Research
The research conducted within the EPR Center includes both technological innovation and application of new techniques to biological problems. The main areas of research are free radicals, spin labeling, metal complexes, and metallo proteins.
How Are We Unique?
Technical Expertise
Application of Techniques
In-House Support
Collaboration
Grants
Ending after ~2000, with EPR Center faculty as Principal Investigator
01/01/2021–11/30/2024
MPI: Candice S. Klug, Michael T. Lerch
EPR spectroscopy is a critically important technique in biomedical research with a unique ability to detect naturally occurring or engineered unpaired electrons in complex biological environments. We will develop two innovative EPR spectrometer technologies with outstanding sample sensitivity that are easy to use and widely available to the scientific community. The resulting state-of-the-art prototypes will provide a transformative increase in throughput that will enable a wide range of new applications in biomedical EPR spectroscopy studies including structural biology, metalloprotein research, redox biology, rational drug design, and clinical diagnostics for a range of disease areas.
R01GM135581
09/20/2019–08/31/2024
PI: Michael T. Lerch
G-protein-coupled receptors are a large and diverse class of cell surface receptors responsible for regulating nearly every physiological process in the human body and are therefore important targets for drug development. In this project, we aim to elucidate the molecular basis for modulation of β2-adrenergic receptor signaling by two post-translational modifications (PTMs), glycosylation and palmitoylation, using a complementary combination of continuous-wave and pulsed electron paramagnetic resonance techniques and functional assays. By detailing the effects of these PTMs on the conformational landscape, the results from these studies will provide insight into the understudied yet critical role of these PTMs as regulators of receptor signaling, thereby increasing researchers' ability to rationally design drugs to achieve the desired therapeutic effect.
R01CA232433
04/15/2019–03/31/2024
MPI: Ming You, Balaraman Kalyanaraman, Laura Kresty
New and effective preventive agents for lung cancer are urgently needed. Selectively inhibiting cancer cell mitochondrial bioenergetics is a novel preventive strategy for lung cancer that has a great potential. By modifying lonidamine (LON), we created the mitochondria-targeted agent, Mito-LON, as a new, safe and potent preventive agent that robustly inhibits bioenergetics and induces autophagic cell death of cancer cells. We will systematically and thoroughly evaluate the chemopreventive potential of Mito-LON using both in vitro and in vivo models of lung cancer and determine its primary mechanism(s) of action.
R01GM108817
09/01/2014–06/30/2023
PI: Candice S. Klug
Endotoxin, or lipopolysaccharide, from important disease-causing bacteria such as Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa induces severe septic shock in humans and can quickly lead to inflammatory disease and/or death. Endotoxin is required for the survival of these bacteria, thus the proteins and interactions involved in its transport within the bacterium are exciting potential new targets for novel antibiotics. The aim of this project is to use structural biology and microbiology assays to obtain a detailed understanding of how the endotoxin-transport proteins move endotoxin within the cell as a foundation for the future development of inventive antibiotics against pathogenic bacteria.
R01AI104922
05/23/2013–08/31/2022
MPI: Dara W. Frank, Jimmy B. Feix
Pseudomonas aeruginosa and a variety of bacterial genera deliver effectors directly into host cells via a specialized injection system. Effectors encode toxic enzymatic activities that cause cell death or dysfunction leading to pathology, tissue destruction and poor outcomes for infected individuals. The long-term goals of this research are to identify how a host encoded cofactor, ubiquitin, interacts with the P. aeruginosa effector, ExoU. Mapping this interface will provide information needed to design inhibitors that may be active against a variety of bacteria, most of which are highly resistant to antibiotics.
R01CA208648
03/01/2017–02/28/2022
MPI: Ming You & Balaraman Kalyanaraman
Chemoprevention of precancerous growths in the lung from progressing to cancer and inhibiting NSCLC's metastasis using novel, potent chemopreventive agents are important strategies to reduce NSCLC mortality. Honokiol (HNK), an active ingredient of the extract of Magnolia bark long popular in traditional Asian medicines, has cancer chemopreventive properties. Here we design a new mitochondria-targeted compound (called Mito- HNK) based on HNK’s structure to facilitate its delivery to mitochondria. We will evaluate the chemopreventive potential of Mito-HNK using both in vitro and in vivo models of lung adenocarcinoma and determine its mechanism of action. At the conclusion of these studies, we will have determined the efficacy of Mito-HNK for inhibiting lung adenocarcinoma progression and metastasis and its suitability for human clinical trials.
07/01/2019–06/30/2021
PI: Candice S. Klug
The research in this study, which used novel state-of-the-art enhancements to a biophysical spectroscopic technique to enable the study of protein structure and functional dynamics, will lead to a better understanding of the physiology of disease processes such as cardiovascular and pulmonary diseases; cystic fibrosis; diabetes; obesity; behavioral, neurological, and psychiatric disorders; Alzheimer's disease; and cancer. This research will also contribute to the development of novel antibiotics and cancer therapeutic agents, and to the design of safer and more effective drugs targeting a broad spectrum of diseases. Additional avenues of research are expected to be uncovered once the success of the initially proposed projects is evident, fostering further opportunities for new interdisciplinary science.
12/01/2019–05/31/2021
PI: Candice S. Klug
04/01/2004–05/31/2021
PI: W. Karol Subczynski
Cataracts are a major cause of blindness throughout the world. At present, surgery is the only effective treatment. The reason for the onset of cataracts is unknown, but a great deal of evidence suggests that the presence of high cholesterol and cholesterol bilayer domains in the eye lens helps to maintain transparency and prevent cataract formation. The goal of this study was to understand how fiber-cell plasma membranes in the lens, in particular their lipid bilayer portion, change during aging and cataract formation so that alternative strategies for preventing, slowing the progression, and curing cataracts can be devised and evaluated.
07/01/2018–06/30/2020
PI: Michael T. Lerch
MCW Cancer Center Pilot Grant
02/01/2019–02/28/2020
PI: Balaraman Kalyanaraman
R01AA022986
12/01/2014–11/30/2019
MPI: Narayan Avadhani, Balaraman Kalyanaraman
Alcohol consumption has been implicated in a multitude of human diseases including alcoholic liver disease (ALD), liver cancer, myocardial fibrosis/infarction, pancreatitis, and disorders of the immune, endocrine and reproductive systems and estimated to cost annually over 1.5 billion dollars in the U.S. in terms of lost productivity and cost of health management. This study will advance our understanding of ALD and critical molecular targets affected. A combination of subcellular targeting of antioxidants and enzyme inhibitors and use of humanized mouse models should provide novel insights into the mechanism of the disease and also lead to development of clinically important drugs for treating or reversing the alcohol liver damage.
R01NS081936
07/01/2016–06/30/2019
MPI: Sidhartha Tan, Jeannette Vasquez Vivar
There is a paucity of effective treatments for cerebral palsy and this proposal tested a promising strategy aimed at a preventive cure for this disease. The studies tested the ways at which a vitamin-like co-factor is involved in brain injury. Using surrogate markers of magnetic resonance imaging, this study examined what happens to brain cells in the early critical phase of injury, which seems to determine the eventual course of events leading to movement disorders of cerebral palsy.
06/01/2015–04/30/2019
PI: Jimmy B. Feix
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that is a leading cause of hospital-acquired infections, and is particularly problematic for patients who are immunosuppressed or require mechanical ventilation. P. aeruginosa persists chronically in cystic fibrosis patients, resulting in irreversible lung damage and mortality. The infectivity of P. aeruginosa is significantly enhanced by the Type III secreted toxin, ExoU. Our biochemical and biophysical studies of ExoU were designed to understand its molecular mechanism of activation, facilitating the development of novel inhibitors to reduce tissue damage or sepsis due to P. aeruginosa infection.
P41EB001980
03/01/1997–03/31/2019
PI: Candice S. Klug (transferred from James S. Hyde)
The mission of the National Biomedical EPR Center was to serve the community of EPR spectroscopists by development of advanced EPR instrumentation and new EPR methodologies.
P41RR001008
05/01/1976–02/28/2002
PI: James S. Hyde
The broad aim of the National Biomedical ESR Center was to create and maintain a comprehensive center with balance in all five categories of a research resource—technological research and development, collaborative research, service, training, and dissemination—with expertise in the three main application areas of ESR spectroscopy—free radicals, transition metals, and spin labels—with outstanding competence in ESR development.
06/01/2017–05/31/2018
PI: Balaraman Kalyanaraman
R01EB002052
07/01/1979–03/31/2016
PI: Candice S. Klug (transferred from James S. Hyde)
Molecular dynamics occur in all biological molecules across a wide range of motional frequencies, some of which are central to biological function. The nitroxide-radical spin-label method, based on EPR, is suitable for the study of molecular dynamics, including dynamics with characteristic motional periods of a millisecond to a microsecond that are biologically relevant. The study applied a new EPR spectrometer with many innovative features and that operates at the high microwave frequency of 94 GHz to characterize cholesterol-mediated lipid interactions in membranes as a function of cholesterol content and temperature.
R01CA152810
06/14/2010–04/30/2015
PI: Balaraman Kalyanaraman
The results obtained from this work likely mitigate the adverse side effects associated with breast cancer chemotherapy. This work also enables early detection of breast cancer in an animal model using a novel imaging technique.
R01GM070642
05/01/2004–07/31/2014
PI: Candice S. Klug
Multidrug resistance is a serious problem in medicine, not only in the often futile treatment of infectious diseases, but also in the treatment of cancer patients. In addition, because of the close similarity of MsbA with other ABC transporters implicated in various common genetic disorders such as the cystic fibrosis transmembrane conductance regulator, any new functional information gained by studying the easily purified MsbA is beneficial to our understanding of structure-function relationships in this very important class of integral membrane proteins. The similarity of MsbA to so many proteins in its general class, and its prevalence in pathogenic bacteria, creates an opportunity for the detailed study of this transporter that will add to our fundamental knowledge of an entire class of potential novel drug targets.
08/01/2010–07/31/2014
Project leader: James S. Hyde
This core provided input from what is generally agreed to be the leading EPR instrumental development site in the world, the National Biomedical EPR Center at the Medical College of Wisconsin. The role of this core was to provide leadership in the development of specific aspects of the technology needed to accomplish the goals of the CMCR. These developments were carried out in collaboration with the projects and with the instrumental Core at Dartmouth, to facilitate the development of the best possible prototype instruments for EPR dosimetry.
R01NS039958
02/01/2009–01/31/2014
MPI: Balaraman Kalyanaraman, Anumantha Kanthasamy
Role of Neuronal NOS & Superoxide in Neurodegeneration
R01NS039958
04/10/2000–03/31/2004
PI: Balaraman Kalyanaraman
Parkinson's disease (PD) is a debilitating neurodegenerative disease. Effective treatment to intervene the progression of neurodegenerative processes in PD remains unavailable. Using a cell culture and a mouse model of PD, we developed a "mitochondria-targeted" antioxidant-based neuroprotective strategy for treating PD. These studies, which brought together chemical and neuropharmacological expertise from two institutions (Medical College of Wisconsin and Iowa State University), helped us develop efficacious mitochondria-targeted antioxidants for treatment of PD as well as understand the possible neuroprotective mechanisms of these novel class of agents.
S10OD011937
04/01/2012–03/31/2013
PI: Candice S. Klug
This application was for an upgrade to Q-band for our current Bruker X-band E580 pulse spectrometer capable of running DEER (double electron-electron resonance), DQC (double quantum coherence), and ENDOR (electron nuclear double resonance) experiments at cryogenic temperatures. The primary use of both the current and upgraded instrument are to quantitate distance measurements between paramagnetic probes on or within biomedically relevant proteins. The major advantages of upgrading to Q-band (35 GHz) DEER from X-band (9 GHz) DEER are a >10-fold increase in sensitivity and overall higher quality distance data. The improvement in resolution, accuracy, identification, signal intensity and the collection of longer distances are of considerable benefit to an array of biological projects.
R01GM068829
09/30/2004–08/31/2012
PI: Jimmy B. Feix
The prevalence of multi-drug resistant infections is one of the most serious problems in health care, both in the United States and worldwide, leading to increased treatment costs and a growing incidence of treatment failure. There is a critical need for the development of new antibiotics, and in particular for new classes of compounds that target non-traditional sites other than cell-wall synthesis and the bacterial ribosome. Antimicrobial peptides, which display remarkable efficacy against a broad spectrum of pathogens, including those resistant to conventional antibiotics, offer a novel approach to the treatment of drug-resistant infections. Developing a more complete understanding of the interactions of antimicrobial peptides with their target cells will enhance our ability to design and develop more effective peptide and peptidomimetic antibiotics.
R01HL067244
12/16/2002–07/31/2012
PI: Jeannette Vasquez Vivar
The broad objectives of this study were designed to bridge the gap in knowledge and were based upon the hypothesis that altering basal tetrahydrobiopterin metabolism by lipid peroxidation products and reactive oxygen species has important consequences in normal nitric oxide/reactive oxygen species fluxes and endothelial physiology favoring phenotypical changes associated with atherogenesis.
R01GM005792
12/10/2001–04/30/2012
R29GM055792
04/01/1997–11/30/2001
PI: Neil Hogg
The goal of this study was to disentangle the cellular effects of nitric oxide from the direct effects of S-nitrosothiols to more fully understand how these species affect cellular function. Importantly, these studies will point to a role of S-nitrosothiols formation not simply as "carriers" of nitric oxide bioactivity but as a distinct bifurcation in nitric oxide signaling pathways.
R01HL063119
07/01/1999–03/31/2012
PI: Balaraman Kalyanaraman
Increased levels of nitrotyrosine and nitrated proteins have been detected in a variety of pulmonary and cardiovascular diseases, and in neurodegenerative and chronic inflammatory disorders. The overall objective of this study was to obtain new mechanistic insight into how the hydrophobic interior of biological membranes facilitates oxidation and nitration reactions of reactive nitrogen species, such as peroxynitrite or nitrogen dioxide radical. This goal of this comprehensive study of reactive nitrogen species reactions in simple well-defined model membrane system was to provide new mechanistic insight for understanding oxidative and nitrosative stress in pulmonary cardiovascular, neurodegenerative, and inflammatory diseases.
R01EB001417
07/01/1979–03/31/2012
PI: James S. Hyde
This goals of this study were device-design driven. Two of the aims focused on development of novel sample resonators for EPR spectroscopy that provide substantially higher signal-to-noise ratios than those used. The third aim focused on development of a novel bimodal resonator for nuclear magnetic resonance signal enhancement by dynamic nuclear polarization.
R13CA150298
04/0/2010–03/31/2011
PI: Balaraman Kalyanaraman
This is the first conference on in vivo spectroscopy, spin trapping, and spin labeling to be held in Puerto Rico. This interdisciplinary scientific conference brought together physicians, chemists, and biologist from the United States and around the globe, who are engaged in research activities involving magnetic resonance, structural and redox biology, radiation, cancer, and other rare diseases. The major purpose of this meeting is to discuss the applications of state-of-the-art EPR methodology in biomedical research with a view to enlightening the younger faculty, postdoctoral fellows, and graduate students on the broad scope of activities in magnetic resonance.
03/01/2004–02/28/2010
PI: Candice S. Klug
The goal of this proposal was to study the structure of the purified inner membrane protein ArnT by site-directed spin labeling EPR spectroscopy in order to provide the first structural information on this newly identified transferase. These studies were anticipated to provide insights into the local and global structure of ArnT, a previously uncharacterized integral membrane protein, which is of fundamental importance in furthering our understanding of the structure and functional dynamics of membrane proteins.
R03TW008052
02/01/2009–12/31/2009
PI: W. Karol Subczynski
Age-related cataracts are a major cause of blindness in developing countries. The reason for the onset of cataracts is unknown, but a great deal of evidence suggests that an increase in oxygen concentration in the lens interior can lead to the development of cataracts. The goal of the studies was to generate important fundamental information about the contribution of cholesterol to the process of oxygen transport within the eye lens, which should increase our understanding of the role cholesterol plays and, in turn, help contribute to the prevention of age-related nuclear cataracts.
07/15/2008–07/14/2009
PI: Candice S. Klug
R13EB007938
04/01/2007–03/31/2009
PI: Balaraman Kalyanaraman
EPR 2007 was a joint conference of the 12th In Vivo EPR Spectroscopy and Imaging meeting and the 9th International EPR Spin Trapping/Spin Labeling meeting. It was held April 29 through May 3, 2007, in Chicago, Illinois, at the the Hilton Suites Chicago/Magnificent Mile. The meeting was sponsored by the Department of Biophysics at the Medical College of Wisconsin and the Department of Radiation and Cellular Oncology at the University of Chicago. The conference was an international workshop that brought together a community of scientists who apply the technique of electron paramagnetic resonance (EPR) to problems intimately related to human physiology and pathophysiology. The primary focus of the meeting was on the use of magnetic resonance technology to investigate the fundamental mechanisms related to technology and structural biology, oxidate cell signaling, and biomedicine. Sessions provided a balance between studies of biological systems and advances in methodology. This helped strengthen the program and promote the effectiveness of science in the United States and around the world. In addition to other invited institutions, all of the NIH-funded EPR centers participated: National EPR Center (Medical College of Wisconsin, Milwaukee, WI), EPR Center for the Study of Viable Systems (Dartmouth College, Hanover, NH), and Center for EPR Imaging in In Vivo Physiology (University of Chicago, Chicago, IL). The EPR Group at the National Cancer Institute also participated in the conference. The meeting also aimed to attract a significant number of participants from other countries in Europe, Asia, Australia, Africa and South America. It was important for the United States to be well-represented at this meeting, so that our scientists were apprised of the latest technological developments from around the world and to establish future collaborations with potential postdoctoral fellows and with research groups.
R01NS040494
07/01/2000–01/31/2009
PI: Balaraman Kalyanaraman
The broad long-term objectives of this project are to understand the direct and indirect mechanisms by which human copper, zinc superoxide dismutase (hSOD1) mutants associated with familial and sporadic amyotrophic lateral sclerosis (ALS) disease cause selective toxicity to motor neurons. The goal of this study was to merge the oxidation and aggregation hypotheses in ALS SOD1-dependent toxicity using isolated hSOD1 proteins, and explore ceramide-induced oxidant signaling in G93A-transfected cells, and G93A mutant mice. Understanding the molecular basis of ALS SOD1 mutant toxicity will help improve overall strategies for developing effective drug therapy for ALS. The use of state-of-the-art analytical techniques coupled with syntheses of mitochondria-targeted spin probes and fluorescent probes should yield new insights on the molecular mechanism for increased toxicity of ALS SOD1 mutants in motor neuron cells.
R01CA077822
01/01/1999–08/31/2008
PI: Balaraman Kalyanaraman
The long-term goal of this project was to unravel the free radical mechanisms by which doxorubicin (DOX), a cancer chemotherapeutic drug that is currently used in the clinic, induces cardiotoxicity in cancer patients.
R01HL073056
03/17/2003–02/29/2008
PI: Balaraman Kalyanaraman
The long-term goal of this proposal is to unravel the role of oxidant-induced iron signaling mechanism in endothelial cell apoptosis.
12/01/2006–11/30/2007
PI: Candice S. Klug
07/15/2002–07/14/2003
PI: Candice S. Klug
Grants
Ending after ~2010, with EPR Center faculty as Co-Investigator or Collaborator
R01NS114972
05/01/2020–02/28/2025
PI: Sidhartha Tan
Co-investigator: Jeannette Vasquez Vivar
There is a paucity of effective treatments for cerebral palsy and this proposal tests new promising drugs aimed at a preventive cure for this disease. These are new drugs aimed at inhibiting an enzyme present in brain called neuronal nitric oxide synthase. New information about how these drugs act, how they affect brain cells, and how effective they are in an animal model of cerebral palsy will be very valuable for future translation to clinical use in humans throughout the world.
R01GM140385
01/01/2021–11/30/2024
MPI: Candice S. Klug, Michael T. Lerch (MCW)
Co-investigators: Neil Hogg, Richard R. Mett, Jason W. Sidabras
EPR spectroscopy is a critically important technique in biomedical research with a unique ability to detect naturally occurring or engineered unpaired electrons in complex biological environments. We will develop two innovative EPR spectrometer technologies with outstanding sample sensitivity that are easy to use and widely available to the scientific community. The resulting state-of-the-art prototypes will provide a transformative increase in throughput that will enable a wide range of new applications in biomedical EPR spectroscopy studies including structural biology, metalloprotein research, redox biology, rational drug design, and clinical diagnostics for a range of disease areas.
12/20/2019–12/19/2023
PI: Marija Raguz (University of Split, Croatia)
Collaborator: W. Karol Subczynski
R01GM135256
01/01/2020–11/30/2023
PI: Christopher J. Kristich (transferred from Candice S. Klug & Christopher J. Kristich [MPI])
Co-investigator: Candice S. Klug
Transmembrane kinases containing PASTA domains control critical processes in most Gram-positive pathogenic bacteria, including antibiotic resistance, toxin production, virulence, cell division, and bacterial viability. The research proposed here promises to reveal new insights into the mechanisms by which this family of kinases functions to coordinate biological adaptations to environmental stimuli. These insights will facilitate development of new treatments for infections caused by Gram-positive bacteria by defining new targets for innovative therapeutics with potentially unique modes of action.
01/01/2004–05/31/2023
PI: Blake R. Hill (MCW)
Co-investigator: Jimmy B. Feix
Mitochondria are components of cells that perform many functions critical for life and are known for being the "power plant" of the cells. The mitochondria have their own life cycle with a mechanism to destroy damaged mitochondria that involves a splitting event that separates a healthy daughter mitochondrion from an unhealthy one that is subsequently removed by the cell. This study will illuminate mechanistic details of these processes and represents an important step towards the discovery of new therapeutic strategies for both rare and common human diseases, including cardiac and neurodegenerative diseases, cancer, diabetes, aging, and neonatal lethality syndrome.
02/11/2014–04/30/2023
PI: Adriano Marchese (MCW)
Co-investigator: Candice S. Klug
The chemokine receptor CXCR4 is overexpressed in metastatic cancers and is associated with poor prognosis, yet the molecular and cellular mechanisms by which CXCR4 contributes to metastatic disease remain poorly understood. The objective of this proposal is to determine the signal transduction mechanisms by which CXCR4 promotes directed cell migration, a cancer-related process required for the spread of cancer to other tissues. Understanding these mechanisms may lead to the identification of new and innovative therapeutic targets to treat and prevent metastatic disease involving CXCR4 signaling.
R01HL058012
05/01/2015–03/31/2024
PI: Daisy Sahoo (MCW)
Co-investigator: Jimmy B. Feix
High plasma cholesterol levels are a major risk factor for heart disease, the leading cause of death worldwide. Our research is designed to understand how we can improve cholesterol removal from the body and lower plasma cholesterol levels. Our findings will help identify new strategies for treating heart disease and other related complications.
R01EY015526
04/01/2004–05/31/2021
PI: W. Karol Subczynski (MCW)
Co-investigator: Jimmy B. Feix
Cataracts are a major cause of blindness throughout the world. At present, surgery is the only effective treatment. The reason for the onset of cataracts is unknown, but a great deal of evidence suggests that the presence of high cholesterol and cholesterol bilayer domains in the eye lens helps to maintain transparency and prevent cataract formation. The goal of this study was to understand how fiber-cell plasma membranes in the lens, in particular their lipid bilayer portion, change during aging and cataract formation so that alternative strategies for preventing, slowing the progression, and curing cataracts can be devised and evaluated.
2016/22/M/NZ1/00187
04/01/2017–03/31/2021
PI: Marta Pasenkiewicz-Gierula ( Jagiellonian University, Poland)
Co-investigator: W. Karol Subczynski
Research Training Program in Vision Science
9/1/2008–12/31/2018
PI: Joseph C. Besharse
Mentor: Candice S. Klug
The goal of the project was to train a new generation of vision science researchers at the predoctoral level that are highly competent in the newest technologies and at the same time mindful of the important role of interdisciplinary, collaborative and translational research in major scientific advances. Our challenge was to expose them to the major problems that need to be solved in vision research while providing in depth training in the technologies essential for research.
P41EB001980
National Biomedical EPR Center
03/01/1997–03/31/2019
PI: Candice S. Klug (transferred from James S. Hyde) (MCW)
Co-Investigators & Collaborators: William E. Antholine, Brian Bennett, Jimmy Feix, Michael T. Lerch, Richard R. Mett, Jason W. Sidabras, Robert A. Strangeway, W. Karol Subczynski
The mission of the National Biomedical EPR Center was to serve the community of EPR spectroscopists by development of advanced EPR instrumentation and new EPR methodologies.
09/01/2009–08/31/2011 & 03/01/2013–02/28/2017
PI: Cynthia M. Czajkowski (University of Wisconsin-Madison)
Co-investigator: Candice S. Klug
Ligand-gated ion channels are proteins that reside in the membranes of all nerve cells. These proteins form channels through the membrane to allow neurons to signal one another at synapses, and thus regulate information flow throughout the brain. Defects in these channels lead to wide variety of neurological diseases and psychiatric conditions and they are the targets of a large number of clinically used drugs. We cannot hope to predict the actions of a drug, design safer and more effective drugs, develop better therapeutic strategies or predict the outcome of a disease-causing mutation without knowledge of how these channels work at a molecular level. The goal of this project was to advance our understanding of how these important channels work.
4/10/2012–3/31/2016
PI: Vsevold Gurevich (Vanderbilt University)
Co-investigator: Candice S. Klug
This study focused on the elucidation of the structural basis of arrestin-dependent activation of the pro-apoptotic JNK family kinases and their activators MKK4/7 using biochemical and biophysical methods. The potential of arrestin mutants with dramatically reduced ability to activate JNKs, that were constructed based on this info, to protect cells against insults and prolong their survival was tested, and the ability of the mutants that activate JNKs more efficiently than wild type arrestins to facilitate cell death also was tested. Molecular tools that specifically increase or block pro-apoptotic signaling have therapeutic potential in disorders associated with excessive cell proliferation (e.g., cancer) or death (e.g., neurodegenerative diseases).
R01EB002052
07/01/1979–03/31/2016
PI: Candice S. Klug (transferred from James S. Hyde)
Co-investigators & Collaborators: Jimmy Feix, Richard R. Mett, Jason W. Sidabras, Robert A. Strangeway, W. Karol Subczynski
Molecular dynamics occur in all biological molecules across a wide range of motional frequencies, some of which are central to biological function. The nitroxide-radical spin-label method, based on EPR, is suitable for the study of molecular dynamics, including dynamics with characteristic motional periods of a millisecond to a microsecond that are biologically relevant. The study applied a new EPR spectrometer with many innovative features and that operates at the high microwave frequency of 94 GHz to characterize cholesterol-mediated lipid interactions in membranes as a function of cholesterol content and temperature.
R01GM081756
09/01/2008–06/30/2012
PI: Vsevold Gurevich (Vanderbilt University)
Co-investigator: Candice S. Klug
Arrestins are multi-functional adaptors that mobilize various signaling molecules to G protein-coupled receptors and microtubules with different functional consequences. The goal of this study was to elucidate the conformations of receptor-bound and microtubule-bound arrestins to understand how arrestin conformation affects its interactions with signaling proteins and the consequences of their binding. This information will set the stage for designing arrestin-based molecular tools for targeted manipulation of cellular signaling that can be used for experimental and therapeutic purposes.
R01HL078937
03/15/2006–02/28/2011
PI: Galen M. Pieper (MCW)
Co-investigator: Jeannette Vasquez Vivar
The loss of cardiac muscle cells is a significant problem in human cardiac transplants that may contribute to poor heart function. Our studies aimed to identify a potential molecular problem intrinsic to cardiac cells that predisposes to cell death and injury. A better understanding of this molecular process may lead to better strategies to prevent injury cardiac cells in these patients.
Publications
Mett RR, Hyde JS. Gordon Coupler with Inductive or Capacitive Iris for Small EPR Resonators for Aqueous Samples. Appl Magn Reson (2022). https://doi.org/10.1007/s00723-021-01432-0
Perry-Hauser NA, Hopkins JB, Zhuo Y, Zheng C, Perez I, Schultz KM, Vishnivetskiy SA, Kaya AI, Sharma P, Dalby KN, Chung KY, Klug CS, Gurevich VV, Iverson TM. The Two Non-Visual Arrestins Engage ERK2 Differently. J Mol Biol. 2022 Apr 15;434(7):167465. doi: 10.1016/j.jmb.2022.167465. Epub 2022 Jan 22. PMID: 35077767; PMCID: PMC8977243.
Hyde JS, Strangeway RA, Sidabras JW. Dispersion EPR: Considerations for Low-Frequency Experiments. Appl Magn Reson. 2022 Jan;53(1):193-206. doi: 10.1007/s00723-021-01352-z. Epub 2021 May 29. PMID: 35464635; PMCID: PMC9030583.
Teucher M, Sidabras JW, Schnegg A. Milliwatt Three- and Four-Pulse Double Electron Electron Resonance for Protein Structure Determination. Phys Chem Chem Phys. 2022 May. https://doi.org/10.1039/D1CP05508A
Stein N, Subczynski WK. Differences in the properties of porcine cortical and nuclear fiber cell plasma membranes revealed by saturation recovery EPR spin labeling measurements. Exp Eye Res. 2021; 206:108536. doi: 10.1016/j.exer.2021.108536. PMID: 33716012. PMCID: PMC8139366
Campanella AJ, Nguyen MT, Zhang J, Ngendahimana T, Antholine WE, Eaton GR, Eaton SS, Glezakou VA, Zadrozny JM. Ligand control of low-frequency electron paramagnetic resonance linewidth in Cr(III) complexes. Dalton Trans. 2021;50(15):5342-5350. doi: 10.1039/d1dt00066g. PMID: 33881070.
Hyde JS, Strangeway RA, Sidabras JW. Dispersion EPR: Considerations for Low-Frequency Experiments. Appl Magn Reson. 2022 Jan;53(1):193-206. doi: 10.1007/s00723-021-01352-z. PMID: 35464635; PMCID: PMC9030583.
Subczynski WK, Widomska J, Stein N, Swartz H. Factors Determining Barrier Properties to Oxygen Transport Across Model and Cell Plasma Membranes Based on EPR Spin-Label Oximetry. Appl Magn Reson. 2021. https://doi.org/10.1007/s00723-021-01412-4
Markiewicz M, Szczelina R, Milanovic B, Subczynski WK, Pasenkiewicz-Gierula M. Chirality affects cholesterol-oxysterol association in water, a computational study. Comput Struct Biotechnol J. 2021 Jul 26;19:4319-4335. doi: 10.1016/j.csbj.2021.07.022. PMID: 34429850; PMCID: PMC8361299.
Stein N, Subczynski WK. Oxygen Transport Parameter in Plasma Membrane of Eye Lens Fiber Cells by Saturation Recovery EPR. Appl Magn Reson. 2021 Jan;52(1):61-80. doi: 10.1007/s00723-020-01237-7. PMID: 33776217; PMCID: PMC7992188.
Subczynski W K, Pasenkiewicz-Gierula M, Widomska J, Stein N. Role of cholesterol in maintaining the physical properties of the plasma membrane. In: Cholesterol: from Biophysics to the Clinics, AN Bukiya and AM Dopico Eds, Elsevier, 2021.
Klug CS, Lerch MT, Feix JB. Applications of Nitroxide Spin Labels to Structural Biology. In: Ouari O, Gigmes D, editors. Nitroxides: Synthesis, Properties and Applications [Internet] London, UK: Royal Society of Chemistry; 2021. Chapter 10; p.392-419.
Mainali L, Pasenkiewicz-Gierula M, Subczynski WK. Formation of cholesterol Bilayer Domains Precedes Formation of Cholesterol Crystals in Membranes Made of the Major Phospholipids of Human Eye Lens Fiber Cell Plasma Membranes. Curr Eye Res. 2020;45(2):162-172. doi:10.1080/02713683.2019.1662058 PMCID: PMC6980519
Del Alamo D, Tessmer MH, Stein RA, Feix JB, Mchaourab HS, Meiler J. Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction. Biophys J. 2020 Jan 21;118(2):366-375. doi: 10.1016/j.bpj.2019.12.011. PMID: 31892409; PMCID: PMC6976798.
Cheng G, Pan J, Podsiadly R, Zielonka J, Garces AM, Dias Duarte Machado LG, Bennett B, McAllister D, Dwinell MB, You M, Kalyanaraman B. Increased formation of reactive oxygen species during tumor growth: Ex vivo low-temperature EPR and in vivo bioluminescence analyses. Free Radic Biol Med. 2020 Feb 1;147:167-174. doi: 10.1016/j.freeradbiomed.2019.12.020. PMID: 31874251; PMCID: PMC6948008.
Boban Z, Puljas A, Kovač D, Subczynski WK, Raguz M. Effect of Electrical Parameters and Cholesterol Concentration on Giant Unilamellar Vesicles Electroformation. Cell Biochem Biophys. 2020 Apr 21. doi: 10.1007/s12013-020-00910-9. PMCID: PMC7608754
Widomska J, SanGiovanni JP, Subczynski WK. Why is Zeaxanthin the Most Concentrated Xanthophyll in the Central Fovea?. Nutrients. 2020;12(5):1333. Published 2020 May 7. doi:10.3390/nu12051333. PMCID: PMC7284714
Hilger D, Kumar KK, Hu H, Pedersen MF, O'Brien ES, Giehm L, Jennings C, Eskici G, Inoue A, Lerch M, Mathiesen JM, Skiniotis G, Kobilka BK. Structural insights into differences in G protein activation by family A and family B GPCRs. Science. 2020;369(6503):eaba3373. doi:10.1126/science.aba3373
Zhuo Y, Gurevich VV, Vishnivetskiy SA, Klug CS, Marchese A. A non-GPCR binding partner interacts with a novel surface on β-arrestin1 to mediate GPCR signaling. J Biol Chem. 2020;jbc.RA120.015074. doi:10.1074/jbc.RA120.015074. PMCID: PMC7426584
Lerch MT, Matt RA, Masureel M, Elgeti M, Kumar KK, Hilger D, Foys B, Kobilka BK, Hubbell WL. Viewing rare conformations of the β2 adrenergic receptor with pressure-resolved DEER spectroscopy. Proc Natl Acad Sci U S A. 2020 Nov 30:202013904. doi: 10.1073/pnas.2013904117. Epub ahead of print. PMID: 33257561; PMCID: PMC7749303.
Tessmer MH, DeCero SA, Del Alamo D, Riegert MO, Meiler J, Frank DW, Feix JB. Characterization of the ExoU activation mechanism using EPR and integrative modeling. Sci Rep. 2020 Nov 12;10(1):19700. doi: 10.1038/s41598-020-76023-3. PMID: 33184362; PMCID: PMC7665212.
Szala M, Grzelakowska A, Modrzejewska J, Siarkiewicz P, Slowinski D, Swierczynska M, Zielonka J, Podsiadly R. Characterization of the reactivity of luciferin boronate - A Probe for inflammatory oxidants with improved stability. Dyes and Pigments 2020 Dec;183:108693.
Chen Q, Zhuo Y, Sharma P, Perez I, Francis DJ, Chakravarthy S, Vishnivetskiy SA, Berndt S, Hanson SM, Zhan X, Brooks EK, Altenbach C, Hubbell WL, Klug CS, Iverson TM, Gurevich VV. An eight amino acid segment controls oligomerization and preferred conformation of the two non-visual arrestins. J Mol Biol. 2020 Dec 30:166790. doi: 10.1016/j.jmb.2020.166790.
Subczynski WK, Pasenkiewicz-Gierula M. Hypothetical Pathway for Formation of Cholesterol Microcrystals Initiating the Atherosclerotic Process. Cell Biochem Biophys. 2020 Sep;78(3):241-247. doi: 10.1007/s12013-020-00925-2. PMID: 32602057; PMCID: PMC7403164.
Mainali L, O'Brien WJ, Subczynski WK. Detection of cholesterol bilayer domains in intact biological membranes: Methodology development and its application to studies of eye lens fiber cell plasma membranes. Exp Eye Res. 2019 January;178:72-81. PMCID: PMC6361697
Feix JB, Kohn S, Tessmer MH, Anderson DM, Frank DW. Conformational Changes and Membrane Interaction of the Bacterial Phospholipase, ExoU: Characterization by Site-Directed Spin Labeling. Cell Biochem Biophys. 2019 March;77(1):79-87. PMCID: PMC6347562
Hyde JS, Sidabras JW, Mett RR. Uniform Field Resonators for EPR Spectroscopy: A Review. Cell Biochem Biophys. 2019 March;77(1):3-14. PMCID: PMC6309773
Tikhonov AN, Subczynski WK. Oxygenic photosynthesis: EPR study of photosynthetic electron transport and oxygen-exchange, an overview. Cell Biochem Biophys. 2019 March;77(1):47-59. PMCID: PMC6524781
Antholine WE, Vasquez-Vivar J, Quirk BJ, Whelan HT, Wu PK, Park JI, Myers CR. Treatment of Cells and Tissues with Chromate Maximizes Mitochondrial 2Fe2S EPR Signals. Int J Mol Sci. 2019 March 6;20(5). PMCID: PMC6429069
Antholine WE. Resolved Hyperfine at L-band for High-Spin CoEDTA, A Model for Co Sites in Proteins. Int J Mol Sci. 2019 May 14;20(10). PMCID: PMC6566446
Antholine WE, Myers CR. Concentration of Fe(3+)-Triapine in BEAS-2B Cells. Int J Mol Sci. 2019 June 22;20(12). PMCID: PMC6627071
Stein N, Mainali L, Hyde JS, Subczynski WK. Characterization of the distribution of spin-lattice relaxation rates of lipid spin labels in fiber cell plasma membranes of eye lenses with a stretched-exponential function. Appl Magn Reson. 2019 July;50(7):903-918. PMCID: PMC6594395
Tessmer MH, Anderson DM, Pickrum AM, Riegert MO, Moretti R, Meiler J, Feix JB, Frank DW. Identification of a ubiquitin-binding interface using Rosetta and DEER. Proc Natl Acad Sci U S A. 2018 January;115(3):525-530. PMCID: PMC5776994
Schultz KM, Klug CS. Characterization of and lipopolysaccharide binding to the E. coli LptC protein dimer. Protein Sci. 2018 February;27(2):381-389. PMCID: PMC5775163
Chitambar CR, Al-Gizawiy MM, Alhajala HS, Pechman KR, Wereley JP, Wujek R, Clark PA, Kuo JS, Antholine WE, Schmainda KM. Gallium Maltolate Disrupts Tumor Iron Metabolism and Retards the Growth of Glioblastoma by Inhibiting Mitochondrial Function and Ribonucleotide Reductase. Mol Cancer Ther. 2018 June;17(6):1240-1250. PMCID: PMC5984712
Schultz KM, Fischer MA, Noey EL, Klug CS. Disruption of the E. coli LptC dimerization interface and characterization of lipopolysaccharide and LptA binding to monomeric LptC. Protein Sci. 2018 August;27(8):1407-1417. PMCID: PMC6153404
Stadtmueller BM, Bridges MD, Dam KM, Lerch MT, Huey-Tubman KE, Hubbell WL, Bjorkman PJ. DEER Spectroscopy Measurements Reveal Multiple Conformations of HIV-1 SOSIP Envelopes that Show Similarities with Envelopes on Native Virions. Immunity. 2018 August 21;49(2):235-246.e4. PMCID: PMC6104740
Yang X, Bennett B, Holz RC. Analyzing the function of the insert region found between the α and β-subunits in the eukaryotic nitrile hydratase from Monosiga brevicollis. Archives Biochem Biophys. 2018 November 1;657:1-7. PMCID: PMC6201762
Antholine WE, Zhang S, Gonzales J, Newman N. Better Resolution of High-Spin Cobalt Hyperfine at Low Frequency: Co-Doped Ba(Zn1/3Ta2/3)O3 as a Model Complex. Int J Mol Sci. 2018 November 9;19(11). PMCID: PMC6274703
Tessmer MH, Anderson DM, Buchaklian A, Frank DW, Feix JB. Cooperative substrate-cofactor interactions and membrane localization of the bacterial PLA2 enzyme, ExoU. J Biol Chem. 2017 Jan 9. pii: jbc.M116.760074. PMCID: PMC5336173
Kalyanaraman B, Cheng G, Hardy M, Ouari O, Sikora A, Zielonka J, Dwinell MB. Modified Metformin as a More Potent Anticancer Drug: Mitochondrial Inhibition, Redox Signaling, Antiproliferative Effects and Future EPR Studies. Cell Biochem Biophys. 2017 Dec;75(3-4):311-317. PMCID: PMC5680142
Subczynski W.K., Widomska J., Mainali L. Factors Determining the Oxygen Permeability of Biological Membranes: Oxygen Transport Across Eye Lens Fiber-Cell Plasma Membranes. Adv Exp Med Biol. 2017;977:27-34. PMCID: PMC5851008
Fischer AW, Anderson DM, Tessmer MH, Frank DW, Feix JB, Meiler J. Structure and Dynamics of Type III Secretion Effector Protein ExoU As determined by SDSL-EPR Spectroscopy in Conjunction with De Novo Protein Folding. ACS Omega. 2017 Jun 30;2(6):2977-2984. PMCID: PMC5494639
Hyde JS. Autobiography of James S. Hyde. Appl. Magn. Reson. 2017 Dec; 48(11-12), 1103-1147. [Part of special issue dedicated to Hyde.] PMCID: PMC6022859
Sarna T, Kalyanaraman B, Berliner L. Xth EPR Workshop on Applications of EPR in Biology and Medicine. Cell Biochem Biophys. 2017; 75(3): 257–258. PMCID: PMC5691121
Sidabras JW, Reijerse EJ, Lubitz W. Uniform Field Re-entrant Cylindrical TE01U Cavity for Pulse Electron Paramagnetic Resonance Spectroscopy at Q-band. Appl. Magn. Reson. 2017.
Mainali L, Camenisch TG, Hyde JS, Subczynski WK. Saturation recovery EPR spin-labeling method for quantification of lipids in biological membrane domains. Appl Magn Reson. 2017 Dec;48(11-12):1355-1373. PMCID: PMC5967259
Schultz KM, Klug CS. High-pressure EPR spectroscopy studies of the E. coli lipopolysaccharide transport proteins LptA and LptC. Appl Magn Reson. 2017 Dec;48(11-12):1341-1353. PMCID: PMC5761346
Hyde JS, Mett RR. EPR Uniform Field Signal ENhancement by Dielectric Tubes in Cavities. Appl Magn Reson. 2017 Dec;48(11-12):1185-1204. PMCID: PMC5761080
Chen Q, Perry NA, Vishnivetskiy SA, Berndt S, Gilbert NC, Zhuo Y, Singh PK, Tholen J, Ohi MD, Gurevich EV, Brautigam CA, Klug CS, Gurevich VV, Iverson TM. Structural basis of arrestin-3 activation and signaling. Nat Commun. 2017 Nov 10;8(1):1427. PMCID: PMC5681653
Herneisen AL, Sahu ID, McCarrick RM, Feix JB, Lorigan GA, Howard KP. A Budding-Defective M2 Mutant Exhibits Reduced Membrane Interaction, Insensitivity to Cholesterol, and Perturbed Interdomain Coupling. Biochemistry. 2017 Nov 7;56(44):5955-5963. PMCID: PMC6112238
Schultz KM, Klug CS. Characterization of and lipopolysaccharide binding to the E. coli LptC protein dimer. Protein Sci. 2018 Feb;27(2):381-389. PMCID: PMC5775163
Suliman M, Santosh V, Seegar TCM, Dalton AC, Schultz KM, Klug CS, Barton WA. Directed evolution provides insight into conformational substrate sampling by SrtA. PLoS One. 2017 Aug 31;12(8):e0184271. PMCID: PMC5578623
Sidabras JW, Sarna T, Mett RR, Hyde JS. Uniform field loop-gap resonator and rectangular TEU02 for aqueous sample EPR at 94GHz. J Magn Reson. 2017 Sep;282:129-135. PMCID: PMC5793860
Widomska J, Subczynski WK, Mainali L, Raguz M. Cholesterol Bilayer Domains in the Eye Lens Health: A Review. Cell Biochem Biophys. 2017 Dec;75(3-4):387-398. PMCID: PMC5691107
Strangeway RA, Hyde JS, Camenisch TG, Sidabras JW, Mett RR, Anderson JR, Ratke JJ, Subczynski WK. Broadband W-band Rapid Frequency Sweep Considerations for Fourier Transform EPR. Cell Biochem Biophys. 2017 Dec;75(3-4):259-273. PMCID: PMC5693649
Stein N, Gumataotao N, Hajnas N, Wu R, Lankathilaka KPW, Bornscheuer UT, Liu D, Fiedler AT, Holz RC, Bennett B. Multiple States of Nitrile Hydratase from Rhodococcus equi TG328-2: Structural and Mechanistic Insights from Electron Paramagnetic Resonance and Density Functional Theory Studies. Biochemistry. 2017 Jun 20;56(24):3068-3077. PMCID: PMC5821057
Schultz KM, Lundquist TJ, Klug CS. Lipopolysaccharide binding to the periplasmic protein LptA. Protein Sci. 2017 Aug;26(8):1517-1523. PMCID: PMC5521551
Subczynski WK, Pasenkiewicz-Gierula M, Widomska J, Mainali L, Raguz M. High Cholesterol/Low Cholesterol: Effects in Biological Membranes: A Review. Cell Biochem Biophys. 2017 Dec;75(3-4):369-385. Review. PMCID: PMC5521551
Langley M, Ghosh A, Charli A, Sarkar S, Ay M, Luo J, Zielonka J, Brenza T, Bennett B, Jin H, Ghaisas S, Schlichtmann B, Kim D, Anantharam V, Kanthasamy A, Narasimhan B, Kalyanaraman B, Kanthasamy AG. Mito-Apocynin Prevents Mitochondrial Dysfunction, Microglial Activation, Oxidative Damage, and Progressive Neurodegeneration in MitoPark Transgenic Mice. Antioxid Redox Signal. 2017 Nov 10;27(14):1048-1066. PMCID: PMC5651937
Sidabras JW, Mett RR, Hyde JS. Extruded dielectric sample tubes of complex cross section for EPR signal enhancement of aqueous samples. J Magn Reson. 2017 Apr;277:45-51. PMCID: PMC5674976
Sidabras JW, Richie JE, Hyde JS. Axially uniform magnetic field-modulation excitation for electron paramagnetic resonance in rectangular and cylindrical cavities by slot cutting. J Magn Reson. 2017 Jan;274:115-124. PMCID: PMC5652332
Mainali L, Raguz M, O'Brien WJ, Subczynski WK. Changes in the Properties and Organization of Human Lens Lipid Membranes Occurring with Age. Curr Eye Res. 2017 May;42(5):721-731. PMCID: PMC5409882
Subczynski WK, Mainali L, Raguz M, O'Brien WJ. Organization of lipids in fiber-cell plasma membranes of the eye lens. Exp Eye Res. 2017 Mar;156:79-86. PMCID: PMC5023447
Subczynski WK, Pasenkiewicz-Gierula M, Widomska J, Mainali L, Raguz M. High Cholesterol/Low Cholesterol: Effects in Biological Membranes: A Review. Cell Biochem Biophys. 2017 December;75(3-4):369-385. PMCID: PMC5645210
Bennett B, Kowalski JM. (2015). EPR Methods for Biological Cu(II): L-band CW and NARS. Methods Enzymol. 563:341-61. PMCID: PMC4772423
Hewage JS, Wanniarachchi S, Morin TJ, Liddle BJ, Banaszynski M, Lindeman SV, Bennett B, Gardinier JR. (2014) Homoleptic nickel(II) complexes of redox-tunable pincer-type ligands. Inorganic chemistry53(19):10070-84. PMCID: PMC5047063
Mandal T, Shin S, Aluvila S, Chen H-C, Grieve C, Choe J-Y, Cheng EH, Hustedt EJ, Oh KJ. (2016). Assembly of Bak homodimers into higher order homooligomers in the mitochondrial apoptotic pore. Sci Rep. 6:30763. PMCID: PMC4973285.
Mainali L, Raguz M, O’Brien WJ, Subczynski WK. (2016). Changes in the properties and organization of human lens lipid membranes occurring with age. Curr Eye Res. 1-11. PMCID: PMC5409882
Mett RR, Sidabras JW, Hyde JS. (2016). MRI surface-coil pair with strong inductive coupling. Rev Sci Inst. Rev. Sci. Instrum. 87, 124704. PMCID: PMC5201604
Mett RR, Sidabras JW, Hyde JS. (2016). Meta-metallic coils and resonators: Methods for high Q-value resonant geometries. Rev Sci Instrum. 87(8):084703. PMCID: PMC5010558
Johnson BJ, Antholine WE, Lindeman SV, Graham MJ, Mankad NP. (2016). A one-hole Cu4S cluster with N2O reductase activity: a structural and functional model for CuZ. J Am Chem Soc. PMCID: PMC5378702
Sidabras JW, Strangeway RA, Mett RR, Anderson JR, Mainali L, Hyde JS. (2016). Hyperbolic-cosine waveguide tapers and oversize rectangular waveguide for reduced broadband insertion loss in W-band electron paramagnetic resonance spectroscopy. II Broadband Characterization. Rev Sci Instrum. 87(3):034704. PMCID: PMC4798996
Stein N, Love D, Judd ET, Elliott SJ, Bennett B, Pacheco AA. (2015). Correlations between the electronic properties of shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its structure: effects of heme oxidation state and active site ligation. Biochemistry. 54(24):3749-58. PMCID: PMC4743497
Subczynski W, Mainali L, Raguz M, O’Brien WJ. (2016). Organization of lipids in fiber-cell plasma membranes of the eye lens. Exp Eye Res. S0014-4835(6)30034-3. PMCID: PMC5023447
Widomska J, Zareba M, Subczynski WK. (2016). Can xanthophyll-membrane interactions explain their selective presence in the retina and brain? Foods. 5(1). pii: 7. PMCID: PMC4809277
Wen T, Wamer WG, Subczynski WK, Hou S, Wu X, Yin JJ. (2016). Enhancement of paramagnetic relaxation by photoexcited gold nanorods. Sci Rep. 6:24101. PMCID: PMC4829829
Zareba M, Widomaka J, Burka JM, Subczynski WK. (2016). Nitroxide free radicals protect macular carotenoids against chemical destruction (bleaching) during lipid peroxidation. Free Rad Biol Med. 101:446-454. PMCID: PMC5154825
Zielonka J, Podsiadły R, Zielonka M, Hardy M, Kalyanaraman K. On the use of peroxy-caged luciferin (PCL-1) probe for bioluminescent detection of inflammatory oxidants in vitro and in vivo - Identification of reaction intermediates and oxidant-specific minor products. Free Radic. Biol. Med. 2016, 99, 32-42. PMCID: PMC5107150
Aitha M, Moritz L, Sahu ID, Sanyurah O, Roche Z, McCarrick R, Lorigan GA, Bennett B, Crowder MW. Conformational dynamics of metallo-β-lactamase CcrA during catalysis investigated by using DEER spectroscopy. J Biol Inorg Chem. 2015 Apr;20(3):585-94. doi: 10.1007/s00775-015-1244-8. PubMed PMID: 25827593; PubMed Central PMCID: PMC4733638.
Anderson DM, Feix JB, Frank DW. Cross Kingdom Activators of Five Classes of Bacterial Effectors. PLoS Pathog. 2015 Jul 23;11(7):e1004944. doi: 10.1371/journal.ppat.1004944. Review. PubMed PMID: 26203905; PubMed Central PMCID: PMC4512716.
Anderson DM, Sato H, Dirck AT, Feix JB, Frank DW. Ubiquitin activates patatin-like phospholipases from multiple bacterial species. J Bacteriol. 2015 Feb;197(3):529-41. doi: 10.1128/JB.02402-14. PubMed PMID: 25404699; PubMed Central PMCID: PMC4285982.
Johnson BJ, Antholine WE, Lindeman SV, Mankad NP. A Cu4S model for the nitrous oxide reductase active sites supported only by nitrogen ligands. Chem Commun (Camb). 2015 Jul 28;51(59):11860-3. doi: 10.1039/c5cc04675k. PubMed PMID: 26111160; PubMed Central PMCID: PMC4731228.
Kim SS, Upshur MA, Saotome K, Sahu ID, McCarrick RM, Feix JB, Lorigan GA, Howard KP. Cholesterol-Dependent Conformational Exchange of the C-Terminal Domain of the Influenza A M2 Protein. Biochemistry. 2015 Dec 15;54(49):7157-67. doi: 10.1021/acs.biochem.5b01065. PubMed PMID: 26569023; PubMed Central PMCID: PMC4734095.
Kittell AW, Hyde JS. Spin-label CW microwave power saturation and rapid passage with triangular non-adiabatic rapid sweep (NARS) and adiabatic rapid passage (ARP) EPR spectroscopy. J Magn Reson. 2015 Jun;255:68-76. doi: 10.1016/j.jmr.2015.03.014. PubMed PMID: 25917132; PubMed Central PMCID: PMC4441560.
Lane AC, Barnes CL, Antholine WE, Wang D, Fiedler AT, Walensky JR. Di- and Trinuclear Mixed-Valence Copper Amidinate Complexes from Reduction of Iodine. Inorg Chem. 2015 Sep 8;54(17):8509-17. doi: 10.1021/acs.inorgchem.5b01161. PubMed PMID: 26252561; PubMed Central PMCID: PMC4733884.
Mainali L, Raguz M, O'Brien WJ, Subczynski WK. Properties of membranes derived from the total lipids extracted from clear and cataractous lenses of 61-70-year-old human donors. Eur Biophys J. 2015 Feb;44(1-2):91-102. doi: 10.1007/s00249-014-1004-7. PubMed PMID: 25502634; PubMed Central PMCID: PMC4323688.
Mainali L, Vasquez-Vivar J, Hyde JS, Subczynski WK. Spin-labeled small unilamellar vesicles with the T1-sensitive saturation-recovery EPR display as an oxygen sensitive analyte for measurement of cellular respiration. Appl Magn Reson. 2015 Aug 1;46(8):885-895. PubMed PMID: 26441482; PubMed Central PMCID: PMC4591545.
Raguz M, Mainali L, O'Brien WJ, Subczynski WK. Lipid domains in intact fiber-cell plasma membranes isolated from cortical and nuclear regions of human eye lenses of donors from different age groups. Exp Eye Res. 2015 Mar;132:78-90. doi: 10.1016/j.exer.2015.01.018. PubMed PMID: 25617680; PubMed Central PMCID: PMC4352400.
Raguz M, Mainali L, O'Brien WJ, Subczynski WK. Amounts of phospholipids and cholesterol in lipid domains formed in intact lens membranes: Methodology development and its application to studies of porcine lens membranes. Exp Eye Res. 2015 Nov;140:179-86. doi: 10.1016/j.exer.2015.09.006. PubMed PMID: 26384651; PubMed Central PMCID: PMC4624471.
Starus A, Nocek B, Bennett B, Larrabee JA, Shaw DL, Sae-Lee W, Russo MT, Gillner DM, Makowska-Grzyska M, Joachimiak A, Holz RC. Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril. Biochemistry. 2015 Aug 11;54(31):4834-44. doi: 0.1021/acs.biochem.5b00475. PubMed PMID: 26186504; PubMed Central PMCID: PMC4671288.
Xu J, Eriksson SE, Cebula M, Sandalova T, Hedström E, Pader I, Cheng Q, Myers CR, Antholine WE, Nagy P, Hellman U, Selivanova G, Lindqvist Y, Arnér ES. The conserved Trp114 residue of thioredoxin reductase 1 has a redox sensor-like function triggering oligomerization and crosslinking upon oxidative stress related to cell death. Cell Death Dis. 2015 Jan 22;6:e1616. doi: 10.1038/cddis.2014.574. PubMed PMID: 25611390; PubMed Central PMCID: PMC4669772.
Zielonka J, Sikora A, Adamus J, Kalyanaraman B. Detection and differentiation between peroxynitrite and hydroperoxides using mitochondria-targeted arylboronic acid. Methods Mol Biol. 2015;1264:171-81. doi: 10.1007/978-1-4939-2257-4_16. PubMed PMID: 25631013; PubMed Central PMCID: PMC4451192.
Cheng G, Zielonka J, McAllister D, Tsai S, Dwinell MB, Kalyanaraman B. Profiling and targeting of cellular bioenergetics: inhibition of pancreatic cancer cell proliferation. Br J Cancer. 2014 Jul 8;111(1):85-93. doi: 10.1038/bjc.2014.272. PMCID: PMC4090735
Diers AR, Broniowska KA, Chang CF, Hill RB, Hogg N. S-Nitrosation of monocarboxylate transporter 1: inhibition of pyruvate-fueled respiration and proliferation of breast cancer cells. Free Radic Biol Med. 2014 Apr;69:229-38. doi: 10.1016/j.freeradbiomed.2014.01.031. PMCID: PMC3982622
Dranka BP, Gifford A, McAllister D, Zielonka J, Joseph J, O'Hara CL, Stucky CL, Kanthasamy AG,Kalyanaraman B. A novel mitochondrially-targeted apocynin derivative prevents hyposmia and loss of motor function in the leucine-rich repeat kinase 2 (LRRK2R1441G) transgenic mouse model of Parkinson's disease. Neurosci Lett. 2014 Sep 25. pii: S0304-3940(14)00779-4. doi: 10.1016/j.neulet.2014.09.042. PMCID: PMC4253647
Hardy M, Poulhés F, Rizzato E, Rockenbauer A, Banaszak K, Karoui H, Lopez M, Zielonka J,Vasquez-Vivar J,Sethumadhavan S, Kalyanaraman B, Tordo P, Ouari O. Mitochondria-targeted spin traps: synthesis, superoxide spin trapping, and mitochondrial uptake. Chem Res Toxicol. 2014 Jul 21;27(7):1155-65. doi: 10.1021/tx500032e. PMCID: PMC5452977
He X, Swarts SG, Demidenko E, Flood AB, Grinberg O, Gui J, Mariani M, Marsh SD, Ruuge AE,Sidabras JW, Tipikin D, Wilcox DE, Swartz HM. Development and validation of an ex vivo electron paramagnetic resonance fingernail biodosimetric method. Radiat Prot Dosimetry. 2014 Jun;159(1-4):172-81. doi: 10.1093/rpd/ncu129. PMCID: PMC4095917
Koto T, Michalski R, Zielonka J, Joseph J, Kalyanaraman B. Detection and identification of oxidants formed during •NO/O2•⁻ reaction: a multi-well plate CW-EPR spectroscopy combined with HPLC analyses. Free Radic Res. 2014 Apr;48(4):478-86. doi: 10.3109/10715762.2014.886774. PMCID: PMC4780754
Kumar A, Chen SH, Kadiiska MB, Hong JS, Zielonka J, Kalyanaraman B, Mason RP. Inducible nitric oxide synthase is key to peroxynitrite-mediated, LPS-induced protein radical formation in murine microglial BV2 cells. Free Radic Biol Med. 2014 Aug;73:51-9. doi: 10.1016/j.freeradbiomed.2014.04.014. PMCID: PMC4111989
Larson MC, Hillery CA, Hogg N. Circulating membrane-derived microvesicles in redox biology. Free Radic BiolMed. 2014 Aug;73:214-28. doi: 10.1016/j.freeradbiomed.2014.04.017. PMCID: PMC4465756
Michalski R, Michalowski B, Sikora A, Zielonka J, Kalyanaraman B. On the use of fluorescence lifetime imaging and dihydroethidium to detect superoxide in intact animals and ex vivo tissues: a reassessment. Free Radic Biol Med. 2014 Feb;67:278-84. doi: 10.1016/j.freeradbiomed.2013.10.816. PMCID: PMC4275029
Michalski R, Zielonka J, Gapys E, Marcinek A, Joseph J, Kalyanaraman B. Real-time measurements of amino acid and protein hydroperoxides using coumarin boronic acid. J Biol Chem. 2014 Aug 8;289(32):22536-53. doi: 10.1074/jbc.M114.553727. PMCID: PMC4139259
Mouradian M, Kikawa KD, Dranka BP, Komas SM, Kalyanaraman B, Pardini RS. Docosahexaenoic acid attenuates breast cancer cell metabolism and the Warburg phenotype by targeting bioenergetic function. Mol Carcinog. 2014 Apr 12. doi: 10.1002/mc.22151.
Pan J, Zhang Q, Liu Q, Komas SM, Kalyanaraman B, Lubet RA, Wang Y, You M. Honokiol Inhibits Lung Tumorigenesis through Inhibition of Mitochondrial Function. Cancer Prev Res (Phila). 2014 Sep 22. pii:canprevres.0091.2014. PMCID: PMC6010030
Raguz M, Mainali L, O'Brien WJ, Subczynski WK. Lipid-protein interactions in plasma membranes of fiber cells isolated from the human eye lens. Exp Eye Res. 2014 Mar;120:138-51. doi: 10.1016/j.exer.2014.01.018. PMCID: PMC3963472
Shah G, Zielonka J, Chen F, Zhang G, Cao Y, Kalyanaraman B, See W. H2O2 Generation by bacillus Calmette-Guérin Induces the Cellular Oxidative Stress Response Required for bacillus Calmette-Guérin Direct Effects on Urothelial Carcinoma Biology. J Urol. 2014 Jun 10. pii: S0022-5347(14)03738-0. doi: 10.1016/j.juro.2014.05.115. PMCID: PMC5798233
Sidabras JW, Varanasi SK, Mett RR, Swarts SG, Swartz HM, Hyde JS. A microwave resonator for limiting depth sensitivity for electron paramagnetic resonance spectroscopy of surfaces. Rev Sci Instrum. 2014 Oct;85(10):104707. doi: 10.1063/1.4898179. PMCID: PMC401662
Widomska J, Subczynski WK. Why has Nature Chosen Lutein and Zeaxanthin to Protect the Retina? J Clin Exp Ophthalmol. 2014 Feb 21;5(1):326. PMCID: PMC4038937
Yu L, Vásquez-Vivar J, Jiang R, Luo K, Derrick M, Tan S. Developmental susceptibility of neurons to transient tetrahydrobiopterin insufficiency and antenatal hypoxia-ischemia in fetal rabbits. Free Radic Biol Med. 2014 Feb;67:426-36. doi: 10.1016/j.freeradbiomed.2013.11.026. PMCID: PMC3945116
Zhuo Y, Vishnivetskiy SA, Zhan X, Gurevich VV, Klug CS. Identification of Receptor Binding-induced Conformational Changes in Non-visual Arrestins. J Biol Chem. 2014 Jul 25;289(30):20991-1002. doi: 10.1074/jbc.M114.560680. PMCID: PMC4110305
Zielonka J, Cheng G, Zielonka M, Ganesh T, Sun A, Joseph J, Michalski R, O'Brien WJ, Lambeth JD, Kalyanaraman B. High-throughput assays for superoxide and hydrogen peroxide: design of a screening workflow to identify inhibitors of NADPH oxidases. J Biol Chem. 2014 Jun 6;289(23):16176-89. doi: 10.1074/jbc.M114.548693. PMCID: PMC4047388
Anderson DM, Feix JB, Monroe AL, Peterson FC, Volkman BF, Haas AL, Frank DW. Identification of the Major Ubiquitin-binding Domain of the Pseudomonas aeruginosa ExoU A2 Phospholipase. J Biol Chem. 2013 Sep 13;288(37):26741-52. doi: 10.1074/jbc.M113.478529. PMCID: PMC3772220
Hyde JS, Bennet B, Kittell AW, Kowalski JM, Sidabris JW. Moving difference (MDIFF) non-adiabatic rapid sweep (NARS) EPR of copper (II). J Magn Reson 236: 15-25, 2013. PMCID: PMC3919454
Mainali L, Hyde JS, Subczynski WK. Using spin-label W-band EPR to study membrane fluidity profiles in samples of small volume. J Magn Reson. 2013 Jan;226:35-44. doi: 10.1016/j.jmr.2012.11.001. PMCID: PMC3529815
Mainali L, Raguz M, O'Brien WJ, Subczynski WK. Properties of membranes derived from the total lipids extracted from the human lens cortex and nucleus. Biochim Biophys Acta. 2013 Jun;1828(6):1432-40. doi: 10.1016/j.bbamem.2013.02.006. PMCID: PMC4323688
Mainali L, Raguz M, Subczynski WK. Formation of cholesterol bilayer domains precedes formation of cholesterol crystals in cholesterol/dimyristoylphosphatidylcholine membranes: EPR and DSC studies. J Phys Chem B. 2013 Aug 1;117(30):8994-9003. doi: 10.1021/jp402394m. PMCID: PMC3762674
Rice AJ, Alvarez FJD, Schultz KM, Klug CS, Davidson AL, Pinkett HW. EPR Spectroscopy of MolB2C2-A Reveals Mechanism of Transport for a Bacterial Type II Molybdate Importer. J. Biol. Chem. 2013;288, 21228-21235. PMCID: PMC3774390 **JBC Paper of the Week
Schultz KM, Feix JB, Klug CS. Disruption of LptA oligomerization and affinity of the LptA-LptC interaction. Protein Sci. 2013 Nov;22(11):1639-45. doi: 10.1002/pro.2369. PMCID: PMC3831678
Valez V, Cassina A, Batinic-Haberle I, Kalyanaraman B, Ferrer-Sueta G, Radi R. Peroxynitrite formation in nitric oxide-exposed submitochondrial particles: detection, oxidative damage and catalytic removal by Mn-porphyrins. Arch Biochem Biophys. 2013 Jan 1;529(1):45-54. doi: 10.1016/j.abb.2012.10.012. PMCID: PMC3534903
Bansal S, Srinivasan S, Anandasadagopan S, Chowdhury AR, Selvaraj V, Kalyanaraman B, Joseph J, Avadhani NG. Additive effects of mitochondria-targeted cytochrome CYP2E1 and alcohol toxicity on cytochrome c oxidase function and stability of respirasome complexes. J Biol Chem. 2012 May 4;287(19):15284-97. PMCID: PMC3346148
Broniowska KA, Hogg N. The Chemical Biology of S-Nitrosothiols. Antioxid Redox Signal. 2012 Oct 1;17(7):969-80. PMCID: PMC3411335
Broniowska KA, Keszler A, Basu S, Kim-Shapiro DB, Hogg N. Cytochrome c-mediated formation of S-nitrosothiol in cells. Biochem J. 2012 Feb 15;442(1):191-7. PMCID: PMC3943432
Cheng G, Zielonka J, Dranka BP, McAllister D, Mackinnon AC Jr, Joseph J, Kalyanaraman B. Mitochondria-targeted drugs synergize with 2-deoxyglucose to trigger breast cancer cell death. Cancer Res. 2012 May 15;72(10):2634-44. PMCID: PMC3700358
Cunniff B, Benson K, Stumpff J, Newick K, Held P, Taatjes D, Joseph J, Kalyanaraman B, Heintz NH. Mitochondrial-targeted nitroxides disrupt mitochondrial architecture and inhibit expression of peroxiredoxin 3 and FOXM1 in malignant mesothelioma cells. J Cell Physiol. 2012 Sep 27. doi: 10.1002/jcp.24232. PMCID: PMC3928986
Diers AR, Broniowska KA, Chang CF, Hogg N. Pyruvate fuels mitochondrial respiration and proliferation of breast cancer cells: effect of monocarboxylate transporter inhibition. Biochem J. 2012 Jun 15;444(3):561- 71. PMCID: PMC4898201
Dranka BP, Zielonka J, Kanthasamy AG, Kalyanaraman B. Alterations in bioenergetic function induced by Parkinson's disease mimetic compounds: lack of correlation with superoxide generation. J Neurochem. 2012 Jun 18. doi: 10.1111/j.1471-4159.2012.07836.x. PMCID: PMC3423581
Drobyshevsky A, Luo K, Derrick M, Yu L, Du H, Prasad PV, Vasquez-Vivar J, Batinic-Haberle I, Tan S. Motor deficits are triggered by reperfusion-reoxygenation injury as diagnosed by MRI and by a mechanism involving oxidants. J Neurosci. 2012 Apr 18;32(16):5500-9. PMCID: PMC3332550
Francis DJ, Hubbell WL, Klug CS. Probing Protein Secondary Structure using EPR: Investigating a Dynamic Region of Visual Arrestin. Appl. Magn. Reson. 2012, Volume 43, Number 3, Pages 405-419. PMCID: PMC4240029
Gadicherla AK, Stowe DF, Antholine WE, Yang M, Camara AK. Damage to mitochondrial complex I during cardiac ischemia reperfusion injury is reduced indirectly by anti-anginal drug ranolazine. Biochim Biophys Acta. 2012 Mar;1817(3):419-29. PMCID: PMC3269517
Ghosh A, Kanthasamy A, Joseph J, Anantharam V, Srivastava P, Dranka BP, Kalyanaraman B, Kanthasamy AG. Anti-inflammatory and neuroprotective effects of an orally active apocynin derivative in pre-clinical models of Parkinson's disease. J Neuroinflammation. 2012 Oct 23;9:241. doi: 10.1186/1742-2094-9-241. PMCID: PMC3488558
Kalyanaraman B, Darley-Usmar V, Davies KJ, Dennery PA, Forman HJ, Grisham MB, Mann GE, Moore K, Roberts LJ 2nd, Ischiropoulos H. Measuring reactive oxygen and nitrogen species with fluorescent probes: challenges and limitations. Free Radic Biol Med. 2012 Jan 1;52(1):1-6. PMCID: PMC3911769
Kittell AW, Hustedt EJ, Hyde JS. Inter-spin distance determination using L-band (1-2GHz) non-adiabatic rapid sweep electron paramagnetic resonance (NARS EPR). J Magn Reson. 2012 Aug;221:51-6. PMCID: PMC3957363
Liddle BJ, Wanniarachchi S, Hewage JS, Lindeman SV, Bennett B, Gardinier JR. Electronic communication across diamagnetic metal bridges: a homoleptic gallium(III) complex of a redox-active diarylamido-based ligand and its oxidized derivatives. Inorg Chem. 2012 Dec 3;51(23):12720-8. doi: 10.1021/ic301437f. PMCID: PMC3601749
Mainali L, Raguz M, O'Brien WJ, Subczynski WK. Properties of fiber cell plasma membranes isolated from the cortex and nucleus of the porcine eye lens. Exp Eye Res. 2012 Apr;97(1):117-29. PMCID: PMC3287047
Mainali L, Raguz M, Subczynski WK. Phases and domains in sphingomyelin-cholesterol membranes: structure and properties using EPR spin-labeling methods. Eur Biophys J. 2012 Feb;41(2):147-59. PMCID: PMC3270143
Mao M, Sudhahar V, Ansenberger-Fricano K, Fernandes DC, Tanaka LY, Fukai T, Laurindo FR, Mason RP, Vasquez-Vivar J, Minshall RD, Stadler K, Bonini MG. Nitroglycerin drives endothelial nitric oxide synthase activation via the phosphatidylinositol 3-kinase/protein kinase B pathway. Free Radic Biol Med. 2012 Jan 15;52(2):427-35. EPMCID: PMC3432314
Merten JA, Schultz KM, Klug CS. Concentration-dependent oligomerization and oligomeric arrangement of LptA. Protein Sci. 2012 Feb;21(2):211-8. doi: 10.1002/pro.2004. PMCID: PMC3324765
Michalski R, Zielonka J, Hardy M, Joseph J, Kalyanaraman B. Hydropropidine: A novel, cell-impermeant fluorogenic probe for detecting extracellular superoxide. Free Radic Biol Med. 2012 Oct 7. doi:pii: S0891- 5849(12)01143-4. 10.1016/j.freeradbiomed.2012.09.018. PMCID: PMC3711142
Mukhopadhyay P, Horváth B, Zsengellėr Z, Bátkai S, Cao Z, Kechrid M, Holovac E, Erdėlyi K, Tanchian G, Liaudet L, Stillman IE, Joseph J, Kalyanaraman B, Pacher P. Mitochondrial reactive oxygen species generation triggers inflammatory response and tissue injury associated with hepatic ischemia-reperfusion: Therapeutic potential of mitochondrially targeted antioxidants. Free Radic Biol Med. 2012 Sep 1;53(5):1123- 38. PMCID: PMC3432152
Mukhopadhyay P, Horváth B, Zsengellér Z, Zielonka J, Tanchian G, Holovac E, Kechrid M, Patel V, Stillman IE, Parikh SM, Joseph J, Kalyanaraman B, Pacher P. Mitochondrial-targeted antioxidants represent a promising approach for prevention of cisplatin-induced nephropathy. Free Radic Biol Med. 2012 Jan 15;52(2):497-506. PMCID: PMC3253235
Petruk AA, Bartesaghi S, Trujillo M, Estrin DA, Murgida D, Kalyanaraman B, Marti MA, Radi R. Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: Computer simulation studies in model tyrosine-cysteine peptides in solution. Arch Biochem Biophys. 2012 Sep 1;525(1):82-91. PMCID: PMC3414218
Plesnar E, Subczynski WK, Pasenkiewicz-Gierula M. Saturation with cholesterol increases vertical order and smoothes the surface of the phosphatidylcholine bilayer: A molecular simulation study. Biochim Biophys Acta. 2012 Mar;1818(3):520-9. PMCID: PMC3273590
Sethumadhavan S, Vasquez-Vivar J, Migrino RQ, Harmann L, Jacob HJ, Lazar J. Mitochondrial DNA variant for complex I reveals a role in diabetic cardiac remodeling. J Biol Chem. 2012 Jun 22;287(26):22174-82. PMCID: PMC3381178
Soberanes S, Gonzalez A, Urich D, Chiarella SE, Radigan KA, Osornio-Vargas A, Joseph J, Kalyanaraman B, Ridge KM, Chandel NS, Mutlu GM, De Vizcaya-Ruiz A, Budinger GR. Particulate matter Air Pollution induces hypermethylation of the p16 promoter Via a mitochondrial ROS-JNK-DNMT1 pathway. Sci Rep. 2012;2:275. PMCID: PMC3281276
Subczynski WK, Raguz M, Widomska J, Mainali L, Konovalov A. Functions of cholesterol and the cholesterol bilayer domain specific to the fiber-cell plasma membrane of the eye lens. J Membr Biol. 2012 Jan;245(1):51-68. PMCID: PMC3288876
Subczynski WK, Wisniewska-Becker A, Widomska J. Can macular xanthophylls replace cholesterol in formation of the liquid-ordered phase in lipid bilayer membranes? Acta Biochim Pol. 2012;59(1):109-14. Epub 2012 Mar 17.
Swartz HM, Flood AB, Williams BB, Dong R, Swarts SG, He X, Grinberg O, Sidabras J, Demidenko E, Gui J, Gladstone DJ, Jarvis LA, Kmiec MM, Kobayashi K, Lesniewski PN, Marsh SD, Matthews TP, Nicolalde RJ, Pennington PM, Raynolds T, Salikhov I, Wilcox DE, Zaki BI. Electron paramagnetic resonance dosimetry for a large-scale radiation incident. Health Phys. 2012 Sep;103(3):255-67. doi: 10.1097/HP.0b013e3182588d92. PMCID: PMC3649772
Tejero J, Basu S, Helms C, Hogg N, King SB, Kim-Shapiro DB, Gladwin MT. Low NO concentration dependence of reductive nitrosylation reaction of hemoglobin. J Biol Chem. 2012 May 25;287(22):18262-74. PMCID: PMC3365727
Wang J, Alexanian A, Ying R, Kizhakekuttu TJ, Dharmashankar K, Vasquez-Vivar J, Gutterman DD, Widlansky ME. Acute Exposure to Low Glucose Rapidly Induces Endothelial Dysfunction and Mitochondrial Oxidative Stress: Role for AMP Kinase. Arterioscler Thromb Vasc Biol. 2012 Mar;32(3):712-20. PMCID: PMC3319449
Wisniewska-Becker A, Nawrocki G, Duda M, Subczynski WK. Structural aspects of the antioxidant activity of lutein in a model of photoreceptor membranes. Acta Biochim Pol. 2012;59(1):119-24. PMCID: PMC4116753
Yin JJ, Fu PP, Lutterodt H, Zhou YT, Antholine WE, Wamer W. Dual Role of Selected Antioxidants Found in Dietary Supplements: Crossover between Anti- and Pro-Oxidant Activities in the Presence of Copper. J Agric Food Chem. 2012 Mar 14;60(10):2554-61. PMCID: PMC3971523
Zielonka J, Sikora A, Hardy M, Joseph J, Dranka BP, Kalyanaraman B. Boronate Probes as Diagnostic Tools for Real Time Monitoring of Peroxynitrite and Hydroperoxides. Chem Res Toxicol. 2012 Sep 17;25(9):1793- 9. PMCID: PMC3501381
Zielonka J, Zielonka M, Sikora A, Adamus J, Joseph J, Hardy M, Ouari O, Dranka BP, Kalyanaraman B. Global Profiling of Reactive Oxygen and Nitrogen Species in Biological Systems: High-Throughput Real-Time Analyses. J Biol Chem. 2012 Jan 27;287(5):2984-95. PMCID: PMC3270955
Zsengellér ZK, Ellezian L, Brown D, Horváth B, Mukhopadhyay P, Kalyanaraman B, Parikh SM, Karumanchi SA, Stillman IE, Pacher P. Cisplatin nephrotoxicity involves mitochondrial injury with impaired tubular mitochondrial enzyme activity. J Histochem Cytochem. 2012 Jul;60(7):521-9. PMCID: PMC3460350
Ahmed MN, Codipilly C, Hogg N, Auten RL. The protective effect of overexpression of extracellular superoxide dismutase on nitric oxide bioavailability in the lung after exposure to hyperoxia stress. Exp. Lung Res. 2011 Feb;37:10-17.
Anderson DM, Schmalzer KM, Sato H, Casey M, Terhune SS, Haas AL, Feix JB, Frank DW. Ubiquitin and ubiquitin-modified proteins activate the Pseudomonas aeruginosa T3SS cytotoxin, ExoU. Mol Microbiol. 2011 Dec;82(6):1454-67. doi: 10.1111/j.1365-2958.2011.07904.x. PMCID: PMC3237844
Belik J, McIntyre BA, Enomoto M, Pan J, Grasemann H, Vasquez-Vivar J. Pulmonary hypertension in the newborn GTP cyclohydrolase I-deficient mouse. Free Radic Biol Med. 2011 Dec 15;51(12):2227-33. PMCID: PMC5050525
Bennett B, Hill BC. Avoiding premature oxidation during the binding of Cu(II) to a dithiolate site in BsSCO. A rapid freeze-quench EPR study. FEBS Lett. 2011 Mar 23;585(6):861-4. PMCID: PMC3109496
Benson MA, Komas SM, Schmalzer KM, Casey MS, Frank DW, Feix JB. Induced conformational changes in the activation of the pseudomonas aeruginosa type III toxin, ExoU. Biophys J. 2011 Mar 2;100(5):1335-43. PMCID: PMC3043214
Chacko BK, Srivastava A, Johnson MS, Benavides GA, Chang MJ, Ye Y, Jhala N, Murphy MP, Kalyanaraman B, Darley-Usmar VM. Mitochondria-targeted ubiquinone (MitoQ) decreases ethanol-dependent micro and macro hepatosteatosis. Hepatology. 2011 Jul;54(1):153-63. doi: 10.1002/hep.24377. PMCID: PMC3125473
Cheng G, Lopez M, Zielonka J, Hauser AD, Joseph J, McAllister D, Rowe JJ, Sugg SL, Williams CL, Kalyanaraman B. Mitochondria-targeted nitroxides exacerbate fluvastatin-mediated cytostatic and cytotoxic effects in breast cancer cells. Cancer Biol Ther. 2011 Oct 15;12(8):707-17. PMCID: PMC3218525
Ge ZD, Ionova IA, Vladic N, Pravdic D, Hirata N, Vásquez-Vivar J, Pratt PF Jr, Warltier DC, Pieper GM, Kersten JR. Cardiac-specific overexpression of GTP cyclohydrolase 1 restores ischemic preconditioning during hyperglycaemia. Cardiovasc Res. 2011 Jul 15;91(2):340-9. PMCID: PMC3125073
Kalyanaraman B. Oxidative chemistry of fluorescent dyes: implications in the detection of reactive oxygen and nitrogen species. Biochem Soc Trans. 2011 Oct;39(5):1221-5.
Kalyanaraman B, Darley-Usmar V, Davies KJ, Dennery PA, Forman HJ, Grisham MB, Mann GE, Moore K, Roberts LJ 2nd, Ischiropoulos H. Measuring reactive oxygen and nitrogen species with fluorescent probes: challenges and limitations. Free Radic Biol Med. 2011 Oct 2;52:1-6. PMCID: PMC3911769
Khan SA, Nanduri J, Yuan G, Kinsman B, Kumar GK, Joseph J, Kalyanaraman B, Prabhakar NR. NADPH oxidase 2 mediates intermittent hypoxia-induced mitochondrial complex I inhibition: relevance to blood pressure changes in rats. Antioxid. Redox Signal. 2011 Feb 15;14:533-542. PMCID: PMC3038125
Kittell AW, Camenisch TG, Ratke JJ, Sidabras JW, Hyde JS. Detection of undistorted continuous wave (CW) electron paramagnetic resonance (EPR) spectra with non-adiabatic rapid sweep (NARS) of the magnetic field. J Magn Reson. 2011 Aug;211(2):228-33. PMCID: PMC3148028
Kolesar JM, Sachidanandam K, Schelman WR, Eickhoff J, Holen KD, Traynor AM, Alberti DB, Thomas JP, Chitambar CR, Wilding G, Antholine WE. Cytotoxic Evaluation of 3-Aminopyridine-2-Carboxaldehyde Thiosemicarbazone, 3-AP, in Peripheral Blood Lymphocytes of Patients with Refractory Solid Tumors using Electron Paramagnetic Resonance. Exp Ther Med. 2011 Jan;2(1):119-123. PMID:21373381
Kowalski JM, Bennett B. Spin Hamiltonian Parameters for Cu(II)-Prion Peptide Complexes from L-Band Electron Paramagnetic Resonance Spectroscopy. J Am Chem Soc. 2011 Jan 25. [Epub ahead of print]
Krishnapuram R, Dhurandhar EJ, Dubuisson O, Kirk-Ballard H, Bajpeyi S, Butte NF, Sothern MS, LarsenMeyer E, Chalew S, Bennett B, Gupta AK, Greenway FL, Johnson WD, Brashear M, Reinhart G, Rankinen T, Bouchard C, Cefalu WT, Ye J, Javier R, Zuberi A, Dhurandhar NV. A template to improve glycemic control without reducing adiposity or dietary fat. Am J Physiol Endocrinol Metab. 2011 May;300(5):E779-89. PMCID: PMC3093976
Kumar SN, Konorev EA, Aggarwal D, Kalyanaraman B. Analysis of proteome changes in doxorubicin-treated adult rat cardiomyocyte. J. Proteomics J Proteomics. 2011 May 1;74(5):683-97. PMCID: PMC3298037
Leskov IL, Whitsett J, Vasquez-Vivar J, Stokes KY. NAD(P)H oxidase and eNOS play differential roles in cytomegalovirus infection-induced microvascular dysfunction. Free Radic Biol Med. 2011 Dec 15;51(12):2300-8. PMCID: PMC3272703
Mainali L, Feix JB, Hyde JS, Subczynski WK. Membrane fluidity profiles as deduced by saturation-recovery EPR measurements of spin-lattice relaxation times of spin labels. J Magn Reson. 2011 Oct;212(2):418-25. PMCID: PMC3214655
Mainali L, Raguz M, Camenisch TG, Hyde JS, Subczynski WK. Spin-label saturation-recovery EPR at Wband: applications to eye lens lipid membranes. J Magn Reson. 2011 Sep;212(1):86-94. PMCID: PMC3163743
Mainali L, Raguz M, Subczynski WK. Phase-separation and domain-formation in cholesterol-sphingomyelin mixture: pulse-EPR oxygen probing. Biophys J. 2011 Aug 17;101(4):837-46. PMCID: PMC3175055
Mett RR, Sidabras JW, Anderson JR, Hyde JS. Hyperbolic-cosine waveguide tapers and oversize rectangular waveguide for reduced broadband insertion loss in W-band electron paramagnetic resonance spectroscopy. Rev Sci Instrum. 2011 Jul;82(7):074704. PMCID: PMC4798996
Murphy MP, Holmgren A, Larsson NG, Halliwell B, Chang CJ, Kalyanaraman B, Rhee SG, Thornalley PJ, Partridge L, Gems D, Nyström T, Belousov V, Schumacker PT, Winterbourn CC. Unraveling the biological roles of reactive oxygen species. Cell. Metab. 2011 Apr 6;13:361-366. PMCID: PMC4445605
Myers JM, Antholine WE, Myers CR. The intracellular redox stress caused by hexavalent chromium is selective for proteins that have key roles in cell survival and thiol redox control. Toxicology. 2011 Mar 15;281(1-3):37-47. PMCID: PMC3039098
Myers JM, Antholine WE, Zielonka J, Myers CR. The iron-chelating drug triapine causes pronounced mitochondrial thiol redox stress. Toxicol Lett. 2011 Mar 5;201(2):130-6. PMCID: PMC21195754
Patel RP, Hogg N, Kim-Shapiro DB. The potential role of the red blood cell in nitrite-dependent regulation of blood flow. Cardiovasc. Res. 2011 Feb;89:507-515. PMCID: PMC3028972
Raguz M, Mainali L, Widomska J, Subczynski WK. The immiscible cholesterol bilayer domain exists as an integral part of phospholipid bilayer membranes. Biochim Biophys Acta. 2011 Apr;1808(4):1072-80. PMCID: PMC3062709
Raguz M, Mainali L, Widomska J, Subczynski WK. Using spin-label electron paramagnetic resonance (EPR) to discriminate and characterize the cholesterol bilayer domain. Chem Phys Lipids. 2011 Aug 9.2011 Nov;164(8):819-29. PMCID: PMC3206151
Schultz KM, Merten JA, Klug CS. Characterization of the E506Q and H537A Dysfunctional Mutants in the E. coli ABC Transporter MsbA. Biochemistry. 2011 May 10;50(18):3599-608. PMCID: PMC3128438
Schultz KM, Merten JA, Klug CS. Effects of the L511P and D512G Mutations on the Escherichia coli ABC Transporter MsbA. Biochemistry. 2011 Apr 5;50(13):2594-602. PMCID: PMC3110719
Sikora A, Zielonka J, Lopez M, Dybala-Defratyka A, Joseph J, Marcinek A, Kalyanaraman B. Reaction between Peroxynitrite and Boronates: EPR Spin-Trapping, HPLC Analyses, and Quantum Mechanical Study of the Free Radical Pathway. Chem Res Toxicol. 2011 May 16;24(5):687-97. PMCID: PMC3743543
Subczynski WK, Mainali L, Camenisch TG, Froncisz W, Hyde JS. Spin-label oximetry at Q- and W-band. J Magn Reson. 2011 Apr;209(2):142-8. PMCID: PMC3065517
Vishnivetskiy SA, Gimenez LE, Francis DJ, Hunson SM, Hubbell WL, Klug CS, Gurevich VV. Few residues within an extensive binding interface drive receptor interaction and determine the specificity of arrestin proteins. J Biol Chem. 2011 Jul 8;286(27):24288-99. PMCID: PMC3129209
Wanniarachchi S, Liddle BJ, Toussaint J, Lindeman SV, Bennett B, Gardinier JR. Using sterics to promote reactivity in fac-Re(CO)(3) complexes of some "non-innocent" NNN-pincer ligands. Dalton Trans. 2011 Sep 21;40(35):8776-87.
Yu L, Derrick M, Ji H, Silverman RB, Whitsett J, Vásquez-Vivar J, Tan S. Neuronal nitric oxide synthase inhibition prevents cerebral palsy following hypoxia-ischemia in fetal rabbits: comparison between JI-8 and 7-nitroindazole. Dev Neurosci. 2011;33(3-4):312-9. PMCID: PMC3225251
Zhu BZ, Mao L, Fan RM, Zhu JG, Zhang YN, Wang J, Kalyanaraman B, Frei B. Ergothioneine prevents copper-induced oxidative damage to DNA and protein by forming a redox-inactive ergothioneine-copper complex. Chem. Res. Toxicol. 2011 Jan 14;24:30-34.
Bodemer GJ, Antholine WA, Basova LV, Saffarini D, Pacheco AA. The effect of detergents and lipids on the properties of the outer-membrane protein OmcA from Shewanella oneidensis. J Biol Inorg Chem. 2010 Jun;15(5):749-58.
Chandran K, McCracken J, Peterson FC, Antholine WE, Volkman BF, Kalyanaraman B. Oxidation of Histidine Residues in Copper-Zinc Superoxide Dismutase by Bicarbonate-Stimulated Peroxidase and Thiol Oxidase Activities: Pulse EPR and NMR Studies. Biochemistry. 2010 Nov 1;49:10616-22.
Cheng Q, Antholine WE, Myers JM, Kalyanaraman B, Arnér ES, Myers CR. The selenium-independent inherent pro-oxidant NADPH oxidase activity of mammalianthioredoxin reductase and its seleniumdependent direct peroxidase activities. J Biol Chem. 2010 Jul 9;285(28):21708-23. PMCID: PMC2898413
Choi DW, Bandow NL, McEllistrem MT, Semrau JD, Antholine WE, Hartsel SC, Gallagher W, Zea CJ, Pohl NL, Zahn JA, DiSpirito AA. Spectral and thermodynamic properties of methanobactin from γ-proteobacterial methane oxidizing bacteria: a case for copper competition on a molecular level. J Inorg Biochem. 2010 Dec;104(12):1240-7.
Farver O, Wherland S, Antholine WE, Gemmen GJ, Chen Y, Pecht I, Fee JA. Pulse radiolysis studies of temperature dependent electron transfers among redox centers in ba3-cytochrome c oxidase from Thermus thermophilus: Comparison of A- and B-type enzymes. Biochemistry. 2010 Oct 28. [Epub ahead of print]
Ghosh A, Chandran K, Kalivendi SV, Joseph J, Antholine WE, Hillard CJ, Kanthasamy A, Kanthasamy A, Kalyanaraman B. Neuroprotection by a mitochondria-targeted drug in a Parkinson's disease model. Free Radic Biol Med. 2010 Dec 1;49(11):1674-84. PMCID: PMC4020411
Goetz BI, Shields HW, Basu S, Wang P, King SB, Hogg N, Gladwin MT, Kim-Shapiro DB. An electron paramagnetic resonance study of the affinity of nitrite for methemoglobin. Nitric Oxide. 2010 Feb 15;22(2):149-54. PMCID: PMC2819623
Hogg N. Detection of nitric oxide by electron paramagnetic resonance spectroscopy. Free Radic Biol Med. 2010 Jul 15;49(2):122-9. PMCID: PMC2916063
Hyde JS, Strangeway RA, Camenisch TG, Ratke JJ, Froncisz W. W-band frequency-swept EPR. J Magn Reson. 2010 Jul;205(1):93-101. PMCID: PMC2885579
Keszler A, Zhang Y, Hogg N. Reaction between nitric oxide, glutathione, and oxygen in the presence and absence of protein: How are S-nitrosothiols formed? Free Radic. Biol. Med. 2010 Jan 1;48:55-64. PMCID: PMC2829852
Limphong P, McKinney RM, Adams NE, Makaroff CA, Bennett B, Crowder MW. The metal ion requirements of Arabidopsis thaliana Glx2-2 for catalytic activity. J. Biol. Inorg. Chem. 2010 Feb;15:249-258.
Myers CR, Antholine WE, Myers JM. The pro-oxidant chromium(VI) inhibits mitochondrial complex I, complex II, and aconitase in the bronchial epithelium: EPR markers for Fe-S proteins. Free Radic Biol Med. 2010 Sep 27;49:1903-1915.
Subczynski WK, Raguz M, Widomska J. Studying lipid organization in biological membranes using liposomes and EPR spin labeling. Methods Mol. Biol. 2010;606:247-269. PMCID: PMC4640678
Subczynski WK, Wisniewska A, Widomska J. Location of macular xanthophylls in the most vulnerable regions of photoreceptor outer-segment membranes. Arch Biochem Biophys. 2010 Dec 1;504(1):61-6. PMCID: PMC2957566
Vishnivetskiy SA, Francis D, Van Eps N, Kim M, Hanson SM, Klug CS, Hubbell WL, Gurevich VV. The role of arrestin alpha-helix I in receptor binding. J. Mol. Biol. 10 Jan;395:42-54. PMCID: PMC2787876
Zhu BZ, Mao L, Fan RM, Zhu JG, Zhang YN, Wang J, Kalyanaraman B, Frei B. Ergothioneine Prevents Copper-Induced Oxidative Damage to DNA and Protein by Forming a Redox-Inactive Ergothioneine-Copper Complex. Chem Res Toxicol. 2010 Nov 3;24:30-34.
Zielonka J, Sikora A, Joseph J, Kalyanaraman B. Peroxynitrite is the major species formed from different flux ratios of co-generated nitric oxide and superoxide: direct reaction with boronate-based fluorescent probe. J Biol Chem. 2010 May 7;285(19):14210-6. PMCID: PMC2863194