Nikolay V. Dokholyan | |
---|---|
Nationality | American |
Occupation(s) | Biophysicist, academic and researcher |
Awards | March of Dimes Basil O’Connor Starter Scholar Research Award Fellow, American Physical Society Michael Hooker Distinguished Professorship G. Thomas Passananti Professorship Distinguished Edmond J. Safra Center Speaker, Tel Aviv University Fellow, American Association for the Advancement of Science Fellow, American Institute for Medical and Biological Engineering (AIMBE) |
Academic background | |
Education | B.S., Physics M.S., Physics Ph.D., Physics |
Alma mater | Moscow Institute of Physics and Technology, Russia Boston University, USA |
Academic work | |
Institutions | Penn State College of Medicine |
Nikolay V. Dokholyan is an American biophysicist,academic and researcher. He is a G. Thomas Passananti Professor and Vice Chair for Research at Penn State College of Medicine. [1]
Dokholyan’s research primarily focuses on translational research,with a particular attention on the applications of basic science in terms of addressing some of the challenging problems in biology and medicine. [2] He is the author of a book entitled Computational Modeling of Biological Systems.
Dokholyan is a fellow of the American Association for the Advancement of Science, [3] and American Physical Society, [4] the founder of the CFold,Inc.,and the founder and President of the Molecules in Action,LLC. [5] He serves as Book Series Editor for Series in Computational Biophysics, [6] Editor-in-Chief for Proteins:Structure,Function,and Bioinformatics, [7] and an Editor for F1000 Research. [8]
Dokholyan studied at Moscow Institute of Physics and Technology and received his Bachelor’s and master's degree in physics in 1992 and 1994,respectively. He then moved to the United States,earning his Doctoral degree in physics from Boston University in 1999 with H. Eugene Stanley. He served as a National Institutes of Health Postdoctoral Fellow in the Department of Chemistry and Chemical Biology at Harvard University till 2002. [9]
Dokholyan started his career in 1988 with a two-year appointment as a Teacher of Physics and Mathematics in a school at Moscow Institute of Physics and Technology. From 2002 till 2008,he served as an assistant professor of biochemistry and biophysics at the University of North Carolina at Chapel Hill,and also held secondary appointments as faculty of Bioinformatics and Computational Biology Training Program,Molecular and Cellular Biophysics Program,and Carolina Center for Genome Sciences. He joined the faculty of Neuroscience Center in 2005,and Lineberger Comprehensive Cancer Center in 2006. In 2008 he was tenured and promoted to associate professor of biochemistry and biophysics,and in 2009,he joined the faculty at Cystic Fibrosis and Pulmonary Research &Treatment Center,and Center for Neurosensory Disorders. He served as a member of The North Carolina Translational and Clinical Sciences Institute from 2010 to 2018,as professor in the department of biochemistry and biophysics from 2011 to 2018,and as Michael Hooker Distinguished Professor from 2014 to 2018 at University of North Carolina at Chapel Hill. In 2017,he held appointment as adjunct professor in the Joint Department of Biomedical Engineering at University of North Carolina at Chapel Hill and North Carolina State University. Currently,he serves as adjunct professor at University of North Carolina at Chapel Hill,and holds adjunct appointments in the Departments of chemistry department and Biomedical Engineering at The Pennsylvania State University. He is also associated with The Huck Institutes of the Life Sciences. [1] He serves as the G. Thomas Passananti Professor and Vice Chair for Research at the Penn State College of Medicine where he holds appointments in the Departments of Pharmacology and Biochemistry &Molecular Biology. [1] In 2021,he became an associate director of the Penn State Clinical and Translational Science Institute. [10]
Dokholyan’s research falls in the areas of computational biology,translational science,biophysics,and biochemistry. [11] His work is focused on developing and understanding basic principles of protein misfolding in neurodegenerative diseases using computational and experimental approaches. His lab has explored the approaches to molecular dynamics simulations and modeling,and drug discovery,while focusing on both biological therapeutics and small molecule screening. [12]
In his study regarding ALS,Dokholyan determined the SOD1 aggregation pathway,and highlighted the occurrence of familial amyotrophic lateral sclerosis-linked SOD1 aggregation due to a mutation-induced increase in dimer dissociation and/or increase in apomonomer formation. [13] He also discovered post-translational modifications of superoxide dismutase (SOD1) in human erythrocytes,and found that glutathionylation promotes SOD1 monomer formation and supports a model in which increased oxidative stress promotes SOD1 aggregation. [14] In 2011,he studied the role of glutathionylation at Cys-111 in terms of inducing dissociation of wild type and FALS mutant SOD1 dimers using computational structural modeling. He further explored the model of ALS etiology,and found out that oxidative stress and aging are linked to protein aggregation. [15]
Dokholyan described the toxicity of nonnative SOD1 trimer in terms of motor neurons,discovered the capability of SOD1 mutants in promoting trimerization increase cell death,and regarded the identification of cytotoxic species as a primary step in context of elucidating the molecular etiology of ALS. [16] In 2018,he conducted a study based on the impacts of Large SOD1 aggregates on cell viability in a model of amyotrophic lateral sclerosis. Results of his study indicated that unlike trimeric SOD,large amyloid aggregates are protective to motor neurons. [17]
Dokholyan developed numerous tools for functional regulation of proteins in living cells. [18] He also introduced concept of nanocomputing agents (NCAs),discussed its benefits in terms of promoting deeper understanding of human biology and disease,and facilitating the development of in situ precision therapeutics. [19] In 2002,he regarded amino acids as nucleation centers for protein folding,and emphasized their "small-world" feature of having a limited set of vertices with large connectivity. [20] Using the approach of Rapaport, [21] he further developed discrete molecular dynamics studies of the folding of a protein-like model. [22]
In 2019,Dokholyan developed epitopes that triggered immune response in rabbits capable of inactivation of live HIV virus. He explored basic structural elements for targets of protective antibodies,and demonstrated that design immunogens with high mimicry to viral proteins lead to the exploration of new templates for vaccine development. [23]
Superoxide dismutase (SOD,EC 1.15.1.1) is an enzyme that alternately catalyzes the dismutation (or partitioning) of the superoxide (O−
2) radical into ordinary molecular oxygen (O2) and hydrogen peroxide (H
2O
2). Superoxide is produced as a by-product of oxygen metabolism and,if not regulated,causes many types of cell damage. Hydrogen peroxide is also damaging and is degraded by other enzymes such as catalase. Thus,SOD is an important antioxidant defense in nearly all living cells exposed to oxygen. One exception is Lactobacillus plantarum and related lactobacilli,which use a different mechanism to prevent damage from reactive O−
2.
Structural biology is a field that is many centuries old which,as defined by the Journal of Structural Biology,deals with structural analysis of living material at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes.
Protein folding is the physical process where a protein chain is translated into its native three-dimensional structure,typically a "folded" conformation,by which the protein becomes biologically functional. Via an expeditious and reproducible process,a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids. At this stage,the polypeptide lacks any stable three-dimensional structure. As the polypeptide chain is being synthesized by a ribosome,the linear chain begins to fold into its three-dimensional structure.
The Max Planck Institute of Biochemistry (MPIB) is a research institute of the Max Planck Society located in Martinsried,a suburb of Munich. The institute was founded in 1973 by the merger of three formerly independent institutes:the Max Planck Institute of Biochemistry,the Max Planck Institute of Protein and Leather Research,and the Max Planck Institute of Cell Chemistry.
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics,chemistry,engineering,mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure,structural organization,and dynamic behaviour at various levels of complexity. This discipline covers topics such as the measurement of molecular forces,molecular associations,allosteric interactions,Brownian motion,and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures,as well as novel experimental approaches.
Gregory A. Petsko is an American biochemist and member of the National Academy of Sciences,the National Academy of Medicine,the American Academy of Arts and Sciences,and the American Philosophical Society. He is currently Professor of Neurology at the Ann Romney Center for Neurologic Diseases at Harvard Medical School and Brigham and Women's Hospital. He formerly had an endowed professorship in Neurology and Neuroscience at Weill Cornell Medical College and is still an adjunct professor of Biomedical Engineering at Cornell University,and is also the Gyula and Katica Tauber Professor,Emeritus,in biochemistry and chemistry at Brandeis University. On October 24,2023,in a ceremony in the East Room of the White House,President Joe Biden presented Gregory Petsko and eight others with the National Medal of Science,the highest honor the United States can bestow on a scientist and engineer.
Superoxide dismutase [Cu-Zn] also known as superoxide dismutase 1 or hSod1 is an enzyme that in humans is encoded by the SOD1 gene,located on chromosome 21. SOD1 is one of three human superoxide dismutases. It is implicated in apoptosis,familial amyotrophic lateral sclerosis and Parkinson's disease.
The serine/threonine-protein kinase/endoribonuclease inositol-requiring enzyme 1 α (IRE1α) is an enzyme that in humans is encoded by the ERN1 gene.
Amyotrophic lateral sclerosis (ALS),also known as motor neurone disease (MND) or Lou Gehrig's disease,is a rare and terminal neurodegenerative disease that results in the progressive loss of motor neurons that control voluntary muscles. ALS is the most common form of the motor neuron diseases. Early symptoms of ALS include stiff muscles,muscle twitches,gradual increasing weakness,and muscle wasting. Limb-onset ALS begins with weakness in the arms or legs,while bulbar-onset ALS begins with difficulty in speaking or swallowing. Around half of people with ALS develop at least mild difficulties with thinking and behavior,and about 15% develop frontotemporal dementia. Motor neuron loss continues until the abilities to eat,speak,move,or,lastly,breathe are lost.
Reginald John Ellis is a British scientist.
Victor Muñoz is a biochemist whose focus has been on protein folding and design. He provided experimental evidence for a mechanism of protein folding called as "downhill folding". He has pioneered various computational and experimental techniques to study this mechanism as well as to gain insights into the general process of protein folding.
Ruth Nussinov is an Israeli-American biologist born in Rehovot who works as a Professor in the Department of Human Genetics,School of Medicine at Tel Aviv University and is the Senior Principal Scientist and Principal Investigator at the National Cancer Institute,National Institutes of Health. Nussinov is also the Editor in Chief of the Current Opinion in Structural Biology and formerly of the journal PLOS Computational Biology.
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred. Usually this common ancestry is inferred from structural alignment and mechanistic similarity,even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent. Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.
Sheena Elizabeth Radford FRS FMedSci is a British biophysicist,and Astbury Professor of Biophysics in the Astbury Centre for Structural Molecular Biology,School of Molecular and Cellular Biology at the University of Leeds. Radford is the Associate Editor of the Journal of Molecular Biology.
Copper chaperone for superoxide dismutase is a metalloprotein that is responsible for the delivery of Cu to superoxide dismutase (SOD1). CCS is a 54kDa protein that is present in mammals and most eukaryotes including yeast. The structure of CCS is composed of three distinct domains that are necessary for its function. Although CCS is important for many organisms,there are CCS independent pathways for SOD1,and many species lack CCS all together,such as C. elegans. In humans the protein is encoded by the CCS gene.
Narayanaswamy Srinivasan was an Indian molecular biophysicist and a professor and the head of Proteins:Structure,Function and Evolutionary Group at the Molecular Biophysics Unit of the Indian Institute of Science. He is known for his researches in the fields of computational genomics and protein structure analysis. An elected fellow of the Indian Academy of Sciences and the National Academy of Sciences,India,he is a J. C. Bose National fellow of the Department of Biotechnology and a recipient of the National Bioscience Award for Career Development of the Department of Science and Technology. The Council of Scientific and Industrial Research,the apex agency of the Government of India for scientific research,awarded him the Shanti Swarup Bhatnagar Prize for Science and Technology,one of the highest Indian science awards,in 2007,for his contributions to biological sciences.
Benjamin Wolozin is an American pharmacologist and neurologist currently at Boston University School of Medicine and an Elected Fellow of the American Association for the Advancement of Science.
There are more than 25 genes known to be associated with amyotrophic lateral sclerosis (ALS) as of June 2018,which collectively account for about 70% of cases of familial ALS (fALS) and 10% of cases of sporadic ALS (sALS). About 5–10% of cases of ALS are directly inherited. Overall,first-degree relatives of an individual with ALS have a 1% risk of developing ALS. ALS has an oligogenic mode of inheritance,meaning that mutations in two or more genes are required to cause disease.
Research on amyotrophic lateral sclerosis (ALS) has focused on animal models of the disease,its mechanisms,ways to diagnose and track it,and treatments.
Jean Baum is an American chemist. She is the distinguished professor of chemistry and chemical biology at Rutgers University,where she is also vice dean for research and graduate education in the school of arts and sciences,and also vice chair of the department of chemistry and chemical biology. Her research investigates protein–protein interaction and protein aggregation using nuclear magnetic resonance spectroscopy (NMR) and other biochemical and biophysical techniques. She serves as treasurer for the Protein Society.