Nikolay Dokholyan

G. Thomas Passananti Professor of Pharmacology; Professor of Biochemistry and Molecular Biology

Nikolay Dokholyan

Research Summary

We are a translational systems research group in the Pharmacology at the Penn State College of Medicine. Our laboratory focuses on understanding etiologies of human diseases, such as cystic fibrosis (CF), amyotrophic lateral sclerosis (ALS), and pain conditions, such as hyperalgesia.

Huck Graduate Students

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Publication Tags

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Proteins Molecular Models Protein Rna Mutation Ligands Src Family Kinases Computational Biology Protein Engineering Cystic Fibrosis Cystic Fibrosis Transmembrane Conductance Regulator Protein Conformation Protein Stability Mutant Proteins Enzyme Activation Nucleic Acid Conformation Genetic Engineering Allosteric Regulation Signal Transduction Lumacaftor Drug Light Pharmacology Thermodynamics Therapeutics

Most Recent Publications

Deciphering the Mechanistic Basis for Perfluoroalkyl-Protein Interactions

Atip Lawanprasert, Janna N. Sloand, Mariangely González Vargas, Harminder Singh, Tomer Eldor, Michael A. Miller, Sopida Pimcharoen, Jian Wang, Scott M. Leighow, Justin R. Pritchard, Nikolay V. Dokholyan, Scott H. Medina, 2023, ChemBioChem

Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase

Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V. Dokholyan, Charles W. Carter, 2023, Structural Dynamics

Big versus small: The impact of aggregate size in disease

Brianna Hnath, Jiaxing Chen, Joshua Reynolds, Esther Choi, Jian Wang, Dongyan Zhang, Congzhou M. Sha, Nikolay V. Dokholyan, 2023, Protein Science

Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs) via Enzymatic Degradation

Damian Beasock, Anh Ha, Justin Halman, Martin Panigaj, Jian Wang, Nikolay V. Dokholyan, Kirill A. Afonin, 2023, Bioconjugate Chemistry on p. 1139-1146

A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments

Jiaxing Chen, Yashavantha L. Vishweshwaraiah, Richard B. Mailman, Erdem D. Tabdanov, Nikolay V. Dokholyan, 2023, Science advances

Structural and dynamic insights into α-synuclein dimer conformations

Joanna Zamel, Jiaxing Chen, Sofia Zaer, Paul David Harris, Paz Drori, Mario Lebendiker, Nir Kalisman, Nikolay V. Dokholyan, Eitan Lerner, 2023, Structure with Folding & design on p. 411-423.e6

Allosteric inactivation of an engineered optogenetic GTPase

Abha Jain, Nikolay V. Dokholyan, Andrew L. Lee, 2023, Proceedings of the National Academy of Sciences of the United States of America

An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity

J. A. Reynolds, Y. L. Vishweshwaraiah, V. R. Chirasani, J. R. Pritchard, N. V. Dokholyan, 2023, Journal of Biological Chemistry

Editorial to “Molecular engineering of biomaterials programmed to operate in living systems”

Kirill A. Afonin, Nikolay V. Dokholyan, 2023, Advanced Drug Delivery Reviews

Structural evolution of Delta lineage of SARS-CoV-2

Mohammad Mahmoudi Gomari, Parastoo Tarighi, Edris Choupani, Shadi Abkhiz, Masoud Mohamadzadeh, Neda Rostami, Esmaeil Sadroddiny, Soukayna Baammi, Vladimir N. Uversky, Nikolay V. Dokholyan, 2023, International Journal of Biological Macromolecules on p. 1116-1140

Most-Cited Papers

Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis

Phuong H. Nguyen, Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Dominguez, Joan Emma Shea, Nikolay V. Dokholyan, Alfonso de Simone, Buyong Ma, Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesné, Guanghong Wei, Fabio Sterpone, Andrew J. Doig, Philippe Derreumaux, 2021, Chemical Reviews on p. 2545-2647

Cystic fibrosis: Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

Deborah M. Cholon, Nancy L. Quinney, M. Leslie Fulcher, Charles R. Esther, Jhuma Das, Nikolay V. Dokholyan, Scott H. Randell, Richard C. Boucher, Martina Gentzsch, 2014, Science Translational Medicine

Allostery in Its Many Disguises: From Theory to Applications

Shoshana J. Wodak, Emanuele Paci, Nikolay V. Dokholyan, Igor N. Berezovsky, Amnon Horovitz, Jing Li, Vincent J. Hilser, Ivet Bahar, John Karanicolas, Gerhard Stock, Peter Hamm, Roland H. Stote, Jerome Eberhardt, Yassmine Chebaro, Annick Dejaegere, Marco Cecchini, Jean Pierre Changeux, Peter G. Bolhuis, Jocelyne Vreede, Pietro Faccioli, Simone Orioli, Riccardo Ravasio, Le Yan, Carolina Brito, Matthieu Wyart, Paraskevi Gkeka, Ivan Rivalta, Giulia Palermo, J. Andrew McCammon, Joanna Panecka-Hofman, Rebecca C. Wade, Antonella Di Pizio, Masha Y. Niv, Ruth Nussinov, Chung Jung Tsai, Hyunbum Jang, Dzmitry Padhorny, Dima Kozakov, Tom McLeish, 2019, Structure with Folding & design on p. 566-578

Controlling Allosteric Networks in Proteins

Nikolay V. Dokholyan, 2016, Chemical Reviews on p. 6463-6487

Engineering extrinsic disorder to control protein activity in living cells

Onur Dagliyan, Miroslaw Tarnawski, Pei Hsuan Chu, David Shirvanyants, Ilme Schlichting, Nikolay V. Dokholyan, Klaus M. Hahn, 2016, Science on p. 1441-1444

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Zhichao Miao, Ryszard W. Adamiak, Marc Frédérick Blanchet, Michal Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Clarence Cheng, Grzegorz Chojnowski, Fang Chieh Chou, Pablo Cordero, José Almeida Cruz, Adrian R. Ferré-D'Amaré, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Stanislaw Dunin-Horkawicz, Wipapat Kladwang, Andrey Krokhotin, Grzegorz Lach, Marcin Magnus, François Major, Thomas H. Mann, Benoît Masquida, Dorota Matelska, Mélanie Meyer, Alla Peselis, Mariusz Popenda, Katarzyna J. Purzycka, Alexander Serganov, Juliusz Stasiewicz, Marta Szachniuk, Arpit Tandon, Siqi Tian, Jian Wang, Yi Xiao, Xiaojun Xu, Jinwei Zhang, Peinan Zhao, Tomasz Zok, Eric Westhof, 2015, RNA on p. 1066-1084

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Robert T. Batey, Alexander J. Becka, Marcin Biesiada, Michał J. Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Clarence Yu Cheng, Fang Chieh Chou, Adrian R. Ferré-D'Amaré, Rhiju Das, Wayne K. Dawson, Feng Ding, Nikolay V. Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E. Łach, François Major, Thomas H. Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J. Patel, Joseph A. Piccirilli, Mariusz Popenda, Katarzyna J. Purzycka, Aiming Ren, Greggory M. Rice, John Santalucia, Joanna Sarzynska, Marta Szachniuk, Arpit Tandon, Jeremiah J. Trausch, Siqi Tian, Jian Wang, Kevin M. Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof, 2017, RNA on p. 655-672

Correctors of δF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

Lihua He, Pradeep Kota, Andrei A. Aleksandrov, Liying Cui, Tim Jensen, Nikolay V. Dokholyan, John R. Riordan, 2013, FASEB Journal on p. 536-545

Single-molecule correlated chemical probing of RNA

Philip J. Homan, Oleg V. Favorov, Christopher A. Lavender, Olcay Kursun, Xiyuan Ge, Steven Busan, Nikolay V. Dokholyan, Kevin M. Weeks, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 13858-13863

Rational design of a ligand-controlled protein conformational switch

Onur Dagliyan, David Shirvanyants, Andrei V. Karginov, Feng Ding, Lanette Fee, Srinivas N. Chandrasekaran, Christina M. Freisinger, Gromoslaw A. Smolen, Anna Huttenlocher, Klaus M. Hahn, Nikolay V. Dokholyan, 2013, Proceedings of the National Academy of Sciences of the United States of America on p. 6800-6804

News Articles Featuring Nikolay Dokholyan

Jul 31, 2023

Penn State CTSI announces seven Bridges to Translation pilot funding recipients

Penn State Clinical and Translational Science Institute is helping to generate innovative health research ideas and promote collaboration through the awarding of pilot grants in its "Bridges to Translation" program.

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May 26, 2023

Protein-based nano-‘computer’ evolves in ability to influence cell behavior

The first protein-based nano-computing agent that functions as a circuit has been created by Penn State researchers.

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Oct 26, 2022

Penn State researchers to explore using quantum computers to design new drugs

The time it takes medicines to move from discovery to approved use for patients can take decades and cost billions of dollars. Now, a $1.2 million National Science Foundation grant will help a team of Penn State researchers study the use of quantum computer-based artificial intelligence (AI) to see if quantum computers can bring drugs to patients faster and cheaper.

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Oct 25, 2022

Penn State scientists developing mutation-proof COVID vaccine

Each year, doctors urge people to get a flu shot because the virus changes and requires a new vaccine. A similar pattern seems to be appearing for COVID every time a new variant is discovered.

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Oct 19, 2022

Penn State researchers engineer protein that could be used to develop 1-dose covid vaccine

Despite receiving one of the three covid-19 vaccines available in the U.S., many Americans continue to become infected with the virus.

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Oct 18, 2022

Newly engineered protein could be used to develop adaptation-proof COVID vaccine

A vaccine design approach that could protect against new variants of SARS-CoV-2 — the virus that causes COVID-19 — but also potentially protects against other coronaviruses is one step closer to reality as a result of research at Penn State College of Medicine.

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Nov 16, 2021

Nanoscale ‘computer’ controls function of protein, influences cell behavior

The creation of nanoscale computers for use in precision health care has long been a dream of many scientists and health care providers. Now, for the first time, researchers at Penn State have produced a nanocomputing agent that can control the function of a particular protein that is involved in cell movement and cancer metastasis.

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Mar 26, 2020

Researchers mobilize to study COVID-19 from multiple angles

Penn State funds 17 research proposals, ranging from vaccine development to improved predictive modeling, with more to come.

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Mar 23, 2020

Penn State funds first round of COVID-19 research proposals

One week after launching a rapid-fire call for proposals, awards are granted to six projects that address the global pandemic, with more to follow

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Nov 26, 2019

Fourteen Penn State faculty recognized with lifetime honor

Fourteen Penn State faculty members in areas ranging from physics and engineering to entomology and plant science have been named fellows of the American Association for the Advancement of Science (AAAS), the world’s largest general scientific society. A lifetime honor bestowed upon members by their peers, a total of 443 individuals are being recognized for their extraordinary achievements in advancing science.

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