Nikolay V. Dokholyan

Penn State Milton S. Hershey Medical Center

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Feng Ding

Shenzhen Third People’s Hospital

Jian Wang

Penn State Milton S. Hershey Medical Center

Elizabeth A. Proctor

Pennsylvania State University

Srinivas Ramachandran

University of Colorado Denver

Pradeep Kota

University of North Carolina at Chapel Hill

Sergey V. Buldyrev

Yeshiva University

H. Eugene Stanley

Boston University

Venkat R. Chirasani

University of North Carolina at Chapel Hill

Feng Ding

Shenzhen Institutes of Advanced Technology

Eugene I. Shakhnovich

Harvard University

Cooperative Institutions

University of North Carolina at Chapel Hill

340

Pennsylvania State University

108

UNC Lineberger Comprehensive Cancer Center

Harvard University

National Institutes of Health

Indiana University School of Medicine

University of North Carolina Health Care

Penn State Milton S. Hershey Medical Center

Stanford University

Howard Hughes Medical Institute

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Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase

Biochemistry (2019)

Paul J. Sapienza Konstantin I. Popov David D. Mowrey Bradley T. Falk Nikolay V. Dokholyan

Thymidylate synthase (TS) is a dimeric enzyme conserved in all life forms that exhibits the allosteric feature of half-the-sites activity. Neither the reason for nor the mechanism of this phenomenon is understood. We used a combined nuclear magnetic resonance (NMR) and molecular dynamics approach to study a stable intermediate preceding hydride transfer, which is the rate-limiting and half-the-sites step. In NMR titrations with ligands leading to this intermediate, we measured chemical shifts of the apoenzyme (lig0), the saturated holoenzyme (lig2), and the typically elusive singly bound (lig1) states. Approximately 40 amides showed quartet patterns providing direct NMR evidence of coupling between the active site and probes >30 Å away in the distal subunit. Quartet peak patterns have symmetrical character, indicating reciprocity in communicating the first and second binding events to the distal protomer. Quartets include key catalytic residues and map to the dimer interface β-sheet, which also represents the shortest path between the two active sites. Simulations corroborate the coupling observed in solution in that there is excellent overlap between quartet residues and main-chain atoms having intersubunit cross-correlated motions. Simulations identify five hot spot residues, three of which lie at the kink in the unique β-bulge abutting the active sites on either end of the sheet. Interstrand cross-correlated motions become more organized and pronounced as the enzyme progresses from lig0 to lig1 and ultimately lig2. Coupling in the apparently symmetrical complex has implications for half-the-sites reactivity and potentially resolves the paradox of inequivalent TS active sites despite the vast majority of X-ray structures appearing to be symmetrical.

10.1021/acs.biochem.9b00486

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Citations (9)

Additional simulation and cross-linking data of α-synuclein monomer

Zenodo (CERN European Organization for Nuclear Research) (2020)

Jiaxing Chen Sofia Zaer Paz Drori Joanna Zamel Khalil Joron

This dataset includes data for the article entitled "The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds".

10.5281/zenodo.4293683

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A Physical Model Reveals the Mechanochemistry Responsible for Dynein's Processive Motion

Biophysical Journal (2011)

Denis Tsygankov Adrian W.R. Serohijos Nikolay V. Dokholyan Timothy C. Elston

Molecular motor

Mechanochemistry

Kinesin

10.1016/j.bpj.2011.05.043

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Citations (12)

Phenylalanine-508 mediates a cytoplasmic–membrane domain contact in the CFTR 3D structure crucial to assembly and channel function

Proceedings of the National Academy of Sciences (2008)

Adrian W.R. Serohijos Tamás Hegedűs Andrei A. Aleksandrov Lihua He Liying Cui

Deletion of phenylalanine-508 (Phe-508) from the N-terminal nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP-binding cassette (ABC) transporter family, disrupts both its folding and function and causes most cystic fibrosis. Most mutant nascent chains do not pass quality control in the ER, and those that do remain thermally unstable, only partially functional, and are rapidly endocytosed and degraded. Although the lack of the Phe-508 peptide backbone diminishes the NBD1 folding yield, the absence of the aromatic side chain is primarily responsible for defective CFTR assembly and channel gating. However, the site of interdomain contact by the side chain is unknown as is the high-resolution 3D structure of the complete protein. Here we present a 3D structure of CFTR, constructed by molecular modeling and supported biochemically, in which Phe-508 mediates a tertiary interaction between the surface of NBD1 and a cytoplasmic loop (CL4) in the C-terminal membrane-spanning domain (MSD2). This crucial cytoplasmic membrane interface, which is dynamically involved in regulation of channel gating, explains the known sensitivity of CFTR assembly to many disease-associated mutations in CL4 as well as NBD1 and provides a sharply focused target for small molecules to treat CF. In addition to identifying a key intramolecular site to be repaired therapeutically, our findings advance understanding of CFTR structure and function and provide a platform for focused biochemical studies of other features of this unique ABC ion channel.

Cyclic nucleotide-binding domain

Chloride channel

10.1073/pnas.0800254105

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Citations (374)

Faculty Opinions recommendation of Probing allostery through DNA.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature (2013)

Nikolay V. Dokholyan Elizabeth A. Proctor

10.3410/f.717980343.793474062

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Citations (0)

Computational Methods Toward Accurate RNA Structure Prediction Using Coarse-Grained and All-Atom Models