Atomic-level characterization of the structural dynamics of proteins

Research output: Contribution to journal › Journal article › Research › peer-review

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Atomic-level characterization of the structural dynamics of proteins. / Shaw, David E; Maragakis, Paul; Lindorff-Larsen, Kresten; Piana, Stefano; Dror, Ron O; Eastwood, Michael P; Bank, Joseph A; Jumper, John M; Salmon, John K; Shan, Yibing; Wriggers, Willy.

In: Science (New York, N.Y.), Vol. 330, No. 6002, 2010, p. 341-6.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Shaw, DE, Maragakis, P, Lindorff-Larsen, K, Piana, S, Dror, RO, Eastwood, MP, Bank, JA, Jumper, JM, Salmon, JK, Shan, Y & Wriggers, W 2010, 'Atomic-level characterization of the structural dynamics of proteins', Science (New York, N.Y.), vol. 330, no. 6002, pp. 341-6. https://doi.org/10.1126/science.1187409

APA

Shaw, D. E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R. O., Eastwood, M. P., Bank, J. A., Jumper, J. M., Salmon, J. K., Shan, Y., & Wriggers, W. (2010). Atomic-level characterization of the structural dynamics of proteins. Science (New York, N.Y.), 330(6002), 341-6. https://doi.org/10.1126/science.1187409

Vancouver

Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP et al. Atomic-level characterization of the structural dynamics of proteins. Science (New York, N.Y.). 2010;330(6002):341-6. https://doi.org/10.1126/science.1187409

Author

Shaw, David E ; Maragakis, Paul ; Lindorff-Larsen, Kresten ; Piana, Stefano ; Dror, Ron O ; Eastwood, Michael P ; Bank, Joseph A ; Jumper, John M ; Salmon, John K ; Shan, Yibing ; Wriggers, Willy. / Atomic-level characterization of the structural dynamics of proteins. In: Science (New York, N.Y.). 2010 ; Vol. 330, No. 6002. pp. 341-6.

Bibtex

@article{d5d6210ca95a4ee793e8ef24456af757,
title = "Atomic-level characterization of the structural dynamics of proteins",
abstract = "Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.",
author = "Shaw, {David E} and Paul Maragakis and Kresten Lindorff-Larsen and Stefano Piana and Dror, {Ron O} and Eastwood, {Michael P} and Bank, {Joseph A} and Jumper, {John M} and Salmon, {John K} and Yibing Shan and Willy Wriggers",
year = "2010",
doi = "10.1126/science.1187409",
language = "English",
volume = "330",
pages = "341--6",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6002",

}

RIS

TY - JOUR

T1 - Atomic-level characterization of the structural dynamics of proteins

AU - Shaw, David E

AU - Maragakis, Paul

AU - Lindorff-Larsen, Kresten

AU - Piana, Stefano

AU - Dror, Ron O

AU - Eastwood, Michael P

AU - Bank, Joseph A

AU - Jumper, John M

AU - Salmon, John K

AU - Shan, Yibing

AU - Wriggers, Willy

PY - 2010

Y1 - 2010

N2 - Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.

AB - Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.

U2 - 10.1126/science.1187409

DO - 10.1126/science.1187409

M3 - Journal article

C2 - 20947758

VL - 330

SP - 341

EP - 346

JO - Science

JF - Science

SN - 0036-8075

IS - 6002

ER -

ID: 37812318