An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations

E Vargas, V Yarov-Yarovoy, F Khalili-Araghi… - Journal of General …, 2012 - rupress.org
Developing an understanding of the mechanism of voltage-gated ion channels in molecular
terms requires knowledge of the structure of the active and resting conformations. Although …

X-ray scattering studies of protein structural dynamics

SP Meisburger, WC Thomas, MB Watkins… - Chemical …, 2017 - ACS Publications
X-ray scattering is uniquely suited to the study of disordered systems and thus has the
potential to provide insight into dynamic processes where diffraction methods fail. In …

Structure of the full-length Shaker potassium channel Kv1. 2 by normal-mode-based X-ray crystallographic refinement

X Chen, Q Wang, F Ni, J Ma - Proceedings of the National …, 2010 - National Acad Sciences
Voltage-dependent potassium channels (Kv) are homotetramers composed of four voltage
sensors and one pore domain. Because of high-level structural flexibility, the first …

Mapping enzyme landscapes by time-resolved crystallography with synchrotron and x-ray free electron laser light

MA Wilson - Annual review of biophysics, 2022 - annualreviews.org
Directly observing enzyme catalysis in real time at the molecular level has been a long-
standing goal of structural enzymology. Time-resolved serial crystallography methods at …

[图书][B] Proteins: energy, heat and signal flow

DM Leitner, JE Straub - 2009 - taylorfrancis.com
Computational modeling can provide a wealth of insight into how energy flow in proteins
mediates protein function. Computational methods can also address fundamental questions …

Validation of crystallographic models containing TLS or other descriptions of anisotropy

F Zucker, PC Champ, EA Merritt - Acta Crystallographica Section D …, 2010 - journals.iucr.org
The use of TLS (translation/libration/screw) models to describe anisotropic displacement of
atoms within a protein crystal structure has become increasingly common. These models …

Comparisons of experimental and computed protein anisotropic temperature factors

L Yang, G Song, RL Jernigan - Proteins: Structure, Function …, 2009 - Wiley Online Library
Because of its appealing simplicity, the anisotropic network model (ANM) has been widely
accepted and applied to study many molecular motion problems: such as ribosome motions …

Recent developments in phasing and structure refinement for macromolecular crystallography

PD Adams, PV Afonine, RW Grosse-Kunstleve… - Current opinion in …, 2009 - Elsevier
Central to crystallographic structure solution is obtaining accurate phases in order to build a
molecular model, ultimately followed by refinement of that model to optimize its fit to the …

Structural basis of actin filament nucleation by tandem W domains

X Chen, F Ni, X Tian, E Kondrashkina, Q Wang, J Ma - Cell reports, 2013 - cell.com
Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells
have evolved a set of actin filament nucleators to promote rapid nucleation and …

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

M Lu, J Ma - Proceedings of the National Academy of …, 2008 - National Acad Sciences
In this article, we report a method for coarse-grained normal mode analysis called the
minimalist network model. The main features of the method are that it can deliver accurate …