Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments

Hydrogen Exchange ◽

Hydrogen Exchange Mass Spectrometry ◽

Dynamics Simulations ◽

Integrating hydrogen–deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins

Nature Protocols ◽

10.1038/s41596-019-0219-6 ◽

2019 ◽

Vol 14 (11) ◽

pp. 3183-3204 ◽

Cited By ~ 10

Author(s):

Chloe Martens ◽

Mrinal Shekhar ◽

Andy M. Lau ◽

Emad Tajkhorshid ◽

Argyris Politis

Keyword(s):

Mass Spectrometry ◽

Molecular Dynamics ◽

Membrane Proteins ◽

Conformational Changes ◽

Hydrogen Deuterium Exchange ◽

Hydrogen Deuterium ◽

Deuterium Exchange Mass Spectrometry ◽

Dynamics Simulations

NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2433563100 ◽

2003 ◽

Vol 100 (25) ◽

pp. 14790-14795 ◽

Cited By ~ 98

Author(s):

K. Kuwata ◽

T. Matumoto ◽

H. Cheng ◽

K. Nagayama ◽

T. L. James ◽

...

Keyword(s):

Molecular Dynamics ◽

Prion Protein ◽

Hydrogen Exchange ◽

Fibril Formation ◽

Protein Fragment ◽

Structural Insight ◽

Dynamics Simulations ◽

Faculty Opinions recommendation of Hydration interaction between phospholipid membranes: insight into different measurement ensembles from atomistic molecular dynamics simulations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718205837.793488403 ◽

2013 ◽

Author(s):

Nathan Baker ◽

Jaehun Chun

Keyword(s):

Molecular Dynamics ◽

Phospholipid Membranes ◽

Dynamics Simulations ◽

Insight into the origin of SARS-CoV-2 through structural analysis of receptor recognition: a molecular simulation study

RSC Advances ◽

10.1039/d1ra00127b ◽

2021 ◽

Vol 11 (15) ◽

pp. 8718-8729

Author(s):

Jixue Sun ◽

Meijiang Liu ◽

Na Yang

Keyword(s):

Molecular Dynamics ◽

Structural Analysis ◽

Molecular Simulation ◽

Simulation Study ◽

Receptor Recognition ◽

Dynamics Simulations ◽

The origin of SARS-CoV-2 through structural analysis of receptor recognition was investigated by molecular dynamics simulations.

Molecular Insight into Cu2+-Induced Conformational Transitions of Amyloid β-Protein from Fast Kinetic Analysis and Molecular Dynamics Simulations

ACS Chemical Neuroscience ◽

10.1021/acschemneuro.0c00502 ◽

2021 ◽

Author(s):

Shaoying Xu ◽

Wenjuan Wang ◽

Xiaoyan Dong ◽

Yan Sun

Keyword(s):

Molecular Dynamics ◽

Kinetic Analysis ◽

Amyloid Β ◽

Conformational Transitions ◽

Amyloid Β Protein ◽

Β Protein ◽

Fast Kinetic ◽

Dynamics Simulations ◽

Monitoring the Folding Pathway of a Protein Over Evolutionary Time using Hydrogen Exchange - Mass Spectrometry (HX-MS)

Biophysical Journal ◽

10.1016/j.bpj.2017.11.350 ◽

2018 ◽

Vol 114 (3) ◽

pp. 54a

Author(s):

Eric Bolin ◽

Shion Lim ◽

Susan Marqusee

Keyword(s):

Mass Spectrometry ◽

Hydrogen Exchange ◽

Folding Pathway ◽

Evolutionary Time ◽

Hydrogen Exchange Mass Spectrometry

Structural Differences in Aβ Amyloid Protofibrils and Fibrils Mapped by Hydrogen Exchange – Mass Spectrometry with On-line Proteolytic Fragmentation

Journal of Molecular Biology ◽

10.1016/j.jmb.2006.06.066 ◽

2006 ◽

Vol 361 (4) ◽

pp. 785-795 ◽

Cited By ~ 98

Author(s):

Indu Kheterpal ◽

Maolian Chen ◽

Kelsey D. Cook ◽

Ronald Wetzel

Keyword(s):

Mass Spectrometry ◽

Hydrogen Exchange ◽

Aβ Amyloid ◽

Structural Differences ◽

Hydrogen Exchange Mass Spectrometry ◽

On Line

Structural insight into epothilones antitumor activity based on the conformational preferences and tubulin binding modes of epothilones A and B obtained from molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2014.911702 ◽

2014 ◽

Vol 33 (4) ◽

pp. 789-803 ◽

Cited By ~ 5

Author(s):

Verónica A. Jiménez ◽

Joel B. Alderete ◽

Karen R. Navarrete

Keyword(s):

Molecular Dynamics ◽

Antitumor Activity ◽

Binding Modes ◽

Conformational Preferences ◽

Tubulin Binding ◽

Structural Insight ◽

Dynamics Simulations ◽

Structure and Dynamics of a Protein–Surfactant Assembly Studied by Ion-Mobility Mass Spectrometry and Molecular Dynamics Simulations

Analytical Chemistry ◽

10.1021/acs.analchem.5b02172 ◽

2015 ◽

Vol 87 (17) ◽

pp. 8970-8976 ◽

Cited By ~ 8

Author(s):

Antoni J. Borysik

Keyword(s):

Mass Spectrometry ◽

Molecular Dynamics ◽

Ion Mobility ◽

Ion Mobility Mass Spectrometry ◽

Structure And Dynamics ◽

Dynamics Simulations

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III)

Structure ◽

10.1016/s0969-2126(97)00282-7 ◽

1997 ◽

Vol 5 (10) ◽

pp. 1297-1311 ◽

Cited By ~ 78

Author(s):

Thomas E Cheatham ◽

Peter A Kollman

Keyword(s):

Molecular Dynamics ◽

Ion Association ◽

Dynamics Simulations ◽