scholarly journals Structural Interpretation of Hydrogen Exchange Protection Factors in Proteins: Characterization of the Native State Fluctuations of CI2

Structure ◽  
2006 ◽  
Vol 14 (1) ◽  
pp. 97-106 ◽  
Author(s):  
Robert B. Best ◽  
Michele Vendruscolo
Keyword(s):  
Hydrogen Exchange ◽  
Native State ◽  
Structural Interpretation

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

Relationship between the Native-State Hydrogen Exchange and Folding Pathways of a Four-Helix Bundle Protein

Biochemistry ◽  
2002 ◽  
Vol 41 (25) ◽  
pp. 7998-8003 ◽  
Author(s):  
Ruiai Chu ◽  
Wuhong Pei ◽  
Jiro Takei ◽  
Yawen Bai
Keyword(s):  
Hydrogen Exchange ◽  
Native State ◽  
Helix Bundle ◽  
Folding Pathways ◽  
Four Helix Bundle ◽  
Bundle Protein

Rapid Characterization of Hydrogen Exchange in Proteins

2013 ◽  
Vol 125 (9) ◽  
pp. 2500-2503 ◽  
Author(s):  
Anushikha Thakur ◽  
Kousik Chandra ◽  
Abhinav Dubey ◽  
Patrick D'Silva ◽  
Hanudatta S. Atreya
Keyword(s):  
Hydrogen Exchange ◽  
Rapid Characterization

scholarly journals Detection of Native-State Nonadditivity in Double Mutant Cycles via Hydrogen Exchange

2010 ◽  
Vol 132 (23) ◽  
pp. 8010-8019 ◽  
Author(s):  
Joshua A. Boyer ◽  
Cristina J. Clay ◽  
K. Scott Luce ◽  
Marshall H. Edgell ◽  
Andrew L. Lee
Keyword(s):  
Double Mutant ◽  
Hydrogen Exchange ◽  
Native State

scholarly journals Protein folding intermediates: native-state hydrogen exchange

Science ◽  
1995 ◽  
Vol 269 (5221) ◽  
pp. 192-197 ◽  
Author(s):  
Y Bai ◽  
T. Sosnick ◽  
L Mayne ◽  
S. Englander
Keyword(s):  
Protein Folding ◽  
Hydrogen Exchange ◽  
Native State ◽  
Folding Intermediates

scholarly journals Characterization of Mg2+-induced conformational change in the 50S ribosomal subunit by differential hydrogen exchange

1980 ◽  
Vol 8 (11) ◽  
pp. 2489-2498 ◽  
Author(s):  
D. Bonnet ◽  
E. Begard ◽  
M. Grunberg-Manago ◽  
G.Hui Bon Hoa
Keyword(s):  
Conformational Change ◽  
Hydrogen Exchange ◽  
Ribosomal Subunit
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