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

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

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

Double mutant of chymotrypsin inhibitor 2 stabilized through increased conformational entropy

2021 ◽  
Author(s):  
Yulian Gavrilov ◽  
Felix Kümmerer ◽  
Simone Orioli ◽  
Andreas Prestel ◽  
Kresten Lindorff-Larsen ◽  
...  
Keyword(s):  
Double Mutant ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Conformational Heterogeneity ◽  
Native State ◽  
Chymotrypsin Inhibitor 2 ◽  
Relaxation Measurements ◽  
The Stability ◽  
Dynamics Simulations ◽  
Mutant Forms

The conformational heterogeneity of a folded protein can affect both its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here we have examined whether changed native state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side-chains with molecular dynamics simulations to quantify the native state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: A reduction in conformational dynamics (and entropy) of the native state of L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native state entropy might be needed to improve the predictions of the effect of mutations on protein stability.

Hydrogen exchange and structural dynamics of proteins and nucleic acids

1983 ◽  
Vol 16 (4) ◽  
pp. 521-655 ◽  
Author(s):  
S. Walter Englander ◽  
Neville R. Kallenbach
Keyword(s):  
Free Energy ◽  
Nucleic Acids ◽  
Structural Dynamics ◽  
Hydrogen Exchange ◽  
Native State ◽  
Structural Work

Though the structures presented in crystallographic models of macromolecules appear to possess rock-like solidity, real proteins and nucleic acids are not particularly rigid. Most structural work to date has centred upon the native state of macromolecules, the most probable macromolecular form. But the native state of a molecule is merely its most abundant form, certainly not its only form. Thermodynamics requires that all other possible structural forms, however improbable, must also exist, albeit with representation corresponding to the factor exp( — Gi/RT) for each state of free energy Gi (see Moelwyn-Hughes, 1961), and one appreciates that each molecule within a population of molecules will in time explore the vast ensemble of possible structural states.

scholarly journals Cytochrome c folding pathway: Kinetic native-state hydrogen exchange

2002 ◽  
Vol 99 (19) ◽  
pp. 12173-12178 ◽  
Author(s):  
L. Hoang ◽  
S. Bedard ◽  
M. M. G. Krishna ◽  
Y. Lin ◽  
S. W. Englander
Keyword(s):  
Cytochrome C ◽  
Hydrogen Exchange ◽  
Folding Pathway ◽  
Native State

Microsecond Protein Folding Kinetics from Native-State Hydrogen Exchange†

Biochemistry ◽  
1997 ◽  
Vol 36 (29) ◽  
pp. 8686-8691 ◽  
Author(s):  
Cammon B. Arrington ◽  
Andrew D. Robertson
Keyword(s):  
Protein Folding ◽  
Hydrogen Exchange ◽  
Folding Kinetics ◽  
Native State

scholarly journals Prediction of Native-State Hydrogen Exchange from Perfectly Funneled Energy Landscapes

2011 ◽  
Vol 133 (43) ◽  
pp. 17463-17472 ◽  
Author(s):  
Patricio O. Craig ◽  
Joachim Lätzer ◽  
Patrick Weinkam ◽  
Ryan M. B. Hoffman ◽  
Diego U. Ferreiro ◽  
...  
Keyword(s):  
Hydrogen Exchange ◽  
Energy Landscapes ◽  
Native State
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