Hydrogen exchange identifies native-state motional domains important in protein folding

Biochemistry ◽  
1993 ◽  
Vol 32 (37) ◽  
pp. 9600-9608 ◽  
Author(s):  
Key Sun Kim ◽  
James A. Fuchs ◽  
Clare K. Woodward
Keyword(s):  
Protein Folding ◽  
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

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 Protein folding and misfolding: mechanism and principles

2007 ◽  
Vol 40 (4) ◽  
pp. 1-41 ◽  
Author(s):  
S. Walter Englander ◽  
Leland Mayne ◽  
Mallela M. G. Krishna
Keyword(s):  
Protein Folding ◽  
Hydrogen Exchange ◽  
Building Blocks ◽  
Native Protein ◽  
Native State ◽  
Stabilization Mechanism ◽  
Structural Units ◽  
Folding Intermediates ◽  
Folding Pathways ◽  
Protein Folding Pathways

AbstractTwo fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.

Self-Similarity of Protein Folding Flows

2012 ◽  
Vol 7 (4) ◽  
pp. 136-141
Author(s):  
I. Kalgin ◽  
Sergey Chekmarev
Keyword(s):  
Protein Folding ◽  
Sh3 Domain ◽  
Atomic Level ◽  
The Self ◽  
Coarse Grained ◽  
Folding Kinetics ◽  
Native State ◽  
Self Similarity ◽  
Folding Dynamics ◽  
Fractal Character

The problem of how a protein folds into its functional (native) state is one of the central problems of molecular biology, which attracts the attention of researchers from biology, physics and chemistry for many years. Of particular interest are general properties of the folding process, because the mechanisms of folding of different proteins can be essentially different. Previously, in the study of folding of fyn SH3 domain, we found that despite all the diversity and complexity of individual folding trajectories, the folding flows possess a well pronounced property of self-similarity, with a fractal character of the flow distributions. In the present paper, we study this phenomenon for another protein – beta3s, which is essentially different from the SH3 domain in its structure and folding kinetics. Also, in contrast to the fyn SH3 domain, for which a coarse-grained representation was used, we perform simulations on the atomic level of resolution. We show that the self-similarity and fractality of folding flows are observed is this case too, which suggests that these properties are characteristic of the protein folding dynamics

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