scholarly journals Side-chain conformational entropy at protein-protein interfaces

2009 ◽  
Vol 11 (12) ◽  
pp. 2860-2870 ◽  
Author(s):  
Christian Cole ◽  
Jim Warwicker
Keyword(s):  
Side Chain ◽  
Conformational Entropy ◽  
Protein Interfaces

scholarly journals Characterization of the dynamics and the conformational entropy in the binding between TAZ1 and CTAD-HIF-1α

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ida Nyqvist ◽  
Jakob Dogan
Keyword(s):  
Entropy Change ◽  
Side Chain ◽  
Transactivation Domain ◽  
Creb Binding Protein ◽  
Conformational Entropy ◽  
Internal Motions ◽  
Relaxation Measurements ◽  
Nanosecond Dynamics

Abstract The interaction between the C-terminal transactivation domain of HIF-1α (CTAD-HIF-1α) and the transcriptional adapter zinc binding 1 (TAZ1) domain of CREB binding protein participate in the initiation of gene transcription during hypoxia. Unbound CTAD-HIF-1α is disordered but undergoes a disorder-to-order transition upon binding to TAZ1. We have here performed NMR side chain and backbone relaxation studies on TAZ1 and side chain relaxation measurements on CTAD-HIF-1α in order to investigate the role of picosecond to nanosecond dynamics. We find that the internal motions are significantly affected upon binding, both on the side chain and the backbone level. The dynamic response corresponds to a conformational entropy change that contributes substantially to the binding thermodynamics for both binding partners. Furthermore, the conformational entropy change for the well-folded TAZ1 varies upon binding to different IDP targets. We further identify a cluster consisting of side chains in bound TAZ1 and CTAD-HIF-1α that experience extensive dynamics and are part of the binding region that involves the N-terminal end of the LPQL motif in CTAD-HIF-1α; a feature that might have an important role in the termination of the hypoxic response.

scholarly journals Protein conformational entropy is not slaved to water

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bryan S. Marques ◽  
Matthew A. Stetz ◽  
Christine Jorge ◽  
Kathleen G. Valentine ◽  
A. Joshua Wand ◽  
...  
Keyword(s):  
Protein Function ◽  
Hydration Shell ◽  
Nmr Relaxation ◽  
Bulk Water ◽  
Side Chain ◽  
Conformational Entropy ◽  
Solvent Water ◽  
Protein Molecules ◽  
Protein Functions ◽  
Internal Side

Abstract Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The “solvent slaving” model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.

Empirical Scale of Side-Chain Conformational Entropy in Protein Folding

1993 ◽  
Vol 231 (3) ◽  
pp. 825-839 ◽  
Author(s):  
Stephen D. Pickett ◽  
Michael J.E. Sternberg
Keyword(s):  
Protein Folding ◽  
Side Chain ◽  
Conformational Entropy

Side-chain rotamer transitions at protein-protein interfaces

2010 ◽  
Vol 78 (15) ◽  
pp. 3219-3225 ◽  
Author(s):  
Mainak Guharoy ◽  
Joël Janin ◽  
Charles H. Robert
Keyword(s):  
Side Chain ◽  
Protein Interfaces

scholarly journals Side-chain conformational entropy in protein folding

1995 ◽  
Vol 4 (11) ◽  
pp. 2247-2251 ◽  
Author(s):  
Andrew J. Doig ◽  
Michael J. E. Sternberg
Keyword(s):  
Protein Folding ◽  
Side Chain ◽  
Conformational Entropy
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