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

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

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 Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction

2011 ◽  
Vol 108 (10) ◽  
pp. 3952-3957 ◽  
Author(s):  
A. Bachmann ◽  
D. Wildemann ◽  
F. Praetorius ◽  
G. Fischer ◽  
T. Kiefhaber
Keyword(s):  
Protein Folding ◽  
Transition State ◽  
Side Chain ◽  
Binding Reaction

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

Simulation of Monomers Selection on Single-Molecular Copolymer Nano-Particles that Mimic Protein Folding

2012 ◽  
Vol 496 ◽  
pp. 58-61
Author(s):  
Wei Zhang
Keyword(s):  
Protein Folding ◽  
Stable Structure ◽  
Nano Particles ◽  
Side Chain ◽  
Nano Particle ◽  
Hp Model ◽  
Α Helix ◽  
Selection Of

The synthesis of protein-like single molecular nano-particle can be simplified by use fewer but longer monomers, which correspond to several old short monomers. The selection of new long monomer subset is optimized and tested in HP model and other models. Results show 2-3 types new monomer are enough to build stable structure, and long monomers should include integer length of one helix, and with interlaced hydrophobic and polar side-chain, thus can form α-helix like structure.

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