scholarly journals Comment on the article `Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase'

IUCrJ ◽  
2018 ◽  
Vol 5 (4) ◽  
pp. 519-519 ◽  
Author(s):  
Massimo Nespolo
IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 130-140 ◽  
Author(s):  
Margarita Dimova ◽  
Yancho D. Devedjiev

Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ida Nyqvist ◽  
Jakob Dogan

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.


2015 ◽  
Vol 301 (1) ◽  
pp. 9-35 ◽  
Author(s):  
Bernhard Schartel ◽  
Birgit Perret ◽  
Bettina Dittrich ◽  
Michael Ciesielski ◽  
Johannes Krämer ◽  
...  

2014 ◽  
Vol 70 (a1) ◽  
pp. C669-C669
Author(s):  
Angshuman Roy Choudhury ◽  
Gurpreet Kaur ◽  
Maheswararao Karanam ◽  
Sandhya Patel

The phrase "Organic fluorine" [1] was introduced by Dunitz and Taylor in 1997 to identify the C–F bonds in organic systems. Different research groups have used the phrase to glorify or deny the influence of C–F bond in crystal lattices. Once Dunitz stated that "Organic Fluorine: Odd Man Out" and Howard et al. questioned the role of "Organic fluorine" in crystal engineering. While some researchers have refuted the role of "organic fluorine" in crystal packing; the others indicated the importance of the interactions involving the same group. A number of publications have shown the importance of "Organic fluorine" in influencing crystal packing. We have been interested in the area of weak interactions in organic solid state chemistry since 1999 [2]; especially interactions involving "Organic fluorine". The study is being conducted following a systematic approach and is still in progress. We have looked at the structures of a number if tetrahydroisoquinoline derivatives, a number of differently substituted imines, phenyleacetanilydes, benzanilides and azobenzenes [3] etc. in order to elucidate the influence of "Organic fluorine" in crystal engineering both in the presence and in the absence of strong hydrogen bonding functional groups present within the molecule. A short summary of our observations will be highlighted in the presentation.


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