Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations

2013 ◽  
Vol 81 (6) ◽  
pp. 1069-1080 ◽  
Author(s):  
Julien Roche ◽  
Jose A. Caro ◽  
Mariano Dellarole ◽  
Ewelina Guca ◽  
Catherine A. Royer ◽  
...  
Keyword(s):  
Staphylococcal Nuclease ◽  
Dynamic Responses ◽  
Native State ◽  
State Ensemble

The native-state ensemble of proteins provides clues for folding, misfolding and function

2006 ◽  
Vol 31 (9) ◽  
pp. 494-496 ◽  
Author(s):  
Nunilo Cremades ◽  
Javier Sancho ◽  
Ernesto Freire
Keyword(s):  
Native State ◽  
State Ensemble ◽  
And Function

Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity

2019 ◽  
Vol 476 (3) ◽  
pp. 613-628 ◽  
Author(s):  
Meenakshi Sharma ◽  
Nancy Jaiswal ◽  
Dinesh Kumar ◽  
Krishna Mohan Poluri
Keyword(s):  
Dynamic Properties ◽  
Nmr Relaxation ◽  
Dynamic Features ◽  
Native State ◽  
Structure Dynamics ◽  
Functional Dynamics ◽  
State Ensemble ◽  
The Stability ◽  
Ph Range ◽  
Relationship Of

Abstract Proteins are dynamic in nature and exist in a set of equilibrium conformations on various timescale motions. The flexibility of proteins governs various biological functions, and therefore elucidation of such functional dynamics is essential. In this context, we have studied the structure–dynamics–stability–activity relationship of bacteriophage T7 lysozyme/endolysin (T7L) native-state ensemble in the pH range of 6–8. Our studies established that T7L native state is conformationally heterogeneous, as several residues of its C-terminal half are present in two conformations (major and minor) in the slow exchange time scale of nuclear magnetic resonance (NMR). Structural and dynamic studies suggested that the residues belonging to minor conformations do exhibit native-like structural and dynamic features. Furthermore, the NMR relaxation experiments unraveled that the native state is highly dynamic and the dynamic behavior is regulated by the pH, as the pH 6 conformation exhibited enhanced dynamics compared with pH 7 and 8. The stability measurements and cell-based activity studies on T7L indicated that the native protein at pH 6 is ∼2 kcal less stable and is ∼50% less active than those of pH 7 and 8. A comprehensive analysis of the T7L active site, unfolding initiation sites and the residues with altered dynamics outlined that the attenuation of stability and activity is a resultant of its enhanced dynamic properties, which, in turn, can be attributed to the protonation/deprotonation of its partially buried His residues. Our study on T7L structure–dynamics–activity paradigm could assist in engineering novel amidase-based endolysins with enhanced activity and stability over a broad pH range.

Revealing the Nature of the Native State Ensemble through Cold Denaturation†

Biochemistry ◽  
2006 ◽  
Vol 45 (34) ◽  
pp. 10163-10174 ◽  
Author(s):  
Steven T. Whitten ◽  
Andrew J. Kurtz ◽  
Maxim S. Pometun ◽  
A. Joshua Wand ◽  
Vincent J. Hilser
Keyword(s):  
Native State ◽  
Cold Denaturation ◽  
State Ensemble

Hierarchy of local structural and dynamics perturbations due to subdenaturing urea in the native state ensemble of DLC8 dimer

2010 ◽  
Vol 153 (1) ◽  
pp. 17-26 ◽  
Author(s):  
P.M. Krishna Mohan ◽  
Swagata Chakraborty ◽  
Ramakrishna V. Hosur
Keyword(s):  
Native State ◽  
State Ensemble

Mapping the structure of a non-native state of staphylococcal nuclease

1996 ◽  
Vol 3 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Mario R. Ermácora ◽  
David W. Ledman ◽  
Robert O. Fox
Keyword(s):  
Staphylococcal Nuclease ◽  
Native State

scholarly journals Effects of sucrose on conformational equilibria and fluctuations within the native-state ensemble of proteins

2003 ◽  
Vol 12 (6) ◽  
pp. 1252-1261 ◽  
Author(s):  
Yong-Sung Kim ◽  
Latoya S. Jones ◽  
Aichun Dong ◽  
Brent S. Kendrick ◽  
Byeong S. Chang ◽  
...  
Keyword(s):  
Native State ◽  
Conformational Equilibria ◽  
State Ensemble

scholarly journals Parallel folding pathway of proline-free staphylococcal nuclease studied by the stopped-flow double-jump method

2003 ◽  
Vol 17 (2-3) ◽  
pp. 203-212 ◽  
Author(s):  
Kiyoto Kamagata ◽  
Kunihiro Kuwajima
Keyword(s):  
Staphylococcal Nuclease ◽  
Folding Pathway ◽  
Stopped Flow ◽  
Native State ◽  
Flow Method ◽  
Folding Mechanism ◽  
Parallel Pathways ◽  
Parallel Folding ◽  
Refolding Kinetics

The folding mechanism of proline‒free staphylococcal nuclease (SNase (pro−)) (P11A, P31A, P42A, P47T, P56A, P117G) was investigated using the double‒jump stopped‒flow method (interrupted refolding). This method has enabled us to specifically monitor the amount of the native molecules during the refolding. The results indicate that the middle and slow phases observed in the refolding kinetics represent the formation of the native state (IM→N, IS→N) and that the folding mechanism of SNase (pro−) is not represented by a single sequential pathway, but at least two parallel pathways are required for interpreting the results.

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