scholarly journals Electrostatic Optimization of the Conformational Energy Landscape in a Metamorphic Protein

Biochemistry ◽  
2012 ◽  
Vol 51 (45) ◽  
pp. 9067-9075 ◽  
Author(s):  
Robert C. Tyler ◽  
Jamie C. Wieting ◽  
Francis C. Peterson ◽  
Brian F. Volkman
Keyword(s):  
Energy Landscape ◽  
Conformational Energy ◽  
Metamorphic Protein

A Predictive Energy Landscape Model of Metamorphic Protein Conformational Specificity

2021 ◽  
Author(s):  
James O. Wrabl ◽  
Keila Voortman-Sheetz ◽  
Vincent J. Hilser
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Large Scale ◽  
Energy Landscape ◽  
Thermodynamic Approach ◽  
High Identity ◽  
Denatured State ◽  
Metamorphic Protein ◽  
The Stability ◽  
The Impact

'Metamorphic' proteins challenge state-of-the-art structure prediction methods reliant on amino acid similarity. Unfortunately, this obviates a more effective thermodynamic approach necessary to properly evaluate the impact of amino acid changes on the stability of two different folds. A vital capability of such a thermodynamic approach would be the quantification of the free energy differences between 1) the energy landscape minima of each native fold, and 2) each fold and the denatured state. Here we develop an energetic framework for conformational specificity, based on an ensemble description of protein thermodynamics. This energetic framework was able to successfully recapitulate the structures of high-identity engineered sequences experimentally shown to adopt either Streptococcus protein GA or GB folds, demonstrating that this approach indeed reflected the energetic determinants of fold. Residue-level decomposition of the conformational specificity suggested several testable hypotheses, notably among them that fold-switching could be affected by local de-stabilization of the populated fold at positions sensitive to equilibrium perturbation. Since this ensemble-based compatibility framework is applicable to any structure and any sequence, it may be practically useful for the future targeted design, or large-scale proteomic detection, of novel metamorphic proteins.

scholarly journals Furanosyl Oxocarbenium Ion Conformational Energy Landscape Maps as a Tool to Study the Glycosylation Stereoselectivity of 2‐Azidofuranoses, 2‐Fluorofuranoses and Methyl Furanosyl Uronates

2019 ◽  
Vol 25 (29) ◽  
pp. 7149-7157 ◽  
Author(s):  
Stefan van der Vorm ◽  
Thomas Hansen ◽  
Erwin R. van Rijssel ◽  
Rolf Dekkers ◽  
Jerre M. Madern ◽  
...  
Keyword(s):  
Energy Landscape ◽  
Conformational Energy ◽  
Oxocarbenium Ion

Conformational Energy Landscape of the Ritonavir Molecule

2016 ◽  
Vol 120 (19) ◽  
pp. 4331-4340 ◽  
Author(s):  
Debayan Chakraborty ◽  
Neelanjana Sengupta ◽  
David J. Wales
Keyword(s):  
Energy Landscape ◽  
Conformational Energy

Sculpting an RNA Conformational Energy Landscape by a Methyl Group Modification—A Single-Molecule FRET Study

2008 ◽  
Vol 47 (23) ◽  
pp. 4326-4330 ◽  
Author(s):  
Andrei Yu. Kobitski ◽  
Martin Hengesbach ◽  
Mark Helm ◽  
G. Ulrich Nienhaus
Keyword(s):  
Single Molecule ◽  
Energy Landscape ◽  
Conformational Energy ◽  
Methyl Group ◽  
Single Molecule Fret ◽  
Group Modification

scholarly journals Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions

2012 ◽  
Vol 29 (6) ◽  
pp. 1683-1694 ◽  
Author(s):  
J.-P. Colletier ◽  
A. Aleksandrov ◽  
N. Coquelle ◽  
S. Mraihi ◽  
E. Mendoza-Barbera ◽  
...  
Keyword(s):  
Energy Landscape ◽  
Conformational Energy ◽  
Hyperthermophilic Protein

scholarly journals Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition

2019 ◽  
Vol 26 (1) ◽  
pp. 121-130.e5 ◽  
Author(s):  
Daniel J. Wood ◽  
Svitlana Korolchuk ◽  
Natalie J. Tatum ◽  
Lan-Zhen Wang ◽  
Jane A. Endicott ◽  
...  
Keyword(s):  
Energy Landscape ◽  
Conformational Energy
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