scholarly journals Protein Dynamics and the Enzymatic Reaction Coordinate

2013 ◽  
pp. 189-208 ◽  
Author(s):  
Steven D. Schwartz
Keyword(s):  
Protein Dynamics ◽  
Enzymatic Reaction ◽  
Reaction Coordinate

Metal coordination and protein dynamics: The allosteric reaction coordinate in hemoglobin

1997 ◽  
Vol 67 (1-4) ◽  
pp. 79
Author(s):  
V. Jayaraman ◽  
K.R. Rodgers ◽  
I. Mukerji ◽  
X. Hu ◽  
T.G. Spiro
Keyword(s):  
Protein Dynamics ◽  
Reaction Coordinate ◽  
Metal Coordination

Uncovering One-Dimensional Reaction Coordinate that Underlies Structure-Function Relationship of Proteins

2022 ◽  
Author(s):  
Shanshan Wu ◽  
Huiyu Li ◽  
Ao Ma
Keyword(s):  
Protein Dynamics ◽  
Computational Cost ◽  
Reaction Coordinate ◽  
Functional Protein ◽  
Complex Molecules ◽  
One Dimensional ◽  
Protein Functions ◽  
Function Relationship ◽  
The One ◽  
Relationship Of

Understanding the mechanism of functional protein dynamics is critical to understanding protein functions. Reaction coordinates is a central topic in protein dynamics and the grail is to find the one-dimensional reaction coordinate that can fully determine the value of committor (i.e. the reaction probability in configuration space) for any protein configuration. We present a powerful new method that can, for the first time, identify the rigorous one-dimensional reaction coordinate in complex molecules. This one-dimensional reaction coordinate is determined by a fundamental mechanical operator--the generalized work functional. This method only requires modest computational cost and can be readily applied to large molecules. Most importantly, the generalized work functional is the physical origin of the collectivity in functional protein dynamics and provides a tentative roadmap that connects the structure of a protein to its function.

scholarly journals Evolution Alters the Enzymatic Reaction Coordinate of Dihydrofolate Reductase

2014 ◽  
Vol 119 (3) ◽  
pp. 989-996 ◽  
Author(s):  
Jean E. Masterson ◽  
Steven D. Schwartz
Keyword(s):  
Dihydrofolate Reductase ◽  
Enzymatic Reaction ◽  
Reaction Coordinate

Snapshots along an Enzymatic Reaction Coordinate:  Analysis of a Retaining β-Glycoside Hydrolase†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (34) ◽  
pp. 11707-11713 ◽  
Author(s):  
Gideon J. Davies ◽  
Lloyd Mackenzie ◽  
Annabelle Varrot ◽  
Miroslawa Dauter ◽  
A. Marek Brzozowski ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Enzymatic Reaction ◽  
Reaction Coordinate

Computer Simulation of Amperometric Biosensor Response to Mixtures of Compounds

2002 ◽  
Vol 7 (2) ◽  
pp. 3-14 ◽  
Author(s):  
R. Baronas ◽  
J. Christensen ◽  
F. Ivanauskas ◽  
J. Kulys
Keyword(s):  
Computer Simulation ◽  
Enzymatic Reaction ◽  
Diffusion Equations ◽  
Response Data ◽  
Finite Difference Technique ◽  
Stationary Diffusion ◽  
Biosensor Array ◽  
Menten Kinetic ◽  
Biosensor Response

A mathematical model of amperometric biosensors has been developed. The model bases on non-stationary diffusion equations containing a non-linear term related to Michaelis-Menten kinetic of the enzymatic reaction. The model describes the biosensor response to mixtures of multiple compounds in two regimes of analysis: batch and flow injection. Using computer simulation, large amount of biosensor response data were synthesised for calibration of a biosensor array to be used for characterization of wastewater. The computer simulation was carried out using the finite difference technique.

Analysis of Actin Protein Dynamics at the Protrusion Process of Cell Movement

2014 ◽  
Vol 134 (2) ◽  
pp. 177-182
Author(s):  
Takuya Miura ◽  
Michiko Sugawara ◽  
Tohru Yagi ◽  
Ken-ichi Tsubota ◽  
Hao Liu
Keyword(s):  
Protein Dynamics ◽  
Cell Movement ◽  
Actin Protein

Bacterial Peptidoglycan Stapling with Functionalized D-Amino Acids

2019 ◽  
Author(s):  
Sylvia L. Rivera ◽  
Akbar Espaillat ◽  
Arjun K. Aditham ◽  
Peyton Shieh ◽  
Chris Muriel-Mundo ◽  
...  
Keyword(s):  
Cell Wall ◽  
Clinical Success ◽  
Bacterial Species ◽  
Enzymatic Reaction ◽  
Amino Acid Derivative ◽  
Wall Structure ◽  
Live Bacteria ◽  
Cross Links ◽  
Osmotic Lysis ◽  
Bacterial Peptidoglycan

Transpeptidation reinforces the structure of cell wall peptidoglycan, an extracellular heteropolymer that protects bacteria from osmotic lysis. The clinical success of transpeptidase-inhibiting β-lactam antibiotics illustrates the essentiality of these cross-linkages for cell wall integrity, but the presence of multiple, seemingly redundant transpeptidases in many bacterial species makes it challenging to determine cross-link function precisely. Here we present a technique to covalently link peptide strands by chemical rather than enzymatic reaction. We employ bio-compatible click chemistry to induce triazole formation between azido- and alkynyl-D-alanine residues that are metabolically installed in the cell walls of Gram-positive and Gram-negative bacteria. Synthetic triazole cross-links can be visualized by substituting azido-D-alanine with azidocoumarin-D-alanine, an amino acid derivative that undergoes fluorescent enhancement upon reaction with terminal alkynes. Cell wall stapling protects the model bacterium Escherichia coli from β-lactam treatment. Chemical control of cell wall structure in live bacteria can provide functional insights that are orthogonal to those obtained by genetics.<br>

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