Chemical and Structural Diversity in Cyclooxygenase Protein Active Sites

2005 ◽  
Vol 2 (11) ◽  
pp. 1533-1552 ◽  
Author(s):  
Ryan G. Huff ◽  
Ersin Bayram ◽  
Huan Tan ◽  
Stacy T. Knutson ◽  
Michael H. Knaggs ◽  
...  
Keyword(s):  
Active Sites ◽  
Structural Diversity ◽  
Protein Active Sites

scholarly journals In VivoImpact of Met221 Substitution in GOB Metallo-β-Lactamase

2012 ◽  
Vol 56 (4) ◽  
pp. 1769-1773 ◽  
Author(s):  
Jorgelina Morán-Barrio ◽  
María-Natalia Lisa ◽  
Alejandro J. Vila
Keyword(s):  
Antibiotic Resistance ◽  
Protein Stability ◽  
Metal Binding ◽  
Active Sites ◽  
Bacterial Resistance ◽  
Structural Diversity ◽  
Hydrophobic Core

ABSTRACTMetallo-β-lactamases (MβLs) represent one of the main mechanisms of bacterial resistance against β-lactam antibiotics. The elucidation of their mechanism has been limited mostly by the structural diversity among their active sites. All MβLs structurally characterized so far present a Cys or a Ser residue at position 221, which is critical for catalysis. GOB lactamases stand as an exception within this picture, possessing a Met residue in this location. We studied different mutants in this position, and we show that Met221 is essential for protein stability, most likely due to its involvement in a hydrophobic core. In contrast to other known MβLs, residue 221 is not involved in metal binding or in catalysis in GOB enzymes, further highlighting the structural diversity of MβLs. We also demonstrate the usefulness of protein periplasmic profiles to assess the contribution of protein stability to antibiotic resistance.

Structural Diversity within the Mononuclear and Binuclear Active Sites ofN-Acetyl-d-glucosamine-6-phosphate Deacetylase†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (27) ◽  
pp. 7953-7962 ◽  
Author(s):  
Richard S. Hall ◽  
Shoshana Brown ◽  
Alexander A. Fedorov ◽  
Elena V. Fedorov ◽  
Chengfu Xu ◽  
...  
Keyword(s):  
Active Sites ◽  
Structural Diversity

scholarly journals The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?

2020 ◽  
Author(s):  
Richard T Bradshaw ◽  
Jacek Dziedzic ◽  
Chris-Kriton Skylaris ◽  
Jonathan W. Essex
Keyword(s):  
Electric Fields ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Force Fields ◽  
Prolyl Isomerase ◽  
Peptidyl Prolyl Isomerase ◽  
Polarizable Force Field ◽  
Polarizable Force Fields ◽  
Protein Active Sites ◽  
Dynamics Simulations

<div><div><div><p>Preorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric fields present inside the active site of the peptidyl-prolyl isomerase cyclophilin A. We compare the molecular mechanical electric fields to those calculated with a fully first principles quantum mechanical (QM) representation of the protein, solvent, and ions, and find that AMOEBA consistently shows far greater correlation with the QM electric fields than either of the additive force fields tested. Catalytically-relevant fields calculated with AMOEBA were typically smaller than those observed with additive potentials, but were generally consistent with an electrostatically-driven mechanism for catalysis. Our results highlight the accuracy and the potential advantages of using polarizable force fields in systems where accurate electrostatics may be crucial for providing mechanistic insights.</p></div></div></div>

Conductive Metal and Covalent Organic Frameworks for Electrocatalysis: Design Principles, Recent Progress and Perspective

Nanoscale ◽  
2021 ◽  
Author(s):  
Jinyan Wang ◽  
Hongyin Hu ◽  
Shuanglong Lu ◽  
Jundie Hu ◽  
Han Zhu ◽  
...  
Keyword(s):  
Active Sites ◽  
Recent Progress ◽  
Structural Diversity ◽  
Design Principles ◽  
Covalent Organic Frameworks

Metal and covalent organic frameworks (MOFs/COFs) are emerging promising candidates in the field of catalysts due to their porous nature, chemically well-defined active sites and structural diversity. However, they are...

Vicinity analysis: a methodology for the identification of similar protein active sites

2008 ◽  
Vol 15 (5) ◽  
pp. 489-498 ◽  
Author(s):  
A. McGready ◽  
A. Stevens ◽  
M. Lipkin ◽  
B. D. Hudson ◽  
D. C. Whitley ◽  
...  
Keyword(s):  
Active Sites ◽  
Similar Protein ◽  
Protein Active Sites

scholarly journals Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines

2008 ◽  
Vol 17 (2) ◽  
pp. 333-341 ◽  
Author(s):  
Wenxu Tong ◽  
Ronald J. Williams ◽  
Ying Wei ◽  
Leonel F. Murga ◽  
Jaeju Ko ◽  
...  
Keyword(s):  
Support Vector Machines ◽  
Active Sites ◽  
Support Vector ◽  
Protein Active Sites ◽  
Vector Machines
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