Generation of Ligand Conformations in Continuum Solvent Consistent with Protein Active Site Topology:  Application to Thrombin

2003 ◽  
Vol 46 (8) ◽  
pp. 1293-1305 ◽  
Author(s):  
Paulette A. Greenidge ◽  
Sandrine A. M. Mérette ◽  
Richard Beck ◽  
Guy Dodson ◽  
Christopher A. Goodwin ◽  
...  
Keyword(s):  
Active Site ◽  
Protein Active Site

Peroxovanadates and Its Bio-Mimicking Relation with Vanadium Haloperoxidases

2016 ◽  
pp. 197-219
Author(s):  
Pranjal Saikia ◽  
Saitanya Kumar Bharadwaj ◽  
Abu Taleb Miah
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
High Efficiency ◽  
Recombinant Enzymes ◽  
Vanadium Compounds ◽  
Reaction Conditions ◽  
The Cost ◽  
Major Emphasis ◽  
Protein Active Site

Vanadium Haloperoxidases (VHPOs) have been used in a variety of biotransformations showing remarkable stereoselectivity and regiospecificity. The high efficiency of the enzyme is influenced by the protein active site and the role of certain amino acids in activation of vanadium(V)-bound peroxide for halide oxidation. The use of natural or recombinant enzymes, or biomimetic vanadium compounds brings up issues regarding the cost of production and reaction conditions. In this chapter, the primary intent is to provide a simple and clear picture of functional mimicking nature of peroxovanadium compounds with haloperoxidases enzymes to the readers. Major emphasis would be given to examine the reactivity of the vanadium haloperoxidases with mechanism.

A Mimic Molecule of Blue Copper Protein Active Site [(−)-Sparteine-N,N‘](maleonitriledithiolato-S,S‘)copper(II)

2001 ◽  
Vol 40 (17) ◽  
pp. 4481-4484 ◽  
Author(s):  
Young-Jin Kim ◽  
Su-Oak Kim ◽  
Young-Inn Kim ◽  
Sung-Nak Choi
Keyword(s):  
Active Site ◽  
Blue Copper Protein ◽  
Blue Copper ◽  
Copper Protein ◽  
Protein Active Site

scholarly journals Comparison of protein active site structures for functional annotation of proteins and drug design

2006 ◽  
Vol 65 (1) ◽  
pp. 124-135 ◽  
Author(s):  
Robert Powers ◽  
Jennifer C. Copeland ◽  
Katherine Germer ◽  
Kelly A. Mercier ◽  
Viswanathan Ramanathan ◽  
...  
Keyword(s):  
Drug Design ◽  
Active Site ◽  
Functional Annotation ◽  
Protein Active Site

scholarly journals PAR-3D: a server to predict protein active site residues

2007 ◽  
Vol 35 (Web Server) ◽  
pp. W503-W505 ◽  
Author(s):  
K. Goyal ◽  
D. Mohanty ◽  
S. C. Mande
Keyword(s):  
Active Site ◽  
Active Site Residues ◽  
Protein Active Site

What Accounts for the Different Function in Photolyases and Cryptochromes: A Computational Study of Critical Events in the Protein Active Site

2019 ◽  
Author(s):  
Daniel Holub ◽  
Thilo Mast ◽  
Tomáš Kubař ◽  
Marcus Elstner ◽  
Natacha Gillet
Keyword(s):  
Experimental Data ◽  
Proton Transfer ◽  
Molecular Mechanism ◽  
Active Site ◽  
Computational Study ◽  
Great Influence ◽  
Functional Differentiation ◽  
E Coli ◽  
Comprehensive Picture ◽  
Protein Active Site

In the current work, we present a combination of various classical and quantum computational protocols to unveil the molecular mechanism of FAD protonation in <i>E. coli</i> photolyase and its mutant. A direct comparison to our previous study on the plant cryptochrome clearly shows the great influence of the electrostatic environment and the flexibility of the FAD pocket on the proton transfer mechanism. Additionally, we propose a proton transfer pathway for WT E. coli photolyase consistent with experimental observations. Taken together, our results and previous experimental data provide a comprehensive picture about the functional differentiation in the cryptochrome-photolyase family.

Sign in / Sign up

Export Citation Format

Share Document