Document Detail


Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding.
MedLine Citation:
PMID:  23210919     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.
Authors:
Joshua P Layfield; Sharon Hammes-Schiffer
Related Documents :
6459779 - Secondary-site binding of glu-plasmin, lys-plasmin and miniplasmin to fibrin.
23991109 - New binding site conformations of the dengue virus ns3 protease accessed by molecular d...
23940029 - Dynamics of cleft closure of the glua2 ligand binding domain in the presence of full an...
23957009 - Mir-1279, mir-548j, mir-548m, and mir-548d-5p binding sites in cdss of paralogous and o...
6725259 - Importance of intramolecular interactions in the control of the fibrin affinity and act...
23834439 - Carbohydrate recognition in the immune system: contributions of neoglycolipid-based mic...
10871039 - Tropomodulin-binding site mapped to residues 7-14 at the n-terminal heptad repeats of t...
6459779 - Secondary-site binding of glu-plasmin, lys-plasmin and miniplasmin to fibrin.
12765239 - Binding of polychlorinated biphenyls/metabolites to hemoglobin.
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-12-31
Journal Detail:
Title:  Journal of the American Chemical Society     Volume:  135     ISSN:  1520-5126     ISO Abbreviation:  J. Am. Chem. Soc.     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-16     Completed Date:  2013-06-19     Revised Date:  2014-01-23    
Medline Journal Info:
Nlm Unique ID:  7503056     Medline TA:  J Am Chem Soc     Country:  United States    
Other Details:
Languages:  eng     Pagination:  717-25     Citation Subset:  IM    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Catalytic Domain
Hydrogen Bonding
Ligands
Models, Molecular
Molecular Dynamics Simulation*
Molecular Structure
Nitriles / chemistry*
Protein Binding
Steroid Isomerases / chemistry*,  metabolism
Vibration
Grant Support
ID/Acronym/Agency:
GM56207/GM/NIGMS NIH HHS; R37 GM056207/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Ligands; 0/Nitriles; EC 5.3.3.-/Steroid Isomerases
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  New TFA-Free Cleavage and Final Deprotection in Fmoc Solid-Phase Peptide Synthesis: Dilute HCl in Fl...
Next Document:  High-performance transistors based on zinc tin oxides by single spin-coating process.