Bio Chem Press  Internet Electronic Journal of Molecular Design is a refereed journal for scientific papers regarding all applications of molecular design
Home | News | Current Issue | Journal Index | IECMD 2004 | Preprint Index | Instructions for Authors | Send the Manuscript | Special Issue
 BioChemPress.com  To bookmark this site press Ctrl D
 
   Home
   News & Announcements
  Journal Info
   Current Issue
   Journal Index
   Preprint Index
   Editor
   Advisory Board
  Conference Info
   IECMD 2004
   Day 1
   Day 2
   Day 3
   Day 4
   Day 5
   Day 6
   Day 7
   Day 8
   Day 9
   Day 10
   IECMD 2003
  BioChem Links
   CoEPrA
   Support Vector Machines
  Author Info
   Instructions for Authors
   Send the Manuscript
   Special Issue
  Contact
   Editorial Office
   Subscription
   Advertising
   Copyright
  User Info
   Terms of Use
   License

Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
ABSTRACT - Internet Electron. J. Mol. Des. May 2006, Volume 5, Number 5, 247-259

Quantitative in silico Analysis of Molecular Recognition and Reactivity of D-Amino Acid Oxidase
Toshihiko Hanai
Internet Electron. J. Mol. Des. 2006, 5, 247-259

Free: Download the paper in PDF format Return to Table of Contents Get Acrobat Reader to view and print the paper

Abstract:
Computational chemical analysis of enantiomer recognition with chromatography was investigated using molecular mechanics calculations. The method was applied to study enantiomer recognition of the protein D-amino acid oxidase (DAAO). The data for several stereo structures were obtained from databases, and then the substrate was replaced with an amino acid, and the new complexes were optimized using a MM2 calculation to study the conformation of the amino acid complex. Mutant and estimated human DAAO were constructed from the sequence data and the known stereo structure of DAAO. The structures of the new complexes with substituted amino acids were also optimized using MM2 calculations, and used to study selectivity. The reactivity was analyzed based on the atomic distances calculated with MM2, and partial atomic charges calculated with the MOPAC PM5 method. The values of atomic distances and partial atomic charges indicate that the cationic hydrogen of the amino acid could be moved to bind with the anionic nitrogen of flavin. The selectivity of DAAO depends on the initial stereo structure measured by X-ray crystallography and on the amino acid included in the oxidation reaction site. Yeast DAAO has a wider open entrance compared to pig kidney DAAO. The selectivity of the co-enzyme was also analyzed using a computational chemical calculation. The phosphate of flavin mononucleotide (FMN) was caught by a guanidino group of the enzyme, but that of flavin adenine dinucleotide (FAD) was free from ion-ion interaction.

Free: Download the paper in PDF format Return to Table of Contents Get Acrobat Reader to view and print the paper

Home | News | Current Issue | Journal Index | IECMD 2004 | Preprint Index | Instructions for Authors | Send the Manuscript | Special Issue
Last changes: January 5, 2006 Webmaster
http://www.biochempress.com/
Copyright © 2001-2006 Ovidiu Ivanciuc