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A Quantitative Measure of Conformational Changes in Apo, Holo and Ligand-Bound Forms of Enzymes

  • Satendra Singh
  • Atul Kumar Singh
  • Gulshan Wadhwa
  • Dev Bukhsh SinghEmail author
  • Seema Dwivedi
  • Budhayash Gautam
  • Pramod W. Ramteke
Original Research Article

Abstract

Determination of the native geometry of the enzymes and ligand complexes is a key step in the process of structure-based drug designing. Enzymes and ligands show flexibility in structural behavior as they come in contact with each other. When ligand binds with active site of the enzyme, in the presence of cofactor some structural changes are expected to occur in the active site. Motivation behind this study is to determine the nature of conformational changes as well as regions where such changes are more pronounced. To measure the structural changes due to cofactor and ligand complex, enzyme in apo, holo and ligand-bound forms is selected. Enzyme data set was retrieved from protein data bank. Fifteen triplet groups were selected for the analysis of structural changes based on selection criteria. Structural features for selected enzymes were compared at the global as well as local region. Accessible surface area for the enzymes in entire triplet set was calculated, which describes the change in accessible surface area upon binding of cofactor and ligand with the enzyme. It was observed that some structural changes take place during binding of ligand in the presence of cofactor. This study will helps in understanding the level of flexibility in protein–ligand interaction for computer-aided drug designing.

Keywords

Flexibility Cofactor Enzymes Structural changes Active site 

Notes

Compliance with Ethical Standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

12539_2015_284_MOESM1_ESM.docx (16 kb)
Supplementary material 1 (docx 16 KB)
12539_2015_284_MOESM2_ESM.docx (27 kb)
Supplementary material 2 (docx 27 KB)

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Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Satendra Singh
    • 1
  • Atul Kumar Singh
    • 2
  • Gulshan Wadhwa
    • 3
  • Dev Bukhsh Singh
    • 4
    Email author
  • Seema Dwivedi
    • 5
  • Budhayash Gautam
    • 1
  • Pramod W. Ramteke
    • 6
  1. 1.Department of Computational Biology and BioinformaticsJSBB, SHIATSAllahabadIndia
  2. 2.Centre for Research in Nanotechnology and ScienceIndian Institute of TechnologyMumbaiIndia
  3. 3.Apex Bioinformatics Centre, Department of BiotechnologyMinistry of Science and TechnologyNew DelhiIndia
  4. 4.Department of Biotechnology, Institute of Biosciences and BiotechnologyChhatrapati Shahu Ji Maharaj UniversityKanpurIndia
  5. 5.School of BiotechnologyGautam Buddha UniversityGreater NoidaIndia
  6. 6.Department of Biological SciencesSHIATSAllahabadIndia

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