भारतीय प्रौद्योगिकी संस्थान दिल्ली
Indian Institute of Technology, Delhi
  • Login
View Item 
  •   Home
  • Faculty Research Publicatons
  • Applied Mechanics
  • View Item
  •   Home
  • Faculty Research Publicatons
  • Applied Mechanics
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

Energetic and kinetic aspects of macromolecular association: computational study of X repressor-operator complexation

Thumbnail
View/Open
jayaramene95.pdf


Collections
  • Applied Mechanics [36]
Metadata
Show full item record
Author: Jayaram, B; Das, A; Aneja, N

Advisor: Advisor

Date: 1996

Publisher: Elsevier S

Citation: Journal of

Series/Report no.:
Item Type:
Keywords: thermodynamic and kinetic; macromolecular; computationally; X repressor-operator; nucleic acid; analyzed

Abstract: A detailed molecular view of structural, thermodynamic and kinetic aspects is essential for a clear understanding of macromolecular association. We have recently assembled a force field to capture the energetics of protein-DNA inter- actions in aqueous solution, and to provide a thermodynamic and kinetic description of association in a computationally expeditious manner. An application of this force field to a X repressor-operator with a partitioning of the interaction energies on a subunit basis has revealed some interesting features. Hydrogen bonding and van der Waals interactions of the turn-recognition helix-turn subunit of the protein with the nucleic acid bases in the major groove appear to determine specificity in binding. Brownian dynamics simulations were performed on several models for the X repressor-operator system to monitor some mechanistic aspects, of relevance to kinetics of B mplexation. The calculated joint probability for a nonspecific association of protein and DNA, driven mostly by electrostatics, followed by a sliding of the protein to the active site (operator region) on the DNA, a search in reduced dimensional configuration space accessible to the system, is much more than the probability of a three-dimensional diffusion of the protein to the active site. Implications of these results to protein-DNA recognition are analyzed and discussed.
Contact Us
Shankar B. Chavan
Computer Applications Division
Central Library, IIT Delhi
shankar.chavan@library.iitd.ac.in
NDLTD
Shodhganga
NDL
ePrints@IISc
etd@IISc
IR@IIT Bombay
NewsClips @IITD
  • facebook
  • twitter
  • youtube
  • instagram
  • pinterest

Browse

All of IITDCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

My Account

LoginRegister
Contact Us
Shankar B. Chavan
Computer Applications Division
Central Library, IIT Delhi
shankar.chavan@library.iitd.ac.in
NDLTD
Shodhganga
NDL
ePrints@IISc
etd@IISc
IR@IIT Bombay
NewsClips @IITD
  • facebook
  • twitter
  • youtube
  • instagram
  • pinterest