Molecular modelling of protein-nucleic acid interactions

Journal of Biomolecular Structure & Dynamics
R ReinM Shibata

Abstract

Computer modeling techniques to study the interaction of proteins with nucleic acids are presented. The methods utilize information from genetic and chemical modification experiments and macromolecular structural constraints. These techniques, in addition to computer model building procedures and theoretical energy calculations, are illustrated for the study of the lac and cro repressor-operator systems. Our predicted interactions between lac and its operator agree with those recently reported for lac based upon sequence alignment with the cro repressor. Several molecular models of the putative helical segment of cro interacting with its OR3 operator are presented. These models are reflective of intermediate conformations experienced by the repressor in recognition of the operator sequence. The results of our studies are further discussed in terms of the design of short peptides interacting with nucleic acid sequences and the evolutionary requirements in establishing these repressor interactions.

References

Apr 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·G M ChurchS H Kim
Nov 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·R Ogata, W Gilbert
Aug 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·D V GoeddelM H Caruthers
Jun 1, 1978·Molecular & General Genetics : MGG·I Saint-Girons, D Margarita
Jan 1, 1975·Progress in Biophysics and Molecular Biology·B Müller-Hill
Jan 21, 1977·Journal of Theoretical Biology·C E Jones, O M Olson
Mar 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·N C SeemanA Rich
Apr 1, 1976·Molecular Biology Reports·A V GurskyB P Gottikh
Apr 1, 1976·Molecular Biology Reports·G V GurskyB P Gottikh
Feb 1, 1974·Proceedings of the National Academy of Sciences of the United States of America·C W Carter, J Kraut
Jun 9, 1972·Nature·K AdlerA Schmitz
Nov 1, 1970·Proceedings of the National Academy of Sciences of the United States of America·M T Sung, G H Dixon
Dec 7, 1981·Journal of Theoretical Biology·P Argos
Dec 5, 1982·Journal of Molecular Biology·F BoschelliY Takeda
Dec 5, 1982·Journal of Molecular Biology·F Boschelli
Jan 1, 1983·Cold Spring Harbor Symposia on Quantitative Biology·R D WellsW Zacharias
Mar 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·B W MatthewsY Takeda
Jan 1, 1980·Progress in Nucleic Acid Research and Molecular Biology·R D WellsS M Stirdivant
Jun 1, 1993·Journal of Biomolecular Structure & Dynamics·R F SetlikR Rein

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Citations

Oct 1, 1986·Journal of Biomolecular Structure & Dynamics·W N HunterO Kennard
Feb 1, 1986·Journal of Biomolecular Structure & Dynamics·V I Poltev, N V Shulyupina
Feb 1, 1991·Journal of Biomolecular Structure & Dynamics·L F Sukhodub, A B Teplitsky
Feb 1, 1996·Journal of Biomolecular Structure & Dynamics·V I PoltevJ H Miller
Feb 1, 1985·Journal of Biomolecular Structure & Dynamics·M VojtískováE Palecek
Feb 1, 1988·Journal of Biomolecular Structure & Dynamics·B Gopalakrishnan, M Bansal

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