Computer simulation of antibody binding specificity

Proteins
M Pellegrini, S Doniach

Abstract

A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives8) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form.

References

Jan 1, 1992·Protein Engineering·N KasinosI Haneef
Dec 1, 1991·Protein Engineering·E L Mehler, T Solmajer
Dec 1, 1991·Protein Engineering·T Solmajer, E L Mehler
Jan 1, 1991·Proteins·J CherfilsJ Janin
Sep 5, 1991·Journal of Molecular Biology·B K Shoichet, I D Kuntz
Apr 20, 1991·Journal of Molecular Biology·T SimonsonG Bricogne
May 5, 1991·Journal of Molecular Biology·F Jiang, S H Kim
Feb 1, 1991·Journal of Computer-aided Molecular Design·M K Gilson, B Honig
Jan 1, 1990·Annual Review of Biochemistry·D R DaviesS Sheriff
Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·S SheriffD R Davies
Jan 1, 1989·Proteins·J J Wendoloski, J B Matthew
Aug 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·E A PadlanD R Davies
Aug 1, 1984·Quarterly Reviews of Biophysics·A Warshel, S T Russell

❮ Previous
Next ❯

Citations

Jul 1, 2011·European Biophysics Journal : EBJ·Udo Riss
Apr 28, 1995·Journal of Molecular Biology·D FischerR Nussinov
Jun 1, 1996·Journal of Critical Care·A P Wheeler, G R Bernard
Apr 1, 1994·Nature Structural Biology·M Totrov, R Abagyan
Oct 15, 1996·Proceedings of the National Academy of Sciences of the United States of America·P D Thomas, K A Dill
May 4, 2000·Protein Science : a Publication of the Protein Society·R I DimaA Maritan
Mar 1, 2000·Methods : a Companion to Methods in Enzymology·C A SotrifferJ M Varga
Jun 11, 2004·Biophysical Journal·Chi ZhangYaoqi Zhou
Mar 28, 1998·Proteins·F SenoJ R Banavar
Jul 13, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·W C LuK M Ho
May 1, 1994·Applied Biochemistry and Biotechnology·D M WebsterA R Rees
Jul 28, 1995·The Journal of Biological Chemistry·J LescarP M Alzari
May 17, 2017·Biophysics Reviews·Nataraj S PagadalaJack Tuszynski

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Bacterial Cell Wall Structure (ASM)

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Antibody Specificity

Antibodies produced by B cells are highly specific for antigen as a result of random gene recombination and somatic hypermutation and affinity maturation. As the main effector of the humoral immune system, antibodies can neutralize foreign cells. Find the latest research on antibody specificity here.