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Journal of Molecular Modeling

, Volume 15, Issue 2, pp 165–171 | Cite as

A disulfide linked model of the complement protein C8γ complexed with C8α indel peptide

  • Athanassios Stavrakoudis
Original Paper

Abstract

In a recent study C8γ (complement protein) with Cys40Ala substitution and a C8α derived peptide with Cys164Ala substitution were co-crystallized and their binding mode was revealed. Computer modeling and molecular dynamics simulations were performed in order to check the hypothesis that the residues Ala164 of C8α and Ala40 of C8γ occupied the right position if cysteine residues were in their place for disulfide bonding. Substitution of these two alanine residues with cysteine along with disulfide bond creation via molecular modeling and subsequent molecular dynamics simulation of the complex corroborated the hypothesis, which was also confirmed from recent crystallographic data. Average RMSD between backbone atoms of the indel peptide during the MD trajectory in comparison with the corresponding sequence of crystal structure of the C8α/γ complex was found only 0.085 nm.

Figure

Modeling the C*y/α comlexation. Ribbon representation of the C8y complexed with C8α indel peptide initial (green/cyan) X-ray structure and the final MD conformation (magenta/orange) after imposing the disulfide link. Average RMSD between backbone atoms of the indel peptide during MD trajectory in comparison with the corresponding sequence of crystal structure of the C8α/y complex was found only 0.085nm.

Keywords

C8α/γ complex Complement protein Computer simulation Membrane attack complex Molecular dynamics 

Notes

Acknowledgment

NAMD parallel execution was performed at the Research Center of Scientific Simulations (RCSS) of University of Ioannina. The open source community is gratefully acknowledged for making publicly available all the computational tools (Linux, NAMD, GNU tools, etc) needed for this research.

Supplementary material

894_2008_412_MOESM1_ESM.mpg (8 mb)
(MPG 8.01 MB)

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of EconomicsUniversity of IoanninaIoanninaGreece

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