Molecular dynamics analysis of HIV-1 matrix protein: clarifying differences between crystallographic and solution structures.
One of the main structural features of the mature HIV-1 virion is the matrix protein (p17). This partially globular protein presents four helixes centrally organized and a fifth one, H5, projecting away from the packed bundle of helixes. Comparison between solution and crystallographic data of p17 indicates a 6 A displacement of a short 3(10) helix and a partial unfolding of H5 in solution related to crystal. While the behavior of the 3(10) helix has been previously addressed to virion assembly, the relevance and origin of H5 partial unfolding is possibly related to the contacts between p17 and other viral elements, such as p24. In this context, we present a 40 ns conformational sampling of monomeric p17 using molecular dynamics simulations. The performed simulations presented a progressive conversion of the p17 crystallographic structure to the NMR conformation, suggesting that the biological form of this protein may have its C-terminal portion partially unfolded.
Verli
Hugo
H
Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, Porto Alegre 90610-000, RS, Brazil. hverli@cbiot.ufrgs.br
Calazans
Alexandre
A
Brindeiro
Rodrigo
R
Tanuri
Amilcar
A
Guimarães
Jorge A
JA
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D015683:Gene Products, gag / Q000737:chemistry*; D015488:HIV Antigens / Q000737:chemistry*; D016655:HIV Core Protein p24 / Q000737:chemistry; D066298:In Vitro Techniques; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017510:Protein Folding; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D012984:Software; D012996:Solutions; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry*; D054301:gag Gene Products, Human Immunodeficiency Virus
D015683:Gene Products, gag; D015488:HIV Antigens; D016655:HIV Core Protein p24; D012996:Solutions; D014764:Viral Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1