A comparative analysis of viral matrix proteins using disorder predictors

doi:10.1186/1743-422X-5-126

Virology Journal

Volume 5

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A comparative analysis of viral matrix proteins using disorder predictors

Gerard Kian-Meng Goh¹^,4 , A Keith Dunker¹ and Vladimir N Uversky¹^,2^,3

¹Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA

²Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA

³Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia

⁴Institute of Molecular & Cell Biology, 138673, Singapore

author email corresponding author email

Virology Journal 2008, 5:126doi:10.1186/1743-422X-5-126


Published:	23 October 2008

Abstract

Background

A previous study (Goh G.K.-M., Dunker A.K., Uversky V.N. (2008) Protein intrinsic disorder toolbox for comparative analysis of viral proteins. BMC Genomics. 9 (Suppl. 2), S4) revealed that HIV matrix protein p17 possesses especially high levels of predicted intrinsic disorder (PID). In this study, we analyzed the PID patterns in matrix proteins of viruses related and unrelated to HIV-1.

Results

Both SIV_macand HIV-1 p17 proteins were predicted by PONDR VLXT to be highly disordered with subtle differences containing 50% and 60% disordered residues, respectively. SIV_macis very closely related to HIV-2. A specific region that is predicted to be disordered in HIV-1 is missing in SIV_mac. The distributions of PID patterns seem to differ in SIV_macand HIV-1 p17 proteins. A high level of PID for the matrix does not seem to be mandatory for retroviruses, since Equine Infectious Anemia Virus (EIAV), an HIV cousin, has been predicted to have low PID level for the matrix; i.e. its matrix protein p15 contains only 21% PID residues. Surprisingly, the PID percentage and the pattern of predicted disorder distribution for p15 resemble those of the influenza matrix protein M1 (25%).

Conclusion

Our data might have important implications in the search for HIV vaccines since disorder in the matrix protein might provide a mechanism for immune evasion.