Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Masso, Majid ^a   Vaisman, Iosif I ^a  

^a GEORGE MASON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

10-FOLD CROSS-VALIDATION; BOOSTED DECISION TREES; COMPUTATIONAL MUTAGENESIS; CORRELATION COEFFICIENT; ENVIRONMENTAL PERTURBATIONS; EVOLUTIONARY INFORMATION; LEAVE-ONE-OUT CROSS VALIDATIONS; STATE-OF-THE-ART METHODS;

COMPUTATIONAL GEOMETRY; DECISION TREES; IMAGE RETRIEVAL; LEARNING ALGORITHMS; MUTAGENESIS; PATIENT TREATMENT; STATISTICAL METHODS; VIRUSES;

DISEASES;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

CHEMOKINE RECEPTOR CCR5; CHEMOKINE RECEPTOR CXCR4; GLYCOPROTEIN GP 120;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETIC DATABASE; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; METABOLISM;

ALGORITHMS; COMPUTER SIMULATION; DATABASES, GENETIC; HIV ENVELOPE PROTEIN GP120; HIV-1; MODELS, MOLECULAR; RECEPTORS, CCR5; RECEPTORS, CXCR4;

EID: 77957271477     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-494     Document Type: Article

References (40)

1. Bernstein HB, Wang G, Plasterer MC, Zack JA, Ramasastry P, Mumenthaler SM, Kitchen CM. CD4+ NK cells can be productively infected with HIV, leading to downregulation of CD4 expression and changes in function. Virology 2009, 387(1):59-66. 10.1016/j.virol.2009.01.044, 2667870, 19251297.
2. Fenyo EM, Albert J, Asjo B. Replicative capacity, cytopathic effect and cell tropism of HIV. Aids 1989, 3(Suppl 1):S5-12. 10.1097/00002030-198901001-00002, 2514754.
3. Schuitemaker H, Koot M, Kootstra NA, Dercksen MW, de Goede RE, van Steenwijk RP, Lange JM, Schattenkerk JK, Miedema F, Tersmette M. Biological phenotype of human immunodeficiency virus type 1 clones at different stages of infection: progression of disease is associated with a shift from monocytotropic to T-cell-tropic virus population. J Virol 1992, 66(3):1354-1360. 240857, 1738194.
4. Berger EA, Doms RW, Fenyo EM, Korber BT, Littman DR, Moore JP, Sattentau QJ, Schuitemaker H, Sodroski J, Weiss RA. A new classification for HIV-1. Nature 1998, 391(6664):240. 10.1038/34571, 9440686.
5. Wu Y. The co-receptor signaling model of HIV-1 pathogenesis in peripheral CD4 T cells. Retrovirology 2009, 6:41. 10.1186/1742-4690-6-41, 2679705, 19409100.
6. Jensen MA, van't Wout AB. Predicting HIV-1 coreceptor usage with sequence analysis. AIDS Rev 2003, 5(2):104-112.
7. Sharon M, Kessler N, Levy R, Zolla-Pazner S, Gorlach M, Anglister J. Alternative conformations of HIV-1 V3 loops mimic beta hairpins in chemokines, suggesting a mechanism for coreceptor selectivity. Structure 2003, 11(2):225-236. 10.1016/S0969-2126(03)00011-X, 12575942.
8. Scheib H, Sperisen P, Hartley O. HIV-1 coreceptor selectivity: structural analogy between HIV-1 V3 regions and chemokine beta-hairpins is not the explanation. Structure 2006, 14(4):645-647. discussion 649-651, 10.1016/j.str.2006.02.009, 16615905.
9. Watabe T, Kishino H, Okuhara Y, Kitazoe Y. Fold recognition of the human immunodeficiency virus type 1 V3 loop and flexibility of its crown structure during the course of adaptation to a host. Genetics 2006, 172(3):1385-1396. 10.1534/genetics.105.051508, 1456290, 16361230.
10. Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L, He T, Kang S, Ceradini D, Jin Z, Yazdanbakhsh K, Kunstman K, Erickson D, Dragon E, Landau NR, Phair J, Ho DD, Koup RA. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med 1996, 2(11):1240-1243. 10.1038/nm1196-1240, 8898752.
11. Dorr P, Westby M, Dobbs S, Griffin P, Irvine B, Macartney M, Mori J, Rickett G, Smith-Burchnell C, Napier C, Webster R, Armour D, Price D, Stammen B, Wood A, Perros M. Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob Agents Chemother 2005, 49(11):4721-4732. 10.1128/AAC.49.11.4721-4732.2005, 1280117, 16251317.
12. Kuritzkes DR. HIV-1 entry inhibitors: an overview. Curr Opin HIV AIDS 2009, 4(2):82-87. 10.1097/COH.0b013e328322402e, 2753507, 19339945.
13. Dau B, Holodniy M. Novel targets for antiretroviral therapy: clinical progress to date. Drugs 2009, 69(1):31-50. 10.2165/00003495-200969010-00003, 19192935.
14. Rose JD, Rhea AM, Weber J, Quinones-Mateu ME. Current tests to evaluate HIV-1 coreceptor tropism. Curr Opin HIV AIDS 2009, 4(2):136-142. 10.1097/COH.0b013e328322f973, 19339953.
15. De Jong JJ, De Ronde A, Keulen W, Tersmette M, Goudsmit J. Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution. J Virol 1992, 66(11):6777-6780. 240176, 1404617.
16. Low AJ, Dong W, Chan D, Sing T, Swanstrom R, Jensen M, Pillai S, Good B, Harrigan PR. Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates. Aids 2007, 21(14):F17-24. 10.1097/QAD.0b013e3282ef81ea, 17721088.
17. Resch W, Hoffman N, Swanstrom R. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 2001, 288(1):51-62. 10.1006/viro.2001.1087, 11543657.
18. Briggs DR, Tuttle DL, Sleasman JW, Goodenow MM. Envelope V3 amino acid sequence predicts HIV-1 phenotype (co-receptor usage and tropism for macrophages). Aids 2000, 14(18):2937-2939. 10.1097/00002030-200012220-00016, 11153675.
19. Jensen MA, Coetzer M, van't Wout AB, Morris L, Mullins JI. A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. J Virol 2006, 80(10):4698-4704. 10.1128/JVI.80.10.4698-4704.2006, 1472078, 16641263.
20. Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, Domingues FS, Buch J, Daumer M, Kaiser R, Lengauer T, Harrigan PR. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther 2007, 12(7):1097-1106.
21. Pillai S, Good B, Richman D, Corbeil J. A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses 2003, 19(2):145-149. 10.1089/088922203762688658, 12643277.
22. Prosperi MC, Fanti I, Ulivi G, Micarelli A, De Luca A, Zazzi M. Robust supervised and unsupervised statistical learning for HIV type 1 coreceptor usage analysis. AIDS Res Hum Retroviruses 2009, 25(3):305-314. 10.1089/aid.2008.0039, 19327050.
23. Sander O, Sing T, Sommer I, Low AJ, Cheung PK, Harrigan PR, Lengauer T, Domingues FS. Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol 2007, 3(3):e58. 10.1371/journal.pcbi.0030058, 1848001, 17397254.
24. Xu S, Huang X, Xu H, Zhang C. Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest. J Microbiol 2007, 45(5):441-446.
25. Masso M, Vaisman II. A novel sequence-structure approach for accurate prediction of resistance to HIV-1 protease inhibitors. Proc IEEE Bioinformatics and Bioengineering 2007, 2:952-958.
26. Vaisman II, Tropsha A, Zheng W. Compositional preferences in quadruplets of nearest neighbor residues in protein structures: statistical geometry analysis. Proc IEEE Symp Int Sys 1998, 163-168.
27. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235-242. 10.1093/nar/28.1.235, 102472, 10592235.
28. Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003, 19(12):1589-1591. 10.1093/bioinformatics/btg224, 12912846.
29. Barber CB, Dobkin DP, Huhdanpaa HT. The quickhull algorithm for convex hulls. ACM Trans Math Software 1996, 22:469-483.
30. Sippl MJ. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des 1993, 7(4):473-501. 10.1007/BF02337562, 8229096.
31. Vranken WF, Budesinsky M, Fant F, Boulez K, Borremans FA. The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution. FEBS Lett 1995, 374(1):117-121. 10.1016/0014-5793(95)01086-T, 7589496.
32. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 2004, 25(13):1605-1612. 10.1002/jcc.20084, 15264254.
33. Masso M, Vaisman II. Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach. Biochem Biophys Res Commun 2003, 305(2):322-326. 10.1016/S0006-291X(03)00760-5, 12745077.
34. Masso M, Lu Z, Vaisman II. Computational mutagenesis studies of protein structure-function correlations. Proteins 2006, 64(1):234-245. 10.1002/prot.20968, 16617425.
35. Masso M, Hijazi K, Parvez N, Vaisman II. Computational mutagenesis of E. coli lac repressor: insight into structure-function relationships and accurate prediction of mutant activity. Lecture Notes in Bioinformatics 2008, 4983:390-401. Heidelberg: Springer, Mandoiu I, Sunderraman R, Zelikovsky A.
36. Masso M, Vaisman II. Accurate prediction of enzyme mutant activity based on a multibody statistical potential. Bioinformatics 2007, 23(23):3155-3161. 10.1093/bioinformatics/btm509, 17977887.
37. Masso M, Vaisman II. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. Bioinformatics 2008, 24(18):2002-2009. 10.1093/bioinformatics/btn353, 18632749.
38. Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253(5016):164-170. 10.1126/science.1853201, 1853201.
39. Frank E, Hall M, Trigg L, Holmes G, Witten IH. Data mining in bioinformatics using Weka. Bioinformatics 2004, 20(15):2479-2481. 10.1093/bioinformatics/bth261, 15073010.
40. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004, 14(6):1188-1190. 10.1101/gr.849004, 419797, 15173120.