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Original Articles

Structure and Polymorphism of the Principal Neutralization Site of Thailand HIV-1 Isolate

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Pages 603-613 | Received 10 Nov 2002, Published online: 15 May 2012

References and Footnotes

  • Leonard , C. K. , Spellman , M. W. , Riddle , L. , Harris , R. J. , Thomas , J. N. and Gregory , T. J. 1990 . J. Biol. Chem. , 265 : 10373 – 10382 .
  • Putney , S. D. , Mathews , T. J. , Robey , W. G. , Lynn , D. I. , Robert-Guroff , M. , Mueller , W. T. , Langlois , A. J. , Ghraycb , J. , Petteway , S. R. , Weinhold , K. J. , Fischinger , P. J. , Wong-Staal , F. , Gallo , R. C. and Bolognesi , D. P. 1986 . Science , 234 : 1392 – 1395 .
  • Robey , W. G. , Arthur , L. O. , Matthews , T. J. , Langlois , A. , Copeland , T. D. , Lerche , N. W. , Oroszlan , S. , Bolognesi , D. P. , Gilden , R. V. and Fischinger , P. J. 1986 . Proc. Natl. Acad. Sci. USA , 83 : 7023 – 7027 .
  • Javaherian , K. , Langlois , A. J. , McDanal , C. , Ross , K. L. , Eckler , L. I. , Jellis , C. L. , Profy , A. T. , Rusche , J. R. , Bolognesi , D. , Putney , S. D. and Matthews , T. J. 1989 . Proc. Natl. Acad. Sci. USA , 86 : 6768 – 6772 .
  • Rusche , J. R. , Javaherian , K. , McDanal , C. , Petro , J. , Lynn , D. L. , Grimaila , R. , Langlois , A. , Gallo , R. C. , Arthur , L. O. , Fischinger , P. J. , Bolognesi , D. P. , Putney , S. D. and Matthews , T. J. 1988 . Proc. Natl. Acad. Sci. USA , 85 : 3198 – 3202 .
  • Palker , T. J. , Clark , M. L. , Langlois , A. J. , Matthews , T. J. , Weinhold , K. J. , Randall , R. , Bolognesi , D. P. and Haynes , B. F. 1988 . Proc. Natl. Acad. Sci. USA , 85 : 1932 – 1936 .
  • LaRosa , G. J. , Davide , J. P. , Weinhold , K. , Waterbury , J. A. , Profy , A. T. , Lewis , J. A. , Langlois , A. J. , Dressman , G. R. , Boswell , R. N. , Shadduk , P. , Holley , L. H. , Karplus , M. , Bolognesi , D. P. , Matthews , T. J. , Emini , E. A. and Putney , S. D. 1990 . Science , 249 : 932 – 935 .
  • Javaherian , K. , Langlois , A. J. , LaRosa , G. J. , Profy , A. T. , Bolognesi , D. P. , Herlihy , W. C. , Putney , S. D. and Matthews , T. J. 1990 . Science , 250 : 1590 – 1593 .
  • Pau , C.-P. , Kai , M. , Holloman-Candal , D. L. , Luo , C.-C. , Kalish , M. L. , Schochetman , G. , Byers , B. and George , J. R. 1994 . AIDS Res. Hum. Retroviruses , 10 : 1369 – 1377 . WHO network for HIV isolation and characterization
  • The data on the X-ray structure of gp120 were published in work (11). However, the separate fragments of protein surface, including the V3 loop of interest, were not taken into account in study cited (see also the file 1gc1 in Protein Data Bank (12, 13))
  • Kwong , P. D. , Wyatt , R. , Robinson , J. , Sweet , R. W. , Sodroski , J. and Hendrickson , W. A. 1998 . Nature , 393 : 648 – 659 .
  • Bernstein , F. C. , Koetzle , T. F. , Williams , G. J. B. , Meyer , E. F. , Brice , M. D. , Rodgers , J. R. , Kennard , O. , Shimanouchi , T. and Tasumi , M. 1977 . J. Mol. Biol. , 112 : 535 – 542 .
  • Berman , H. M. , Westbrook , J. , Feng , Z. , Gilliland , G. , Bhat , T. N. , Weissig , H. , Shindyalov , I. N. and Bourne , P. E. 2000 . Nucleic Acids Research , 28 : 235 – 242 .
  • Chandrasekhar , K. , Profy , A. T. and Dyson , H. J. 1991 . Biochemistry , 30 : 9187 – 9194 .
  • Gupta , G. , Anantharamaiah , G. M. , Scott , D. R. , Eldridge , J. H. and Myers , G. 1993 . J. Biomol. Struct. Dynam. , 11 : 345 – 366 .
  • Catasti , P. , Fontenot , J. D. , Bradbury , E. M. and Gupta , G. 1995 . J. Biol. Chem. , 270 : 2224 – 2232 .
  • Catasti , P. , Bradbury , E. M. and Gupta , G. 1996 . J. Biol. Chem. , 271 : 8236 – 8242 .
  • Andrianov , A. M. 2002 . J. Biomol. Struct. Dynam. , 19 : 973 – 990 .
  • Sherman , S. A. , Andrianov , A. M. and Akhrem , A. A. 1987 . J. Biomol. Struct. Dynam. , 4 : 869884
  • Andrianov , A. M. and Sherman , S. A. 1989 . Studia Biophys. , 131 : 161 – 168 .
  • Andrianov , A. M. and Sherman , S. A. 1990 . “ Modelling and Computer Methods in Molecular Biology and Genetics ” . In Abstracts of the International Conference Edited by: Kolchanov , N. A. and Ratner , V. A. 83 – 84 . Russia : Novosibirsk .
  • Andrianov , A. M. and Akhrem , A. A. 1991 . Molecular Biology (Engl. Tr.) , 25 : 162 – 171 .
  • Andrianov , A. M. 1991 . Molecular Biology (Engl. Tr.) , 25 : 951 – 959 .
  • Sherman , S. A. , Andrianov , A. M. and Akhrem , A. A. 1988 . J. Biomol. Struct. Dynam. , 5 : 785 – 801 .
  • Andrianov , A. M. and Sherman , S. A. 1990 . Stud. Biophys. , 135 : 107 – 114 .
  • Freed , E. O. , Myers , D. J. and Risser , R. 1991 . J. Virol. , 65 : 190 – 194 .
  • Freed , E. O. , Meyers , D. J. and Risser , R. 1991 . J. Virol. , 65 : 333 – 336 .
  • Hwang , S. S. , Boyle , T. J. , Lyerly , H. K. and Cullen , B. R. 1991 . Science , 253 : 71 – 74 .
  • Chesebro , B. , Wehrly , K. , Nishio , J. and Perryman , S. 1992 . J. Virol. , 66 : 6547 – 6554 .
  • Andrianov , A. M. 1999 . J. Biomol. Struct. Dynam. , 16 : 931 – 953 .
  • Stewart , J. J. P. 1989 . Comput. Chem. , 10 : 221 – 227 .
  • Lewis , P. N. , Momany , F. A. and Scheraga , H. A. 1973 . Biochim. Biophys. Acta , 303 : 211 – 229 .
  • Popov , E. M. 1989 . Strukturnayay organizatsiya belkov (Structural Organization of Proteins) 352 Moscow : Nauka .
  • Milner-White , E. J. , Ross , B. M. , Ismail , R. , Belhaj-Mostefa , K. and Poet , R. 1988 . J. Mol. Biol. , 204 : 777 – 782 .
  • Sherman , S. A. , Andrianov , A. M. and Akhrem , A. A. 1989 . Konformatsionnyi analiz i ustanovlenie prostranstvennoi struktury belkovykh molekul (Conformational Analysis and Establishment of Spatial Protein Structure) 240 Nauka i Tekhnika : Minsk .
  • Ghiara , J. B. , Stura , E. A. , Stanfield , R. L. , Profy , A. T. and Wilson , I. A. 1994 . Science , 264 : 82 – 85 .
  • Ghiara , J. B. , Ferguson , D. C. , Satterthwait , A. C. , Dyson , H. J. and Wilson , I. A. 1997 . J. Mol. Biol. , 266 : 31 – 42 .
  • Sherman , S. A. and Johnson , M. E. 1993 . Prog. Biophys. Mol. Biol. , 59 : 285 – 339 .
  • These computations were implemented using the starting values of φ, ψ dihedrals (Table I) by their optimization in the AMBER force field (40).
  • Weiner , P. K. and Kollman , P. A. 1981 . J. Comput. Chem. , 2 : 287 – 303 .
  • Dashevsky , V. G. 1974 . Konformatsii organicheskikh molekul (Conformations of organic molecules) 432 Khimiya : Moscow .
  • Isogai , Y. , Nemethy , G. , Rackovsky , S. , Leach , S. J. and Scheraga , H. A. 1980 . Biopolymers , 19 : 1183 – 1210 .
  • MacArthur , M. W. and Thornton , J. M. 1993 . Proteins: Structure, Function, and Genetics , 17 : 232 – 251 .
  • Here we use the classification of Sippl (45) whereby the peptides are considered as (i) stable (unique conformation), (ii) flip-flop (limited set of structural clusters), (iii) metastable (dominant structure with other conformations admissible), and (iv) unstable (a large number of different conformers)
  • Sippl , M. J. 1990 . J. Mol. Biol. , 213 : 859 – 883 .
  • Andrianov , A. M. 1998 . J. Biomol. Struct. Dynam. , 15 : 1101 – 1113 .

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