Dual Spatial Folds and Different Local Structures of the HIV-1 Immunogenic Crown in Various Virus Isolates

References and Footnotes

• Skinner , M. A. , Langlois , A. J. , McDanal , C. B. , McDougal , J. A. , Bolognesi , D. P. and Matthews , T. J. 1988 . J. Virol. , 62 : 4195 – 4200 .
   PubMedGoogle Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Schreiber , M. , Wachsmuth , C. , Muller , H. , Odemuyiwa , S. , Schmitz , H. , Meyer , S. , Meyer , B. and Schneider-Mergener , J. 1997 . J. Virol. , 71 : 9198 – 9205 .
   PubMed Web of Science ®Google Scholar
• Gorny , M. K. , Xu , J.-Y. , Karwowska , S. , Buchbinder , A. and Zolla-Pazner , S. 1993 . J. Immun. , 150 : 635 – 643 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Wu , L. , Gerard , N. P. , Wyatt , R. , Choe , H. , Parolin , C. , Ruffin , N. , Borsetti , A. , Cardoso , A. A. , Desjardin , E. , Newman , W. , Gerard , C. and Sodroski , J. 1996 . Nature , 384 : 179 – 183 .
   PubMed Web of Science ®Google Scholar
• Trkola , A. , Dragic , T. , Arthos , J. , Binley , J. M. , Olson , W. , Allaway , G. P. , Cheng Mayer , C. , Robinson , J. , Maddon , P. J. and Moore , J. P. 1996 . Nature , 384 : 184 – 187 .
   PubMed Web of Science ®Google Scholar
• Dettin , M. , Ferranti , P. , Scarinci , C. , Picariello , G. and Bello , C. D. 2003 . Biochemistry , 42 : 9007 – 9012 .
   PubMedGoogle Scholar
• Chavda , S. C. , Griffin , P. , Han-Liu , Z. , Keys , B. , Vekony , M. A. and Cann , A. J. 1994 . J. Gen. Virol. , 75 : 3249 – 3253 .
   PubMed Web of Science ®Google Scholar
• Mammano , F. , Salvatori , F. , Ometto , L. , Panozzo , M. , Chieco-Bianchi , L. and Rossi , A. D. 1995 . J. Virol , 69 : 82 – 92 .
   PubMed Web of Science ®Google Scholar
• Milich , L. , Margolin , B. H. and Swanstrom , R. 1993 . J. Virol. , 67 : 5623 – 5634 .
   PubMed Web of Science ®Google Scholar
• Shioda , T. , Levy , J. A. and Cheng-Mayer , C. 1992 . Proc. Natl. Acad. Sci. USA , 89 : 9434 – 9438 .
   PubMed Web of Science ®Google Scholar
• Yamashita , A. , Yamamoto , N. , Matsuda , J. and Koyanagi , Y. 1994 . Virology , 204 : 170 – 179 .
   PubMedGoogle Scholar
• Goudsmit , J. , Debouck , C. , Meloen , R. H. , Smit , L. , Bakker , M. , Asher , D. M. , Wolff , A. V. , Gibbs , C. J. Jr. and Gajdusek , D. C. 1988 . Proc. Natl. Acad. Sci. USA , 85 : 4478 – 4482 .
   PubMed Web of Science ®Google Scholar
• Clements , G. J. , Price-Jones , M. J. , Stephens , P. E. , Sutton , C. , Schulz , T. F. , Clapham , P. R. , McKeating , J. A. , McClure , M. O. , Thomson , S. , Marsh , M. , Kay , J. , Weiss , R. A. and Moore , J. P. 1991 . AIDS Res. Hum. Retroviruses , 71 : 3 – 16 .
   Google Scholar
• Callebeaut , C. , Krust , B. , Jacotor , E. and Hovanessian , A. G. 1993 . Science , 262 : 2045 – 2050 .
   PubMedGoogle Scholar
• Moore , J. P. and Nara , P. L. 1991 . AIDS , 5 : 21 – 33 .
   PubMedGoogle Scholar
• The data on the X-ray structure of gp120 were published in work (22) . However, the separate fragments of protein surface, including the V3 loop of interest, were not taken into account in the study cited (see also the file 1gc1 in Protein Data Bank (23, 24))
   Google Scholar
• Kwong , P. D. , Wyatt , R. , Robinson , J. , Sweet , R. W. , Sodroski , J. and Hendrickson , W. A. 1998 . Nature , 393 : 648 – 659 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Rini , J. M. , Stanfield , R. L. , Stura , E. A. , Salinas , P. A. , Profy , A. T. and Wilson , I. A. 1993 . Proc. Natl. Acad. Sci. USA , 90 : 6325 – 6329 .
   PubMed Web of Science ®Google Scholar
• Ghiara , J. B. , Stura , E. A. , Stanfield , R. L. , Profy , A. T. and Wilson , I. A. 1994 . Science , 264 : 82 – 85 .
   PubMed Web of Science ®Google Scholar
• Ghiara , J. B. , Ferguson , D. C. , Satterthwait , A. C. , Dyson , H. J. and Wilson , I. A. 1997 . J. Mol. Biol. , 266 : 31 – 42 .
   PubMed Web of Science ®Google Scholar
• Stanfield , R. L. , Cabezas , E. , Satterthwait , A. C. , Stura , E. A. , Profy , A. T. and Wilson , I. A. 1999 . Structure , 7 : 131 – 142 .
   PubMed Web of Science ®Google Scholar
• Stanfield , R. L. , Ghiara , J. B. , Saphire , E. O. , Profy , A. T. and Wilson , I. A. 2003 . Virology , 315 : 159 – 173 .
   PubMed Web of Science ®Google Scholar
• Stanfield , R. L. , Gorny , M. K. , Williams , C. , Zolla-Pazner , S. and Wilson , I. A. 2004 . Structure , 12 : 193 – 204 .
   PubMed Web of Science ®Google Scholar
• Ding , J. , Smith , A. D. , Geisler , S. C. , Ma , X. , Arnold , G. F. and Arnold , E. 2002 . Structure , 10 : 999 – 1011 .
   PubMed Web of Science ®Google Scholar
• Catasti , P. , Fontenot , J. D. , Bradbury , E. M. and Gupta , G. 1995 . J. Biol. Chem. , 270 : 2224 – 2232 .
   PubMed Web of Science ®Google Scholar
• Gupta , G. , Anantharamaiah , G. M. , Scott , D. R. , Eldridge , J. H. and Myers , G. 1993 . J. Biomol. Struct. Dynam. , 11 : 345 – 366 .
   PubMed Web of Science ®Google Scholar
• Chandrasekhar , K. , Profy , A. T. and Dyson , H. J. 1991 . Biochemistry , 30 : 9187 – 9194 .
   PubMed Web of Science ®Google Scholar
• Vu , H. M. , de Lorimier , R. , Moody , M. A. , Haynes , B. F. and Spicer , L. D. 1996 . Biochemistry , 35 : 5158 – 5165 .
   PubMed Web of Science ®Google Scholar
• Vranken , W. F. , Budesinsky , M. and Martins , J. C. 1996 . Eur. J. Biochem. , 236 : 100 – 108 .
   PubMedGoogle Scholar
• Sarma , A. V. , Raju , T. V. and Kunwar , A. C. 1997 . J. Biochem. Biophys. Methods , 34 : 83 – 98 .
   PubMedGoogle Scholar
• Tolman , R. L. , Bednarek , M. A. , Johnson , B. A. , Leanza , W. , Marburg , S. , Underwood , D. J. , Emini , E. A. and Conley , A. J. 1993 . Int. J. Pept. Protein Res. , 41 : 455 – 466 .
   PubMedGoogle Scholar
• Jelinek , R. , Terry , T. D. , Gesell , J. J. , Malik , P. , Perham , R. N. and Opella , S. 1997 . J. Mol. Biol. , 266 : 649 – 655 .
   PubMed Web of Science ®Google Scholar
• Huang , X. , Smith , M. C. , Berzofsky , J. A. and Barchi , J. J. Jr. 1996 . FEBSLett. , 393 : 280 – 286 .
   PubMed Web of Science ®Google Scholar
• Huang , X. , Barchi , J. J. , Lung , F. D. , Roller , P. P. , Nara , P. L. , Muschik , J. and Garrity , R. R. 1997 . Biochemistry , 36 : 10846 – 10856 .
   PubMed Web of Science ®Google Scholar
• Markert , R. L. , Ruppach , H. , Gehring , S. , Dietrich , U. , Mierke , D. F. , Kock , M. , Rubsamen- Waigmann , H. and Griesinger , C. 1996 . Eur. J. Biochem. , 237 : 188 – 204 .
   PubMedGoogle Scholar
• Zvi , A. , Kustanovich , I. , Hayek , Y. , Matsushita , S. and Anglister , J. 1995 . FEBS Lett. , 368 : 267 – 270 .
   PubMedGoogle Scholar
• Zvi , A. , Feigelson , D. J. , Hayek , Y. and Anglister , J. 1997 . Biochemistry , 36 : 8619 – 8627 .
   PubMed Web of Science ®Google Scholar
• Tugarinov , V. , Zvi , A. , Levy , R. , Hayek , Y. , Matsushita , S. and Anglister , J. 2000 . Structure , 8 : 385 – 395 .
   PubMed Web of Science ®Google Scholar
• Weliky , D. P. , Benett , A. E. , Zvi , A. , Anglister , J. , Steinbach , P. J. and Tycko , R. 1999 . Nat. Struct. Biol. , 6 : 141 – 145 .
   PubMedGoogle Scholar
• Vranken , W. F. , Fant , F. , Budesinsky , M. and Borremans , F. A. M. 2001 . Eur. J. Biochem. , 268 : 2620 – 2628 .
   PubMedGoogle Scholar
• Wu , G. , MacKenzie , R. , Durda , P. J. and Tsang , P. 2000 . J. Biol. Chem. , 275 : 36645 – 36652 .
   PubMed Web of Science ®Google Scholar
• Sharpe , S. , Kessler , N. , Anglister , J. A. , Yau , W. M. and Tycko , R. 2004 . J. Amer. Chem. Soc. , 126 : 4979 – 4990 .
   PubMedGoogle Scholar
• Andrianov , A. M. 2002 . J. Biomol. Struct. Dynam. , 19 : 973 – 990 .
   PubMed Web of Science ®Google Scholar
• Andrianov , A. M. and Sokolov , Yu. A. 2003 . J. Biomol. Struct. Dynam. , 20 : 603 – 614 .
   PubMed Web of Science ®Google Scholar
• Andrianov , A. M. and Sokolov , Yu. A. 2004 . J. Biomol. Struct. Dynam. , 21 : 577 – 590 .
   PubMed Web of Science ®Google Scholar
• Here and further I use the numeration of amino acid sequences for synthetic peptides (55) imitating the primary structures of HIV-Haiti and HIV-RF V3 loops .
   Google Scholar
• The length of fragments was chosen in agreement with the results of study (56) displaying that the preferred hexapeptide conformations are stabilized owing to interactions with the nearest neighbours in the polypeptide chain, and this stabilizing effect is preserved in longer V3 loop peptides .
   Google Scholar
• Catasti , P. , Bradbury , E. M. and Gupta , G. 1996 . J. Biol. Chem. , 271 : 8236 – 8242 .
   PubMed Web of Science ®Google Scholar
• Andrianov , A. M. 1999 . J. Biomol. Struct. Dynam. , 16 : 931 – 953 .
   PubMed Web of Science ®Google Scholar
• Sherman , S. A. , Andrianov , A. M. and Akhrem , A. A. 1987 . J. Biomol. Struct. Dynam. , 4 : 869 – 884 .
   PubMed Web of Science ®Google Scholar
• 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 Minsk : Nauka i Tekhnika .
   Google Scholar
• Sherman , S. A. , Andrianov , A. M. and Akhrem , A. A. 1988 . J. Biomol. Struct. Dynam. , 5 : 785 – 801 .
   PubMed Web of Science ®Google Scholar
• Andrianov , A. M. and Sherman , S. A. 1990 . Stud. Biophys. , 135 : 107 – 114 .
   Google Scholar
• Stewart , J. J. P. 1989 . Comput. Chem. , 10 : 221 – 227 .
   Google Scholar
• Lewis , P. N. , Momany , F. A. and Scheraga , H. A. 1973 . Biochim. Biophys. Acta , 303 : 211 – 229 .
   PubMed Web of Science ®Google Scholar
• Popov , E. M. 1989 . Strukturnayay organizatsiya belkov (Structural Organization of Proteins) 352 Moscow : Nauka .
   Google Scholar
• Milner-White , E. J. , Ross , B. M. , Ismail , R. , Belhaj-Mostefa , K. and Poet , R. 1988 . J. Mol. Biol. , 204 : 777 – 782 .
   PubMed Web of Science ®Google Scholar
• Sherman , S. A. and Johnson , M. E. 1993 . Prog. Biophys. Mol. Biol. , 59 : 285 – 339 .
   PubMed Web of Science ®Google Scholar
• Kar , L. , Sherman , S. A. and Johnson , M. E. 1994 . J. Biomol. Struct. Dynam. , 12 : 527 – 558 .
   PubMed Web of Science ®Google Scholar
• Sippl , M. J. 1990 . J. Mol. Biol. , 213 : 859 – 883 .
   PubMed Web of Science ®Google Scholar
• The qualitative estimation of the relative populations of simulated conformers in the analyzed ensemble was performed using the Boltzmann equation in the approximation of “isolated molecule” . (see, e.g. (69)
   Google Scholar
• Dashevsky , V. G. 1974 . Konformatsii organicheskikh molekul (Conformations of organic molecules) 432 Moscow : Khimiya .
   Google Scholar
• Freed , E. O. , Myers , D. J. and Risser , R. 1991 . J. Virol. , 65 : 190 – 194 .
   PubMed Web of Science ®Google Scholar
• Freed , E. O. , Meyers , D. J. and Risser , R. 1991 . J. Virol. , 65 : 333 – 336 .
   Google Scholar
• Hwang , S. S. , Boyle , T. J. , Lyerly , H. K. and Cullen , B. R. 1991 . Science , 253 : 71 – 74 .
   PubMed Web of Science ®Google Scholar
• Chesebro , B. , Wehrly , K. , Nishio , J. and Perryman , S. 1992 . J. Virol. , 66 : 6547 – 6554 .
   PubMed Web of Science ®Google Scholar
• Ling , H. , Usami , O. , Xiao , P. , Gu , H. X. and Hattori , T. 2004 . AIDS Res. Hum. Retroviruses , 20 : 213 – 218 .
   PubMedGoogle Scholar
• Gorny , M. K. , Revesz , K. , Williams , C. , Volsky , B. , Louder , M. K. , Anyangwe , C. A. , Krachmarov , C. , Kayman , S. C. , Pinter , A. , Nadas , A. , Nyambi , P. N. , Mascola , J. R. and Zolla- Pazner , S. 2004 . J. Virol. , 78 : 2394 – 2404 .
   PubMedGoogle Scholar
• Cabezas , E. , Wang , M. , Parren , P. W. , Stanfield , R. and Satterthwait , A. C. 2000 . Biochemistry , 39 : 14377 – 14391 .
   PubMedGoogle Scholar
• Hsu , S. T. and Bonvin , A. M. 2004 . Proteins , 55 : 582 – 593 .
   PubMed Web of Science ®Google Scholar