zbMATH — the first resource for mathematics

Overcoming the key challenges in de novo protein design: enhancing computational efficiency and incorporating true backbone flexibility. (English) Zbl 1382.92209
Mondaini, Rubem P. (ed.) et al., Mathematical modelling of biosystems. Berlin: Springer (ISBN 978-3-540-76783-1/hbk). Applied Optimization 102, 133-183 (2008).
Summary: De novo protein design is initiated with a postulated or known flexible threedimensional protein structure and aims at identifying amino acid sequences compatible with such a structure. The problem was first denoted as the “inverse folding problem” [K. E. Drexler, “Molecular engineering: an approach to the development of general capabilities for molecular manipulation”, Proc. Natl. Acad. Sci. 78, No. 9, 5275–5278 (1981; doi:10.1073/pnas.78.9.5275); C. Pabo, “Molecular technology: designing proteins and peptides”, Nature 301, 200 (1983; doi:10.1038/301200a0)] since protein design has intimate links to the well-known protein folding problem [C. Hardin et al., “Ab initio protein structure prediction”, Curr. Opinion Struct. Biol. 12, No. 2, 176–181 (2002; doi:10.1016/s0959-440x(02)00306-8)]. While the protein folding problem aims at determining the single structure for a sequence, the de novo protein design problem exhibits a high level of degeneracy; that is, a large number of sequences are always found to share a common fold, although the sequences will vary with respect to properties such as activity and stability.
For the entire collection see [Zbl 1134.92001].
92D20 Protein sequences, DNA sequences
92-08 Computational methods for problems pertaining to biology
Full Text: DOI
[1] Kiepeis, J.L., Floudas, C.A., Morikis, D., Tsokos, C.G., Argyropoulos, E., Spruce, L., Lambris, J.D.: Integrated structural, computational and experimental approach for lead optimization: deisgn of compstatin variants with improved activity. J. Am. Chem. Soc., 125, 8422-8423 (2003)
[2] Klepeis, J.L., Floudas, C.A., Morikis, D., Tsokos, C.G., Lambris, J.D.: Design of peptide analogs with improved activity using a novel de novo protein design approach. Ind. Eng. Chem. Res., 43, 3817-3826 (2004)
[3] Jin, W., Kambara, O., Sasakawa, H., Tamura, A., Takada, S.: De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification. Structure, 11, 581-590 (2003)
[4] Drexler, K.E.: Molecular engineering: an approach to the development of general capabilities for molecular manipulation. Proc. Natl. Acad. Sci. USA, 78, 5275-5278 (1981)
[5] Pabo, C.: Molecular technology: designing proteins and peptides. Nature, 301, 200 (1983)
[6] Hardin, C., Pogorelov, T.V., Luthey-Schulten, Z.: Ab initio protein structure prediction. Curr. Opin. Struc. Biol., 12, 176-181 (2002)
[7] Moore, J.C., Arnold, F.H.: Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents. Nat. Biotechnol., 14, 458-467 (1996)
[8] Voigt, C.A., Mayo, S.L., Arnold, F.H., Wang, Z-G.: Computational method to reduce the search space for directed protein evolution. Proc. Natl. Acad. Sci. USA, 98, 3778-3783 (2001)
[9] Skandalis, A., Encell, L.P., Loeb, L.A.: Creating novel enzymes by applied molecular evolution. Chem. Biol., 4, 889-898 (1997)
[10] Ponder, J.W., Richards, F.M.: Tertiary templates for proteins. J. Mol. Biol., 193, 775-791 (1987)
[11] Desjarlais, J.R., Handel, T.M.: De novo design of the hydrophobic cores of proteins. Protein Sci., 4, 2006-2018 (1995)
[12] Koehl, P., Levitt, M.: De novo protein design I. In search of stability and specificity. J. Mol. Biol., 293, 1161-1181 (1999)
[13] Voigt, C.A., Gordon, D.B., Mayo, S.L.: Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design. J. Mol. Biol., 299, 789-803 (2000)
[14] Desjarlais, J.R., Handel, T.M.: Side chain and backbone exibility in protein core design. J. Mol. Biol., 290, 305-318 (1999)
[15] Desmet, J., De Maeyer, M., Hazes, B., Lasters, L: The dead-end elimination theorem and its use in side-chain positioning. Nature, 356, 539-542 (1992)
[16] Dahiyat, B.I., Mayo, S.L.: De novo protein design: fully automated sequence selection. Science, 278, 82-87 (1997)
[17] Tobi, D., Elber, R.: Distance-dependent pair potential for protein folding: results from linear optimization. Proteins: Structure, Function, and Bioinformatics, 41, 40-46 (2000)
[18] Tobi, D., Shafran, G., Linial, N., Elber, R.: On the design and analysis of protein folding potentials. Proteins: Structure, Function, and Bioinformatics, 40, 71-85 (2000)
[19] Loose, C., Kiepeis, J.L., Floudas, C.A.: A new pairwise folding potential based on improved decoy generation and side chain packing. Proteins: Structure, Function, and Bioinformatics, 54, 303-314 (2004)
[20] CPLEX: Using the CPLEX Callable Library. ILOG, Inc. Mountain View, California (1997)
[21] Sherali, H.D., Adams, W.P.: A Reformulation Linearization Technique for Solving Discrete and Continuous Nonconvex Problems. Kluwer Academic Publishing, Boston (1999) · Zbl 0926.90078
[22] Floudas, C.A.: Nonlinear and Mixed-Integer Optimization: Fundamentals and Applications. Oxford University Press, New York (1995) · Zbl 0886.90106
[23] Kiepeis, J.L., Schafroth, H.D., Westerberg, K.M., Floudas, C.A.: Deterministic global optimization and ab initio approaches for the structure prediction of polypeptides, dynamics of protein folding and proteinprotein interaction. In: Friesner, R.A. (ed) Advances in Chemical Physics. Wiley, New York (2002)
[24] Kiepeis, J.L., Floudas, C.A., Morikis, D., Lambris, J.D.: Predicting peptide structures using NMR data and deterministic global optimization. J. Comput. Chem., 20, 1354-1370 (1999)
[25] Kiepeis, J.L., Floudas, C.A.: Ab initio tertiary structure prediction of proteins. J. Global. Optim., 25, 113-140 (2003) · Zbl 1045.92018
[26] Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., Scheraga, H.A.: Energy parameters in polypeptides. 10. J. Phys. Chem., 96, 6472-6484 (1992)
[27] Floudas, C. A.: Deterministic Global Optimization: Theory, Methods and Applications. Kluwer Academic Publishers, New York (2000)
[28] Adjiman, C., Androulakis, I., Floudas, C.A.: A global optimization method, aBB, for general twice-differential constrained NPLs-1. Theoretical advances. Computers Chem. Engng., 22, 1137-1158 (1998)
[29] Adjiman, C., Androulakis, I., Floudas, C.A.: A global optimization method, aBB, for general twice-differentiable constrained NLPs-II. Implementation and computational results. Computers Chem. Engng., 22, 1159-1179 (1998)
[30] Adjiman, C., Androulakis, I., Floudas, C.A.: Global optimization of mixedinteger nonlinear problems. AIChE Journal, 46, 1769-1797 (2000)
[31] Sahu, A., Lambris, J. D.: Structure and biology of complement protein C3, a connecting link between innate and acquired immunity. Immunol. Rev., 180, 35-48 (2001)
[32] Sahu, A., Kay, B.K., Lambris, J.D.: Inhibition of human complement by a C3-binding peptide isolated from a phage displayed random peptide library. J. Immunol., 157, 884-891 (1996)
[33] Sahu, A., Soulika, A.M., Morikis, D., Spruce, L., Moore, W.T., Lambris, J.D.: Binding kinetics, structure activity relationship and biotransformation of the complement inhibitor compstatin. J. Immunol, 165, 2491-2499 (2000)
[34] Morikis, D., Roy, M., Sahu, A., Torganis, A., Jennings, P.A., Tsokos, G.C., Lambris, J.D.: The structural basis of compstatin activity examined by structure-function-based design of peptide analogs and NMR. J. Biol. Chem., 277, 14942-14953 (2002)
[35] Soulika, A.M., Morikis, D., Sarias, M.R., Roy, M., Spruce, L., Sahu, A., Lambris, J.D.: Studies of structure-activity relations of complement inhibitor compstatin. J. Immunology, 170, 1881-1890 (2003)
[36] Soulika, A.M., Khan, M.M., Hattori, T., Bowen, F.W., Richardson, B.A., Hack, C.E., Sahu, A., Edmunds, L.H., Lambris, J.D.: Inhibition of heparin/protamine complex-induced complement activation by comsptatin in baboons. Clin. Immunology, 96, 212-221 (2000)
[37] Nilsson, B., Larsson, R., Hong, J., Elgue, G., Ekdahl, K.N., Sahu, A., Lambris, J.D.: Compstatin inhibits complement and cellular activation in whole blood in two models of extracorporeal circulation. Blood, 92, 1661-1667 (1998)
[38] Fiane, A.E., Mollnes, T.E., Videm, V., Hovig, T., Hogasen, K., Mellbye, O.J., Spruce, L., Moore, W.T., Sahu, A., Lambris, J.D.: Compstatin, a peptide inhibitor of C3, prolongs survival of ex-vivo perfused pig xenografts. Xenotransplantation, 6, 52-65 (1999)
[39] Mollnes, T.E., Brekke, O.L., Fung, M., Fure, H., Christiansen, D., Bergseth, G., Videm, V., Lappegard, K.T., Kohl, J., Lambris, J.D.: Essential role of the C5a receptor in E coli-induced oxidative burst and phagocytosis revealed by a novel lepirudin-based human whole blood model of in animation. Blood, 100, 1869-1877 (2002)
[40] Klegeris, A., Singh, E.A., McGeer, P.L.: Effects of c-reactive protein and pentosan polysulphate on human complement activation. Immunology, 106, 381-388 (2002)
[41] Sahu, A., Morikis, D., Lambris, J.D.: Compstatin, a peptide inhibitor of complement, exhibits species-specific binging to complement component c3. Mol. Immunology, 39, 557-566 (2003)
[42] Gordon, B.B., Horn, G.K., Mayo, S.L., Pierce, N.A.: Exact rotamer optimization for protein design. J. Comput. Chem., 24, 232-243 (2003)
[43] Pierce, N.L., Spriet, J.A., Desmet, J., Mayo, S.L.: Conformational splitting: a more powerful criterion for dead-end elimination. J. Comput. Chem., 21, 999-1009 (2000)
[44] Zou, J.M., Saven, J.G.: Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure. J. Mol. Bio., 296, 281-294 (2000)
[45] Kuhlman, B., O’Neill, J.W., Kim, D.E., Zhang, K.Y.J., Baker, D.: Accurate computer-based design of a new backbone conformation in the second turn of protein 1. J. Mol. Bio., 315, 471-477 (2002)
[46] Kuhlman, B., Dantae, G., Ireton, G.C., Verani, G., Stoddard, B., Baker, D.: Design of a novel globular protein fold with atomic-level accuracy. Science, 302, 1364-1368 (2003)
[47] Kuhlman, B., Baker, D.: Native Protein Sequences Are Close to Optimal for Their Structures. Proc. Natl. Acad. Sci. USA, 97, 10383-10388 (2000)
[48] Dantas, G., Kuhlman, B., Callender, D., Wong, M., Baker, D.: A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J. Mol. Biol., 332, 449-460 (2003)
[49] Watters, A.L., Baker, D.: Searching for folded proteins in vitro and in silico. Eur. J. Biochem., 271, 1615-1622 (2004)
[50] Kuhlman, B., Baker, D.: Exploring folding free energy landscapes using computational protein design. Current Opinion in Structural Biology, 14, 89-95 (2004)
[51] Kortemme, T., Baker, D.: Computational design of protein-protein interactions. Current Opinion in Chemical Biology, 8, 91-97 (2004)
[52] Benson, D.E., Wisz, M.S., Hellinga, H.W.: Rational design of nascent metalloenzymes. Proc. Natl. Acad. Sci. USA, 97, 6292-6297 (2000)
[53] Goldstein, R.F.: Effcient rotamer elimination applied to protein sidechains and related spin glasses. Biophysics Journal, 66, 1335-1340 (1994)
[54] Looger, L.L., Dwyer, M.W., Smith, J.J., Hellinga, H.W.: Computational design of receptor and sensor proteins with novel functions. Nature, 423, 185-190 (2003)
[55] Richards, F.M., Hellinga, H.W.: Optimal sequence selection in proteins of known structure by simulated evolution. Proc. Natl. Acad. Sci. USA, 91, 5803-5807 (1994)
[56] Richards, F.M., Hellinga, H.W.: Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with predefined geometry. J. Mol. Biol., 222, 763-785 (1991)
[57] Richards, F.M., Caradonna, J.P., Hellinga, H.W.: Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J. Mol. Biol., 222, 787-803 (1991)
[58] Yang, W., Jones, L.M., Isley, L., Ye, Y., Lee, H-W., Wilkins, A., Liu, Z.R., Hellinga, H.W., Malchow, R., Ghazi, M., Yang, J.J.: Rational design of a calcium-binding protein. J. Am. Chem. Soc., 125, 6165-6171 (2003)
[59] Kraemer-Pecore, C.M., Wollacott, A.M., Desjarlais, J.R.: Computational protein design. Current Opinion in Chemical Biology, 5, 690-695 (2001)
[60] Kraemer-Pecore, C.M., Lecomte, J.T., Desjarlais, J.R.: A de novo redesign of the ww domain. Protein Science., 12, 2194-2205 (2003)
[61] Lim, W.A., Hodel, A., Sauer, R.T., Richards, F.M.: The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc. Natl. Acad. Sci. USA, 91, 423-427 (1994)
[62] Ember, J.A., Johansen, N.L., Hugli, T.E.: Designing synthetic superagonists of c3a anaphylatoxin. Biochemistry, 30, 3603-3612 (1991)
[63] Dahiyat, B.I., Mayo, S.L.: Protein design automation. Protein Science, 5, 895-903 (1996)
[64] Su, A., Mayo, S.L.: Coupling backbone exibility and amino acid sequence selection in protein design. Protein Science, 6, 1701-1707 (1997)
[65] Malakauskas, S.M., Mayo, S.L.: Design, structure, and stability of a hyperthermophilic protein variant. Nat. Struct. Biol., 5, 470-475 (1998)
[66] Shimaoka, M., Shifman, J.M., Jing, H., Takagi, L., Mayo, S.L., Springer, T.A.: Computational design of an intergrin I domain stabilized in the open high affinity conformation. Nat. Struct. Biol., 7, 674-678 (2000)
[67] Mooers, B.H.M., Datta, D., Baase, W.A., Zollars, E.S., Mayo, S.L., Matthews, B.W.: Repacking the core of T4 lysozyme by automated design. J. Mol. Biol., 332, 741-756 (2003)
[68] Gillespie, B., Vu, D.M., Shah, P.S., Marshall, S.A., Dyer, R.B., Mayo, S.L., Plaxco, K.W.: NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics. J. Mol. Biol., 330, 813-819 (2003)
[69] Zhu, Y., Alonso, D.O., Maki, K., Huang, C.Y., Lahr, S.J., Daggett, V., Roder, H., DeGrado, W.F., Gai, F.: Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein. Proc. Natl. Acad. Sci. USA, 100, 15486-15491 (2003)
[70] Kono, H., Saven, J.G.: Statistical theory for protein combinatorial libraries. Packing interactions, backbone exibility, and the sequence variability of a mainchain structure. J. Mol. Biol., 306, 607-628 (2001)
[71] Park, S., Yang, X., Saven, J.G.: Advances in computational protein design. Current Opinion in Structural Biology, 14, 487-494 (2004)
[72] Pokala, N., Handel, T.M.: Review: protein design-where we were, where we are, where we’re going. Journal of Structural Biology, 134, 269-281 (2001)
[73] Dill, K.A.: Dominant forces in protein folding. Biochemisty, 29, 7133-7155 (1990)
[74] Lee, C.: Predicting protein mutant energetics by self-consistent ensemble optimization. J. Mol. Biol., 236, 918-939 (1994)
[75] Kiepeis, J.L., Floudas, C.A.: Free energy calculations for peptides via deterministic global optimization. J. Chem. Phys., 110, 7491 (1999)
[76] Huber, R., Scholze, H., Paques, E.P., Deisenhofer, J.: Crystal structure analysis and molecular model of human c3a anaphylatoxin. Hoppe-Seylers Z Physiol Chemie, 361, 1389-1399 (1980)
[77] Tuffery, P., Etchebest, C., Hazout, S., Lavery, R.: A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn., 8, 1267-1289 (1991)
[78] Wilson, C., Mace, J.E., Agard, D.A.: Computational method for the design of enzymes with altered substrate specificity. J. Mol. Biol., 220, 495-506 (1991)
[79] Farinas, E., Regan, L. The de novo design of a rubredoxin-like Fe site. Protein Science, 7, 1939-1946 (1998)
[80] O. Prokopyev and H.X. Huang and P.M. Pardalos: Multi-quadratic Binary Programming. University of Florida, Research Report (2004)
[81] Oral, M., Kettani, O.: A linearization procedure for quadratic and cubic mixedinteger problems. Operations Research, 40, S109-S116 (1990)
[82] Oral, M., Kettani, O.: Reformulating nonlinear combinatorial optimization problems for higher computational efficiency. European Journal of Operational Research, 58, 236-249 (1992) · Zbl 0766.90060
[83] Pierce, N.A., Winfree, E.: Protein design is np-hard. Protein Engineering, 15, 779-782 (2002)
[84] Mallik, B., Katragadda, M., Spruce, L.A., Carafides, C., Tsokos, C.G., Morikis, D., Lambris, J.D.: Design and nmr characterization of active analogues of compstatin containing non-natural amino acids. Journal of Medicinal Chemistry, 48, 274-286 (2005)
[85] Fung, H.K., Rao, S., Floudas, C.A., Prokopyev, O., Pardalos, P.M., Rendl, F.: Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in de novo protein design. J. Comb. Optim., 10, 41-60 (2005) · Zbl 1077.92019
[86] Saunders, C.T., Baker, D.: Recapitulation of protein family divergence using exible backbone protein design. J. Mol. Biol., 346, 631-644 (2005)
[87] Rajgaria, R., McAllister, S.R., Floudas, C.A.: Development of a novel high resolution calpha-calpha distance dependent force field using a high quality decoy set. Proteins: Structure, Function, and Bioinformatics, accepted for publication (2006)
[88] Floudas, C.A.: Research challenges, opportunities and synergism in systems engineering and computational biology. AIChE Journal, 51, 1872-1884 (2005)
[89] Fung, H.K., Taylor, M.S., Floudas, C.A.: Novel formulation for the sequence selection problem in de novo protein design with exible templates. Optim. Methods & Software, in print (2006) · Zbl 1116.92027
[90] Guntert, P., Mumenthaler, C., Wuthrich, K.: Torsion angle dynamics for nmr structure calculation with the new program DYANA. J. Mol. Bio., 273, 283-298 (1997)
[91] Guntert, P.: Automated nmr structure calculation with CYANA. J. Mol. Bio., 278, 353-378 (2004)
[92] Ponder, J.: TINKER, software tools for molecular design. 1998. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine. St. Louis, MO. (1998)
[93] Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., Kollman, P.A.: A 2nd generation force-field for the simulation Of proteins, nucleic-Acids, and organicmolecules. J. Am. Chem. Soc., 117, 5179-5197 (1995)
[94] Janssen, B.J.C., Huizinga, E.G., Raaijmakers, H.C.A., Roos, A., Daha, M.R., Nilsson-Ekdahl, K., Nilsson, B., Gros, P.: Structures of complement component C3 provide insights into the function and evolution of immunity. Nature, 437, 505-511 (2005)
[95] Dwyer, M.A., Looger, L.L., Hellinga, H.W.: Computational design of a biologically active enzyme. Science, 304, 1967-1971 (2004)
[96] Dwyer, M.A., Hellinga, H.W.: Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr. Opin. Struc. Biol., 14, 495-504 (2004)
[97] Swift, J., Wehbi, W.A., Kelly, B.D., Stowell, X.F., Saven, J.G., Dmochowski, I.J.: Design of functional ferritin-like proteins with hydrophobic cavities. J. Am. Chem. Soc., 128, 6611-6619 (2006)
[98] Bunagan, M.R., Yang, X., Saven, J.G., Gai, F.: Ultrafast folding of a computationally designed trp-cage mutant: trp-cage. J. Phys. Chem. B., 110, 3759-3763 (2006)
[99] Cochran, F.V., Wu, S.P., Wang, W., Nanda, V., Saven, J.G., Therien, M.J., DeGrado, W.F.: Computational de novo design and characterization of a fourhelix bundle protein that selectively binds a nonbiological cofactor. J. Am. Chem. Soc., 127, 1346-1347 (2005)
[100] Sood, V.D., Baker, D.: Recapitulation and design of protein binding peptide structures and sequences. J. Mol. Biol., 357, 917-927 (2006)
[101] Korkegian, A., Black, M.E., Baker, D., Stoddard, B.L.: Computational thermostabilization of an enzyme. Science, 308, 857-860 (2005)
[102] Lazar, G.A., Marshall, S.A., Plecs, J.J., Mayo, S.L., Desjarlais, J.R.: Designing proteins for therapeutic applications. Curr. Opin. Struc. Biol., 13, 513-518 (2003)
[103] Shukla, U.J., Marino, H., Huang, P., Mayo, S.L., Love, J.J.: A designed protein interface that blocks fibril formation. J. Am. Chem. Soc., 126, 13914-13915 (2004)
[104] Song, G., Lazar, G.A., Kortemme, T., Shimaoka, M., Desjarlais, J.R., Baker, D., Springer, T.A. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J. Biol. Chem., 281, 5042-5049 (2006)
[105] Glover, F.: Improved linear integer programming formulations of nonlinear integer problems. Management Science, 22, 455-460 (1975) · Zbl 0318.90044
[106] Floudas, C.A., Fung, H.K.: Mathematical modeling and optimization methods for de novo protein design. In: Rigoutsos, I., Stephanopoulos, G. (eds) Systems Biology II. Oxford University, New York, NY (2006)
[107] Chan, D.C., Fass, D., Berger, J.M., Kim, P.S.: Core structure of gp41 from the HIV envelope glycoprotein. Cell, 89, 263-273 (1997)
[108] Malashkevich, V.N., Chan, D.C., Chutkowski, C.T., Kim, P.S.: Crystal structure of the simian immunodeficiency virus (SIV) gp41 core: conserved helical interactions underlie the broad inhibitory activity of gp41 peptides. Proc. Natl. Acad. Sci., 95, 9134-9139 (1998)
[109] Baritaki, S., Dittmar, M.T., Spandidos, D.A., Krambovitis, E.: In vitro inhibition of R5 HIV-1 infectivity by X4 V3-derived synthesis peptides. International Journal of Molecular Medicine, 16, 333-336 (2005)
[110] Bagnarelli, P., Fiorelli, L., Vecchi, M., Monachetti, A., Menzo, S., Clementi, M.: Analysis of the functional relationship between v3 loop and gpl20 conext with regards to human immunodeficiency virus coreceptor usage using naturally selected sequences and different viral backbones. Virology, 307, 328-340 (2003)
[111] Galanakis, P.A., Spyroulias, G.A., Rizos, A., Samolis, P., Krambovitis, E. Conformational properties of HIV-1 gpl20/v3 immunogenic domains. Current Medicinal Chemistry, 12, 1551-1568 (2005)
[112] Huang, C., Tang, M., Zhang, M., Majeed, S., Montabana, E., Stanfield, R.L., Dimitrov, D.S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P.D.: Structure of a v3-containing HIV-1 gpl20 core. Science, 310, 1025-1028 (2005)
[113] Zolla-Pazner, S.: Identifying epitopes of HIV-1 that induce protective antibodies. Nature Reviews Immunology, 4, 199-210 (2004)
[114] Sia, S.K., Carr, P.A., Cochran, A.G., Malashkevich, V.N., Kim, P.S.: Short constrained peptides that inhibit HIV-1 entry. PNAS, 99, 14664-14669 (2002)
[115] Fung, H.K., Taylor, M.S., Floudas, C.A., Morikis, D., Lambris, J.D.: Redesigning complement 3a based on exible templates from both xray crystallography and molecular dynamics simulation. In preparation (2006)
[116] Hoover, D.M., Rajashankar, K.R., Blumenthal, R., Puri, A., Oppenheim, J.J., Chertov, O., Lubkowski, J.: The structure of human β-defensin-2 shows evidence of higher order oligomeration. J. Biol. Chem., 275, 32911-32918 (2000)
[117] García, J.R.C., Florian, J., Schulz, S., Krause, A., Rodriguez-Jiménez, F.J., Forssmann, U., Adermann, K., Kluver, E., Vogelmeier, C., Becker, D., Hedrich, R., Forssmann, W.G., Bals, R.: Identification of a novel, multifunctional β - defensin (human β-defensin 3) with specific antimicrobial activity. Cell and Tissue Research, 306, 257-264 (2001)
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.