Rational and computational design of stabilized variants of cyanovirin-N that retain affinity and specificity for glycan ligands

Biochemistry

Volumn 50, Issue 49, 2011, Pages 10698-10712

  Patsalo, Vadim ^a,b   Raleigh, Daniel P ^b   Green, David F ^a,b  

^a Stony Brook University   (United States)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIPHATIC GROUPS; CARBOHYDRATE BINDING; CHEMICAL DENATURATION; COMPUTATIONAL DESIGN; ENVELOPE GLYCOPROTEINS; FREE ENERGY LANDSCAPE; GLYCAN MICROARRAYS; GLYCANS; HIGH AFFINITY; HUMAN IMMUNODEFICIENCY VIRUS; POISSON-BOLTZMANN; POLAR SIDE CHAINS; PROTEIN CORE; PROTEIN FOLDS; REPACKING ALGORITHM; SPECIFICITY PROFILE; THERMAL DENATURATIONS; THERMO DYNAMIC ANALYSIS; THERMODYNAMIC PARAMETER; TWO-STATE TRANSITIONS;

CARBOHYDRATES; DENATURATION; PROTEIN FOLDING; PROTEINS; PYROLYSIS; THERMOANALYSIS; VIRUSES;

BINDING ENERGY;

CARBOHYDRATE BINDING PROTEIN; CYANOVIRIN N; GLYCAN; GUANIDINE; SERINE; THREONINE;

ARTICLE; BINDING AFFINITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN MICROARRAY; PROTEIN STABILITY; PROTEIN UNFOLDING; STATIC ELECTRICITY; THERMODYNAMICS;

AMINO ACID SUBSTITUTION; ANTI-HIV AGENTS; BACTERIAL PROTEINS; BINDING SITES; CARBOHYDRATE SEQUENCE; CARRIER PROTEINS; CIRCULAR DICHROISM; DRUG DESIGN; GUANIDINE; LIGANDS; MICROARRAY ANALYSIS; MOLECULAR SEQUENCE DATA; MUTATION; POLYSACCHARIDES; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY;

EID: 82955169560     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201411c     Document Type: Article

References (92)

1. Gustafson, K. R., Sowder, R. C., Henderson, L. E., Cardellina, J. H., McMahon, J. B., Rajamani, U., Pannell, L. K., and Boyd, M. R. (1997) Isolation, primary sequence determination, and disulfide bond structure of cyanovirin-N, an anti-HIV (human immunodeficiency virus) protein from the cyanobacterium Nostoc ellipsosporum Biochem. Biophys. Res. Commun. 238, 223-228 (Pubitemid 27453305)
2. Boyd, M. R., Gustafson, K. R., McMahon, J. B., Shoemaker, R. H., O'Keefe, B. R., Mori, T., Gulakowski, R. J., Wu, L., Rivera, M. I., Laurencot, C. M., Currens, M. J., Cardellina, J. H., Buckheit, R. W., Nara, P. L., Pannell, L. K., Sowder, R. C., and Henderson, L. E. (1997) Discovery of cyanovirin-N, a novel human immunodeficiency virus-inactivating protein that binds viral surface envelope glycoprotein gp120: Potential applications to microbicide development Antimicrob. Agents Chemother. 41, 1521-1530 (Pubitemid 27289680)
3. Balzarini, J. (2007) Targeting the glycans of glycoproteins: A novel paradigm for antiviral therapy Nat. Rev. Microbiol. 5, 583-597 (Pubitemid 47074114)
4. Dey, B., Lerner, D. L., Lusso, P., Boyd, M. R., Elder, J. H., and Berger, E. A. (2000) Multiple antiviral activities of cyanovirin-N: Blocking of human immunodeficiency virus type 1 gp120 interaction with CD4 and coreceptor and inhibition of diverse enveloped viruses J. Virol. 74, 4562-4569 (Pubitemid 30237881)
5. Wei, X., Decker, J. M., Wang, S., Hui, H., Kappes, J. C., Wu, X., Salazar-Gonzalez, J. F., Salazar, M. G., Kilby, J. M., Saag, M. S., Komarova, N. L., Nowak, M. A., Hahn, B. H., Kwong, P. D., and Shaw, G. M. (2003) Antibody neutralization and escape by HIV-1 Nature 422, 307-312 (Pubitemid 36378357)
6. Scanlan, C. N., Offer, J., Zitzmann, N., and Dwek, R. A. (2007) Exploiting the defensive sugars of HIV-1 for drug and vaccine design Nature 446, 1038-1045 (Pubitemid 46676066)
7. Barrientos, L. G., O'Keefe, B. R., Bray, M., Sanchez, A., Gronenborn, A. M., and Boyd, M. R. (2003) Cyanovirin-N binds to the viral surface glycoprotein, GP1,2 and inhibits infectivity of Ebola virus Antiviral Res. 58, 47-56 (Pubitemid 36507221)
8. Tiwari, V., Shukla, S. Y., and Shukla, D. (2009) A sugar binding protein cyanovirin-N blocks herpes simplex virus type-1 entry and cell fusion Antiviral Res. 84, 67-75
9. O'Keefe, B. R., Smee, D. F., Turpin, J. A., Saucedo, C. J., Gustafson, K. R., Mori, T., Blakeslee, D., Buckheit, R., and Boyd, M. R. (2003) Potent anti-influenza activity of cyanovirin-N and interactions with viral hemagglutinin Antimicrob. Agents Chemother. 47, 2518-2525 (Pubitemid 36919454)
10. Barrientos, L. G., Louis, J. M., Botos, I., Mori, T., Han, Z., O'Keefe, B. R., Boyd, M. R., Wlodawer, A., and Gronenborn, A. M. (2002) The domain-swapped dimer of cyanovirin-N is in a metastable folded state: Reconciliation of X-ray and NMR structures Structure 10, 673-686 (Pubitemid 34518710)
11. Colleluori, D. M., Tien, D., Kang, F., Pagliei, T., Kuss, R., McCormick, T., Watson, K., McFadden, K., Chaiken, I., Buckheit, R. W., and Romano, J. W. (2005) Expression, purification, and characterization of recombinant cyanovirin-N for vaginal anti-HIV microbicide development Protein Expression Purif. 39, 229-236 (Pubitemid 40084609)
12. Mori, T., Barrientos, L. G., Han, Z., Gronenborn, A. M., Turpin, J. A., and Boyd, M. R. (2002) Functional homologs of cyanovirin-N amenable to mass production in prokaryotic and eukaryotic hosts Protein Expression Purif. 26, 42-49 (Pubitemid 35307485)
13. Sexton, A., Drake, P. M., Mahmood, N., Harman, S. J., Shattock, R. J., and Ma, J. K.-C. (2006) Transgenic plant production of cyanovirin-N, an HIV microbicide FASEB J. 20, 356-388
14. Matei, E., Zheng, A., Furey, W., Rose, J., Aiken, C., and Gronenborn, A. M. (2010) Anti-HIV activity of defective cyanovirin-N mutants is restored by dimerization J. Biol. Chem. 285, 13057-13065
15. Matei, E., Furey, W., and Gronenborn, A. M. (2008) Solution and crystal structures of a sugar binding site mutant of cyanovirin-N: No evidence of domain swapping Structure 16, 1183-1194
16. Fromme, R., Katiliene, Z., Giomarelli, B., Bogani, F., Mahon, J. M., Mori, T., Fromme, P., and Ghirlanda, G. (2007) A monovalent mutant of cyanovirin-N provides insight into the role of multiple interactions with gp120 for antiviral activity Biochemistry 46, 9199-9207 (Pubitemid 47255034)
17. Barrientos, L. G., Matei, E., Lasala, F., Delgado, R., and Gronenborn, A. M. (2006) Dissecting carbohydrate-cyanovirin-N binding by structure-guided mutagenesis: Functional implications for viral entry inhibition Protein Eng., Des. Sel. 19, 525-535 (Pubitemid 44950458)
18. Chang, L. C. and Bewley, C. A. (2002) Potent inhibition of HIV-1 fusion by cyanovirin-N requires only a single high affinity carbohydrate binding site: Characterization of low affinity carbohydrate binding site knockout mutants J. Mol. Biol. 318, 1-8 (Pubitemid 34729380)
19. Keeffe, J. R., Gnanapragasam, P. N. P., Gillespie, S. K., Yong, J., Bjorkman, P. J., and Mayo, S. L. (2011) Designed oligomers of cyanovirin-N show enhanced HIV neutralization Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1108777108
20. Dahiyat, B. I. and Mayo, S. L. (1997) Probing the role of packing specificity in protein design Proc. Natl. Acad. Sci. U.S.A. 94, 10172-10177 (Pubitemid 27407013)
21. Blaber, M., Lindstrom, J. D., Gassner, N., Xu, J., Heinz, D. W., and Matthews, B. W. (1993) Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala → Ser and Val → Thr substitutions in T4 lysozyme Biochemistry 32, 11363-11373 (Pubitemid 23332048)
22. Hendsch, Z. S., Jonsson, T., Sauer, R. T., and Tidor, B. (1996) Protein stabilization by removal of unsatisfied polar groups: Computational approaches and experimental tests Biochemistry 35, 7621-7625 (Pubitemid 26202502)
23. Mok, Y. K., Elisseeva, E. L., Davidson, A. R., and Forman-Kay, J. D. (2001) Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states J. Mol. Biol. 307, 913-928 (Pubitemid 33027668)
24. Spector, S., Wang, M., Carp, S. A., Robblee, J., Hendsch, Z. S., Fairman, R., Tidor, B., and Raleigh, D. P. (2000) Rational modification of protein stability by the mutation of charged surface residues Biochemistry 39, 872-879 (Pubitemid 30075313)
25. Robinson, C. R. and Sauer, R. T. (2000) Striking stabilization of Arc repressor by an engineered disulfide bond Biochemistry 39, 12494-12502
26. Nauli, S., Kuhlman, B., and Baker, D. (2001) Computer-based redesign of a protein folding pathway Nat. Struct. Biol. 8, 602-605 (Pubitemid 32613008)
27. Zhou, H. X., Hoess, R. H., and DeGrado, W. F. (1996) In vitro evolution of thermodynamically stable turns Nat. Struct. Biol. 3, 446-451 (Pubitemid 26139444)
28. Predki, P. F., Agrawal, V., Brünger, A. T., and Regan, L. (1996) Amino-acid substitutions in a surface turn modulate protein stability Nat. Struct. Biol. 3, 54-48
29. Anil, B., Song, B., Tang, Y., and Raleigh, D. P. (2004) Exploiting the right side of the Ramachandran plot: Substitution of glycines by d -alanine can significantly increase protein stability J. Am. Chem. Soc. 126, 13194-13195 (Pubitemid 39382725)
30. Cho, J.-H., Sato, S., and Raleigh, D. P. (2004) Thermodynamics and kinetics of non-native interactions in protein folding: A single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state J. Mol. Biol. 338, 827-837 (Pubitemid 38507425)
31. Malakauskas, S. M. and Mayo, S. L. (1998) Design, structure and stability of a hyperthermophilic protein variant Nat. Struct. Biol. 5, 470-475 (Pubitemid 28265030)
32. Green, D. F. and Tidor, B. (2002) Evaluation of electrostatic interactions. Current Protocols in Bioinformatics, Chapter 8, Unit 8.3, Wiley, New York.
33. Gilson, M. K., Rashin, A., Fine, R., and Honig, B. (1985) On the calculation of electrostatic interactions in proteins J. Mol. Biol. 184, 503-516 (Pubitemid 15013023)
34. Honig, B. and Nicholls, A. (1995) Classical electrostatics in biology and chemistry Science 268, 1144-1149
35. Nina, M., Beglov, D., and Roux, B. (1997) Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations J. Phys. Chem. B 101, 5239-5248 (Pubitemid 127609289)
36. Green, D. F., Dennis, A. T., Fam, P. S., Tidor, B., and Jasanoff, A. (2006) Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide Biochemistry 45, 12547-12559 (Pubitemid 44583697)
37. Looger, L. L. and Hellinga, H. W. (2001) Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics J. Mol. Biol. 307, 429-445 (Pubitemid 33029991)
38. Gordon, D. B. and Mayo, S. L. (1998) Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem J. Comput. Chem. 19, 1505-1514
39. Leach, A. R. and Lemon, A. P. (1998) Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm Proteins 33, 227-239 (Pubitemid 28457975)
40. Maeyer, M. D., Desmet, J., and Lasters, I. (2000) The dead-end elimination theorem: Mathematical aspects, implementation, optimizations, evaluation, and performance Methods Mol. Biol. 143, 265-304
41. Lasters, I., Maeyer, M. D., and Desmet, J. (1995) Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains Protein Eng. 8, 815-822
42. Desmet, J., Maeyer, M., Hazes, B., and Lasters, I. (1992) The dead-end elimination theorem and its use in protein side-chain positioning Nature 356, 539-542
43. Lovell, S. C., Word, J. M., Richardson, J. S., and Richardson, D. C. (2000) The penultimate rotamer library Proteins 40, 389-408 (Pubitemid 30624447)
44. Brooks, B. R., Brooks, C. L., III, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R. W., Post, C. B., Pu, J. Z., Schaefer, M., Tidor, B., Venable, R. M., Woodcock, H. L., Wu, X., Yang, W., York, D. M., and Karplus, M. (2009) CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 30, 1545-1614
45. MacKerell, A., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J., Field, M., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F., Mattos, C., Michnick, S., Ngo, T., Nguyen, D., Prodhom, B., Reiher, W., Roux, B., Schlenkrich, M., Smith, J., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102, 3586-3616 (Pubitemid 128576688)
46. Schaefer, M. and Karplus, M. (1996) A comprehensive analytical treatment of continuum electrostatics J. Phys. Chem. 100, 1578-1599 (Pubitemid 126789971)
47. Greenfield, N. J. (2006) Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions Nat. Protoc. 1, 2527-2535
48. Greenfield, N. J. (2006) Determination of the folding of proteins as a function of denaturants, osmolytes or ligands using circular dichroism Nat. Protoc. 1, 2733-2741
49. R Development Core Team (2011) R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna.
50. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6, 277-293
51. Bewley, C. A. (2001) Solution structure of a cyanovirin-N:Manα1- 2Manα complex: Structural basis for high-affinity carbohydrate-mediated binding to gp120 Structure 9, 931-940 (Pubitemid 32972159)
52. 9 with nanomolar affinity: Implications for binding to the HIV envelope protein gp120 J. Am. Chem. Soc. 123, 3892-3902 (Pubitemid 32899476)
53. Yang, F., Bewley, C. A., Louis, J. M., Gustafson, K. R., Boyd, M. R., Gronenborn, A. M., Clore, G. M., and Wlodawer, A. (1999) Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping J. Mol. Biol. 288, 403-412 (Pubitemid 29221810)
54. Bowie, J. U., Reidhaar-Olson, J. F., Lim, W. A., and Sauer, R. T. (1990) Deciphering the message in protein sequences: Tolerance to amino acid substitutions Science 247, 1306-1310
55. Bewley, C. A., Gustafson, K. R., Boyd, M. R., Covell, D. G., Bax, A., Clore, G. M., and Gronenborn, A. M. (1998) Solution structure of cyanovirin-N, a potent HIV-inactivating protein Nat. Struct. Biol. 5, 571-578
56. Hendsch, Z. S. and Tidor, B. (1994) Do salt bridges stabilize proteins? A continuum electrostatic analysis Protein Sci. 3, 211-226 (Pubitemid 24086354)
57. Lippow, S. M., Wittrup, K. D., and Tidor, B. (2007) Computational design of antibody-affinity improvement beyond in vivo maturation Nat. Biotechnol. 25, 1171-1176 (Pubitemid 47538113)
58. Kehr, J.-C., Zilliges, Y., Springer, A., Disney, M. D., Ratner, D. D., Bouchier, C., Seeberger, P. H., de Marsac, N. T., and Dittmann, E. (2006) A mannan binding lectin is involved in cell-cell attachment in a toxic strain of Microcystis aeruginosa Mol. Microbiol. 59, 893-906
59. Percudani, R., Montanini, B., and Ottonello, S. (2005) The anti-HIV cyanovirin-N domain is evolutionarily conserved and occurs as a protein module in eukaryotes Proteins 60, 670-678 (Pubitemid 41266424)
60. Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E. L. L., Eddy, S. R., and Bateman, A. (2010) The Pfam protein families database Nucleic Acids Res. 38, D211-D222
61. Koharudin, L. M. I., Viscomi, A. R., Jee, J.-G., Ottonello, S., and Gronenborn, A. M. (2008) The evolutionarily conserved family of cyanovirin-N homologs: Structures and carbohydrate specificity Structure 16, 570-584 (Pubitemid 351458704)
62. Shahzad-ul-Hussan, S., Gustchina, E., Ghirlando, R., Clore, G. M., and Bewley, C. A. (2011) Solution structure of the monovalent lectin microvirin in complex with Manα(1-2)Man provides a basis for anti-HIV activity with low toxicity J. Biol. Chem. 286, 20788-20796
63. Koharudin, L. M. I., Viscomi, A. R., Montanini, B., Kershaw, M. J., Talbot, N. J., Ottonello, S., and Gronenborn, A. M. (2011) Structure-function analysis of a CVNH-LysM lectin expressed during plant infection by the rice blast fungus Magnaporthe oryzae Structure 19, 662-674
64. Schneider, T. D. and Stephens, R. M. (1990) Sequence logos: A new way to display consensus sequences Nucleic Acids Res. 18, 6097-6100
65. Neher, E. (1994) How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. U.S.A. 91, 98-102 (Pubitemid 24018650)
66. Lockless, S. W. and Ranganathan, R. (1999) Evolutionarily conserved pathways of energetic connectivity in protein families Science 286, 295-299 (Pubitemid 29484693)
67. Mori, T., Shoemaker, R. H., Gulakowski, R. J., Krepps, B. L., McMahon, J. B., Gustafson, K. R., Pannell, L. K., and Boyd, M. R. (1997) Analysis of sequence requirements for biological activity of cyanovirin-N, a potent HIV (human immunodeficiency virus)-inactivating protein Biochem. Biophys. Res. Commun. 238, 218-222 (Pubitemid 27453304)
68. Mori, T., Gustafson, K. R., Pannell, L. K., Shoemaker, R. H., Wu, L., McMahon, J. B., and Boyd, M. R. (1998) Recombinant production of cyanovirin-N, a potent human immunodeficiency virus-inactivating protein derived from a cultured cyanobacterium Protein Expression Purif. 12, 151-158 (Pubitemid 28360439)
69. Shenoy, S. R., Barrientos, L. G., Ratner, D. M., O'Keefe, B. R., Seeberger, P. H., Gronenborn, A. M., and Boyd, M. R. (2002) Multisite and multivalent binding between cyanovirin-N and branched oligomannosides: calorimetric and NMR characterization Chem. Biol. 9, 1109-1118 (Pubitemid 35240933)
70. Barrientos, L. G., Louis, J. M., Hung, J., Smith, T. H., O'Keefe, B. R., Gardella, R. S., Mori, T., Boyd, M. R., and Gronenborn, A. M. (2002) Design and initial characterization of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N Proteins 46, 153-160 (Pubitemid 34052068)
71. Han, Z., Xiong, C., Mori, T., and Boyd, M. R. (2002) Discovery of a stable dimeric mutant of cyanovirin-N (CV-N) from a T7 phage-displayed CV-N mutant library Biochem. Biophys. Res. Commun. 292, 1036-1043 (Pubitemid 34687309)
72. Dill, K. A. and Shortle, D. (1991) Denatured states of proteins Annu. Rev. Biochem. 60, 795-825
73. Henry, E. and Hofrichter, J. (1992) Singular value decomposition: Application to analysis of experimental data Methods Enzymol. 210, 129-192
74. Segel, D. J., Fink, A. L., Hodgson, K. O., and Doniach, S. (1998) Protein denaturation: A small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c. Biochemistry 37, 12443-12451 (Pubitemid 28427528)
75. Latypov, R. F., Cheng, H., Roder, N. A., Zhang, J., and Roder, H. (2006) Structural characterization of an equilibrium unfolding intermediate in cytochrome c J. Mol. Biol. 357, 1009-1025
76. Blixt, O., Head, S., Mondala, T., Scanlan, C., Huflejt, M. E., Alvarez, R., Bryan, M. C., Fazio, F., Calarese, D., Stevens, J., Razi, N., Stevens, D. J., Skehel, J. J., van Die, I., Burton, D. R., Wilson, I. A., Cummings, R., Bovin, N., Wong, C.-H., and Paulson, J. C. (2004) Printed covalent glycan array for ligand profiling of diverse glycan binding proteins Proc. Natl. Acad. Sci. U.S.A. 101, 17033-17038 (Pubitemid 39627769)
77. Fujimoto, Y. K., Terbush, R. N., Patsalo, V., and Green, D. F. (2008) Computational models explain the oligosaccharide specificity of cyanovirin-N Protein Sci. 17, 2008-2014
78. Waldburger, C. D., Schildbach, J. F., and Sauer, R. T. (1995) Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2, 122-128 (Pubitemid 26040648)
79. Harbury, P. B., Plecs, J. J., Tidor, B., Alber, T., and Kim, P. S. (1998) High-resolution protein design with backbone freedom Science 282, 1462-1467 (Pubitemid 28538602)
80. Mandell, D. J. and Kortemme, T. (2009) Computer-aided design of functional protein interactions Nat. Chem. Biol. 5, 797-807
81. Eisenberg, D. and McLachlan, A. D. (1986) Solvation energy in protein folding and binding Nature 319, 199-203 (Pubitemid 16128783)
82. Barrientos, L. G., Lasala, F., Delgado, R., Sanchez, A., and Gronenborn, A. M. (2004) Flipping the switch from monomeric to dimeric CV-N has little effect on antiviral activity Structure 12, 1799-1807 (Pubitemid 39298964)
83. Hazes, B. and Dijkstra, B. W. (1988) Model building of disulfide bonds in proteins with known three-dimensional structure Protein Eng. 2, 119-125
84. MacKerel, A., Jr., Brooks, C., III, Nilsson, L., Roux, B., Won, Y., and Karplus, M. (1998) CHARMM: The energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry (v. R. Schleyer, P., Eds.) Vol. 1, pp 271-277, John Wiley & Sons, Chichester, U.K.
85. Cornell, W., Cieplak, P., Bayly, C., Gould, I., Merz, K., Ferguson, D., Spellmeyer, D., Fox, T., Caldwell, J., and Kollman, P. (1996) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 118, 5179-5197
86. Laurents, D. V. and Baldwin, R. L. (1997) Characterization of the unfolding pathway of hen egg white lysozyme Biochemistry 36, 1496-1504 (Pubitemid 27074974)
87. Munson, M., O'Brien, R., Sturtevant, J. M., and Regan, L. (1994) Redesigning the hydrophobic core of a four-helix-bundle protein Protein Sci. 3, 2015-2022
88. Smith, C. K., Withka, J. M., and Regan, L. (1994) A thermodynamic scale for the β-sheet forming tendencies of the amino acids Biochemistry 33, 5510-5517
89. Chaudhuri, T. K., Horii, K., Yoda, T., Arai, M., Nagata, S., Terada, T. P., Uchiyama, H., Ikura, T., Tsumoto, K., Kataoka, H., Matsushima, M., Kuwajima, K., and Kumagai, I. (1999) Effect of the extra N-terminal methionine residue on the stability and folding of recombinant α-lactalbumin expressed in Escherichia coli J. Mol. Biol. 285, 1179-1194 (Pubitemid 29054325)
90. Chaudhuri, T. K., Arai, M., Terada, T. P., Ikura, T., and Kuwajima, K. (2000) Equilibrium and kinetic studies on folding of the authentic and recombinant forms of human α-lactalbumin by circular dichroism spectroscopy Biochemistry 39, 15643-15651 (Pubitemid 32002794)
91. Hubbard, S. J. and Thornton, J. M. (1993) 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.
92. Crooks, G. E., Hon, G., Chandonia, J.-M., and Brenner, S. E. (2004) WebLogo: A sequence logo generator Genome Res. 14, 1188-1190 (Pubitemid 38811555)