The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
Tài liệu tham khảo
Argos, 1988, An investigation of protein subunit and domain interfaces, Protein Eng., 2, 101, 10.1093/protein/2.2.101
Ban, 1994, Crystal structure of an idiotype-anti-idiotype Fab complex, Proc. Natl Acad. Sci. USA, 91, 1604, 10.1073/pnas.91.5.1604
Banner, 1996, The crystal structure of the complex of blood coagulation factor VIIA with soluble tissue factor, Nature, 380, 41, 10.1038/380041a0
Bernstein, 1977, The Protein Data Bank. A computer-based archival file for macromolecular structures, J. Mol. Biol., 112, 535, 10.1016/S0022-2836(77)80200-3
Bhat, 1994, Bound water molecules and conformational stabilization help mediate an antigen-antibody association, Proc. Natl Acad. Sci. USA, 91, 1089, 10.1073/pnas.91.3.1089
Bigay, 1994, Roles of lipid modifications of transducin subunits in their GDP-dependent association and membrane binding, Biochemistry, 33, 14081, 10.1021/bi00251a017
Bigler, 1993, Binding of aminoacid side chains to preformed cavities, Protein Sci., 2, 786, 10.1002/pro.5560020509
Bode, 1978, The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding, J. Mol. Biol., 118, 99, 10.1016/0022-2836(78)90246-2
Bode, 1986, X-ray crystal structure of the complex of human leukocyte (Pmn elastase) and the third domain of the turkey ovomucoid inhibitor, EMBO J., 5, 2453, 10.1002/j.1460-2075.1986.tb04521.x
Bode, 1987, The high resolution X-ray crystal structure of the complex formed between subtilsin Carlsberg and eglin C, an elastase inhibitor from the leech Hirudo medicinalis, Eur. J. Biochem., 166, 673, 10.1111/j.1432-1033.1987.tb13566.x
Bogan, 1998, An analysis of hot spots in protein interfaces, J. Mol. Biol., 280, 1, 10.1006/jmbi.1998.1843
Bolognesi, 1982, Three-dimensional structure of the complex between pancreatic secretory inhibitor (Kazal type) and trypsinogen at 1.8 Å resolution, J. Mol. Biol., 162, 839, 10.1016/0022-2836(82)90550-2
Bompard-Gilles, 1996, Substrate mimicry in the active center of mammalian α-amylase, Structure, 4, 1441, 10.1016/S0969-2126(96)00151-7
Bossart-Whitaker, 1995, The crystal structure of the antibody N10-Staphylococcal nuclease complex at 2.9 Å resolution, J. Mol. Biol., 253, 559, 10.1006/jmbi.1995.0573
Braden, 1994, Three-dimensional structures of the free and antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1, J. Mol. Biol., 242, 767, 10.1016/0022-2836(94)90046-9
Braden, 1996, Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 Å resolution, J. Mol. Biol., 264, 137, 10.1006/jmbi.1996.0629
Buckle, 1994, Protein-protein recognition, Biochemistry, 33, 8878, 10.1021/bi00196a004
Castro, 1996, Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitor, Biochemistry, 35, 11435, 10.1021/bi960515w
Chen, 1983, Refined 2.5 Å X-ray crystal structure of the complex formed by porcine kallikrein A and the bovine pancreatic trypsin inhibitor, J. Mol. Biol., 164, 283, 10.1016/0022-2836(83)90078-5
Chitarra, 1993, Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex, Proc. Natl Acad. Sci. USA, 90, 7711, 10.1073/pnas.90.16.7711
Chothia, 1975, Structural invariants in protein folding, Nature, 254, 304, 10.1038/254304a0
Chothia, 1997, Protein-protein and protein-carbohydrate recognition
Chothia, 1975, Principles of protein-protein recognition, Nature, 256, 705, 10.1038/256705a0
Clackson, 1995, A hot spot of binding energy in a hormone-receptor interface, Science, 267, 383, 10.1126/science.7529940
Cunningham, 1993, Comparison of a structural and functional epitope, J. Mol. Biol., 234, 554, 10.1006/jmbi.1993.1611
Dall’Acqua, 1996, A mutational analysis of bthe inding of two different proteins to the same antibody, Biochemistry, 35, 9667, 10.1021/bi960819i
Dall’Acqua, 1998, A mutational analysis of binding interactions in an antigen-antibody protein-protein complex, Biochemistry, 37, 7981, 10.1021/bi980148j
Davies, 1996, Interactions of protein antigens with antibodies, Proc. Natl Acad. Sci. USA, 93, 7, 10.1073/pnas.93.1.7
Deisenhofer, 1981, Crystallographic refinement and atonic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9 and 2.8 Å resolution, Biochemistry, 20, 2361, 10.1021/bi00512a001
Derrick, 1994, The third IgG-binding domain from streptococcal protein G, J. Mol. Biol., 243, 906, 10.1006/jmbi.1994.1691
Desmyter, 1996, Crystal structure of a single-domain Vh antibody fragment in complex with lysozyme, Nature Struct. Biol., 3, 803, 10.1038/nsb0996-803
Engh, 1996, Crystal structures of catalytic subunit of cAMP-dependent protein kinase in complex with isoquinolinesulfonyl protein kinase inhibitor H7, H8 and H89. Structural implications for selectivity, J. Biol. Chem., 271, 26157, 10.1074/jbc.271.42.26157
Frigerio, 1992, Crystal and molecular structure of the bovine a-chymotrypsin-eglin C complex at 2.0 Å resolution, J. Mol. Biol., 225, 107, 10.1016/0022-2836(92)91029-O
Fujinaga, 1987, Crystal and molecular structures of α-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution, J. Mol. Biol., 195, 397, 10.1016/0022-2836(87)90659-0
Gamble, 1996, Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV1 capsid, Cell, 87, 1285, 10.1016/S0092-8674(00)81823-1
Garboczi, 1996, Structure of the complex between human T-cell receptor, viral peptide and HLA-A2, Nature, 384, 134, 10.1038/384134a0
Gaudet, 1996, Crystal structure at 2.4 Å resolution of the complex of transducin βγ and its regulator, phosducin, Cell, 87, 577, 10.1016/S0092-8674(00)81376-8
Gerstein, 1995, The volume of atoms on the protein surface calculated from simulation using Voronoi polyhedra, J. Mol. Biol., 249, 955, 10.1006/jmbi.1995.0351
Goldman, 1997, Analysis of binding interactions in an idiotope-antiidiotope protein-protein complex by double mutant cycles, Biochemistry, 36, 49, 10.1021/bi961769k
Gorina, 1996, Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2, Science, 274, 1001, 10.1126/science.274.5289.1001
Griffith, 1995, X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex, Cell, 82, 507, 10.1016/0092-8674(95)90439-5
Guillet, 1993, Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar, Structure, 1, 165, 10.1016/0969-2126(93)90018-C
Harel, 1995, Crystal structure of an acetylcholinesterase-fasciclin complex, Structure, 3, 1355, 10.1016/S0969-2126(01)00273-8
Harrison, 1997, Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK, Science, 276, 431, 10.1126/science.276.5311.431
Harpaz, 1994, Volume changes on protein folding, Structure, 2, 641, 10.1016/S0969-2126(00)00065-4
Housset, 1997, The three-dimensional structure of a T-cell antigen receptor Vα-Vβ heterodimer reveals a novel rearrangement of the Vβ domain, EMBO J., 16, 4205, 10.1093/emboj/16.14.4205
Huang, 1993, The refined 1.6 Å resolution crystal structure of the complex formed between porcine β-trypsin and MCTI-A, a trypsin inhibitor of the squash family, J. Mol. Biol., 229, 1022, 10.1006/jmbi.1993.1102
Huang, 1995, Water molecules participate in protease-inhibitor interactions, Protein Sci., 4, 1985, 10.1002/pro.5560041004
Huber, 1974, Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II Crystallographic refinement at 1.9 Å resolution, J. Mol. Biol., 89, 73, 10.1016/0022-2836(74)90163-6
Hurley, 1993, Structure of the regulatory complex of E. coli IIIGel with glycerol kinase, Science, 259, 673, 10.1126/science.8430315
Janin, 1995, Principles of protein-protein recognition from structure to thermodynamics, Biochimie, 77, 497, 10.1016/0300-9084(96)88166-1
Janin, 1996, Protein-protein recognition, Prog. Biophys. Mol. Biol., 64, 145, 10.1016/S0079-6107(96)00001-6
Janin, 1976, Stability and specificity of protein-protein interactions, J. Mol. Biol., 100, 197, 10.1016/S0022-2836(76)80148-9
Janin, 1990, The structure of protein-protein recognition sites, J. Biol. Chem., 265, 16027, 10.1016/S0021-9258(17)46181-3
Janin, 1988, Surface, subunit interfaces and interior of oligomeric proteins, J. Mol. Biol., 204, 155, 10.1016/0022-2836(88)90606-7
Jardetzky, 1994, Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen, Nature, 368, 711, 10.1038/368711a0
Jeffrey, 1995, Mechanism of CDK activation revealed by the structure of a cyclin A-CDK2 complex, Nature, 376, 313, 10.1038/376313a0
Jones, 1995, Protein-protein interaction, Prog. Biophys. Mol. Biol., 63, 131, 10.1016/0079-6107(94)00008-W
Jones, 1996, Principles of protein-protein interactions, Proc. Natl Acad. Sci. USA, 93, 13, 10.1073/pnas.93.1.13
Jones, 1997, Analysis of protein-protein interaction sites using surface patches, J. Mol. Biol., 272, 121, 10.1006/jmbi.1997.1234
Kabsch, 1990, Atomic structure of the actin:DNAse I complex, Nature, 347, 37, 10.1038/347037a0
Kawashima, 1996, The structure of the E. coli EF-Tu. EF-Ts complex at 2.5 Å resolution, Nature, 379, 511, 10.1038/379511a0
Kelley, 1995, Analysis of the factor VIIa binding site on human tissue factor, Biochemistry, 34, 10383, 10.1021/bi00033a009
Kobe, 1995, A structural basis of the interactions between leucine rich repeats and protein ligands, Nature, 374, 183, 10.1038/374183a0
Lambright, 1994, Structural determinants for activation of the α-subunit of a heterotrimeric G protein, Nature, 369, 621, 10.1038/369621a0
Lambright, 1996, The 2.0 Å crystal structure of a heterotrimeric G-protein, Nature, 379, 311, 10.1038/379311a0
Lawrence, 1993, Shape complementarity at protein/protein interfaces, J. Mol. Biol., 234, 946, 10.1006/jmbi.1993.1648
Lee, 1971, The interpretation of protein structures, J. Mol. Biol., 55, 379, 10.1016/0022-2836(71)90324-X
Lee, 1996, Crystal structure of the conserved coreof HIV-1 nef complexed with a Src family SH3 domain, Cell, 85, 831, 10.1016/S0092-8674(00)81276-3
Lescar, 1995, Crystal Structure of a cross reaction complex between Fab F9.13.7 and guinea fowl lysozyme, J. Biol. Chem., 270, 18067, 10.1074/jbc.270.30.18067
Li, 1997, Crystal structure of Lyme disease antigen OspA complexed with a Fab, Proc. Natl Acad. Sci. USA, 94, 3584, 10.1073/pnas.94.8.3584
Livnah, 1996, Functional mimicry of a protein hormone by a peptide agonist, Science, 273, 464, 10.1126/science.273.5274.464
Malby, 1994, The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping site of the NC41 antibody, Structure, 2, 733, 10.1016/S0969-2126(00)00074-5
Malkowski, 1997, The co-crystal structure of unliganded bovine α-thrombin and prethrombin-2:movement of the Tyr-Pro-Pro-Trp segment upon ligand binding, Protein Sci., 6, 1438, 10.1002/pro.5560060708
Marquart, 1983, The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors, Acta Crystallog. sect. B, 39, 480, 10.1107/S010876818300275X
McDonald, 1994, Satisfying hydrogen bonding potential in proteins, J. Mol. Biol., 238, 777, 10.1006/jmbi.1994.1334
McPhalen, 1987, Structural comparison of two serine proteinase-protein inhibitor complexes. Eglin C-subtilisin Carlsberg and CI 2-subtilisin novo, Biochemistry, 27, 6582, 10.1021/bi00417a058
Miller, 1987, Interior and surface of monomeric proteins, J. Mol. Biol., 196, 641, 10.1016/0022-2836(87)90038-6
Miller, 1987, The accessible surface area and stability of oligomeric proteins, Nature, 328, 834, 10.1038/328834a0
Mittl, 1997, A new structural class of serine protease inhibitors revealed by the structure of the hirustatin-kallikrein complex, Structure, 5, 253, 10.1016/S0969-2126(97)00183-4
Nassar, 1996, The 2.2 Å crystal structure of the ras-binding domain of the serine/threonine kinase c-Raf1 in a complex with Rap1A and a GTP analogue, Nature, 375, 554, 10.1038/375554a0
Nicholls, 1992, Protein folding and association, Proteins: Struct. Funct. Genet., 11, 281, 10.1002/prot.340110407
Noel, 1993, The 2.2 Å crystal structure of transducin complexes with GTPgS, Nature, 366, 654, 10.1038/366654a0
Padlan, 1989, Structure of an antibody-antigen complex, Proc. Natl Acad. Sci. USA, 86, 5938, 10.1073/pnas.86.15.5938
Pelletier, 1992, Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochromec, Science, 258, 1748, 10.1126/science.1334573
Prasad, 1993, Evaluation of mutagenesis for epitope mapping, J. Biol. Chem., 268, 10705, 10.1016/S0021-9258(18)82041-5
Read, 1983, Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8 Å resolution, Biochemistry, 22, 4420, 10.1021/bi00288a012
Rees, 1982, Refined crystal structure of potato inhibitor complex of carboxypeptidase A at 2.5 Å resolution, J. Mol. Biol., 160, 475, 10.1016/0022-2836(82)90309-6
Richards, 1974, The interpretation of protein structures, J. Mol. Biol., 82, 1, 10.1016/0022-2836(74)90570-1
Rittinger, 1997, Structure at 1.65 Å of RhoA and its GTPase-activating protein in complex with a transition-state analogue, Nature, 389, 758, 10.1038/39651
Rydel, 1991, The refined crystal structure of the hirudin-thrombin complex, J. Mol. Biol., 221, 583, 10.1016/0022-2836(91)80074-5
Savva, 1995, Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycoslase inhibitor protein complex, Nature Struct. Biol., 2, 752, 10.1038/nsb0995-752
Scheidig, 1997, Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer’s amyloid b-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI), Protein Sci., 6, 1806, 10.1002/pro.5560060902
Schreiber, 1993, Interaction of barnase with its polypeptide inhibitor barstat studied by protein engineering, Biochemistry, 32, 5145, 10.1021/bi00070a025
Schreiber, 1995, Energetics of protein-protein interactions, J. Mol. Biol., 248, 478, 10.1016/S0022-2836(95)80064-6
Schutt, 1993, The structure of crystalline profilin-β-actin, Nature, 365, 810, 10.1038/365810a0
Sheriff, 1987, Three-dimensional structure of an antibody-antigen complex, Proc. Natl Acad. Sci. USA, 84, 8075, 10.1073/pnas.84.22.8075
Sondek, 1996, Crystal structure of a GA protein βγ dimer at 2. 1 Å resolution, Nature, 379, 369, 10.1038/379369a0
Song, 1998, Kunitz-type soybean trypsin inhibitor revisited, J. Mol. Biol., 275, 347, 10.1006/jmbi.1997.1469
Stewart, 1998, Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran, J. Mol. Biol., 277, 635, 10.1006/jmbi.1997.1602
Strynadka, 1996, A potent new mode of β-lactamase inhibition revealed by the 1.7 Å X-ray crystallographic structute of the TEM-1-BLIP complex, Nature Struct. Biol., 3, 290, 10.1038/nsb0396-290
Stubbs, 1990, The refined 2.4 Å X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinease papain, EMBO J., 9, 1939, 10.1002/j.1460-2075.1990.tb08321.x
Sundström, 1996, Crystal structure of an antagonist mutant of human growth hormon G120R in complex with its receptor at 2.9 Å resolution, J. Biol. Chem., 271, 32197, 10.1074/jbc.271.50.32197
Takeuchi, 1991, Refined crystal structure of the complex subtilisin BPN and Streptomyces subtilisin inhibitor at 1.8 Å resolution, J. Mol. Biol., 221, 309
Tesmer, 1997, Structure of RGS4 bound to AlF4− activated Giα1, Cell, 89, 251, 10.1016/S0092-8674(00)80204-4
Tsai, 1997, Hydrophobic folding units at protein-protein interfaces, Protein Sci., 6, 1426, 10.1002/pro.5560060707
Tsai, 1996, A dataset of protein-protein interfaces generated with a sequence order-independent comparison technique, J. Mol. Biol., 260, 604, 10.1006/jmbi.1996.0424
Tsunemi, 1996, Crystal structure of an elastase-specific inhibitor elafin complexed with porcine pancreatic elastase, Biochemistry, 35, 11570, 10.1021/bi960900l
Tulip, 1992, Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex, J. Mol. Biol., 227, 122, 10.1016/0022-2836(92)90687-F
van de Locht, 1995, Two heads are better than one, EMBO J., 14, 5149, 10.1002/j.1460-2075.1995.tb00199.x
van de Locht, 1996, The ornithodorin-thrombin crystal structure, a key to the TAP enigma?, EMBO J., 15, 6011, 10.1002/j.1460-2075.1996.tb00989.x
van de Locht, 1997, The thrombin E192Q-BPTI complex reveals gross structural rearrangements, EMBO J., 16, 2977, 10.1093/emboj/16.11.2977
Vos, 1992, Human growth hormone and extracellular domain of its receptor, Science, 255, 306, 10.1126/science.1549776
Wall, 1995, The structure of the G protein heterotrimer Giα1β1γ2, Cell, 83, 1047, 10.1016/0092-8674(95)90220-1
Wang, 1997, Crystal structure of the EF-Tu. EF-Ts complex from Thermus thermophilus, Nature Struct. Biol., 4, 650, 10.1038/nsb0897-650
Wang, 1998, Atomic structure of an αβ T-cell receptor (TCR) heterodimer in complex with an anti-TCR Fab fragment derived from a mitogenic antibody, EMBO J., 17, 10, 10.1093/emboj/17.1.10
Welch, 1997, Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY, Nature Struct. Biol., 5, 25, 10.1038/nsb0198-25
Wells, 1996, Binding in the growth hormone receptor complex, Proc. Natl Acad. Sci. USA, 93, 1, 10.1073/pnas.93.1.1
Xu, 1997, Hydrogen bonds and salt bridges across protein-protein interfaces, Protein Eng., 10, 999, 10.1093/protein/10.9.999
Young, 1994, A role for surface hydrophobicity in protein-protein recognition, Protein Sci., 3, 717, 10.1002/pro.5560030501
Ysern, 1998, Imperfect interfaces, Nature Struct. Biol., 5, 412, 10.1038/nsb0698-412