Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method

Proteins: Structure, Function and Genetics

Volumn 56, Issue 4, 2004, Pages 828-838

  Sherman, Douglas B ^a   Zhang, Shuxing ^b   Pitner, J Bruce ^a   Tropsha, Alexander ^b  

^a BD Technologies   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Conformational stability change; Delaunay tessellation; Differential SNAPP profile analysis; Ligand binding; Periplasmic binding proteins

Indexed keywords

BACTERIAL PROTEIN; LIGAND; PERIPLASMIC BINDING PROTEIN; PROTEIN;

AMINO ACID COMPOSITION; ANALYTIC METHOD; ARTICLE; CHEMICAL REACTION; CRYSTALLIZATION; DELAUNAY TESSELLATION; ENERGY TRANSFER; LIGAND BINDING; LOG LIKELIHOOD SCORE; NEIGHBORHOOD ANALYSIS OF PROTEIN PACKING METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN STABILITY; SCORING SYSTEM; SITE DIRECTED MUTAGENESIS; SNAPP SCORE; SNAPP STATISTICAL SCORING FUNCTION; STRUCTURE ANALYSIS;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; IONS; LIGANDS; MONOSACCHARIDES; OLIGOPEPTIDES; OLIGOSACCHARIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, QUATERNARY; PROTEINS; VITAMINS;

BACTERIA (MICROORGANISMS);

EID: 4043095448     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20131     Document Type: Article

References (74)

1. Ames GF-L. Bacterial periplasmic transport systems: structure, mechanism, and evolution. Annu Rev Biochem 1986;55:397-425.
2. Furlong CE. Osmotic-shock-sensitive transport systems. In: Neidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE, editors. Escherichia coli and Salmonella typhimurium: cellular and molecular biology. Washington, DC: American Society for Microbiology; 1987. p 768-796.
3. Tam R, Saier MH Jr. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 1993;57:320-346.
4. Gerstein M, Lesk AM, Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 1994;33:6739-6749.
5. Quiocho FA, Ledvina PS. Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes. Mol Microbiol 1996;20:17-25.
6. Quiocho FA, Vyas NK. Novel stereospecificity of the L-arabinose-binding protein. Nature 1984;310:381-386.
7. Sack JS, Saper MA, Quiocho FA. Periplasmic binding protein structure and function: refined X-ray structures of the leucine/ isoleucine/valine-binding protein and its complex with leucine. J Mol Biol 1989;206:171-191.
8. Sack JS, Trakhanov SD, Tsigannik IH, Quiocho FA. Structure of the L-leucine-binding protein refined at 2.4 Å resolution and comparison with the Leu/Ile/Val-binding protein structure. J Mol Biol 1989;206:193-207.
9. Oh BH, Kang CH, De Bondt H, Kim SH, Nikaido K, Joshi AK, Ames GF-L. The bacterial periplasmic histidine-binding protein: structure/function analysis of the ligand-binding site and comparison with related proteins. J Biol Chem 1994;269:4135-4143.
10. Yao N, Trakhanov S, Quiocho FA. Refined 1.89 Å structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins. Biochemistry 1994;33:4769-4779.
11. Hu Y, Rech S, Gunsalus RP, Rees DC. Crystal structure of the molybdate binding protein ModA. Nat Struct Biol 1997;4:703-707.
12. Pflugrath JW, Quiocho FA. Sulphate sequestered in the sulphate-binding protein of Salmonella typhimurium is bound solely by hydrogen bonds. Nature 1985;314:257-260.
13. Pflugrath JW, Quiocho FA. The 2 Å resolution structure of the sulfate-binding protein involved in active transport in Salmonella typhimurium. J Mol Biol 1988;200:163-180.
14. Luecke H, Quiocho FA. High specificity of a phosphate transport protein determined by hydrogen bonds. Nature 1990;347:402-406.
15. Wang Z, Luecke H, Yao N, Quiocho FA. A low energy short hydrogen bond in very high resolution structures of protein receptor-phosphate complexes. Nat Struct Biol 1997;4:519-522.
16. Yao N, Ledvina PS, Choudhary A, Quiocho FA. Modulation of a salt link does not affect binding of phosphate to its specific active transport receptor. Biochemistry 1996;35:2079-2085.
17. Flocco MM, Mowbray SL. The 1.9 Å X-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium. J Biol Chem 1994;269:8931-8936.
18. Mowbray SL, Smith RD, Cole LB. Structure of the periplasmic glucose/galactose receptor of Salmonella typhimurium. Receptor 1990;1:41-53.
19. Vyas NK, Vyas MN, Quiocho FA. Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 1988;242:1290-1295.
20. Zou JY, Flocco MM, Mowbray SL. The 1.7 Å refined X-ray structure of the periplasmic glucose/galactose receptor from Salmonella typhimurium. J Mol Biol 1993;233:739-752.
21. Björkman AJ, Binnie RA, Zhang H, Cole LB, Hermodson MA, Mowbray SL. Probing protein-protein interactions: the ribose-binding protein in bacterial transport and chemotaxis. J Biol Chem 1994;269:30206-30211.
22. Björkman AJ, Mowbray SL. Multiple open forms of ribose-binding protein trace the path of its conformational change. J Mol Biol 1998;279:651-664.
23. Mahendroo M, Cole LB, Mowbray SL. Preliminary X-ray data for the periplasmic ribose receptor from Escherichia coli. J Mol Biol 1990;211:689-690.
24. Mowbray SL, Cole LB. 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli. J Mol Biol 1992;225:155-175.
25. Hsiao CD, Sun YJ, Rose J, Cottam PF, Ho C, Wang BC. Crystals of glutamine-binding protein in various conformational states. J Mol Biol 1994;240:87-91.
26. Hsiao CD, Sun YJ, Rose J, Wang BC. The crystal structure of glutamine-binding protein from Escherichia coli. J Mol Biol 1996;262:225-242.
27. Sun YJ, Rose J, Wang BC, Hsiao CD. The structure of glutamine-binding protein complexed with glutamine at 1.94 Å resolution: comparisons with other amino acid binding proteins. J Mol Biol 1998;278:219-229.
28. Kang CH, Shin WC, Yamagata Y, Gokcen S, Ames GF-L, Kim SH. Crystal structure of the lysine-, arginine-, ornithine-binding protein (LAO) from Salmonella typhimurium at 2.7 Å resolution. J Biol Chem 1991;266:23893-23899.
29. Oh BH, Pandit J, Kang CH, Nikaido K, Gokcen S, Ames GF-L, Kim SH. Three-dimensional structures of the periplasmic lysine/ arginine/ornithine- binding protein with and without a ligand. J Biol Chem 1993;268:11348-11355.
30. Chaudhuri BN, Ko J, Park C, Jones TA, Mowbray SL. Structure of D-allose binding protein from Escherichia coli bound to D-allose at 1.8 Å resolution. J Mol Biol 1999;286:1519-1531.
31. Magnusson U, Chaudhuri BN, Ko J, Park C, Jones TA, Mowbary SL. Hinge-bending motion of D-allose-binding protein from Escherichia coli: three open conformations. J Biol Chem 2002;277:14077-14084.
32. +3-binding protein reveals convergent evolution within a superfamily. Nat Struct Biol 1997;4:919-924.
33. 3+-binding protein. Biochemistry 2001;40:15631-15637.
34. Karpowich NK, Huang HH, Smith PC, Hunt JF. Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding. J Biol Chem 2003;278:8429-8434.
35. Lee YH, Deka RK, Norgard MV, Radolf JD, Hasemann CA. Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone. Nat Struct Biol 1999;6:628-633.
36. Lee YH, Dorwart MR, Hazlett KR, Deka RKO, Norgard MV, Radolf JD, Hasemann CA. The crystal structure of Zn(II)-free Treponema pallidum TroA, a periplasmic metal-binding protein, reveals a closed conformation. J Bacteriol 2002;184:2300-2304.
37. Dunten P, Mowbray SL. Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis. Protein Sci 1995;4:2327-2334.
38. Dunten PW, Harris JH, Feiz V, Mowbray SL. Crystallization and preliminary X-ray analysis of the periplasmic dipeptide binding protein from Escherichia coli. J Mol Biol 1993;231:145-147.
39. Nickitenko AV, Trakhanov S, Quiocho FA. 2 Å resolution structure of DppA, a periplasmic dipeptide transport/chemosensory receptor. Biochemistry 1995;34:16585-16595.
40. Davies TG, Hubbard RE, Tame JRH. Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci 1999;8:1432-1444.
41. Sleigh SH, Tame JRH, Dodson EJ, Wilkinson AJ. Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine. Biochemistry 1997;36:9747-9758.
42. Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JRH. Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol 1999;291:393-415.
43. Tame JRH, Murshudov GN, Dodson EJ, Neil TK, Dodson GG, Higgins CF, Wilkinson AJ. The structural basis of sequence-independent peptide binding by OppA protein. Science 1994;264: 1578-1581.
44. Tame JRH, Dodson EJ, Murshudov G, Higgins CF, Wilkinson AJ. The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands. Structure 1995;3:1395-1406.
45. Tame JRH, Sleigh SH, Wilkinson AJ, Ladbury JE. The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nat Struct Biol 1996;3:998-1001.
46. Duan X, Hall JA, Nikaido H, Quiocho FA. Crystal structures of the maltodextrin/maltose-binding protein complexed with reduced oligosaccharides: flexibility of tertiary structure and ligand binding. J Mol Biol 2001;306:1115-1126.
47. Duan X, Quiocho FA. Structural evidence for a dominant role of nonpolar interactions in the binding of a transport/chemosensory receptor to its highly polar ligands. Biochemistry 2002;41:706-712.
48. Quiocho FA, Spurlino JC, Rodseth LE. Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. Structure 1997; 5:997-1015.
49. Sharff AJ, Rodseth LE, Spurlino JC, Quiocho FA. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 1992; 31:10657-10663.
50. Sharff AJ, Rodseth LE, Quiocho FA. Refined 1.8 Å structure reveals the mode of binding of β-cyclodextrin to the maltodextrin binding protein. Biochemistry 1993;32:10553-10559.
51. Spurlino JC, Lu GY, Quiocho FA. The 2.3 Å resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. J Biol Chem 1991;266: 5202-5219.
52. Newcomer ME, Lewis BA, Quiocho FA. The radius of gyration of L-arabinose-binding protein decreases upon binding of ligand. J Biol Chem 1981;256:13218-13222.
53. Shilton BH, Flocco MM, Nilsson M, Mowbray SL. Conformational changes of three periplasmic receptors for bacterial chemotaxis and transport: the maltose-, glucose/galactose- and ribose-binding proteins. J Mol Biol 1996;264:350-363.
54. Careaga CL, Sutherland J, Sabeti J, Falke JJ. Large amplitude twisting motions of an interdomain hinge: a disulfide trapping study of the galactose-glucose binding protein. Biochemistry 1995;34:3048-3055.
55. 19F NMR studies of the D-galactose chemosensory receptor. 1. Sugar binding yields a global structural change. Biochemistry 1991;30:4248-4256.
56. Mao B, Pear MR, McCammon JA, Quiocho FA. Hinge-bending in L-arabinose-binding protein: the "Venus's-flytrap" model. J Biol Chem 1982;257:1131-1133.
57. Cammer SA, Carter CW Jr, Tropsha A. Identification of sequence-specific tertiary packing motifs in protein structures using Delaunay tessellation. In: Gan HH, Schlick T, editors. Computational Methods for Macromolecules: Challenges and Applications, Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, Oct. 12-14, 2000. Lecture Notes in Computational Science and Engineering (LNCSE). New York: Springer Verlag; 2002. p 477-494.
58. Carter CW Jr, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 2001;311:625-638.
59. Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 2003;19:1540-1548.
60. Masso M, Vaisman II. Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach. Biochem Biophys Res Commun 2003;305:322-326.
61. Singh RK, Tropsha A, Vaisman II. Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comput Biol 1996;3:213-221.
62. Zheng W, Cho SJ, Vaisman II, Tropsha A. A new approach to protein fold recognition based on Delaunay tessellation of protein structure. In: Altman RB, Dunker AK, Hunter L, Klein TE, editors. Pacific Symposium on Biocomputing '97. Singapore: World Scientific; 1997. p 486-497.
63. Aurenhammer F. Voronoi diagrams: A survey of a fundamental data structure. ACM Comput Surveys 1991;23:345-405.
64. Li L, Shakhnovich EI. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc Natl Acad Sci USA 2001;98:13014-13018.
65. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
66. Sawaya MR, Kraut J. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 1997;36:586-603.
67. Berry MB, Meador B, Bilderback T, Liang P, Glaser M, Phillips GN Jr. The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP. Proteins 1994;19:183-198.
68. 5A refined at 1.9 Å resolution: a model for a catalytic transition state. J Mol Biol 1992;224:159-177.
69. Müller CW, Schlauderer GJ, Reinstein J, Schulz GE. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 1996;4:147-156.
70. Chattopadhyaya R, Meador WE, Means AR, Quiocho FA. Calmodulin structure refined at 1.7 Å resolution. J Mol Biol 1992;228:1177-1191.
71. Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee CB, Bax A. Solution structure of calcium-free calmodulin. Nat Struct Biol 1995;2:768-776.
72. 2+-calmodulin. Nat Struct Biol 1994;1:795-801.
73. Wang T, Wade RC. Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics. J Med Chem 2002;45:4828-4837.
74. Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF. Protein flexibility predictions using graph theory. Proteins 2001;44:150-165.