Comparative modelling of protein structure and its impact on microbial cell factories

Microbial Cell Factories

Volumn 4, Issue , 2005, Pages

  Centeno, Nuria B ^a   Planas Iglesias, Joan ^a   Oliva, Baldomero ^a  

^a INST MUNIC D INVESTIGACIO MEDICA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MICROORGANISM PROTEIN;

CELL FUNCTION; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; DNA TEMPLATE; GENE INSERTION SEQUENCE; GENETIC SELECTION; MOLECULAR EVOLUTION; NONHUMAN; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS;

EID: 26844535367     PISSN: 14752859     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-4-20     Document Type: Review

References (99)

1. Baneyx F: Recombinant protein expression in Escherichia coli. Curr Opin Biotechnol 1999, 10(5):411-421.
2. Baneyx F, Mujacic M: Recombinant protein folding and misfolding in Escherichia coli. Nat Biotechnol 2004, 22(11):1399-1408.
3. Gerngross TU: Advances in the production of human therapeutic proteins in yeasts and filamentous fungi. Nat Biotechnol 2004, 22(11):1409-1414.
4. Blundell TL, Sibanda BL, Sternberg MJ, Thornton JM: Knowledge-based prediction of protein structures and the design of novel molecules. Nature 1987, 326(11):347-352.
5. Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, Madhusudhan MS, Mirkovic N, Sali A: Protein structure modeling for structural genomics. Nat Struct Biol 2000, 7(Suppl):986-990.
6. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000, 29:291-325.
7. Chothia C, Lesk AM: The relation between the divergence of sequence and structure in proteins. Embo J 1986, 5(4):823-826.
8. Lesk AM, Chothia C: How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 1980, 136(3):225-270.
9. McPherson A: Protein crystallization in the structural genomics era. J Struct Funct Genomics 2004, 5(1-2):1-2.
10. Baker D, Sali A: Protein structure prediction and structural genomics. Science 2001, 294(5540):93-96.
11. Fiser A, Feig M, Brooks CL 3rd, Sali A: Evolution and physics in comparative protein structure modeling. Acc Chem Res 2002, 35(6):413-421.
12. Edwards YJ, Cottage A: Bioinformatics methods to predict protein structure and function. A practical approach. Mol Biotechnol 2003, 23(2):139-166.
13. Krieger E, Nabuurs SB, Vriend G: Homology modeling. Methods Biochem Anal 2003, 44:509-523.
14. Kretsinger RH, Ison RE, Hovmoller S: Prediction of protein structure. Methods Enzymol 2004, 383:1-27.
15. Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM: A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 2003, 53(Suppl 6):369-379.
16. Rost B: Twilight zone of protein sequence alignments. Protein Eng 1999, 12(2):85-94.
17. Rost B, Schneider R, Sander C: Protein fold recognition by prediction-based threading. J Mol Biol 1997, 270(3):471-480.
18. Doolittle RF: Of URFs and ORFs: a primer on how to analyze derived amino acid sequences Mill Valley, CA, USA: University Science Books; 1986.
19. Vogt G, Etzold T, Argos P: An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J Mol Biol 1995, 249(4):816-831.
20. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
21. Park J, Teichmann SA, Hubbard T, Chothia C: Intermediate sequences increase the detection of homology between sequences. J Mol Biol 1997, 273(1):349-354.
22. Li W, Pio F, Pawlowski K, Godzik A: Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 2000, 16(12):1105-1110.
23. John B, Sali A: Detection of homologous proteins by an intermediate sequence search. Protein Sci 2004, 13(1):54-62.
24. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D: Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 1994, 235(5):1501-1531.
25. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al.: The Pfam protein families database. Nucleic Acids Res 2004:D138-141.
26. Shi J, Blundell TL, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001, 310(1):243-257.
27. Jones DT, Taylor WR, Thornton JM: A new approach to protein fold recognition. Nature 1992, 358(6381):86-89.
28. Kelley LA, MacCallum RM, Sternberg MJ: Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000, 299(2):499-520.
29. Garriga D, Diez J, Oliva B: Modeling the helicase domain of Brome mosaic virus 1a replicase. J Mol Model (Online) 2004, 10(5-6):5-6.
30. Espadaler J, Aragues R, Eswar N, Marti-Renom MA, Querol E, Aviles FX, Sali A, Oliva B: Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A 2005, 102(20):7151-7156.
31. Felsenstein: Confidence-limits on phylogeneis - an approach using the bootstrap. Evolution 1985, 39:783-791.
32. Tramontano A, Leplae R, Morea V: Analysis and assessment of comparative modeling predictions in CASP4. Proteins 2001:22-38.
33. Qian B, Ortiz AR, Baker D: Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc Natl Acad Sci U S A 2004, 101(43):15346-15351.
34. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ: Multiple sequence alignment with Clustal X. Trends Biochem Sci 1998, 23(10):403-405.
35. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14(9):755-763.
36. Russell RB, Barton GJ: Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 1992, 14(2):309-323.
37. Shindyalov IN, Bourne PE: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 11(9):739-747.
38. Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637.
39. Sutcliffe MJ, Haneef I, Carney D, Blundell TL: Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1987, 1(5):377-384.
40. Guex N, Peitsch MC: SWISS-MODEL and the Swiss-Pdb-Viewer: an environment for comparative protein modeling. Electrophoresis 1997, 18(15):2714-2723.
41. Schwede T, Kopp J, Guex N, Peitsch MC: SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 2003, 31(13):3381-3385.
42. Kopp J, Schwede T: The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res 2004:D230-234.
43. Unger R, Harel D, Wherland S, Sussman JL: A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 1989, 5(4):355-373.
44. Bates PA, Kelley LA, MacCallum RM, Sternberg MJ: Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins 2001:39-46.
45. Havel TF, Snow ME: A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 1991, 217(1):1-7.
46. Sali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3):779-815.
47. Sali A: Modeling mutations and homologous proteins. Curr Opin Biotechnol 1995, 6(4):437-451.
48. Sanchez R, Sali A: Advances in comparative protein-structure modelling. Curr Opin Struct Biol 1997, 7(2):206-214.
49. Fiser A, Do RK, Sali A: Modeling of loops in protein structures. Protein Sci 2000, 9(9):1753-1773.
50. Fiser A, Sali A: ModLoop: automated modeling of loops in protein structures. Bioinformatics 2003, 19(18):2500-2501.
51. Espadaler J, Fernandez-Fuentes N, Hermoso A, Querol E, Aviles FX, Sternberg MJ, Oliva B: ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res 2004:D185-188.
52. Burke DF, Deane CM, Blundell TL: Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. Bioinformatics 2000, 16(6):513-519.
53. Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJ, Oliva B: Prediction of the conformation and geometry of loops in globular proteins. Testing ArchDB, a structural classification of loops. Proteins 2005 in press.
54. Vasquez M: Modeling side-chain conformation. Curr Opin Struct Biol 1996, 6(2):217-221.
55. Vriend G: WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990, 8(1):52-56.
56. Canutescu AA, Shelenkov AA, Dunbrack RL Jr: A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003, 12(9):2001-2014.
57. Repiso A, Oliva B, Vives Corrons JL, Carreras J, Climent F: Glucose phosphate isomerase deficiency: enzymatic and familial characterization of Arg346His mutation. Biochim Biophys Acta 2005, 1740(3):467-471.
58. de Atauri P, Repiso A, Oliva B, Lluis Vives-Corrons J, Climent F, Carreras J: Characterization of the first described mutation of human red blood cell phosphoglycerate mutase. Biochim Biophys Acta 2005, 1740(3):403-410.
59. Andres AM, Soldevila M, Navarro A, Kidd KK, Oliva B, Bertranpetit J: Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage. Hum Genet 2004, 115(5):377-386.
60. Moult J, Fidelis K, Zemla A, Hubbard T: Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins 2001:2-7.
61. Venclovas C: Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment. Proteins 2001:47-54.
62. van Vlijmen HW, Karplus M: PDB-based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol 1997, 267(4):975-1001.
63. Mehler EL, Periole X, Hassan SA, Weinstein H: Key issues in the computational simulation of GPCR function: representation of loop domains. J Comput Aided Mol Des 2002, 16(11):841-853.
64. Fan H, Mark AE: Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 2004, 13(1):211-220.
65. Carrieri A, Centeno NB, Rodrigo J, Sanz F, Carotti A: Theoretical evidence of a salt bridge disruption as the initiating process for the alpha1 d-adrenergic receptor activation: a molecular dynamics and docking study. Proteins 2001, 43(4):382-394.
66. Gutierrez-de-Teran H, Centeno NB, Pastor M, Sanz F: Novel approaches for modeling of the A1 adenosine receptor and its agonist binding site. Proteins 2004, 54(4):705-715.
67. Laskowski RA, MacArthur MW, Moss DB, Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993, 26:283-291.
68. Sippl MJ: Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990, 213(4):859-883.
69. Luthy R, Bowie JU, Eisenberg D: Assessment of protein models with three-dimensional profiles. Nature 1992, 356(6364):83-85.
70. Sippl MJ: Recognition of errors in three-dimensional structures of proteins. Proteins 1993, 17(4):355-362.
71. Zheng QC, Li ZS, Xiao JF, Sun M, Zhang Y, Sun CC: Homology modeling and PAPS ligand (cofactor) binding study of bovine phenol sulfotransferase. J Mol Model (Online) 2005.
72. Aloy P, Mas JM, Marti-Renom MA, Querol E, Aviles FX, Oliva B: Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2. J Comput Aided Mol Des 2000, 14(1):83-92.
73. Hansson T, Oostenbrink C, van Gunsteren W: Molecular dynamics simulations. Curr Opin Struct Biol 2002, 12(2):190-196.
74. Scott WRP, Hunenberger PH, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF: The GROMOS biomiolecular simulation program package. J Phys Chem A 1999, 103:3596-3607.
75. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M: CHARMM - A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983, 16(2):513-519.
76. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seib el G, Collman P: AMBER, a package of computer-programs for applying molecular mechanics,
77. Tramontano A, Morea V: Assessment of homology-based predictions in CASP5. Proteins 2003, 53(Suppl 6):352-368.
78. Flohil JA, Vriend G, Berendsen HJ: Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis. Proteins 2002, 48(4):593-604.
79. Iverson GM, Reddel S, Victoria EJ, Cockerill KA, Wang YX, Marti-Renom MA, Sali A, Marquis DM, Krilis SA, Linnik MD: Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol 2002, 169(12):7097-7103.
80. Feliu JX, Benito A, Oliva B, Aviles FX, Villaverde A: Conformational flexibility in a highly mobile protein loop of foot-and-mouth disease virus: distinct structural requirements for integrin and antibody binding. J Mol Biol 1998, 283(2):331-338.
81. Sathyanarayanan PV, Siems WF, Jones JP, Poovaiah BW: Calcium-stimulated autophosphorylation site of plant chimeric calcium/calmodulin-dependent protein kinase. J Biol Chem 2001, 276(35):32940-32947.
82. Gloyn AL, Odili S, Zelent D, Buettger C, Castleden HA, Steele AM, Stride A, Shiota C, Magnuson MA, Lorini R, et al.: Insights into the structure and regulation of glucokinase from a novel mutation (V62M), which causes maturity-onset diabetes of the young. J Biol Chem 2005, 280(14):14105-14113.
83. Matsui E, Abe J, Yokoyama H, Matsui I: Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii. J Biol Chem 2004, 279(16):16687-16696.
84. Ishino T, Pasut G, Scibek J, Chaiken I: Kinetic interaction analysis of human interleukin 5 receptor alpha mutants reveals a unique binding topology and charge distribution for cytokine recognition. J Biol Chem 2004, 279(10):9547-9556.
85. Valdar WS, Thornton JM: Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 2001, 313(2):399-416.
86. Villa-Freixa J, Bonet J, Khan AK, Johnston M: Evaluating the relationship between residue stability and enzyme active site preorganization in protein regulated enzymes. Theor Chem Acc 2005 in press.
87. Yokoyama S: Protein expression systems for structural genomics and proteomics. Curr Opin Chem Biol 2003, 7(1):39-43.
88. Carrio M, Gonzalez-Montalban N, Vera A, Villaverde A, Ventura S: Amylod-like properties of bacterial inclusion bodies. J Mol Biol 2005, 347(5):1025-1037.
89. Wodak SJ, Mendez R: Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004, 14(2):242-249.
90. Schneidman-Duhovny D, Nussinov R, Wolfson HJ: Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr Med Chem 2004, 11(1):91-107.
91. Seri M, Savino M, Bordo D, Cusano R, Rocca B, Meloni I, Di Bari F, Koivisto PA, Bolognesi M, Ghiggeri GM, et al.: Epstein syndrome: another renal disorder with mutations in the nonmuscle myosin heavy chain 9 gene. Hum Genet 2002, 110(2):182-186.
92. Almstedt K, Lundqvist M, Carlsson J, Karlsson M, Persson B, Jonsson BH, Carlsson U, Hammarstrom P: Unfolding a folding disease: folding, misfolding and aggregation of the marble brain syndrome-associated mutant H107Y of human carbonic anhydrase II. J Mol Biol 2004, 342(2):619-633.
93. Kim SH: Shining a light on structural genomics. Nat Struct Biol 1998, 5(Suppl):643-645.
94. Goldsmith-Fischman S, Honig B: Structural genomics: computational methods for structure analysis. Protein Sci 2003, 12(9):1813-1821.
95. Montelione GT, Anderson S: Structural genomics: keystone for a Human Proteome Project. Nat Struct Biol 1999, 6(1):11-12.
96. Edwards AM, Arrowsmith CH, Christendat D, Dharamsi A, Friesen JD, Greenblatt JF, Vedadi M: Protein production: feeding the crystallographers and NMR spectroscopists. Nat Struct Biol 2000, 7(Suppl):970-972.
97. Brenner SE: Target selection for structural genomics. Nat Struct Biol 2000, 7(Suppl):967-969.
98. CASP5. Proceedings of the 5th Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. 1-5 December Asilomar, California, USA. Proteins 2002, 53(Suppl 6):333-595.
99. Becker OM, Shacham S, Marantz Y, Noiman S: Modeling the 3D structure of GPCRs: advances and application to drug discovery. Curr Opin Drug Discov Devel 2003, 6(3):353-361.