Prots: A fragment based protein thermo-stability potential

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 1, 2012, Pages 81-92

  Li, Yunqi ^a   Zhang, Jian ^b   Tai, David ^a   Russell Middaugh, C ^a   Zhang, Yang ^b   Fang, Jianwen ^a  

^a UNIVERSITY OF KANSAS   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Datamining; Prediction; Protein stability; Thermophilic; Thermostability potential

Indexed keywords

AMINO ACID;

ARTICLE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEIN STRUCTURE; REVERTANT; SEQUENCE ANALYSIS; TEMPERATURE; THERMOSTABILITY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; CHICKENS; COMPUTER SIMULATION; FIBROBLAST GROWTH FACTOR 1; HUMANS; LINEAR MODELS; MODELS, MOLECULAR; MURAMIDASE; MUTATION, MISSENSE; PROTEIN ENGINEERING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; ROC CURVE; SOFTWARE; THERMODYNAMICS; TRANSITION TEMPERATURE;

EID: 83455206743     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23163     Document Type: Article

References (66)

1. Dahiyat BI. In silico design for protein stabilization. Curr Opin Biotech 1999; 10: 387-390.
2. Korkegian A, Black ME, Baker D, Stoddard BL. Computational thermostabilization of an enzyme. Science 2005; 308: 857-860.
3. Lazar GA, Marshall SA, Plecs JJ, Mayo SL, Desjarlais JR. Designing proteins for therapeutic applications. Curr Opin Struct Biol 2003; 13: 513-518.
4. Schweiker KL, Makhatadze GI. Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biology 2009; 490: 261-283.
5. Sterner R, Liebl W. Thermophilic adaptation of proteins. Crit Rev Biochem Mol Biol 2001; 36: 39-106.
6. Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL. Design of therapeutic proteins with enhanced stability. Proc Natl Acad Sci USA 2009; 106: 11937-11942.
7. Unsworth LD, van der Oost J, Koutsopoulos S. Hyperthermophilic enzymes-stability, activity and implementation strategies for high temperature applications. FEBS J 2007; 274: 4044-4056.
8. Schoemaker HE, Mink D, Wubbolts MG. Dispelling the myths-biocatalysis in industrial synthesis. Science 2003; 299: 1694-1697.
9. Frokjaer S, Otzen DE. Protein drug stability: a formulation challenge. Nat Rev Drug Discov 2005; 4: 298-306.
10. Lippow SM, Tidor B. Progress in computational protein design. Curr Opin Biotech 2007; 18: 305-311.
11. Potapov V, Cohen M, Schreiber G. Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 2009; 22: 553-560.
12. Berezovsky IN, Shakhnovich EI. Physics and evolution of thermophilic adaptation. Proc Natl Acad Sci USA 2005; 102: 12742-12747.
13. Berezovsky IN, Zeldovich KB, Shakhnovich EI. Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol 2007; 3: e52.
14. Gianese G, Argos P, Pascarella S. Structural adaptation of enzymes to low temperatures. Protein Eng 2001; 14: 141-148.
15. Mandrich L, Pezzullo M, Del Vecchio P, Barone G, Rossi M, Manco G. Analysis of thermal adaptation in the HSL enzyme family. J Mol Biol 2004; 335: 357-369.
16. McDonald JH. Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol Biol Evol 2001; 18: 741-749.
17. Menendez-Arias L, Argos P. Engineering protein thermal stability. Sequence statistics point to residue substitutions in alpha-helices. JMol Biol 1989; 206: 397-406.
18. Metpally RP, Reddy BV. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: insights into the molecular basis of cold adaptation of proteins. BMC Genomics 2009; 10: 11.
19. Razvi A, Scholtz JM. Lessons in stability from thermophilic proteins. Protein Sci 2006; 15: 1569-1578.
20. Zeldovich KB, Berezovsky IN, Shakhnovich EI. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 2007; 3: e5.
21. Zhou XX, Wang YB, Pan YJ, Li WF. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids 2008; 34: 25-33.
22. Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, Olsen GJ. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci USA 1999; 96: 3578-3583.
23. Glyakina AV, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV. Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatics 2007; 23: 2231-2238.
24. Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002; 320: 369-387.
25. Gu J, Hilser VJ. Sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome. Mol Biol Evol 2009; 26: 2217-2227.
26. Gu J, Hilser VJ. Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome. Structure 2008; 16: 1627-1637.
27. Chan CH, Liang HK, Hsiao NW, Ko MT, Lyu PC, Hwang JK. Relationship between local structural entropy and protein thermostability. Proteins 2004; 57: 684-691.
28. Pokala N, Handel TM. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 2005; 347: 203-227.
29. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2726.
30. Yin S, Ding F, Dokholyan NV. Modeling backbone flexibility improves protein stability estimation. Structure 2007; 15: 1567-1576.
31. Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic acids research 2005; 33(Web Server issue): W306-W310.
32. Cheng J, Randall A, Baldi P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 2006; 62: 1125-1132.
33. Masso M, Vaisman, II. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. Bioinformatics 2008; 24: 2002-2009.
34. Montanucci L, Fariselli P, Martelli PL, Casadio R. Predicting protein thermostability changes from sequence upon multiple mutations. Bioinformatics 2008; 24: I190-I195.
35. Wu LC, Lee JX, Huang HD, Liu BJ, Horng JT. An expert system to predict protein thermostability using decision tree. Expert Systems Appl 2009; 36: 9007-9014.
36. Gromiha MM, Oobatake M, Sarai A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys Chem 1999; 82: 51-67.
37. Huang LT, Gromiha MM. Reliable prediction of protein thermostability change upon double mutation from amino acid sequence. Bioinformatics 2009; 25: 2181-2187.
38. Singh RK, Tropsha A, Vaisman II. Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comp Biol 1996; 3: 213-221.
39. Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009; 19: 145-155.
40. Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007; 5: 17.
41. Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007; 69( Suppl 8): 108-117.
42. Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009; 77( Suppl 9): 100-113.
43. Li Y, Middaugh CR, Fang J. A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants. BMC Bioinformatics 2010; 11: 62.
44. Becktel WJ, Schellman JA. Protein stability curves. Biopolymers 1987; 26: 1859-1877.
45. Li YQ, Fang JW. Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. Biochem Biophys Res Commun 2010; 396: 736-741.
46. Kryshtafovych A, Krysko O, Daniluk P, Dmytriv Z, Fidelis K. Protein structure prediction center in CASP8. Proteins-Struct Funct Bioinformatics 2009; 77: 5-9.
47. Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction-round VII. Proteins-Struct Funct Bioinformatics 2007; 69: 3-9.
48. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 2007; 35: 3375-3382.
49. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004; 25: 865-871.
50. Li Y, Zhang Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins-Structure Function and Bioinformatics 2009; 76: 665-676.
51. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008; 9: 40.
52. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004; 57: 702-710.
53. Kumar MD, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, Uedaira H, Sarai A. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res 2006; 34(Database issue): D204-D206.
54. Li Y, Drummond DA, Sawayama AM, Snow CD, Bloom JD, Arnold FH. A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Nat Biotechnol 2007; 25: 1051-1056.
55. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.
56. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
57. Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 1998; 7: 1884-1897.
58. Masso M, Vaisman, II. Accurate prediction of enzyme mutant activity based on a multibody statistical potential. Bioinformatics 2007; 23: 3155-3161.
59. Deutsch C, Krishnamoorthy B. Four-body scoring function for mutagenesis. Bioinformatics 2007; 23: 3009-3015.
60. Gromiha MM, Huang L-T, Lai L-F. Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins. Lecture Notes Comput Sci 2008; 5265: 1-12.
61. Kim H, Moon EJ, Moon S, Jung HJ, Yang YL, Park YH, Heo M, Cheon M, Chang I, Han DS. New method of evaluating relative thermal stabilities of proteins based on their amino acid sequences; Targetstar. Int J Modern Phys C 2007; 18: 1513-1526.
62. Brych SR, Blaber SI, Logan TM, Blaber M. Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil. Protein Sci 2001; 10: 2587-2599.
63. Culajay JF, Blaber SI, Khurana A, Blaber M. Thermodynamic characterization of mutants of human fibroblast growth factor 1 with an increased physiological half-life. Biochemistry 2000; 39: 7153-7158.
64. Dalluge R, Oschmann J, Birkenmeier O, Lucke C, Lilie H, Rudolph R, Lange C. A tetrapeptide fragment-based design method results in highly stable artificial proteins. Proteins-Struct Funct Bioinformatics 2007; 68: 839-849.
65. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008; 36(Database issue): D281-D288.
66. Bae E, Bannen RM, Phillips GN, Jr. Bioinformatic method for protein thermal stabilization by structural entropy optimization. Proc Natl Acad Sci USA 2008; 105: 9594-9597.