Predicting the melting point of human C-type lysozyme mutants

Current Protein and Peptide Science

Volumn 11, Issue 7, 2010, Pages 562-572

  Verma, Deeptak ^a   Jacobs, Donald J ^b   Livesay, Dennis R ^a  

^a University of North Carolina at Charlotte   (United States)

^b UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

Author keywords

Distance constraint model; Heat capacity; Lysozyme; Melting point; Mutation; Protein stability

Indexed keywords

LYSOZYME; LYSOZYME TYPE C; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ANALYSIS; ENZYME STRUCTURE; IONIC STRENGTH; MELTING POINT; MOLECULAR INTERACTION; MUTATION; PH; PROTEIN STABILITY; THERMODYNAMICS;

CALORIMETRY, DIFFERENTIAL SCANNING; COMPUTER SIMULATION; DATABASES, PROTEIN; ENTROPY; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; MURAMIDASE; MUTANT PROTEINS; PROTEIN STABILITY; PROTEIN STRUCTURE, TERTIARY; TRANSITION TEMPERATURE;

EID: 79251478002     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920310794109210     Document Type: Article

References (45)

1. Huang, L.T.; Saraboji, K.; Ho, S.Y.; Hwang, S.F.; Ponnuswamy, M.N.; Gromiha, M.M. Prediction of protein mutant stability using classification and regression tool. Biophys. Chem., 2007, 125(2-3), 462-470.
2. Huang, L.T.; Gromiha, M.M.; Ho, S.Y. Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model. J. Mol. Model, 2007, 13(8), 879-890.
3. Huang, L.T.; Gromiha, M.M.; Ho, S.Y. iPTREE-STAB, interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics, 2007, 23(10), 1292-1293.
4. Cheng, J.; Randall, A.; Baldi, P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins, 2006, 62(4), 1125-1132.
5. Capriotti, E.; Fariselli, P.; Calabrese, R.; Casadio, R. Predicting protein stability changes from sequences using support vector machines. Bioinformatics, 2005, 21 Suppl 2, ii54-58.
6. Capriotti, E.; Fariselli, P.; Casadio, R. I-Mutant2.0, predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res., 2005, 33(Web Server issue), W306-310.
7. Rost, B.; Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 1994, 19(1), 55-72.
8. Caballero, J.; Fernandez, L.; Abreu, J.I.; Fernandez, M. Amino Acid Sequence Autocorrelation vectors and ensembles of Bayesian-Regularized Genetic Neural Networks for prediction of conformational stability of human lysozyme mutants. J. Chem. Inf. Model, 2006, 46(3), 1255-1268.
9. Capriotti, E.; Fariselli, P.; Casadio, R. A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics, 2004, 20(Suppl 1), i63-68.
10. Alber, T. Mutational effects on protein stability. Annu. Rev. Biochem., 1989, 58, 765-798.
11. Strickler, S.S.; Gribenko, A.V.; Keiffer, T.R.; Tomlinson, J.; Reihle, T.; Loladze, V.V.; Makhatadze, G.I. Protein stability and surface electrostatics, a charged relationship. Biochemistry, 2006, 45(9), 2761-2766.
12. Makhatadze, G.I.; Loladze, V.V.; Ermolenko, D.N.; Chen, X.; Thomas, S.T. Contribution of surface salt bridges to protein stability, guidelines for protein engineering. J. Mol. Biol., 2003, 327(5), 1135-1148.
13. Makhatadze, G.I.; Loladze, V.V.; Gribenko, A.V.; Lopez, M.M. Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions. J. Mol. Biol., 2004, 336(4), 929-942.
14. Torrez, M.; Schultehenrich, M.; Livesay, D.R. Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces. Biophys. J., 2003, 85(5), 2845-2853.
15. Dong, F.; Vijayakumar, M.; Zhou, H.X. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J., 2003, 85(1), 49-60.
16. Zhou, H.X.; Dong, F. Electrostatic contributions to the stability of a thermophilic cold shock protein. Biophys. J., 2003, 84(4), 2216-2222.
17. Dong, F.; Zhou, H.X. Electrostatic contributions to T4 lysozyme stability, solvent-exposed charges versus semi-buried salt bridges. Biophys. J., 2002, 83(3), 1341-1347.
18. Jacobs, D.J.; Dallakyan, S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophys. J., 2005, 88(2), 903-915.
19. Livesay, D.R.; Dallakyan, S.; Wood, G.G.; Jacobs, D.J. A flexible approach for understanding protein stability. FEBS Lett., 2004, 576(3), 468-476.
20. Razvi, A.; Scholtz, J.M. Lessons in stability from thermophilic proteins. Protein Sci., 2006, 15(7), 1569-1578.
21. Meirovitch, H. Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Curr. Opin. Struct. Biol., 2007, 17(2), 181-186.
22. Dill, K.A. Additivity principles in biochemistry. J. Biol. Chem., 1997, 272(2), 701-704.
23. Mark, A.E.; van Gunsteren, W.F. Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. J. Mol. Biol., 1994, 240(2), 167-176.
24. Jacobs, D.J.; Dallakyan, S.; Wood, G.G.; Heckathorne, A. Network rigidity at finite temperature, relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 2003, 68(6 Pt 1), 061109.
25. Jacobs, D.J.; Rader, A.J.; Kuhn, L.A.; Thorpe, M.F. Protein flexibility predictions using graph theory. Proteins, 2001, 44(2), 150-165.
26. Jacobs, D.J.; Thorpe, M.F. Generic rigidity percolation, The pebble game. Phys. Rev. Lett., 1995, 75(22), 4051-4054.
27. Vorov, O.K.; Livesay, D.R.; Jacobs, D.J. Helix/coil nucleation, a local response to global demands. Biophys. J., 2009, 97(11), 3000-3009.
28. Dahiyat, B.I.; Gordon, D.B.; Mayo, S.L. Automated design of the surface positions of protein helices. Protein Sci., 1997, 6(6), 1333-1337.
29. Fernandez, A.; Kardos, J.; Goto, Y. Protein folding, could hydrophobic collapse be coupled with hydrogen-bond formation? FEBS Lett., 2003, 536(1-3), 187-192.
30. Livesay, D.R.; Jacobs, D.J. Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Proteins, 2006, 62(1), 130-143.
31. Jacobs, D.J.; Livesay, D.R.; Hules, J.; Tasayco, M.L. Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. J. Mol. Biol., 2006, 358(3), 882-904.
32. Livesay, D.R.; Huynh, D.H.; Dallakyan, S.; Jacobs, D.J. Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Chem. Cent. J., 2008, 2, 17.
33. Mottonen, J.M.; Xu, M.; Jacobs, D.J.; Livesay, D.R. Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Proteins, 2009, 75(3), 610-627.
34. Yamagata, Y.; Kubota, M.; Sumikawa, Y.; Funahashi, J.; Takano, K.; Fujii, S.; Yutani, K. Contribution of hydrogen bonds to the conformational stability of human lysozyme, calorimetry and X-ray analysis of six tyrosine → phenylalanine mutants. Biochemistry, 1998, 37(26), 9355-9362.
35. Takano, K.; Yamagata, Y.; Fujii, S.; Yutani, K. Contribution of the hydrophobic effect to the stability of human lysozyme, calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants. Biochemistry, 1997, 36(4), 688-698.
36. Takano, K.; Ota, M.; Ogasahara, K.; Yamagata, Y.; Nishikawa, K.; Yutani, K. Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. Protein Eng., 1999, 12(8), 663-672.
37. Takano, K.; Tsuchimori, K.; Yamagata, Y.; Yutani, K. Effect of foreign N-terminal residues on the conformational stability of human lysozyme. Eur. J. Biochem., 1999, 266(2), 675-682.
38. Funahashi, J.; Takano, K.; Yamagata, Y.; Yutani, K. Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme. Protein Eng., 1999, 12(10), 841-850.
39. Funahashi, J.; Takano, K.; Ogasahara, K.; Yamagata, Y.; Yutani, K. The structure, stability, and folding process of amyloidogenic mutant human lysozyme. J. Biochem., 1996, 120(6), 1216-1223.
40. Herning, T.; Yutani, K.; Inaka, K.; Kuroki, R.; Matsushima, M.; Kikuchi, M. Role of proline residues in human lysozyme stability, a scanning calorimetric study combined with X-ray structure analysis of proline mutants. Biochemistry, 1992, 31(31), 7077-7085.
41. Robertson, A.D.; Murphy, K.P. Protein structure and the energetics of protein stability. Chem. Rev., 1997, 97(5), 1251-1268.
42. Gordon, J.C.; Myers, J.B.; Folta, T.; Shoja, V.; Heath, L.S.; Onufriev, A. H++, a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res., 2005, 33(Web Server issue), W368-371.
43. Gomez, J.; Hilser, V.J.; Xie, D.; Freire, E. The heat capacity of proteins. Proteins, 1995, 22(4), 404-412.
44. Pace, C.N.; Shirley, B.A.; McNutt, M.; Gajiwala, K. Forces contributing to the conformational stability of proteins. FASEB J., 1996, 10(1), 75-83.
45. Guerois, R.; Nielsen, J.E.; Serrano, L. Predicting changes in the stability of proteins and protein complexes, a study of more than 1000 mutations. J. Mol. Biol., 2002, 320(2), 369-387.