Point Mutations in Protein Globular Domains: Contributions from Function, Stability and Misfolding

Journal of Molecular Biology

Volumn 363, Issue 2, 2006, Pages 422-432

  Sanchez I E ^a   Tejero, J ^b   Gomez Moreno C ^b   Medina, M ^b   Serrano, L ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF ZARAGOZA   (Spain)

Author keywords

aggregation; amyloid; function; mutation; protein stability

Indexed keywords

GLOBULAR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; POINT MUTATION; PRESSURE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY;

EID: 33748945709     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.08.020     Document Type: Article

References (76)

1. Lichtarge O., Bourne H.R., and Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257 (1996) 342-358
2. Bartlett G.J., Porter C.T., Borkakoti N., and Thornton J.M. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324 (2002) 105-121
3. Steipe B., Schiller B., Pluckthun A., and Steinbacher S. Sequence statistics reliably predict stabilizing mutations in a protein domain. J. Mol. Biol. 240 (1994) 188-192
4. Kuhlman B., and Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 97 (2000) 10383-10388
5. Lehmann M., Kostrewa D., Wyss M., Brugger R., D'Arcy A., Pasamontes L., and van Loon A.P. From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase. Protein Eng. 13 (2000) 49-57
6. Di Nardo A.A., Larson S.M., and Davidson A.R. The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core. J. Mol. Biol. 333 (2003) 641-655
7. Steipe B. Consensus-based engineering of protein stability: from intrabodies to thermostable enzymes. Methods Enzymol. 388 (2004) 176-186
8. Godoy-Ruiz R., Perez-Jimenez R., Ibarra-Molero B., and Sanchez-Ruiz J.M. A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization. Biophys. J. 89 (2005) 3320-3331
9. Steward A., Adhya S., and Clarke J. Sequence conservation in Ig-like domains: the role of highly conserved proline residues in the fibronectin type III superfamily. J. Mol. Biol. 318 (2002) 935-940
10. Lopez de la Paz M., and Serrano L. Sequence determinants of amyloid fibril formation. Proc. Natl Acad. Sci. USA 101 (2004) 87-92
11. Parrini C., Taddei N., Ramazzotti M., Degl'Innocenti D., Ramponi G., Dobson C.M., and Chiti F. Glycine residues appear to be evolutionarily conserved for their ability to inhibit aggregation. Structure (Camb) 13 (2005) 1143-1151
12. Broome B.M., and Hecht M.H. Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J. Mol. Biol. 296 (2000) 961-968
13. Schwartz R., Istrail S., and King J. Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. Protein Sci. 10 (2001) 1023-1031
14. Richardson J.S., and Richardson D.C. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl Acad. Sci. USA 99 (2002) 2754-2759
15. Rousseau F., Serrano L., and Schymkowitz J.W. How evolutionary pressure against protein aggregation shaped chaperone specificity. J. Mol. Biol. 355 (2006) 1037-1047
16. Meiering E.M., Serrano L., and Fersht A.R. Effect of active site residues in barnase on activity and stability. J. Mol. Biol. 225 (1992) 585-589
17. Shoichet B.K., Baase W.A., Kuroki R., and Matthews B.W. A relationship between protein stability and protein function. Proc. Natl Acad. Sci. USA 92 (1995) 452-456
18. Schreiber G., Buckle A.M., and Fersht A.R. Stability and function: two constraints in the evolution of barstar and other proteins. Structure 2 (1994) 945-951
19. Garcia C., Nishimura C., Cavagnero S., Dyson H.J., and Wright P.E. Changes in the apomyoglobin folding pathway caused by mutation of the distal histidine residue. Biochemistry 39 (2000) 11227-11237
20. Greene L.H., Grobler J.A., Malinovskii V.A., Tian J., Acharya K.R., and Brew K. Stability, activity and flexibility in alpha-lactalbumin. Protein Eng. 12 (1999) 581-587
21. Lee K.N., Park S.D., and Yu M.H. Probing the native strain iin alpha1-antitrypsin. Nature Struct. Biol. 3 (1996) 497-500
22. Haruki M., Noguchi E., Nakai C., Liu Y.Y., Oobatake M., Itaya M., and Kanaya S. Investigating the role of conserved residue Asp134 in Escherichia coli ribonuclease HI by site-directed random mutagenesis. Eur. J. Biochem. 220 (1994) 623-631
23. Zhi W., Srere P.A., and Evans C.T. Conformational stability of pig citrate synthase and some active-site mutants. Biochemistry 30 (1991) 9281-9286
24. Zhang J., Liu Z.P., Jones T.A., Gierasch L.M., and Sambrook J.F. Mutating the charged residues in the binding pocket of cellular retinoic acid-binding protein simultaneously reduces its binding affinity to retinoic acid and increases its thermostability. Proteins: Struct. Funct. Genet. 13 (1992) 87-99
25. Di Nardo A.A., Korzhnev D.M., Stogios P.J., Zarrine-Afsar A., Kay L.E., and Davidson A.R. Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Proc. Natl Acad. Sci. USA 101 (2004) 7954-7959
26. Quirk D.J., Park C., Thompson J.E., and Raines R.T. His...Asp catalytic dyad of ribonuclease A: conformational stability of the wild-type, D121N, D121A, and H119A enzymes. Biochemistry 37 (1998) 17958-17964
27. Jackson S.E., and Fersht A.R. Contribution of residues in the reactive site loop of chymotrypsin inhibitor 2 to protein stability and activity. Biochemistry 33 (1994) 13880-13887
28. Chatani E., Tanimizu N., Ueno H., and Hayashi R. Structural and functional changes in bovine pancreatic ribonuclease a by the replacement of Phe120 with other hydrophobic residues. J. Biochem. (Tokyo) 129 (2001) 917-922
29. Schindler T., Perl D., Graumann P., Sieber V., Marahiel M.A., and Schmid F.X. Surface-exposed phenylalanines in the RNP1/RNP2 motif stabilize the cold-shock protein CspB from Bacillus subtilis. Proteins: Struct. Funct. Genet. 30 (1998) 401-406
30. Hillier B.J., Rodriguez H.M., and Gregoret L.M. Coupling protein stability and protein function in Escherichia coli CspA. Fold. Des. 3 (1998) 87-93
31. Kragelund B.B., Poulsen K., Andersen K.V., Baldursson T., Kroll J.B., Neergard T.B., et al. Conserved residues and their role in the structure, function, and stability of acyl-coenzyme A binding protein. Biochemistry 38 (1999) 2386-2394
32. Eberhardt E.S., Wittmayer P.K., Templer B.M., and Raines R.T. Contribution of a tyrosine side chain to ribonuclease A catalysis and stability. Protein Sci. 5 (1996) 1697-1703
33. Fetrow J.S., Spitzer J.S., Gilden B.M., Mellender S.J., Begley T.J., Haas B.J., and Boose T.L. Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and glycine 77 in omega-loop D of yeast iso-1-cytochrome c. Biochemistry 37 (1998) 2477-2487
34. Rochet J.C., and Lansbury Jr. P.T. Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struct. Biol. 10 (2000) 60-68
35. Linding R., Schymkowitz J., Rousseau F., Diella F., and Serrano L. A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J. Mol. Biol. 342 (2004) 345-353
36. Porter C.T., Bartlett G.J., and Thornton J.M. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucl. Acids Res. 32 (2004) D129-D133
37. Wallace A.C., Laskowski R.A., and Thornton J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8 (1995) 127-134
38. Luscombe N.M., Laskowski R.A., and Thornton J.M. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucl. Acids Res. 25 (1997) 4940-4945
39. Diemand A.V., and Scheib H. iMolTalk: an interactive, internet-based protein structure analysis server. Nucl. Acids Res. 32 (2004) W512-W516
40. Fernandez-Escamilla A.M., Rousseau F., Schymkowitz J., and Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nature Biotechnol. 22 (2004) 1302-1306
41. Kumar M.D., Bava K.A., Gromiha M.M., Prabakaran P., Kitajima K., Uedaira H., and Sarai A. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucl. Acids Res. 34 (2006) D204-D206
42. Parsell D.A., and Sauer R.T. The structural stability of a protein is an important determinant of its proteolytic susceptibility in Escherichia coli. J. Biol. Chem. 264 (1989) 7590-7595
43. Ghaemmaghami S., Fitzgerald M.C., and Oas T.G. A quantitative, high-throughput screen for protein stability. Proc. Natl Acad. Sci. USA 97 (2000) 8296-8301
44. Barlow M., and Hall B.G. Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase. Genetics 160 (2002) 823-832
45. Cochran J.R., Kim Y.S., Lippow S.M., Rao B., and Wittrup K.D. Improved mutants from directed evolution are biased to orthologous substitutions. Protein Eng. 19 (2006) 245-253
46. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., et al. The Pfam protein families database. Nucl. Acids Res. 32 (2004) D138-D141
47. Sanchez I.E., and Kiefhaber T. Origin of unusual phi-values in protein folding: evidence against specific nucleation sites. J. Mol. Biol. 334 (2003) 1077-1085
48. Capriotti E., Fariselli P., and Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucl. Acids Res. 33 (2005) W306-W310
49. Guerois R., Nielsen J.E., and Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320 (2002) 369-387
50. Wang Q., Buckle A.M., Foster N.W., Johnson C.M., and Fersht A.R. Design of highly stable functional GroEL minichaperones. Protein Sci. 8 (1999) 2186-2193
51. Keefe A.D., and Szostak J.W. Functional proteins from a random-sequence library. Nature 410 (2001) 715-718
52. Jaenicke R., and Zavodszky P. Proteins under extreme physical conditions. FEBS Letters 268 (1990) 344-349
53. Ota M., Kinoshita K., and Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J. Mol. Biol. 327 (2003) 1053-1064
54. Chelliah V., Chen L., Blundell T.L., and Lovell S.C. Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J. Mol. Biol. 342 (2004) 1487-1504
55. Cheng G., Qian B., Samudrala R., and Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucl. Acids Res. 33 (2005) 5861-5867
56. Chelliah V., Blundell T.L., and Fernandez-Recio J. Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J. Mol. Biol. 357 (2006) 1669-1682
57. Chakrabarti R., Klibanov A.M., and Friesner R.A. Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc. Natl Acad. Sci. USA 102 (2005) 10153-10158
58. Rousseau F., Schymkowitz J., and Serrano L. Protein aggregation and amyloidosis: confusion of the kinds?. Curr. Opin. Struct. Biol. 16 (2006) 118-126
59. Lopez De La Paz M., Goldie K., Zurdo J., Lacroix E., Dobson C.M., Hoenger A., and Serrano L. De novo designed peptide-based amyloid fibrils. Proc. Natl Acad. Sci. USA 99 (2002) 16052-16057
60. Gassner N.C., Baase W.A., and Matthews B.W. A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc. Natl Acad. Sci. USA 93 (1996) 12155-12158
61. Brown B.M., and Sauer R.T. Tolerance of Arc repressor to multiple-alanine substitutions. Proc. Natl Acad. Sci. USA 96 (1999) 1983-1988
62. Chasman D., and Adams R.M. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J. Mol. Biol. 307 (2001) 683-706
63. Lockless S.W., and Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
64. Larson S.M., Di Nardo A.A., and Davidson A.R. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303 (2000) 433-446
65. England J.L., Shakhnovich B.E., and Shakhnovich E.I. Natural selection of more designable folds: a mechanism for thermophilic adaptation. Proc. Natl Acad. Sci. USA 100 (2003) 8727-8731
66. Drummond D.A., Bloom J.D., Adami C., Wilke C.O., and Arnold F.H. Why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 102 (2005) 14338-14343
67. Bastolla U., Moya A., Viguera E., and van Ham R.C. Genomic determinants of protein folding thermodynamics in prokaryotic organisms. J. Mol. Biol. 343 (2004) 1451-1466
68. Tartaglia G.G., Pellarin R., Cavalli A., and Caflisch A. Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Sci. 14 (2005) 2735-2740
69. Benner S.A., Cohen M.A., and Gonnet G.H. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng. 7 (1994) 1323-1332
70. Flores T.P., Orengo C.A., Moss D.S., and Thornton J.M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2 (1993) 1811-1826
71. Littler S.J., and Hubbard S.J. Conservation of orientation and sequence in protein domain-domain interactions. J. Mol. Biol. 345 (2005) 1265-1279
72. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
73. Rost B., and Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins: Struct. Funct. Genet. 20 (1994) 216-226
74. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242
75. de los Rios M.A., Muralidhara B.K., Wildes D., Sosnick T.R., Marqusee S., Wittung-Stafshede P., et al. On the precision of experimentally determined protein folding rates and phi-values. Protein Sci. 15 (2006) 553-563
76. Henikoff S., and Henikoff J.G. Position-based sequence weights. J. Mol. Biol. 243 (1994) 574-578