Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins

Current Opinion in Structural Biology

Volumn 32, Issue , 2015, Pages 18-24

  Kucukkal, Tugba G ^a   Petukh, Marharyta ^a   Li, Lin ^a   Alexov, Emil ^a  

^a CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; PROTEIN; PROTEIN BINDING;

CHEMICAL INTERACTION; ENERGY CONSUMPTION; GENE MUTATION; GEOMETRY; HYDROGEN BOND; HYDROPHOBICITY; MACROMOLECULE; MOLECULAR DYNAMICS; NON SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISM; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; SALT BRIDGE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; CHEMISTRY; GENETIC PREDISPOSITION; GENETICS; HUMAN; METABOLISM; MOLECULAR MODEL; MUTATION; PROTEIN CONFORMATION;

ANIMALS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, MOLECULAR; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPS; PROTEIN STABILITY; PROTEINS;

EID: 84922176356     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2015.01.003     Document Type: Review

References (59)

1. Alexov E. Advances in human biology: combining genetics and molecular biophysics to pave the way for personalized diagnostics and medicine. Adv Biol 2014, 2014. Article ID 471836.
2. Sayers E.W., Barrett T., Benson D.A., Bolton E., Bryant S.H., Canese K., Chetvernin V., Church D.M., Dicuccio M., Federhen S., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2012, 40:D13-D25.
3. Kucukkal T.G., Yang Y., Chapman S.C., Cao W., Alexov E. Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci 2014, 15:9670-9717.
4. Stanley C.M., Sunyaev S.R., Greenblatt M.S., Oetting W.S. Clinically relevant variants-identifying, collecting, interpreting, and disseminating: the 2013 annual scientific meeting of the Human Genome Variation Society. Hum Mutat 2014, 35:505-510.
5. Yates C.M., Sternberg M.J. The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions. J Mol Biol 2013, 425:3949-3963.
6. Bartlett A.I., Radford S.E. An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 2009, 16:582-588.
7. Stefl S., Nishi H., Petukh M., Panchenko A.R., Alexov E. Molecular mechanisms of disease-causing missense mutations. J Mol Biol 2013, 425:3919-3936.
8. Zhang Z., Miteva M.A., Wang L., Alexov E. Analyzing effects of naturally occurring missense mutations. Comput Math Methods Med 2012, 2012:805827.
9. Chipot C. Free energy calculations: theory and applications in chemistry and biology. Springer Series in Chemical Physics 2007, vol 86. Springer-Verlag, Berlin.
10. Zhang Z., Wang L., Gao Y., Zhang J., Zhenirovskyy M., Alexov E. Predicting folding free energy changes upon single point mutations. Bioinformatics 2012, 28:664-671.
11. Benedix A., Becker C.M., de Groot B.L., Caflisch A., Bockmann R.A. Predicting free energy changes using structural ensembles. Nat Methods 2009, 6:3-4.
12. Pastore A., Lori C., Lantella A., Pasquo A., Alexander L.T., Knapp S., Chiaraluce R., Consalvi V. Effect of single amino acid substitution observed in cancer on Pim-1 kinase thermodynamic stability and structure. PLoS ONE 2013, 8:e64824.
13. Khan R.H., Chaturvedi D., Mahalakshmi R. Methionine mutations of outer membrane protein X influence structural stability and beta-barrel unfolding. PLoS ONE 2013, 8:e79351.
14. Grothe H.L., Little M.R., Sjogren P.P., Chang A.A., Nelson E.F., Yuan C. Altered protein conformation and lower stability of the dystrophic transforming growth factor beta-induced protein mutants. Mol Vis 2013, 19:593.
15. Takano K., Liu D., Tarpey P., Gallant E., Lam A., Witham S., Alexov E., Chaubey A., Stevenson R.E., Schwartz C.E., Board P.G., Dulhunty A.F. An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity. Hum Mol Genet 2012, 21:4497-4507.
16. Lori C., Pasquo A., Montanari R., Capelli D., Consalvi V., Chiaraluce R., Cervoni L., Loiodice F., Laghezza A., Aschi M., Giorgi A., Pochetti G. Structural basis of the transactivation deficiency of the human PPARgamma F360L mutant associated with familial partial lipodystrophy. Acta Crystallogr D Biol Crystallogr 2014, 70:1965-1976.
17. Monticone S., Bandulik S., Stindl J., Zilbermint M., Dedov I., Mulatero P., Allgaeuer M., Richard Lee C.C., Stratakis C.A., Ann Williams T., Tiulpakov A. A case of severe hyperaldosteronism caused by a de novo mutation affecting a critical 'salt bridge' Kir3.4 residue. J Clin Endocrinol Metab 2014, 100:E114-E118.
18. Witham S., Takano K., Schwartz C., Alexov E. A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics. Proteins 2011, 79:2444-2454.
19. Zhang Z., Norris J., Schwartz C., Alexov E. In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase. PLoS One 2011, 6:e20373.
20. Zhang Z., Zheng Y., Petukh M., Pegg A., Ikeguchi Y., Alexov E. Enhancing human spermine synthase activity by engineered mutations. PLoS Comput Biol 2013, 9:e1002924.
21. Boccuto L., Aoki K., Flanagan-Steet H., Chen C.F., Fan X., Bartel F., Petukh M., Pittman A., Saul R., Chaubey A., Alexov E., Tiemeyer M., Steet R., Schwartz C.E. A mutation in a ganglioside biosynthetic enzyme ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation. Hum Mol Genet 2014, 23:418-433.
22. Zhang Z., Norris J., Kalscheuer V., Wood T., Wang L., Schwartz C., Alexov E., Van Esch H. A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome. Hum Mol Genet 2013, 22:3789-3797.
23. Zhang Z., Teng S., Wang L., Schwartz C.E., Alexov E. Computational analysis of missense mutations causing Snyder-Robinson syndrome. Hum Mutat 2010, 31:1043-1049.
24. Chiariotti L., Doss C.G.P., NagaSundaram N. Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach. PLoS ONE 2012, 7:e31677.
25. Kumar A., Rajendran V., Sethumadhavan R., Purohit R. Molecular dynamic simulation reveals damaging impact of RAC1 F28L mutation in the switch I region. PLoS One 2013, 8:e7745.
26. Jeninga E.H., van Beekum O., van Dijk A.D., Hamers N., Hendriks-Stegeman B.I., Bonvin A.M., Berger R., Kalkhoven E. Impaired peroxisome proliferator-activated receptor gamma function through mutation of a conserved salt bridge (R425C) in familial partial lipodystrophy. Mol Endocrinol 2007, 21:1049-1065.
27. Nussinov R., Tsai C.-J. Allostery in disease and in drug discovery. Cell 2013, 153:293-305.
28. Motlagh H.N., Wrabl J.O., Li J., Hilser V.J. The ensemble nature of allostery. Nature 2014, 508:331-339.
29. Kleckner I.R., Foster M.P. An introduction to NMR-based approaches for measuring protein dynamics. Biochim Biophys Acta 2011, 1814:942-968.
30. Medintz I., Hildebrandt N. FRET-Förster Resonance Energy Transfer: from Theory to Applications 2013, John Wiley & Sons.
31. Dror R.O., Jensen M.O., Borhani D.W., Shaw D.E. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol 2010, 135:555-562.
32. Bouvignies G., Vallurupalli P., Hansen D.F., Correia B.E., Lange O., Bah A., Vernon R.M., Dahlquist F.W., Baker D., Kay L.E. Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 2011, 477:111-114.
33. Wen Y., Li J., Xiong M., Peng Y., Yao W., Hong J., Lin D. Solution structure and dynamics of the I214V mutant of the rabbit prion protein. PLoS ONE 2010, 5:e13273.
34. Caron N.S., Desmond C.R., Xia J., Truant R. Polyglutamine domain flexibility mediates the proximity between flanking sequences in huntingtin. Proc Natl Acad Sci 2013, 110:14610-14615.
35. Zhong X., Liu Y., Zhu L., Meng X., Wang R., Van Petegem F., Wagenknecht T., Chen S.R., Liu Z. Conformational dynamics inside amino-terminal disease hotspot of ryanodine receptor. Structure 2013, 21:2051-2060.
36. Kumar A., Purohit R. Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PLoS Comput Biol 2014, 10:e1003318.
37. Bandaranayake R.M., Ungureanu D., Shan Y., Shaw D.E., Silvennoinen O., Hubbard S.R. Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F. Nat Struct Mol Biol 2012, 19:754-759.
38. Moretti R., Fleishman S.J., Agius R., Torchala M., Bates P.A., Kastritis P.L., Rodrigues J.P.G.L.M., Trellet M., Bonvin A.M.J.J., Cui M., et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins 2013, 81:1980-1987.
39. Fong J.H., Shoemaker B.A., Panchenko A.R. Intrinsic protein disorder in human pathways. Mol Biosyst 2012, 8:320-326.
40. Buljan M., Chalancon G., Dunker A.K., Bateman A., Balaji S., Fuxreiter M., Babu M.M. Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol 2013, 23:443-450.
41. Schreiber G., Keating A.E. Protein binding specificity versus promiscuity. Curr Opin Struct Biol 2011, 21:50-61.
42. Carbonell P., Nussinov R., del Sol A. Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics 2009, 9:1744-1753.
43. Zhang Z., Witham S., Alexov E. On the role of electrostatics in protein-protein interactions. Phys Biol 2011, 8:035001.
44. Moal I.H., Fernandez-Recio J. SKEMPI: a structural kinetic and energetic database of mutant protein interactions and its use in empirical models. Bioinformatics 2012, 28:2600-2607.
45. Ghai R., Falconer R.J., Collins B.M. Applications of isothermal titration calorimetry in pure and applied research-survey of the literature from 2010. J Mol Recognit 2012, 25:32-52.
46. Phillip Y., Kiss V., Schreiber G. Protein-binding dynamics imaged in a living cell. Proc Natl Acad Sci U S A 2012, 109:1461-1466.
47. Masi A., Cicchi R., Carloni A., Pavone F.S., Arcangeli A. Optical methods in the study of protein-protein interactions. Adv Exp Med Biol 2010, 674:33-42.
48. Kastritis P.L., Bonvin A.M. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2013, 10:20120835.
49. Domoszlai T., Martincuks A., Fahrenkamp D., Schmitz-Van de Leur H., Kuster A., Muller-Newen G. Consequences of the disease-related L78R mutation for dimerization and activity of STAT3. J Cell Sci 2014, 127:1899-1910.
50. Placone J., Hristova K. Direct assessment of the effect of the Gly380Arg achondroplasia mutation on FGFR3 dimerization using quantitative imaging FRET. PLoS One 2012, 7:e46678.
51. Placone J., He L., Del Piccolo N., Hristova K. Strong dimerization of wild-type ErbB2/Neu transmembrane domain and the oncogenic Val664Glu mutant in mammalian plasma membranes. Biochim Biophys Acta 2014, 1838:2326-2330.
52. Yang F., Wu M., Li Y., Zheng G.Y., Cao H.Q., Sun W., Yang R., Zhang H., Sheng Y.H., Kong X.Q., Tian X.L., Zhou L. Mutation p.S335X in GATA4 reduces its DNA binding affinity and enhances cell apoptosis associated with ventricular septal defect. Curr Mol Med 2013, 13:993-999.
53. Nishi H., Tyagi M., Teng S., Shoemaker B.A., Hashimoto K., Alexov E., Wuchty S., Panchenko A.R. Cancer missense mutations alter binding properties of proteins and their interaction networks. PLoS One 2013, 8:e66273.
54. Teng S., Madej T., Panchenko A., Alexov E. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J 2009, 96:2178-2188.
55. Berliner N., Teyra J., Colak R., Garcia Lopez S., Kim P.M. Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation. PLoS One 2014, 9:e107353.
56. Zeng J., Jia X., Zhang J.Z., Mei Y. The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect. J Comput Chem 2013, 34:2677-2686.
57. Di Marino D., Oteri F., Morozzo Della Rocca B., Chillemi G., Falconi M. ADP/ATP mitochondrial carrier MD simulations to shed light on the structural-dynamical events that, after an additional mutation, restore the function in a pathological single mutant. J Struct Biol 2010, 172:225-232.
58. Capriotti E., Calabrese R., Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 2006, 22:2729-2734.
59. Wei Q., Dunbrack R.L. The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS ONE 2013, 8:e67863.