All Title Author
Keywords Abstract

PLOS ONE  2013 

An In Silico Analysis of Troponin I Mutations in Hypertrophic Cardiomyopathy of Indian Origin

DOI: 10.1371/journal.pone.0070704

Full-Text   Cite this paper   Add to My Lib

Abstract:

Hypertrophic Cardiomyopathy (HCM) is an autosomal dominant disorder of the myocardium which is hypertrophied resulting in arrhythmias and heart failure leading to sudden cardiac death (SCD). Several sarcomeric proteins and modifier genes have been implicated in this disease. Troponin I, being a part of the Troponin complex (troponin I, troponin C, troponin T), is an important gene for sarcomeric function. Four mutations (1 novel) were identified in Indian HCM cases, namely, Pro82Ser, Arg98Gln, Arg141Gln and Arg162Gln in Troponin I protein, which are in functionally significant domains. In order to analyse the effect of the mutations on protein stability and protein-protein interactions within the Troponin complex, an in silico study was carried out. The freely available X-ray crystal structure (PDB ID: 1JIE) was used as the template to model the protein followed by loop generation and development of troponin complex for both the troponin I wild type and four mutants (NCBI ID: PRJNA194382). The structural study was carried out to determine the effect of mutation on the structural stability and protein-protein interactions between three subunits in the complex. These mutations, especially the arginine to glutamine substitutions were found to result in local perturbations within the troponin complex by creating/removing inter/intra molecular hydrogen bonds with troponin T and troponin C. This has led to a decrease in the protein stability and loss of important interactions between the three subunits. It could have a significant impact on the disease progression when coupled with allelic heterogeneity which was observed in the cases carrying these mutations. However, this can be further confirmed by functional studies on protein levels in the identified cases.

References

[1]  Lim DS, Roberts R, Marian AJ (2001) Expression Profiling of Cardiac Genes in Human Hypertrophic Cardiomyopathy: Insight Into the Pathogenesis of Phenotypes. J Am Coll Cardiol 38: 1175–80.
[2]  Robinson P, Griffiths PJ, Watkins H, Redwood CH (2007) Dilated and Hypertrophic Cardiomyopathy Mutations in Troponin and a-Tropomyosin Have Opposing Effects on the Calcium Affinity of Cardiac Thin Filaments. Circ Res 101: 1266–1273.
[3]  Burton D, Abdulrazzak H, Knott A, Elliott K, Redwood C, et al. (2002) Two mutations in troponin I that cause hypertrophic cardiomyopathy have contrasting effects on cardiac muscle contractility. Biochem. J 362: 443–451.
[4]  Ushasree B, Shivani V, Narsimhan C, Pratibha N (2009) Novel Mutations in Beta Myosin Heavy Chain, Actin and Troponin I genes associated with Dilated Cardiomyopathy in Indian Population. J Gen 88: 3.
[5]  James J, Zhang Y, Osinska H, Sanbe A, Klevitsky R, et al. (2000) Transgenic Modeling of a Cardiac Troponin I Mutation Linked to Familial Hypertrophic Cardiomyopathy. Circ Res 87: 805–811.
[6]  Westfall MV, Metzger JM (2001) Troponin I Isoforms and Chimeras: Tuning the Molecular Switch of Cardiac Contraction. News Physiol Sci 16.
[7]  Kobayashi T, Solaro RJ (2006) Increased Ca2+ Affinity of Cardiac Thin Filaments Reconstituted with Cardiomyopathy-related Mutant Cardiac Troponin I. JBC. 281: 13471–13477.
[8]  Grand RJ, Levine BA, Perry SV (1982) Proton-magnetic-resonance studies on the interaction of rabbit skeletal-muscle troponin I with troponin C and actin. Biochem J 203: 61–68.
[9]  Malnic B, Farah CS, Reinach FC (1998) Regulatory properties of the NH2- and COOH-terminal domains of troponin T-ATPase activation and binding to troponin I and troponin C. J Biol Chem. 273: 10594–10601.
[10]  Deepa SR, Pratibha N, Singh P, Narasimhan C, Singh L, et al. (2012) High prevalence of Arginine to Glutamine Substitution at 98,141 and 162 positions in Troponin I (TNNI3) associated with hypertrophic cardiomyopathy among Indians. BMC Med Gen 13(69): 1–8.
[11]  Betts MJ, Russell RB (2003) Amino Acid Properties and Consequences of Substitutions. Volume: 4 Publisher: John Wiley & Sons Ltd Pages: 289–316.
[12]  Day A (1996) The Source of Stability in Proteins. PPS course participant
[13]  Summers KM (1996) Relationship between genotype and phenotype in monogenic diseases: relevance to polygenic diseases. Hum Mutat 7: 283–293.
[14]  Scriver CR, Waters PJ (1999) Monogenic traits are not simple: lessons from phenylketonuria. Trends Genet 15: 267–272.
[15]  Dipple KM, McCabe ERB (2000) Phenotypes of patients with “simple” Mendelian disorders are complex traits: thresholds, modifiers, and systems dynamics. Am J Hum. Genet 66: 1729–1735.
[16]  Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8: r49–r62.
[17]  Gu W, Zhou T, Ma J, Sun X, Lu Z (2004) The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. Biosystems 73: 89–97.
[18]  D’Onofrio G (2002) Expression patterns and gene distribution in the human genome. Gene 300: 155–160.
[19]  Waters PJ (2001) Degradation of Mutant Proteins, Underlying “Loss of Function” Phenotypes, Plays a Major Role in Genetic Disease. Curr Issues Mol Biol 3(3): 57–65.
[20]  Takeda S, Yamashita A, Maieda K, Maida Y (2003) Structure of the core domain of human cardiac troponin in the Ca (2+)-saturated form. Nature 424: 35–41.
[21]  Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779–815.
[22]  Fiser A, Do RKG, Sali A (2000) Modelling of loops in protein structures. Protein Science 9: 1753–1773.
[23]  Discovery Studio 2.0 (2007) Molecular modeling program package. Accelrys Software Inc San Diego CA USA.
[24]  Fletcher R, Reeves CM (1964) Function Minimization by Conjugate Gradients. The Computer Journal 7: 149–154.
[25]  Kirkpatrick S, Gelatt CD Jr, Vecchi MP (1983) Optimization by simulated annealing. Science 220 (4598): 671–680.
[26]  Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sciences 15: 2507–2524.
[27]  Spassov VZ, Yan L, Flook PK (2007) The Dominant Role of Side-Chain Backbone Interactions in Structural Realization of Amino Acid-Code. ChiRotor: A Side-Chain Prediction Algorithm Based on Side-Chain Backbone Interactions. Protein Science 16: 494–506.
[28]  Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4: 187–217.
[29]  Momany FA, Rone R (1992) Validation of the general purpose QUANTA ?3.2/CHARMm? force field. J Comp Chem 13: 888–900.
[30]  Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277: 396–404.
[31]  Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK – a program to check the stereochemical quality of protein structures. J App Cryst 26: 283–291.
[32]  Wei Z, Qi L, Jiang H (1997) Some convergence properties of descent methods. Journal of Optimization Theory and Applications 95: 177–188.

Full-Text

comments powered by Disqus