- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 697051, 13 pages
In Silico Screening and Molecular Dynamics Simulation of Disease-Associated nsSNP in TYRP1 Gene and Its Structural Consequences in OCA3
1School of Bio Sciences and Technology (SBST), Bioinformatics Division, Vellore Institute of Technology University, Vellore, Tamil Nadu 632014, India
2Human Genetics Foundation, Torino, Via Nizza 52, 10126 Torino, Italy
Received 20 April 2013; Revised 23 May 2013; Accepted 23 May 2013
Academic Editor: Claudio M. Soares
Copyright © 2013 Balu Kamaraj and Rituraj Purohit. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- V. V. V. S. Murty, B. Bouchard, S. Mathew, S. Vijayasaradhi, and A. N. Houghton, “Assignment of the human TYRP (brown) locus to chromosome region 9p23 by nonradioactive in situ hybridization,” Genomics, vol. 13, no. 1, pp. 227–229, 1992.
- S. Shibahara, H. Taguchi, R. M. Muller et al., “Structural organization of the pigment cell-specific gene located at the brown locus in mouse: its promoter activity and alternatively spliced transcripts,” The Journal of Biological Chemistry, vol. 266, no. 24, pp. 15895–15901, 1991.
- R. A. Sturm, B. J. O'Sullivan, N. F. Box et al., “Chromosomal structure of the human TYRP1 and TYRP2 loci and comparison of the tyrosinase-related protein gene family,” Genomics, vol. 29, no. 1, pp. 24–34, 1995.
- N. F. Box, J. R. Wyeth, C. J. Mayne, L. E. O'Gorman, N. G. Martin, and R. A. Sturm, “Complete sequence and polymorphism study of the human TYRP1 gene encoding tyrosinase-related protein 1,” Mammalian Genome, vol. 9, no. 1, pp. 50–53, 1998.
- S. Vijayasaradhi, P. M. Doskoch, and A. N. Houghton, “Biosynthesis and intracellular movement of the melanosomal membrane glycoprotein gp75, the human b (Brown) locus product,” Experimental Cell Research, vol. 196, no. 2, pp. 233–240, 1991.
- R. Halaban and G. Moellmann, “Murine and human b locus pigmentation genes encode a glycoprotein (gp75) with catalase activity,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4809–4813, 1990.
- G. Prota, Melanins and Melanogenesis, Academic Press, New York, NY, USA, 1992.
- V. J. Hearing Jr., “Mammalian monophenol monooxygenase (tyrosinase): purification, properties, and reactions catalyzed,” Methods in Enzymology, vol. 142, pp. 154–165, 1987.
- G. Prota, “Some new aspects of eumelanin chemistry,” Progress in Clinical and Biological Research, vol. 256, pp. 101–124, 1988.
- S. Alonso, N. Izagirre, I. Smith-Zubiaga et al., “Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans,” BMC Evolutionary Biology, vol. 8, no. 1, article 74, 2008.
- S. Ito, “A chemist's view of melanogenesis,” Pigment Cell Research, vol. 16, no. 3, pp. 230–236, 2003.
- C. Jiménez-Cervantes, F. Solano, T. Kobayashi et al., “A new enzymatic function in the melanogenic pathway. The 5,6- dihydroxyindole-2-carboxylic acid oxidase activity of tyrosinase-related protein-1 (TRP1),” The Journal of Biological Chemistry, vol. 269, no. 27, pp. 17993–18000, 1994.
- T. Kobayashi, K. Urabe, A. Winder et al., “Tyrosinase related protein 1 (TRP1) functions as a DHICA oxidase in melanin biosynthesis,” The EMBO Journal, vol. 13, no. 24, pp. 5818–5825, 1994.
- T. Kobayashi, W. D. Vieira, B. Potterf, C. Sakai, G. Imokawa, and V. J. Hearing, “Modulation of melanogenic protein expression during the switch from eu- to pheomelanogenesis,” Journal of Cell Science, vol. 108, no. 6, pp. 2301–2309, 1995.
- T. Kobayashi, G. Imokawa, D. C. Bennett, and V. J. Hearing, “Tyrosinase stabilization by Tyrp1 (the brown locus protein),” The Journal of Biological Chemistry, vol. 273, no. 48, pp. 31801–31805, 1999.
- T. Hirobe and H. Abe, “Genetic and epigenetic control of the proliferation and differentiation of mouse epidermal melanocytes in culture,” Pigment Cell Research, vol. 12, no. 3, pp. 147–163, 1999.
- R. Johnson and I. J. Jackson, “Light is a dominant mouse mutation resulting in premature cell death,” Nature Genetics, vol. 1, no. 3, pp. 226–229, 1992.
- D. Fang, Y. Tsuji, and V. Setaluri, “Selective down-regulation of tyrosinase family gene TYRP1 by inhibition of the activity of melanocyte transcription factor, MITF,” Nucleic Acids Research, vol. 30, no. 14, pp. 3096–3106, 2002.
- R. Sarangarajan and R. E. Boissy, “Tyrp1 and oculocutaneous albinism type 3,” Pigment Cell Research, vol. 14, no. 6, pp. 437–444, 2001.
- R. E. Boissy, C. Sakai, H. Zhao, T. Kobayashi, and V. J. Hearing, “Human tyrosinase related protein-1 (TRP-1) does not function as a DHICA oxidase activity in contrast to murine TRP-1,” Experimental Dermatology, vol. 7, no. 4, pp. 198–204, 1998.
- H. Zhao, Y. Zhao, J. J. Nordlund, and R. E. Boissy, “Human TRP-1 has tyrosine hydroxylase but no dopa oxidase activity,” Pigment Cell Research, vol. 7, no. 3, pp. 131–140, 1994.
- K. Urabe, P. Aroca, and V. J. Hearing, “From gene to protein: determination of melanin synthesis,” Pigment Cell Research, vol. 6, no. 4, pp. 186–192, 1993.
- C. Olivares, C. Jiménez-Cervantes, J. A. Lozano, F. Solano, and J. C. García-Borrón, “The 5,6-dihydroxyindole-2-carboxylic acid (DHICA) oxidase activity of human tyrosinase,” Biochemical Journal, vol. 354, no. 1, pp. 131–139, 2001.
- P. Manga, K. Sato, L. Ye, F. Beermann, M. Lynn Lamoreux, and S. J. Orlow, “Mutational analysis of the modulation of tyrosinase by tyrosinase-related proteins 1 and 2 in vitro,” Pigment Cell Research, vol. 13, no. 5, pp. 364–374, 2000.
- M. A. Carvalho, S. M. Marsillac, R. Karchin et al., “Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis,” Cancer Research, vol. 67, no. 4, pp. 1494–1501, 2007.
- M. Carvalho, M. A. Pino, R. Karchin et al., “Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1,” Mutation Research, vol. 660, no. 1-2, pp. 1–11, 2009.
- D. E. Goldgar, D. F. Easton, A. M. Deffenbaugh, A. N. A. Monteiro, S. V. Tavtigian, and F. J. Couch, “Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2,” American Journal of Human Genetics, vol. 75, no. 4, pp. 535–544, 2004.
- R. Karchin, “Next generation tools for the annotation of human SNPs,” Briefings in Bioinformatics, vol. 10, no. 1, pp. 35–52, 2009.
- K. Balu and R. Purohit, “Mutational analysis of TYR gene and its structural consequences in OCA1A,” Gene, vol. 513, no. 1, pp. 184–195, 2013.
- R. Purohit, V. Rajendran, and R. Sethumadhavan, “Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis,” Journal of Molecular Modeling, vol. 17, no. 4, pp. 869–877, 2011.
- R. Purohit, V. Rajendran, and R. Sethumadhavan, “Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants,” Journal of Biomolecular Structure and Dynamics, vol. 29, no. 1, pp. 137–152, 2011.
- A. Kumar, V. Rajendran, R. Sethumadhavan, and R. Purohit, “In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ),” FEBS Open Biology, vol. 2, pp. 285–293, 2012.
- A. Kumar, V. Rajendran, R. Sethumadhavan, and R. Purohit, “Relationship between a point mutation S97C in CK1δ protein and its affect on ATP-binding affinity,” Journal of Biomolecular Structure & Dynamics, 2013.
- V. Rajendran and R. Sethumadhavan, “Drug resistance mechanism of PncA in Mycobacterium tuberculosis,” Journal of Biomolecular Structure and Dynamics, 2013.
- V. Rajendran, R. Purohit, and R. Sethumadhavan, “In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein,” Amino Acids, vol. 43, no. 2, pp. 603–615, 2012.
- K. Balu and R. Purohit, “In-silico analysis of Betaine Aldehyde Dehydrogenase2 of Oryza sativa and significant mutations responsible for fragrance,” Journal of Plant Interactions, pp. 1–13, 2012.
- K. Balu, V. Rajendran, R. Sethumadhavan, and R. Purohit, “Investigation of binding phenomenon of NSP3 and p130Cas mutants and their effect on cell signalling,” Cell Biochemistry and Biophysics, pp. 1–11, 2013.
- I. A. Adzhubei, S. Schmidt, L. Peshkin et al., “A method and server for predicting damaging missense mutations,” Nature Methods, vol. 7, no. 4, pp. 248–249, 2010.
- P. Kumar, S. Henikoff, and P. C. Ng, “Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm,” Nature Protocols, vol. 4, no. 7, pp. 1073–1082, 2009.
- E. Capriotti, P. Fariselli, I. Rossi, and R. Casadio, “A three-state prediction of single point mutations on protein stability changes,” BMC Bioinformatics, vol. 9, no. 2, article S6, 2008.
- P. D. Thomas, M. J. Campbell, A. Kejariwal et al., “PANTHER: a library of protein families and subfamilies indexed by function,” Genome Research, vol. 13, no. 9, pp. 2129–2141, 2003.
- E. Capriotti, R. Calabrese, and R. Casadio, “Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information,” Bioinformatics, vol. 22, no. 22, pp. 2729–2734, 2006.
- R. Calabrese, E. Capriotti, P. Fariselli, P. L. Martelli, and R. Casadio, “Functional annotations improve the predictive score of human disease-related mutations in proteins,” Human Mutation, vol. 30, no. 8, pp. 1237–1244, 2009.
- C. Ferrer-Costa, J. L. Gelpí, L. Zamakola, I. Parraga, X. de la Cruz, and M. Orozco, “PMUT: a web-based tool for the annotation of pathological mutations on proteins,” Bioinformatics, vol. 21, no. 14, pp. 3176–3178, 2005.
- B. Li, V. G. Krishnan, M. E. Mort et al., “Automated inference of molecular mechanisms of disease from amino acid substitutions,” Bioinformatics, vol. 25, no. 21, pp. 2744–2750, 2009.
- J. Amberger, C. A. Bocchini, A. F. Scott, and A. Hamosh, “McKusick's Online Mendelian Inheritance in Man (OMIM®),” Nucleic Acids Research, vol. 37, no. 1, pp. D793–D796, 2009.
- S. T. Sherry, M.-H. Ward, M. Kholodov et al., “DbSNP: the NCBI database of genetic variation,” Nucleic Acids Research, vol. 29, no. 1, pp. 308–311, 2001.
- Y. L. Yip, H. Scheib, A. V. Diemand et al., “The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants,” Human Mutation, vol. 23, no. 5, pp. 464–470, 2004.
- Y. L. Yip, M. Famiglietti, A. Gos et al., “Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase,” Human Mutation, vol. 29, no. 3, pp. 361–366, 2008.
- B. Boeckmann, A. Bairoch, R. Apweiler et al., “The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003,” Nucleic Acids Research, vol. 31, no. 1, pp. 365–370, 2003.
- W. Kaplan and T. G. Littlejohn, “Swiss-PDB viewer (Deep View),” Briefings in Bioinformatics, vol. 2, no. 2, pp. 195–197, 2001.
- B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GRGMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation,” Journal of Chemical Theory and Computation, vol. 4, no. 3, pp. 435–447, 2008.
- Y. Zhang, “I-TASSER server for protein 3D structure prediction,” BMC Bioinformatics, vol. 9, article 40, 2008.
- R. A. Laskowski, J. A. C. Rullmann, M. W. MacArthur, R. Kaptein, and J. M. Thornton, “AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR,” Journal of Biomolecular NMR, vol. 8, no. 4, pp. 477–486, 1996.
- M. Wiederstein and M. J. Sippl, “ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins,” Nucleic Acids Research, vol. 35, pp. W407–W410, 2007.
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984.
- T. E. Cheatham III, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman, “Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins,” Journal of the American Chemical Society, vol. 117, no. 14, pp. 4193–4194, 1995.
- P. J. Turner, XMGRACE, Version 5.1.19, Center For Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology, Beaverton, Ore, USA, 2005.
- A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, “Essential dynamics of proteins,” Proteins: Structure, Function and Genetics, vol. 17, no. 4, pp. 412–425, 1993.
- J. Thusberg and M. Vihinen, “Pathogenic or not? and if so, then how? Studying the effects of missense mutations using bioinformatics methods,” Human Mutation, vol. 30, no. 5, pp. 703–714, 2009.
- S. Hicks, D. A. Wheeler, S. E. Plon, and M. Kimmel, “Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed,” Human Mutation, vol. 32, no. 6, pp. 661–668, 2011.
- K.-H. Zhang, Z. Li, J. Lei et al., “Oculocutaneous Albinism type 3 (OCA3): analysis of two novel mutations in TYRP1 gene in two Chinese patients,” Cell Biochemistry and Biophysics, vol. 61, no. 3, pp. 523–529, 2011.
- D. R. Livesay, S. Dallakyan, G. G. Wood, and D. J. Jacobs, “A flexible approach for understanding protein stability,” FEBS Letters, vol. 576, no. 3, pp. 468–476, 2004.
- D. Verma, D. J. Jacobs, and D. R. Livesay, “Changes in lysozyme flexibility upon mutation are frequent, large and long-ranged,” PLoS Computational Biology, vol. 8, no. 3, Article ID 100240, 2012.
- A. A. Ribeiro and R. B. de Alencastro, “Mixed Monte Carlo/molecular dynamics simulations of the prion protein,” Journal of Molecular Graphics and Modelling, vol. 42, pp. 1–6, 2013.
- W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers, vol. 22, no. 12, pp. 2577–2637, 1983.
- D. R. Simeonov, X. Wang, C. Wang, et al., “DNA variations in oculocutaneous Albinism: an updated mutation List and current outstanding issues in molecular diagnostics,” Human Mutation, vol. 34, no. 6, pp. 827–835, 2013.