234
Views
6
CrossRef citations to date
0
Altmetric
Articles

Tryptophan to Glycine mutation in the position 116 leads to protein aggregation and decreases the stability of the LITAF protein

, , &
Pages 1695-1709 | Received 12 Feb 2014, Accepted 18 Sep 2014, Published online: 13 Oct 2014

References

  • Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., … Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7, 248–249.10.1038/nmeth0410-248
  • Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17, 412–425.10.1002/(ISSN)1097-0134
  • Amberger, J., Bocchini, C. A., Scott, A. F., & Hamosh, A. (2009). McKusick’s online mendelian inheritance in man (OMIM(R)). Nucleic Acids Research, 37, D793–D796.10.1093/nar/gkn665
  • Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F. V., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In B. Pullman (Ed.), Intermolecular forces (pp. 331–342). Dordrecht: D. Riedel.10.1007/978-94-015-7658-1
  • Buchthal, F., & Behse, F. (1977). Peroneal muscular atrophy (PMA) and related disorders. Brain, 100, 41–66.10.1093/brain/100.1.41
  • Calabrese, R., Capriotti, E., Fariselli, P., Martelli, P. L., & Casadio, R. (2009). Functional annotations improve the predictive score of human disease-related mutations in proteins. Human Mutation, 30, 1237–1244.10.1002/humu.v30:8
  • Campbell, R., Dorey, H., Naegeli, M., Grubstein, L. K., Bennett, K. K., Bonter, F., … Davidson, W. S. (2004). An empowerment evaluation model for sexual assault programs: Empirical evidence of effectiveness. American Journal of Community Psychology, 34, 251–262.10.1007/s10464-004-7418-0
  • Capriotti, E., Fariselli, P., Rossi, I., & Casadio, R. (2008). A three state prediction of single point mutations on protein stability changes. BMC Bioinformatics, 9, S6.10.1186/1471-2105-9-S2-S6
  • Carvalho, M. A., Marsillac, S. M., Karchin, R., Manoukian, S., Grist, S., Swaby, R. F., … Monteiro, A. N. (2007). Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Research, 67, 1494–1501.10.1158/0008-5472.CAN-06-3297
  • Carvalho, M., Pino, M. A., Karchin, R., Beddor, J., Godinho-Netto, M., Mesquita, R. D., … Billack, B. (2009). Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 660, 1–11.10.1016/j.mrfmmm.2008.09.017
  • Dixit, A., Torkamani, A., Schork, N. J., & Verkhivker, G. (2009). Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: The impact on protein structure, dynamics, and stability. Biophysical Journal, 96, 858–874.10.1016/j.bpj.2008.10.041
  • Dyck, P. J., & Lambert, E. H. (1968). Lower motor and primary sensory neuron diseases with peroneal muscular atrophy. Archives of Neurology, 18, 603–618.10.1001/archneur.1968.00470360025002
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103, 8577–8593.10.1063/1.470117
  • Eswar, N., Marti-Renom, M. A., Webb, B., Madhusudhan, M. S., Eramian, D., Shen, M., … Sali, A. (2006). Comparative protein structure modeling with MODELLER. Current Protocols in Bioinformatics, 15, 5.6.1–5.6.30.
  • Gerding, W. M., Koetting, J., Epplen, J. T., & Neusch, C. (2009). Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF. Neuromuscular Disorders, 19, 701–703.10.1016/j.nmd.2009.05.006
  • Goldgar, D. E., Easton, D. F., Deffenbaugh, A. M., Monteiro, A. N., Tavtigian, S. V., & Couch, F. J. (2004). Integrated evaluation of DNA sequence variants of unknown clinical significance: Application to BRCA1 and BRCA2. The American Journal of Human Genetics, 75, 535–544.10.1086/424388
  • Grossfield, A., Feller, S. E., & Pitman, M. C. (2006). A role for direct interactions in the modulation of rhodopsin by ω-3 polyunsaturated lipids. Proceedings of the National Academy of Sciences, 103, 4888–4893.10.1073/pnas.0508352103
  • Grossfield, A., Feller, S. E., & Pitman, M. C. (2007). Convergence of molecular dynamics simulations of membrane proteins. Proteins: Structure, Function, and Bioinformatics, 67, 31–40.10.1002/prot.21308
  • Grossfield, A., & Zuckerman, D. M. (2009). Quantifying uncertainty and sampling quality in biomolecular simulations. Annual reports in computational chemistry, 5, 23–48.10.1016/S1574-1400(09)00502-7
  • Gunsteren, W. F. V., Billeter, S. R., Eising, A. A., Hunenberger, P. H., Kruger, P. K., Mark, A. E., … Tironi, I. G. (1996). Biomolecular simulation: The GROMOS96 manual and user guide (pp. 1–1024). Zurich: Verlag der Fachvereine.
  • Guo, J., Ning, L., Ren, H., Liu, H., & Yao, X. (2012). Influence of the pathogenic mutations T188K/R/A on the structural stability and misfolding of human prion protein: Insight from molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) – General Subjects, 1820, 116–123.10.1016/j.bbagen.2011.11.013
  • Harding, A. E., & Thomas, P. K. (1980). The clinical features of hereditary motor and sensory neuropathy types I and II. Brain, 103, 259–280.10.1093/brain/103.2.259
  • Henne, W. M., Buchkovich, N. J., & Emr, S. D. (2011). The ESCRT pathway. Developmental Cell, 21, 77–91.10.1016/j.devcel.2011.05.015
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.10.1002/(ISSN)1096-987X
  • Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.10.1021/ct700301q
  • Hicks, S., Wheeler, D. A., Plon, S. E., & Kimmel, M. (2011). Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Human Mutation, 32, 661–668.10.1002/humu.21490
  • Karchin, R. (2009). Next generation tools for the annotation of human SNPs. Briefings in Bioinformatics, 10, 35–52.
  • Katzmann, D. J., Odorizzi, G., & Emr, S. D. (2002). Receptor downregulation and multivesicular-body sorting. Nature Reviews Molecular Cell Biology, 3, 893–905.10.1038/nrm973
  • Klose, D. P., Wallace, B. A., & Janes, R. W. (2010). 2Struc: The secondary structure server. Bioinformatics, 26, 2624–2625.10.1093/bioinformatics/btq480
  • Kumar, P., Henikoff, S., & Ng, P. C. (2009). Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols, 4, 1073–1081.10.1038/nprot.2009.86
  • Laskowski, R. A. (1997). PDBsum: A web-based database of summaries and analyses of all PDB structures. Trends in Biochemical Sciences, 22, 488–490.10.1016/S0968-0004(97)01140-7
  • Latour, P., Gonnaud, P. M., Ollagnon, E., Chan, V., Perelman, S., Stojkovic, T., … Maire, I. (2006). SIMPLE mutation analysis in dominant demyelinating Charcot–Marie–Tooth disease: Three novel mutations. Journal of the Peripheral Nervous System, 11, 148–155.10.1111/jns.2006.11.issue-2
  • Lee, S. M., Chin, L. S., & Li, L. (2012). Charcot–Marie–Tooth disease-linked protein SIMPLE functions with the ESCRT machinery in endosomal trafficking. Journal of Cell Biology, 199, 799–816.
  • Lee, S. M., Olzmann, J. A., Chin, L.-S., & Li, L. (2011). Mutations associated with Charcot–Marie–Tooth disease cause SIMPLE protein mislocalization and degradation by the proteasome and aggresome–autophagy pathways. Journal of Cell Science, 124, 3319–3331.10.1242/jcs.087114
  • Li, B., Krishnan, V. G., Mort, M. E., Xin, F., Kamati, K. K., Cooper, D. N., … Radivojac, P. (2009). Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics, 25, 2744–2750.10.1093/bioinformatics/btp528
  • Lupski, J. R. (1998). Charcot–Marie–Tooth disease: Lessons in genetic mechanisms. Molecular Medicine, 4, 3–11.
  • Lupski, J. R., de Oca-Luna, R., Slaugenhaupt, S., Pentao, L., Guzzetta, V., Trask, B. J., … Patel, P. I. (1991). DNA duplication associated with Charcot–Marie–Tooth disease type 1A. Cell, 66, 219–232.10.1016/0092-8674(91)90613-4
  • Matsunami, N., Smith, B., Ballard, L., William Lensch, M., Robertson, M., Albertsen, H., … Chance, P. F. (1992). Peripheral myelin protein-22 gene maps in the duplication in chromosome 17p11.2 associated with Charcot–Marie–Tooth 1A. Nature Genetics, 1, 176–179.10.1038/ng0692-176
  • Moriwaki, Y., Begum, N. A., Kobayashi, M., Matsumoto, M., Toyoshima, K., & Seya, T. (2001). Mycobacterium bovis Bacillus Calmette-Guerin and its cell wall complex induce a novel lysosomal membrane protein, SIMPLE, that bridges the missing link between lipopolysaccharide and p53-inducible gene, LITAF(PIG7), and estrogen-inducible gene, EET-1. Journal of Biological Chemistry, 276, 23065–23076.10.1074/jbc.M011660200
  • Oostenbrink, C., Villa, A., Mark, A. E., & Gunsteren, W. F. V. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25, 1656–1676.10.1002/(ISSN)1096-987X
  • Patel, P. I., Roa, B. B., Welcher, A. A., Schoener-Scott, R., Trask, B. J., Pentao, L., … Suter, U. (1992). The gene for the peripheral myelin protein PMP-22 is a candidate for Charcot–Marie–Tooth disease type 1A. Nature Genetics, 1, 159–165.10.1038/ng0692-159
  • Raeymaekers, P., Timmerman, V., Nelis, E., De Jonghe, P., Hoogenduk, J. E., Baas, F., … Van Broeckhoven, C. (1991). Duplication in chromosome 17p11.2 in Charcot–Marie–Tooth neuropathy type 1a (CMT 1a). Neuromuscular Disorders, 1, 93–97.10.1016/0960-8966(91)90055-W
  • Roxrud, I., Stenmark, H., & Malerød, L. (2010). ESCRT & Co. Biology of the Cell, 102, 293–318.10.1042/BC20090161
  • Saifi, G. M., Szigeti, K., Wiszniewski, W., Shy, M. E., Krajewski, K., Hausmanowa-Petrusewicz, I., … Lupski, J. R. (2005). SIMPLE mutations in Charcot–Marie–Tooth disease and the potential role of its protein product in protein degradation. Human Mutation, 25, 372–383.10.1002/humu.v25:4
  • Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M., & Sirotkin, K. (2001). dbSNP: The NCBI database of genetic variation. Nucleic Acids Research, 29, 308–311.10.1093/nar/29.1.308
  • Skre, H. (1974). Genetic and clinical aspects of Charcot–Marie–Tooth’s disease. Clinical Genetics, 6, 98–118.
  • Street, V. A., Bennett, C. L., Goldy, J. D., Shirk, A. J., Kleopa, K. A., Tempel, B. L., … Chance, P. F. (2003). Mutation of a putative protein degradation gene LITAF/SIMPLE in Charcot–Marie–Tooth disease 1C. Neurology, 60, 22–26.10.1212/WNL.60.1.22
  • Thusberg, J., & Vihinen, M. (2009). Pathogenic or not? and if so, then how? Studying the effects of missense mutations using bioinformatics methods. Human Mutation, 30, 703–714.10.1002/humu.v30:5
  • Timmerman, V., Nelis, E., Van Hul, W., Nieuwenhuijsen, B. W., Chen, K. L., Wang, S., … Van Broeckhoven, C. (1992). The peripheral myelin protein gene PMP-22 is contained within the Charcot–Marie–Tooth disease type 1A duplication. Nature Genetics, 1, 171–175.10.1038/ng0692-171
  • Turner, P. J. (2005). XMGRACE, Version 5.1.19. Beaverton, OR: Central for costal and Land-Margin Research; Oregon Graduate Institute of Science and Technology.
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.10.1002/(ISSN)1096-987X
  • Vinay Kumar, C., Kumar, K. M., Swetha, R., Ramaiah, S., & Anbarasu, A. (2014). Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis. Journal of Theoretical Biology, 354, 72–80.10.1016/j.jtbi.2014.03.027
  • Warner, L. E., Mancias, P., Butler, I. J., McDonald, C. M., Keppen, L., Koob, K., & Lupski, J. R. (1998). Mutations in the early growth response 2 (EGR2) gene are associated with hereditary myelinopathies. Nature Genetics, 18, 382–384.10.1038/ng0498-382
  • Warner, L. E., Roa, B. B., & Lupski, J. R. (1996). Absence ofPMP22 coding region mutations in CMT1A duplication patients: Further evidence supporting gene dosage as a mechanism for charcot-marie-tooth disease type 1A. Human Mutation, 8, 362–365.10.1002/(ISSN)1098-1004
  • Waterman, H., & Yarden, Y. (2001). Molecular mechanisms underlying endocytosis and sorting of ErbB receptor tyrosine kinases. FEBS Letters, 490, 142–152.10.1016/S0014-5793(01)02117-2
  • Wu, X., Yang, G., Zu, Y., Fu, Y., Zhou, L., & Yuan, X. (2011). The Trp-cage miniprotein with single-site mutations: Studies of stability and dynamics using molecular dynamics. Computational and Theoretical Chemistry, 973, 1–8.10.1016/j.comptc.2011.06.018
  • Zhang, K. H., Li, Z., Lei, J., Pang, T., Xu, B., Jiang, W. Y., & Li, H. Y. (2011). Oculocutaneous Albinism type 3 (OCA3): Analysis of two novel mutations in TYRP1 gene in two Chinese patients. Cell Biochemistry and Biophysics, 61, 523–529.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.