Structural insight with mutational impact on tyrosinase and PKC-β interaction from Homo sapiens : Molecular modeling and docking studies for melanogenesis, albinism and increased risk for melanoma

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 25, 403, 10.1016/S0022-2836(05)80360-2 Analysis Tool Web Services from the EMBL-EBI, 2013, 41, W597 Bagchi, 2014, Structural characterizations of metal ion binding transcriptional regulator CueR from opportunistic pathogen Pseudomonasaeruginosa to identify its possible involvements in virulence, Appl. Biochem. Biotechnol. Baker, 2001, Protein structure prediction and structural genomics, Science, 294, 93, 10.1126/science.1065659 Baldwin, 1996, How Hofmeister ion interactions affect protein stability, Biophys. J., 71, 2056, 10.1016/S0006-3495(96)79404-3 Banerjee, 2015, 404, 43 Banerjee, 2016, Molecular modeling, mutational analysis and conformational switching in IL27: an in silico structural insight towards AIDS research, Gene, 576, 72, 10.1016/j.gene.2015.09.075 Banerjee, 2016, An optimized in silico neuroinformatics approach: positive regulation via DNA interaction in cellular decisions for Arg to Ala mutation in SOX11, 802 Banerjee, 2016, Structural exploration and conformational transitions in MDM2 upon DHFR interaction from Homo sapiens: a computational outlook for malignancy via epigenetic disruption, Scientifica, 2016, 1, 10.1155/2016/9420692 Berman, 2000, The protein data bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 Bhattacharya, 2014, Hypoglycosylation of dystroglycan due to T192M mutation: a molecular insight behind the fact, Gene, 537, 108, 10.1016/j.gene.2013.11.071 Bin-Guang, 2007, What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms, J. Mol. Biol., 370, 439, 10.1016/j.jmb.2007.04.051 Brooks, 1983, CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J.Comp. Chem., 4, 187, 10.1002/jcc.540040211 Cartmill, 2011 Chen, 2003, ZDOCK: an initial-stage protein docking algorithms, Proteins, 51, 82 Colovos, 1993, Verification of protein structures: patterns of nonbonded atomic interactions, Protein Sci., 2, 1511, 10.1002/pro.5560020916 Comeau, 2004, ClusPro: an automated docking and discrimination method for the prediction of protein complexes, Bioinformatics, 20, 45, 10.1093/bioinformatics/btg371 DeLano, 2002 Eisenberg, 1997, VERIFY3D: assessment of protein models with three-dimensional profiles, Methods Enzymol., 277, 396, 10.1016/S0076-6879(97)77022-8 Fiser, 2003, ModLoop: automated modeling of loops in protein structures, Bioinformatics, 19, 2500, 10.1093/bioinformatics/btg362 George, 2002, An analysis of protein domain linkers: their classification and role in protein folding, Protein Eng., 15, 871, 10.1093/protein/15.11.871 Gerstein, 1992, A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites, Acta Cryst, A48, 271, 10.1107/S0108767391012680 Groves, 2001 Hee-Young, 1999, Protein kinase C-β activates tyrosinase by phosphorylating serine residues in its cytoplasmic domain, J. Biol. Chem., 274, 16470, 10.1074/jbc.274.23.16470 Huang, 2013, Allosite: a method for predicting allosteric sites, Bioinformatics, 29, 2357, 10.1093/bioinformatics/btt399 Huang, 2015, ASBench: benchmarking sets for allosteric discovery, Bioinformatics, 31, 2598, 10.1093/bioinformatics/btv169 Jian, 2011, Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling, Structure, 19, 1784, 10.1016/j.str.2011.09.022 Johannes, 2005, The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res., 33, W244, 10.1093/nar/gki408 Jones, 1998, Domain assignment for protein structures using a consensus approach: characterization and analysis, Protein Sci., 7, 233, 10.1002/pro.5560070202 Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymes, 22, 2577, 10.1002/bip.360221211 Kozakov, 2015, The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins, Nat. Protoc., 10, 733, 10.1038/nprot.2015.043 Krieger, 2003 Laskowski, 1993, PROCHECK: a program to check the stereochemistry of protein structures, J. Appl. Crystallogr., 26, 283, 10.1107/S0021889892009944 Mark, 2003, Application of the random coil index to studying protein flexibility, J. Biomol. NMR, 40, 31 Marti-Renom, 2000, Comparative protein structure modeling of genes and genomes, Annu. Rev. Biophys. Biomol. Struct., 29, 291, 10.1146/annurev.biophys.29.1.291 McWilliam, 2013, Analysis tool web services from the EMBL-EBI, Nucleic Acids Res., 41, W597, 10.1093/nar/gkt376 Olivares, 2009, New insights into the active site structure and catalytic mechanism of tyrosinase and its related proteins, Pigment Cell Melanoma Res., 22, 750, 10.1111/j.1755-148X.2009.00636.x Opara, 2010, Skin cancers in albinos in a teaching hospital in eastern Nigeria—presentation and challenges of care, World J. Surg. Oncol., 8, 73, 10.1186/1477-7819-8-73 Paul, 1993, Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation, Protein Sci., 2, 2050, 10.1002/pro.5560021206 Plonka, 2006, Melanin synthesis in microorganisms—biotechnological and medical aspects, Acta Biochim. Pol., 53, 429, 10.18388/abp.2006_3314 Punta, 2011, The Pfam protein families database, Nucleic Acids Res., 40, D290, 10.1093/nar/gkr1065 Ramachandran, 1968, Conformation of polypeptides and proteins, Adv. Protein Chem., 23, 283, 10.1016/S0065-3233(08)60402-7 Ramachandran, 2011, PROTEINS: structure, Funct. Bioinform., 79, 261, 10.1002/prot.22879 Ray, 2016, In silico perspective into interactions and mutations in human TLR4 and Ebola glycoprotein, 209 Richard, 2003, Comparison of the genomes of human and mouse lays the foundation of genome zoology, Hum. Mol. Genet., 12, 701, 10.1093/hmg/ddg078 Sali, 1993, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol., 234, 779, 10.1006/jmbi.1993.1626 Sander, 1991, Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins, 9, 56, 10.1002/prot.340090107 Scherer, 2010, Genetics of pigmentation in skin cancer—a review, Mutat. Res., 705, 141, 10.1016/j.mrrev.2010.06.002 Shen, 2016, ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks, Nucleic Acids Res., 44, D527, 10.1093/nar/gkv902 Simmosis, 2005, PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information, Nucleic Acid Res., 33, W289, 10.1093/nar/gki390 Tartaglia, 2008, Prediction of aggregation-prone regions in structured proteins, J. Mol. Biol., 380, 425, 10.1016/j.jmb.2008.05.013 Thompson, 1994, Nucl. Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Tina, 2007, PIC: protein interactions calculator, Nucleic Acids Res., 35, W473, 10.1093/nar/gkm423 Vakser, 1995, Protein docking for low-resolution structures, Protein Eng., 8, 371, 10.1093/protein/8.4.371 Weiderstein, 2007, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acid Residues, 35, W407, 10.1093/nar/gkm290 Wiederstein, 2004 Xiang, 2006, Advances in homology protein structure modeling, Curr. Protein Pept. Sci., 7, 217, 10.2174/138920306777452312 Xu, 2011, Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization, Biophys. J., 101, 2525, 10.1016/j.bpj.2011.10.024 Xu, 1999, Crystal structures of c-Src reveal features of its autoinhibitory mechanism, Mol.Cell., 3, 629, 10.1016/S1097-2765(00)80356-1 Yamaguchi, 2009, Physiological factors that regulate skin pigmentation, Biofactors, 35, 193, 10.1002/biof.29 Zhang, 2005, TM-align: a protein structure alignment algorithm based on TM-score, Nucleic Acids Res., 33, 2302, 10.1093/nar/gki524