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Proteomic Tools for the Analysis of Cytoskeleton Proteins

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Cytoskeleton Methods and Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1365))

Abstract

Proteomic analyses have become an essential part of the toolkit of the molecular biologist, given the widespread availability of genomic data and open source or freely accessible bioinformatics software. Tools are available for detecting homologous sequences, recognizing functional domains, and modeling the three-dimensional structure for any given protein sequence. Although a wealth of structural and functional information is available for a large number of cytoskeletal proteins, with representatives spanning all of the major subfamilies, the majority of cytoskeletal proteins remain partially or totally uncharacterized. Moreover, bioinformatics tools provide a means for studying the effects of synthetic mutations or naturally occurring variants of these cytoskeletal proteins. This chapter discusses various freely available proteomic analysis tools, with a focus on in silico prediction of protein structure and function. The selected tools are notable for providing an easily accessible interface for the novice, while retaining advanced functionality for more experienced computational biologists.

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References

  1. Pettersen EF et al (2004) UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612

    Article  CAS  PubMed  Google Scholar 

  2. Benson DA et al (2014) GenBank. Nucleic Acids Res 41:D36

    Article  Google Scholar 

  3. Kulikova T et al (2007) EMBL nucleotide sequence database in 2006. Nucleic Acids Res 35(Database issue):D16–D20

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Tateno Y et al (2002) DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res 30(1):27–30

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Pruitt KD et al (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 42(Database issue):D756–D763

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. UniProt C (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42(Database issue):D191–D198

    Google Scholar 

  7. Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  8. Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Web Server issue):W29–W37

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Sievers F et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539

    Article  PubMed Central  PubMed  Google Scholar 

  11. Di Tommaso P et al (2011) T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res 39(Web Server issue):W13–W17

    Article  PubMed Central  PubMed  Google Scholar 

  12. Katoh K et al (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Do CB et al (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15(2):330–340

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. de Castro E et al (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34(Web Server issue):W362–W365

    Article  PubMed Central  PubMed  Google Scholar 

  16. Jonassen I, Collins JF, Higgins DG (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci 4(8):1587–1595

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Finn RD et al (2014) Pfam: the protein families database. Nucleic Acids Res 42(Database issue):D222–D230

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Geer LY et al (2002) CDART: protein homology by domain architecture. Genome Res 12(10):1619–1623

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Schultz J et al (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28(1):231–234

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Letunic I, Doerks T, Bork P (2014) SMART: recent updates, new developments and status in 2015. Nucleic Acids Res 43:D257

    Article  PubMed Central  PubMed  Google Scholar 

  21. Biegert A, Soding J (2008) De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics 24(6):807–814

    Article  CAS  PubMed  Google Scholar 

  22. George RA, Heringa J (2000) The REPRO server: finding protein internal sequence repeats through the Web. Trends Biochem Sci 25(10):515–517

    Article  CAS  PubMed  Google Scholar 

  23. Buchan DW et al (2013) Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res 41(Web Server issue):W349–W357

    Article  PubMed Central  PubMed  Google Scholar 

  24. Kallberg M et al (2012) Template-based protein structure modeling using the RaptorX web server. Nat Protoc 7(8):1511–1522

    Article  CAS  PubMed  Google Scholar 

  25. Yang J et al (2015) The I-TASSER Suite: Protein structure and function prediction. Nature Methods 12: 7–8

    Google Scholar 

  26. Berman HM, The Protein Data Bank et al (2000) Nucleic Acids Res 28(1):235–242

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Moult J (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 15(3):285–289

    Article  CAS  PubMed  Google Scholar 

  28. John B, Sali A (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 31(14):3982–3992

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Fernandez-Fuentes N et al (2007) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 23(19):2558–2565

    Article  CAS  PubMed  Google Scholar 

  30. Sali A et al (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23(3):318–326

    Article  CAS  PubMed  Google Scholar 

  31. Eisenberg D, Luthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404

    Article  CAS  PubMed  Google Scholar 

  32. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(Web Server issue):W407–W410

    Article  PubMed Central  PubMed  Google Scholar 

  33. Laskowski RA et al (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J App Cryst 26:283–291

    Article  CAS  Google Scholar 

  34. Lane L et al (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acids Res 40(Database issue):D76–D83

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Barker WC et al (2001) Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Res 29(1):29–32

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Biegert A, Soding J (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci U S A 106(10):3770–3775

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Remmert M et al (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9(2):173–175

    Article  CAS  Google Scholar 

  38. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85(8):2444–2448

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  39. Bawono P, Heringa J (2014) PRALINE: a versatile multiple sequence alignment toolkit. Methods Mol Biol 1079:245–262

    Article  CAS  PubMed  Google Scholar 

  40. Sadreyev RI et al (2009) COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res 37(Web Server issue):W90–W94

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Pei J, Grishin NV (2014) PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol 1079:263–271

    Article  PubMed Central  PubMed  Google Scholar 

  42. Chikkagoudar S, Roshan U, Livesay D (2007) eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. Nucleic Acids Res 35(Web Server issue):W675–W677

    Article  PubMed Central  PubMed  Google Scholar 

  43. Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36(Web Server issue):W197–W201

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Petersen B et al (2009) A generic method for assignment of reliability scores applied to solvent accessibility predictions. BMC Struct Biol 9:51

    Article  PubMed Central  PubMed  Google Scholar 

  45. Yachdav G et al (2014) PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res 42(Web Server issue):W337–W343

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Pollastri G, McLysaght A (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 21(8):1719–1720

    Article  CAS  PubMed  Google Scholar 

  47. Geourjon C, Deleage G (1995) SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11(6):681–684

    CAS  PubMed  Google Scholar 

  48. Crooks GE et al (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  49. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40

    Article  Google Scholar 

  50. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue):W244–W248

    Article  PubMed Central  PubMed  Google Scholar 

  51. Wu S, Zhang Y (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35(10):3375–3382

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Bennett-Lovsey RM et al (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70(3):611–625

    Article  CAS  PubMed  Google Scholar 

  53. Lobley A, Sadowski MI, Jones DT (2009) pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics 25(14):1761–1767

    Article  CAS  PubMed  Google Scholar 

  54. Shi J, Blundell TL, Mizuguchi K (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310(1):243–257

    Article  CAS  PubMed  Google Scholar 

  55. Yang Y et al (2011) Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics 27(15):2076–2082

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  56. McGuffin LJ, Buenavista MT, Roche DB (2013) The ModFOLD4 server for the quality assessment of 3D protein models. Nucleic Acids Res 41(Web Server issue):W368–W372

    Article  PubMed Central  PubMed  Google Scholar 

  57. Benkert P, Kunzli M, Schwede T (2009) QMEAN server for protein model quality estimation. Nucleic Acids Res 37(Web Server issue):W510–W514

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  58. Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57(4):702–710

    Article  CAS  PubMed  Google Scholar 

  59. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66(4):778–795

    Article  CAS  PubMed  Google Scholar 

  60. Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12(5):1073–1086

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  61. Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15(11):2507–2524

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  62. Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42(Web Server issue):W320–W324

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Stivala A et al (2011) Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics 27(23):3315–3316

    Article  CAS  PubMed  Google Scholar 

  64. Waterhouse AM et al (2009) Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Biochemistry Program, The Graduate Center, City University of New York, New York, NY, USA

    Mary Ellen Heavner & Shaneen Singh

  2. Department of Biology, Brooklyn College, City University of New York, 209 Ingersoll Hall Extension, 2900 Bedford Ave., Brooklyn, NY, 11210, USA

    Shaneen Singh

  3. Biology Program, The Graduate Center, City University of New York, New York, NY, USA

    Michael Scarpati, Eliza Wiech & Shaneen Singh

Authors
  1. Michael Scarpati
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  2. Mary Ellen Heavner
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  3. Eliza Wiech
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  4. Shaneen Singh
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Corresponding author

Correspondence to Shaneen Singh .

Editor information

Editors and Affiliations

  1. Brooklyn College, Brooklyn, New York, USA

    Ray H. Gavin

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Scarpati, M., Heavner, M.E., Wiech, E., Singh, S. (2016). Proteomic Tools for the Analysis of Cytoskeleton Proteins. In: Gavin, R. (eds) Cytoskeleton Methods and Protocols. Methods in Molecular Biology, vol 1365. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3124-8_23

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  • DOI: https://doi.org/10.1007/978-1-4939-3124-8_23

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3123-1

  • Online ISBN: 978-1-4939-3124-8

  • eBook Packages: Springer Protocols

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