Proteomic Tools for the Analysis of Cytoskeleton Proteins.
Comparative modeling
Docking analysis
Homology modeling
Multiple sequence alignment
Protein domains
Protein-protein interactions
Proteomics
Secondary structure prediction
Sequence similarity
Structure analysis
Threading
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
20
9
2021
pubmed:
21
9
2021
medline:
8
1
2022
Statut:
ppublish
Résumé
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, as well as for predicting interactions with other proteins or macromolecules. Although a wealth of structural and functional information is available for many 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.
Identifiants
pubmed: 34542864
doi: 10.1007/978-1-0716-1661-1_19
doi:
Substances chimiques
Cytoskeletal Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
363-425Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Pettersen EF et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612
pubmed: 15264254
doi: 10.1002/jcc.20084
The PyMOL Molecular Graphics System, Version 2.4, Schrödinger, LLC
Webb B, Sali A (2016) Comparative protein structure modeling using modeller. Curr Protoc Bioinformatics 54:5.6.1–5.6.37
doi: 10.1002/cpbi.3
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
pubmed: 11752245
pmcid: 99140
doi: 10.1093/nar/30.1.27
Kulikova T et al (2007) EMBL nucleotide sequence database in 2006. Nucleic Acids Res 35(Database issue):D16–D20
pubmed: 17148479
doi: 10.1093/nar/gkl913
Benson DA et al (2014) GenBank. Nucleic Acids Res 41:D36
doi: 10.1093/nar/gks1195
UniProt C (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42(Database issue):D191–D198
MacDougall A et al (2020) UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinformatics 36(17):4643–4648. https://doi.org/10.1093/bioinformatics/btaa485
doi: 10.1093/bioinformatics/btaa485
pubmed: 32399560
pmcid: 7750954
Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
pubmed: 2231712
pmcid: 2231712
doi: 10.1016/S0022-2836(05)80360-2
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
pubmed: 9254694
pmcid: 9254694
doi: 10.1093/nar/25.17.3389
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Web Server issue):W29–W37
pubmed: 21593126
pmcid: 3125773
doi: 10.1093/nar/gkr367
Sievers F et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539
pubmed: 21988835
pmcid: 3261699
doi: 10.1038/msb.2011.75
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
pubmed: 21558174
pmcid: 3125728
doi: 10.1093/nar/gkr245
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
pubmed: 12136088
pmcid: 135756
doi: 10.1093/nar/gkf436
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
pubmed: 15034147
pmcid: 390337
doi: 10.1093/nar/gkh340
Do CB et al (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15(2):330–340
pubmed: 15687296
pmcid: 546535
doi: 10.1101/gr.2821705
Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42(W1):W320–W324
pubmed: 24753421
pmcid: 4086106
doi: 10.1093/nar/gku316
Wiech EM, Cheng HP, Singh SM (2015) Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. Protein Sci 24(3):319–327
pubmed: 25492513
doi: 10.1002/pro.2616
Mitchell AL et al (2019) InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res 47(D1):D351–D360
pubmed: 30398656
doi: 10.1093/nar/gky1100
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
pubmed: 16845026
pmcid: 1538847
doi: 10.1093/nar/gkl124
Jonassen I, Collins JF, Higgins DG (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci 4(8):1587–1595
pubmed: 8520485
pmcid: 2143188
doi: 10.1002/pro.5560040817
Hulo N et al (2008) The 20 years of PROSITE. Nucleic Acids Res 36(Database issue):D245–D249
pubmed: 18003654
Wenzhong L et al (2015) IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics 31(20):3359–3361
doi: 10.1093/bioinformatics/btv362
Finn RD et al (2014) Pfam: the protein families database. Nucleic Acids Res 42(Database issue):D222–D230
pubmed: 24288371
doi: 10.1093/nar/gkt1223
Marchler-Bauer A et al (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39(D):225–229
doi: 10.1093/nar/gkq1189
Schultz J et al (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28(1):231–234
pubmed: 10592234
pmcid: 102444
doi: 10.1093/nar/28.1.231
Biegert A, Soding J (2008) De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics 24(6):807–814
pubmed: 18245125
doi: 10.1093/bioinformatics/btn039
George RA, Heringa J (2000) The REPRO server: finding protein internal sequence repeats through the Web. Trends Biochem Sci 25(10):515–517
pubmed: 11203383
doi: 10.1016/S0968-0004(00)01643-1
Buchan DW et al (2013) Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res 41(Web Server issue):W349–W357
pubmed: 23748958
pmcid: 3692098
doi: 10.1093/nar/gkt381
Wang Z et al (2011) Protein 8-class secondary structure prediction using conditional neural fields. Proteomics 11(19):3786–3792
pubmed: 21805636
pmcid: 3341732
doi: 10.1002/pmic.201100196
Yan R, Xu D, Yang J, Walker S, Zhang Y (2013) A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Report 3:2619
doi: 10.1038/srep02619
Pollastri G et al (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47:228–235
pubmed: 11933069
doi: 10.1002/prot.10082
Drozdetskiy A et al (2015) JPred4: a protein secondary structure prediction server. Nucleic Acids Res 4(W1):W389–W394
doi: 10.1093/nar/gkv332
Romero O, Dunker K (1997) Sequence data analysis for long disordered regions prediction in the Calcineurin Family. Genome Inform Ser Workshop Genome Inform 8:110–124
pubmed: 11072311
Ward JJ et al (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337:635–645
pubmed: 15019783
doi: 10.1016/j.jmb.2004.02.002
Mizianty MJ et al (2013) MFDp2-accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles. Intrinsically Disordered Proteins 1(1):e24428
pubmed: 28516009
pmcid: 5424793
doi: 10.4161/idp.24428
Ishida T, Kinoshita K (2007) PrDOS:prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 35(Web Server issue):W460–W464
pubmed: 17567614
pmcid: 1933209
doi: 10.1093/nar/gkm363
Berman HM et al (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235–242
pubmed: 10592235
pmcid: 102472
doi: 10.1093/nar/28.1.235
Moult J (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 15(3):285–289
pubmed: 15939584
doi: 10.1016/j.sbi.2005.05.011
John B, Sali A (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 31(14):3982–3992
pubmed: 12853614
pmcid: 165975
doi: 10.1093/nar/gkg460
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
pubmed: 17823132
doi: 10.1093/bioinformatics/btm377
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
pubmed: 15980461
pmcid: 1160169
doi: 10.1093/nar/gki408
Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40
doi: 10.1186/1471-2105-9-40
Dong X, Yang Z (2011) Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J 101:2525–2534
doi: 10.1016/j.bpj.2011.10.024
Krivov GG, Shapovalov MV, Dunbrack RL (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77(4):778–795
pubmed: 19603484
pmcid: 2885146
doi: 10.1002/prot.22488
Bhattacharya D et al (2016) 3Drefine: an interactive web server for efficient protein structure refinement. Nucleic Acids Res 44(W1):W406–W409
pubmed: 27131371
pmcid: 4987902
doi: 10.1093/nar/gkw336
Shuid AN, Kempster R, McGuffin LJ (2017) ReFOLD: a server for the refinement of 3D models of proteins guided by accurate quality estimates. Nucleic Acids Res 45:W422–W428
pubmed: 28402475
pmcid: 5570150
doi: 10.1093/nar/gkx249
Bhattacharya D (2019) refineD: improved protein structure refinement using machine learning based restrained relaxation. Bioinformatics 35:3320–3328
pubmed: 30759180
doi: 10.1093/bioinformatics/btz101
Eisenberg D, Luthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profi les. Methods Enzymol 277:396–404
pubmed: 9379925
pmcid: 9379925
doi: 10.1016/S0076-6879(97)77022-8
Olechnovič K, Venclovas Č (2017) VoroMQA: assessment of protein structure quality using interatomic contact areas. Proteins 85(6):1131–1145
pubmed: 28263393
doi: 10.1002/prot.25278
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
pubmed: 17517781
pmcid: 1933241
doi: 10.1093/nar/gkm290
Uziela K et al (2017) ProQ3D: Improved model quality assessments using Deep Learning. Bioinformatics 33(10):1578–1580
pubmed: 28052925
Hermjakob H et al (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32:D452–D455
pubmed: 14681455
pmcid: 308786
doi: 10.1093/nar/gkh052
Jensen LJ et al (2009) STRING8—a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37:D412–D416
pubmed: 18940858
doi: 10.1093/nar/gkn760
Oughtred R et al (2019) The BioGRID interaction database: 2019 update. Nucleic Acids Res 47(D1):D529–D541
pubmed: 30476227
doi: 10.1093/nar/gky1079
Morris GM et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J Comput Chem 16:2785–2791
doi: 10.1002/jcc.21256
Zhang N et al (2006) Enriching screening libraries with bioactive fragment space. Bioorg Med Chem 26(15):3594–3597
doi: 10.1016/j.bmcl.2016.06.013
Vajda S et al (2017) New additions to the ClusPro server motivated by CAPRI. Proteins 85(3):435–444
pubmed: 27936493
pmcid: 5313348
doi: 10.1002/prot.25219
Laskowski RA et al (2018) PDBsum: structural summaries of PDB entries. Protein 27:129–134
doi: 10.1002/pro.3289
O'Leary NA et al (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44(D1):D733–D745
pubmed: 26553804
doi: 10.1093/nar/gkv1189
Goodsell DS et al (2020) RCSB Protein Data Bank: enabling biomedical research and drug discovery. Protein Sci 29:52–65
pubmed: 31531901
doi: 10.1002/pro.3730
Lane L et al (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acids Res 40(Database issue):D76–D83
pubmed: 22139911
doi: 10.1093/nar/gkr1179
Barker WC et al (2001) Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Res 29(1):29–32
pubmed: 11125041
pmcid: 29802
doi: 10.1093/nar/29.1.29
Remmert M et al (2012) HHblits: lightningfast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9(2):173–175
doi: 10.1038/nmeth.1818
Madeira F et al (2019) The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 47(W1):W636–W641
pubmed: 30976793
pmcid: 6602479
doi: 10.1093/nar/gkz268
Bawono P, Heringa J (2014) PRALINE: a versatile multiple sequence alignment toolkit. Methods Mol Biol 1079:245–262
pubmed: 24170407
doi: 10.1007/978-1-62703-646-7_16
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
pubmed: 19435884
pmcid: 2703893
doi: 10.1093/nar/gkp360
Pei J, Grishin NV (2014) PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol 1079:263–271
pubmed: 24170408
pmcid: 4506754
doi: 10.1007/978-1-62703-646-7_17
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
pubmed: 17485479
pmcid: 1933135
doi: 10.1093/nar/gkm267
Klausen MS et al (2019) NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning. Proteins 87:520–527
pubmed: 30785653
doi: 10.1002/prot.25674
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
pubmed: 24799431
pmcid: 4086098
doi: 10.1093/nar/gku366
Pollastri G, McLysaght A (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 21(8):1719–1720
pubmed: 15585524
doi: 10.1093/bioinformatics/bti203
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
pubmed: 8808585
Lin K et al (2005) A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 21:152–159
pubmed: 15377504
doi: 10.1093/bioinformatics/bth487
Adamczak A, Porollo A, Meller J (2004) Accurate prediction of solvent accessibility using neural networks based regression. Proteins 56:753–767
pubmed: 15281128
doi: 10.1002/prot.20176
Yang J et al (2020) Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci 117(3):1496–1503
pubmed: 31896580
pmcid: 6983395
doi: 10.1073/pnas.1914677117
Xu D, Zhang Y (2013) Toward optimal fragment generations for ab initio protein structure assembly. Proteins 81:229–239
pubmed: 22972754
doi: 10.1002/prot.24179
Ma J et al (2013) Protein threading using context-specific alignment potential. Bioinformatics 29(13):i257–i265
pubmed: 23812991
pmcid: 3694651
doi: 10.1093/bioinformatics/btt210
Wu S, Zhang Y (2007) LOMETS: a local metathreading-server for protein structure prediction. Nucleic Acids Res 35(10):3375–3382
pubmed: 17478507
pmcid: 1904280
doi: 10.1093/nar/gkm251
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
pubmed: 17876813
doi: 10.1002/prot.21688
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
pubmed: 19429599
doi: 10.1093/bioinformatics/btp302
Waterhouse A et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46(W1):W296–W303
pubmed: 29788355
pmcid: 29788355
doi: 10.1093/nar/gky427
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
pubmed: 21666270
pmcid: 3137224
doi: 10.1093/bioinformatics/btr350
Combet C et al (2002) Geno3D: automatic comparative molecular modelling of protein. Bioinformatics 18:213–214
pubmed: 11836238
doi: 10.1093/bioinformatics/18.1.213
McGuffin LJ et al (2019) IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Res 47:W408–W413
pubmed: 31045208
pmcid: 6602432
doi: 10.1093/nar/gkz322
Bates PA et al (2001) Enhancement of protein modelling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins (Suppl 5):39–46
Wallner B et al (2003) Automatic consensus based fold recognition using Pcons, ProQ and Pmodeller. Proteins (Suppl 6):534–541
Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12(5):1073–1086
pubmed: 12717029
pmcid: 2323877
doi: 10.1110/ps.0236803
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
pubmed: 23620298
pmcid: 3692122
doi: 10.1093/nar/gkt294
Benkert P, Kunzli M, Schwede T (2009) QMEAN server for protein model quality estimation. Nucleic Acids Res 37(Web Server issue):W510–W514
pubmed: 19429685
pmcid: 2703985
doi: 10.1093/nar/gkp322
Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57(4):702–710
pubmed: 15476259
doi: 10.1002/prot.20264
Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66(4):778–795
pubmed: 17186527
doi: 10.1002/prot.21165
Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15(11):2507–2524
pubmed: 17075131
pmcid: 2242414
doi: 10.1110/ps.062416606
Williams CJ et al (2018) MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci 27:293–315
pubmed: 29067766
doi: 10.1002/pro.3330
Bhattacharya D, Cheng J (unpublished) REFINEpro: a conformation ensemble approach for protein structure refinement. http://sysbio.rnet.missouri.edu/REFINEpro/faq.html
Waterhouse AM et al (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191
pubmed: 19151095
pmcid: 2672624
doi: 10.1093/bioinformatics/btp033
Stivala A et al (2011) Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics 27(23):3315–3316
pubmed: 21994221
doi: 10.1093/bioinformatics/btr575
Crooks GE et al (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190
pubmed: 15173120
pmcid: 419797
doi: 10.1101/gr.849004
Linding R et al (2003) Protein disorder prediction: implications for structural proteomics. Structure 11(11):1453–1459
pubmed: 14604535
doi: 10.1016/j.str.2003.10.002
Kozlowski LP, Bujnicki JM (2012) MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics 13:111
pubmed: 22624656
pmcid: 3465245
doi: 10.1186/1471-2105-13-111
Walsh AJM, Martin T, Di Domenico T, Tosatto SCE (2012) Espritz: accurate and fast prediction of protein disorder. Bioinformatics 28(4):503–509
pubmed: 22190692
doi: 10.1093/bioinformatics/btr682
Warde-Farley D et al (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38(Web Server issue):W214–W220
pubmed: 20576703
pmcid: 2896186
doi: 10.1093/nar/gkq537
Grosdidier A, Zoete V, Michielin O (2011) SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res 39(Web Server issue):W270–W277
pubmed: 21624888
pmcid: 3125772
doi: 10.1093/nar/gkr366
Van Zundert GCP et al (2016) The HADDOCK2.2 webserver: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428:720–725
pubmed: 26410586
doi: 10.1016/j.jmb.2015.09.014
Schneidman-Duhovny D et al (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33:W363–W367
pubmed: 15980490
pmcid: 1160241
doi: 10.1093/nar/gki481
Humphrey W et al (1996) VMD—visual molecular dynamics. J Mol Graph 14:33–38
pubmed: 8744570
doi: 10.1016/0263-7855(96)00018-5