Systematic analysis of short internal indels and their impact on protein folding

BMC Structural Biology

Volumn 10, Issue , 2010, Pages

  Kim, RyangGuk ^a   Guo, Jun Tao ^a  

^a University of North Carolina at Charlotte   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; INDEL MUTATION; PLASTICITY; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; GENETIC DATABASE; GENETICS; INTERNET; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN RENATURATION; PROTEIN STABILITY; SEQUENCE HOMOLOGY;

EUKARYOTA;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASES, GENETIC; INDEL MUTATION; INTERNET; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN RENATURATION; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 77955103653     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-10-24     Document Type: Article

References (47)

1. Why do humans have so few genes? E Pennisi, Science (New York, NY) 2005 309 5731 80.
2. Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes. Y Xing C Lee, Nature reviews 2006 7 7 499 509 10.1038/nrg1896 16770337
3. Alternative isoform regulation in human tissue transcriptomes. ET Wang R Sandberg S Luo I Khrebtukova L Zhang C Mayr SF Kingsmore GP Schroth CB Burge, Nature 2008 456 7221 470 476 10.1038/nature07509 18978772
4. The implications of alternative splicing in the ENCODE protein complement. ML Tress PL Martelli A Frankish GA Reeves JJ Wesselink C Yeats PI Olason M Albrecht H Hegyi A Giorgetti D Raimondo J Lagarde RA Laskowski G Lopez MI Sadowski JD Watson P Fariselli I Rossi A Nagy W Kai Z Storling M Orsini Y Assenov H Blankenburg C Huthmacher F Ramirez A Schlicker F Denoeud P Jones S Kerrien, et al. Proceedings of the National Academy of Sciences of the United States of America 2007 104 13 5495 5500 10.1073/pnas.0700800104 17372197
5. The Universal Protein Resource (UniProt) 2009. UniProt-Consortium, Nucleic acids research 2009 37 Database 169 174 18836194
6. The Protein Data Bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne, Nucleic acids research 2000 28 1 235 242 10.1093/nar/28.1.235 10592235
7. Structural and functional diversity generated by alternative mRNA splicing. J Stetefeld MA Ruegg, Trends in biochemical sciences 2005 30 9 515 521 10.1016/j.tibs.2005.07.001 16023350
8. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. DA Keedy CJ Williams JJ Headd WB Arendall VB Chen GJ Kapral RA Gillespie JN Block A Zemla DC Richardson JS Richardson, Proteins 2009 77 Suppl 9 29 49 19731372
9. A conformational switch in the Piccolo C2A domain regulated by alternative splicing. J Garcia SH Gerber S Sugita TC Sudhof J Rizo, Nature structural & molecular biology 2004 11 1 45 53
10. Analysis of insertions/deletions in protein structures. S Pascarella P Argos, Journal of molecular biology 1992 224 2 461 471 10.1016/0022-2836(92) 91008-D 1560462
11. The importance of loop length in the folding of an immunoglobulin domain. CF Wright J Christodoulou CM Dobson J Clarke, Protein Eng Des Sel 2004 17 5 443 453 10.1093/protein/gzh052 15208402
12. Understanding the molecular machinery of genetics through 3 D structures. RA Laskowski JM Thornton, Nature reviews 2008 9 2 141 151 18160966
13. How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme. DW Heinz WA Baase FW Dahlquist BW Matthews, Nature 1993 361 6412 561 564 10.1038/361561a0 8429913
14. Sequential reorganization of beta-sheet topology by insertion of a single strand. M Sagermann WA Baase BW Matthews, Protein Sci 2006 15 5 1085 1092 10.1110/ps.052018006 16597830
15. Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme. IR Vetter WA Baase DW Heinz JP Xiong S Snow BW Matthews, Protein Sci 1996 5 12 2399 2415 10.1002/pro.5560051203 8976549
16. Structural genomics analysis of alternative splicing and application to isoform structure modeling. P Wang B Yan JT Guo C Hicks Y Xu, Proceedings of the National Academy of Sciences of the United States of America 2005 102 52 18920 18925 10.1073/pnas.0506770102 16354838
17. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. PR Romero S Zaidi YY Fang VN Uversky P Radivojac CJ Oldfield MS Cortese M Sickmeier T LeGall Z Obradovic AK Dunker, Proceedings of the National Academy of Sciences of the United States of America 2006 103 22 8390 8395 10.1073/pnas.0507916103 16717195
18. Alternative splicing and protein structure evolution. F Birzele G Csaba R Zimmer, Nucleic acids research 2008 36 2 550 558 10.1093/nar/gkm1054 18055499
19. Flexibility and packing in proteins. B Halle, Proceedings of the National Academy of Sciences of the United States of America 2002 99 3 1274 1279 10.1073/pnas.032522499 11818549
20. Predicting Protein Disorder for N-, C-, and Internal Regions. X Li P Romero M Rani AK Dunker Z Obradovic, Genome Inform Ser Workshop Genome Inform 1999 10 30 40 11072340
21. The protein as a variable in protein crystallization. GE Dale C Oefner A D'Arcy, Journal of structural biology 2003 142 1 88 97 10.1016/S1047-8477(03) 00041-8 12718922
22. His-tag impact on structure. M Carson DH Johnson H McDonald C Brouillette LJ Delucas, Acta Crystallogr D Biol Crystallogr 2007 63 Pt 3 295 301 10.1107/S0907444906052024 17327666
23. SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. FP David YL Yip, BMC bioinformatics 2008 9 391 10.1186/1471-2105-9-391 18811932
24. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. SA Benner MA Cohen GH Gonnet, Journal of molecular biology 1993 229 4 1065 1082 10.1006/jmbi.1993.1105 8445636
25. Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. JO Wrabl NV Grishin, Proteins 2004 54 1 71 87 10.1002/prot.10508 14705025
26. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. MS Chang SA Benner, Journal of molecular biology 2004 341 2 617 631 10.1016/j.jmb.2004.05.045 15276848
27. Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. M Hsing A Cherkasov, BMC bioinformatics 2008 9 293 10.1186/1471-2105-9-293 18578882
28. A systematic study of homologous protein structures with insertions/deletions. RM Kim J-T J Guo, Computational Systems Bioinformatics: 2009 Stanford, CA, USA: Life Sciences Society 2009 000 103 113
29. Intrinsically disordered protein. AK Dunker JD Lawson CJ Brown RM Williams P Romero JS Oh CJ Oldfield AM Campen CM Ratliff KW Hipps J Ausio MS Nissen R Reeves C Kang CR Kissinger RW Bailey MD Griswold W Chiu EC Garner Z Obradovic, J Mol Graph Model 2001 19 1 26 59 10.1016/S1093-3263(00)00138-8 11381529
30. Intrinsic disorder in cell-signaling and cancer-associated proteins. LM Iakoucheva CJ Brown JD Lawson Z Obradovic AK Dunker, Journal of molecular biology 2002 323 3 573 584 10.1016/S0022-2836(02)00969-5 12381310
31. The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. S Birtalan Y Zhang FA Fellouse L Shao G Schaefer SS Sidhu, Journal of molecular biology 2008 377 5 1518 1528 10.1016/j.jmb.2008.01.093 18336836
32. Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures. M Zemlin M Klinger J Link C Zemlin K Bauer JA Engler HW Schroeder Jr PM Kirkham, Journal of molecular biology 2003 334 4 733 749 10.1016/j.jmb.2003.10.007 14636599
33. PISCES: a protein sequence culling server. G Wang RL Dunbrack Jr, Bioinformatics (Oxford, England) 2003 19 12 1589 1591 10.1093/bioinformatics/ btg224 12912846
34. BLASTClust. http://www.ncbi.nlm.nih.gov/
35. A general method applicable to the search for similarities in the amino acid sequence of two proteins. SB Needleman CD Wunsch, Journal of molecular biology 1970 48 3 443 453 10.1016/0022-2836(70)90057-4 5420325
36. EMBOSS: the European Molecular Biology Open Software Suite. P Rice I Longden A Bleasby, Trends Genet 2000 16 6 276 277 10.1016/S0168-9525(00)02024-2 10827456
37. Between order and disorder in protein structures: analysis of "dual personality" fragments in proteins. Y Zhang B Stec A Godzik, Structure 2007 15 9 1141 1147 10.1016/j.str.2007.07.012 17850753
38. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W Kabsch C Sander, Biopolymers 1983 22 12 2577 2637 10.1002/bip.360221211 6667333
39. DisProt: a database of protein disorder. S Vucetic Z Obradovic V Vacic P Radivojac K Peng LM Iakoucheva MS Cortese JD Lawson CJ Brown JG Sikes CD Newton AK Dunker, Bioinformatics (Oxford, England) 2005 21 1 137 140 10.1093/bioinformatics/bth476 15310560
40. Interior and surface of monomeric proteins. S Miller J Janin AM Lesk C Chothia, Journal of molecular biology 1987 196 3 641 656 10.1016/0022-2836(87) 90038-6 3681970
41. PROSPECT II: protein structure prediction program for genome-scale applications. D Kim D Xu JT Guo K Ellrott Y Xu, Protein engineering 2003 16 9 641 650 10.1093/protein/gzg081 14560049
42. FAST: a novel protein structure alignment algorithm. J Zhu Z Weng, Proteins 2005 58 3 618 627 10.1002/prot.20331 15609341
43. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. IN Shindyalov PE Bourne, Protein engineering 1998 11 9 739 747 10.1093/protein/11.9.739 9796821
44. SCOP database in 2004: refinements integrate structure and sequence family data. A Andreeva D Howorth SE Brenner TJ Hubbard C Chothia AG Murzin, Nucleic acids research 2004 32 Database 226 229 10.1093/nar/gkh039 14681400
45. Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. JL Xu MM Davis, Immunity 2000 13 1 37 45 10.1016/S1074-7613(00) 00006-6 10933393
46. Fold change in evolution of protein structures. NV Grishin, Journal of structural biology 2001 134 2-3 167 185 10.1006/jsbi.2001.4335 11551177
47. Analysis of chameleon sequences and their implications in biological processes. JT Guo JW Jaromczyk Y Xu, Proteins 2007 67 3 548 558 10.1002/prot.21285 17299764