Fragment-based modeling of membrane protein loops: Successes, failures, and prospects for the future

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 2, 2014, Pages 175-186

  Kelm, Sebastian ^a   Vangone, Anna ^a,b   Choi, Yoonjoo ^a   Ebejer, Jean Paul ^a   Shi, Jiye ^c,d   Deane, Charlotte M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF SALERNO   (Italy)

^c UCB PHARMA   (Belgium)

^d SHANGHAI INSTITUTE OF APPLIED PHYSICS   (China)

Author keywords

Database loop structure prediction; FREAD; Homology modeling; MEDELLER; PyFREAD

Indexed keywords

MEMBRANE PROTEIN;

ACCURACY; ALGORITHM; ARTICLE; DATA BASE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; VALIDITY;

DATABASE LOOP STRUCTURE PREDICTION; FREAD; HOMOLOGY MODELING; MEDELLER; PYFREAD;

AMINO ACID MOTIFS; COMPUTER SIMULATION; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84892677204     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24299     Document Type: Article

References (43)

1. von Heijne G. The membrane protein universe: what's out there and why bother? Intern Med 2007;261:543-557.
2. Forrest L, Tang C, Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 2006;91:508-517.
3. von Heijne G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J 1986;5:3021-3027.
4. von Heijne G. Membrane protein structure prediction: hydrophobicity analysis and the positive-inside rule. J Mol Biol 1992;225:487-494.
5. Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
6. Shenkin PS, Yarmush DL, Fine RM, Wang H, Levinthal C. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ring-like structures. Biopolymers 1987;26:2053-2085.
7. Hurst T. Flexible 3D searching: the directed tweak technique. J Chem Inf Comput Sci 1994;34:190-196.
8. Lee J, Lee D, Park H, Coutsias EA, Seok C. Protein loop modeling by using fragment assembly and analytical loop closure. Proteins 2010;78:3428-3436.
9. Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55:351-367.
10. Zhu K, Pincus DL, Zhao S, Friesner RA. Long loop prediction using the protein local optimization program. Proteins 2006;65:438-452.
11. DePristo MA, de Bakker PIW, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 2003;51:41-55.
12. de Bakker PIW, DePristo MA, Burke DF, Blundell TL. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the amber force field with the generalized born solvation model. Proteins 2003;51:21-40.
13. Fiser A, Do RKG, Šali A. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
14. Abagyan R, Totrov M, Kuznetsov D. ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 1994;15:488-506.
15. Abagyan RA, Totrov M. Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. J Comput Phys 1999;151:402-421.
16. Arnautova YA, Abagyan RA, Totrov M. Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins 2011;79:477-498.
17. Choi Y, Deane CM. FREAD revisited: accurate loop structure prediction using a database search algorithm. Proteins 2010;78:1431-1440.
18. Zhao S, Zhu K, Li J, Friesner RA. Progress in super long loop prediction. Proteins 2011;79:2920-2935.
19. Michalsky E, Goede A, Preissner R. Loops in proteins (lip)-a comprehensive loop database for homology modelling. Protein Eng 2003;16:979-985.
20. Fernandez-Fuentes N, Oliva B, Fiser A. A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res 2006;34:2085-2097.
21. Peng HP, Yang AS. Modeling protein loops with knowledge-based prediction of sequence-structure alignment. Bioinformatics 2007;23:2836-2842.
22. Hildebrand PW, Goede A, Bauer RA, Gruening B, Ismer J, Michalsky E, Preissner R. Superlooper-a prediction server for the modeling of loops in globular and membrane proteins. Nucleic Acids Res 2009;37:W571-W574.
23. Deane CM, Blundell TL. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 2001;10:599-612.
24. Lessel U, Schomburg D. Importance of anchor group positioning in protein loop prediction. Proteins 1999;37:56-64.
25. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
26. Fernandez-Fuentes N, Fiser A. Saturating representation of loop conformational fragments in structure databanks. BMC Struct Biol 2006;6:15.
27. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The protein data bank. Nucleic Acids Res 2000;28:235-242.
28. Jones TA, Thirup S. Using known substructures in protein model building and crystallography. EMBO 1986;5:819-822.
29. Choi Y, Deane CM. Predicting antibody complementarity determining region structures without classification. Mol BioSyst 2011;7:3327-3334.
30. Tusnády GE, Dosztányi Z, Simon I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 2005;33:D275-D278.
31. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI. OPM: orientations of proteins in membranes database. Bioinformatics 2006;22:623-625.
32. Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MSP. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 2008;16:621-630.
33. Wang G, Dunbrack R. Pisces: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
34. Kelm S, Shi J, Deane CM. iMembrane: homology-based membrane-insertion of proteins. Bioinformatics 2009;25:1086-1088.
35. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP. JOY: protein sequence-structure representation and analysis. Bioinformatics 1998;14:617-623.
36. Sokal R, Michener C. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 1958;38:1409-1438.
37. Kelm S, Shi J, Deane CM. MEDELLER: homology-based coordinate generation for membrane proteins. Bioinformatics 2010;26:2833-2840.
38. Bugalho M, Oliveira A. Constant time clash detection in protein folding. J Bioinf Comput Biol 2009;7:55-74.
39. Hill JR, Kelm S, Shi J, Deane CM. Environment specific substitution tables improve membrane protein alignment. Bioinformatics 2011;27:i15-i23.
40. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309.
41. Goldfeld DA, Zhu K, Beuming T, Friesner RA. Loop prediction for a GPCR homology model: algorithms and results. Proteins 2013;81:214-228.
42. Nugent T, Jones DT. Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proceedings of the National Academy of Sciences 2012;109:E1540-E1547.
43. Hill JR, Deane CM. MP-T: improving membrane protein alignment for structure prediction. Bioinformatics 2012;29:54-61.