Going beyond clustering in MD trajectory analysis: An application to villin headpiece folding

PLoS ONE

Volumn 5, Issue 4, 2010, Pages

  Rajan, Aruna ^a   Freddolino, Peter L ^b,c   Schulten, Klaus ^a,b  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VILLIN; ACTIN BINDING PROTEIN;

ARTICLE; CLUSTER ANALYSIS; GEOMETRY; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN FOLDING; SIMULATION; CHEMISTRY; COMPARATIVE STUDY; EVALUATION; METHODOLOGY; STANDARD; STATISTICS;

CLUSTER ANALYSIS; MICROFILAMENT PROTEINS; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; STATISTICS AS TOPIC;

EID: 77956298149     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009890     Document Type: Article

References (35)

1. Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J (2006) Submicrosecond protein folding. J Mol Biol 359: 546-553.
2. Kulbeka J, Hofritcher J, Eaton WA (2004) The protein folding speed limit. Curr Opin Struct Biol 14: 76-88.
3. Maragakis P, Lindorff-Larson K, Eastwood MP, Dror RO, Klepeis JL, et al. (2008) Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. J Phys Chem B 112: 6155-6158.
4. Ensign DL, Kasson PM, Pande VS (2007) Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol 374: 806-816.
5. Freddolino PL, Liu F, Gruebele M, Schulten K (2008) Ten-microsecond MD simulation of a fast-folding WW domain. Biophys J 94: L75-L77.
6. Freddolino PL, Schulten K (2009) Common structural transitions in explicitsolvent simulations of villin headpiece folding. Biophys J 97: 2337-2346.
7. Duan Y, Kollman P (1998) Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution. Science 282: 740-744.
8. Karpen ME, Tobias DJ, Brooks CL (1993) Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochem 32: 412-420.
9. Hubner IA, Deeds EJ, Shakhnovich EI (2006) Understanding ensemble protein folding at atomic detail. PNAS 103: 17747-17752.
10. Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, et al. (1999) Peptide folding: When simulation meets experiment. Angew Chem Int Ed 38: 236-240.
11. van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: Fast, flexible, and free. J Comput Chem. pp 1701-1718.
12. Krivov SV, Muff S, Caflisch A, Karplus M (2008) One-Dimensional Barrier- Preserving Free-Energy Projections of a beta-sheet Miniprotein: New Insights into the Folding Process. J Phys Chem B 112: 8701-8714.
13. Handl J, Knowles J, Kell DB (2005) Computational cluster validation in postgenomic data analysis. Bioinformatics 21: 3201-3212.
14. Garca AE (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68: 2696-2699.
15. Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KFA, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived Ubiquitin ensemble in solution. Science 320: 1471-1475.
16. Yang LW, Eyal E, Bahar I, Kitao A (2009) Principal component analysis of native ensembles of biomolecular structures PCA_NEST: insights into functional dynamics. Bioinformatics 25: 606-614.
17. Balsera MA, Wriggers W, Oono Y, Schulten K (1996) Principal Component Analysis and long time protein dynamics. J Phys Chem 100: 2567-2572.
18. Levitt M (1983) Molecular dynamics of native protein ii: Analysis of nature of motion. J Mol Bio 168: 621-657.
19. Li A, Daggett V (1996) Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Bio 257: 412-429.
20. Shepard RN (1962) The analysis of proximities: multidimensional scaling with an unknown distance function I. Psychometrika 27: 125-139.
21. Shepard RN (1962) The analysis of proximities: multidimensional scaling with an unknown distance function II. Psychometrika 27: 219-246.
22. Kruskal JB (1964) Multidimensional scaling by optimizing goodness-of-fit to a nonmetric hypothesis. Psychometrika 29: 1-29.
23. Kruskal JB (1964) Nonmetric multidimensional scaling: A numerical method. Psychometrika 29: 115-129.
24. Taguchi YH, Oono Y (2004) Nonmetric multidimensional scaling as a datamining tool: new algorithm and new targets. Geometrical Structures of Phase Space, Multidimensional Chaos, Special Volume of Adv Chem Phys 130: 315-351.
25. Coifman RR, Lafon S, Lee AB, Maggioni M, Nadler B, et al. (2005) Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps. PNAS 102: 7426-7431.
26. Green P, Carmone Jr. FJ, Smith S (1970) Multidimensional Scaling: Concepts and Applications. Boston, MA: Allyn and Bacon.
27. Borg I, Groenen P (1997) Modern Multidimensional Scaling, theory and applications Springer.
28. Rajaram S (2009) Phenomenological approaches to the analysis of highthroughput biological experiments. Ph.D. thesis, University of Illinois, Dept. of Phys., Urbana-Champaign, IL.
29. Taguchi YH, Oono Y (2005) Relational patterns of gene expression via nonmetric multidimensional scaling analysis. Bioinformatics 21: 730-740.
30. Rajaram S (2009) A novel meta-analysis method exploiting consistency of highthroughput experiments. Bioinformatics 25: 636-642.
31. Rajaram S, Oono Y (2010) NeatMap - non-clustering heat map alternatives in R. BMC Bioinformatics 11: 45.
32. S Rajaram YO, h Taguchi Y (2005) Some implications of renormalization group theoretical ideas to statistics. Physica D 205: 207-214.
33. Wang J, Brüschweiler R (2006) 2d entropy of discrete molecular ensembles. J Chem Theory Comput 2: 18-24.
34. Ota M, Ikeguchi M, Kidera A (2004) Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. PNAS 101: 17658-17663.
35. Udgaonkar J (2008) Multiple routes and structural heterogeneity in protein folding. Ann Rev Biophys 37: 489-510.