A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

PLoS Computational Biology

Volumn 9, Issue 7, 2013, Pages

  Petrov, Drazen ^a   Margreitter, Christian ^a,b   Grandits, Melanie ^b   Oostenbrink, Chris ^b   Zagrovic, Bojan ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTATIONAL CHEMISTRY; HYDRATION; PROTEINS; SIGNAL TRANSDUCTION;

AMINO-ACIDS; CELL-CYCLE CONTROLS; CELLULAR PROCESS; DYNAMIC NETWORK; DYNAMICS SIMULATION; INTERACTION NETWORKS; POST-TRANSLATIONAL MODIFICATIONS; STRUCTURE DYNAMICS; STRUCTURE NETWORK; SYSTEMATIC FRAMEWORK;

MOLECULAR DYNAMICS;

AMINO ACID; PROTEIN;

ACCURACY; ACETYLATION; AMINO ACID ANALYSIS; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; HYDRATION; HYDROPHOBICITY; HYDROXYLATION; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PHYSICAL CHEMISTRY; PROTEIN METHYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; QUANTITATIVE ANALYSIS;

EID: 84880818881     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003154     Document Type: Article

References (50)

1. Mann M, Jensen ON, (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21: 255-261.
2. Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr, (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 44: 7342-7372.
3. Bartova E, Krejci J, Harnicarova A, Galiova G, Kozubek S, (2008) Histone modifications and nuclear architecture: A review. J Histochem Cytochem 56: 711-721.
4. Berlett BS, Stadtman ER, (1997) Protein oxidation in aging, disease, and oxidative stress. J Biol Chem 272: 20313-20316.
5. Nystrom T, (2005) Role of oxidative carbonylation in protein quality control and senescence. EMBO J 24: 1311-1317.
6. Deribe YL, Pawson T, Dikic I, (2010) Post-translational modifications in signal integration. Nat Struct Mol Biol 17: 666-672.
7. van Rossum B, Fischle W, Selenko P, (2012) Asymmetrically modified nucleosomes expand the histone code. Nat Struct Mol Biol 19: 1064-1066.
8. van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, et al. (2006) Biomolecular modeling: goals, problems, perspectives. Angew Chem Int Ed Engl 45: 4064-4092.
9. Kruschel D, Zagrovic B, (2009) Conformational averaging in structural biology: issues, challenges and computational solutions. Mol Biosyst 5: 1606-1616.
10. Best RB, (2012) Atomistic molecular simulations of protein folding. Curr Opin Struct Biol 22: 52-61.
11. Petrov D, Zagrovic B, (2011) Microscopic analysis of protein oxidative damage: effect of carbonylation on structure, dynamics, and aggregability of villin headpiece. J Am Chem Soc 133: 7016-7024.
12. Polyansky AA, Zagrovic B, (2012) Protein Electrostatic Properties Predefining the Level of Surface Hydrophobicity Change upon Phosphorylation. J Phys Chem Lett 3: 973-976.
13. Potoyan DA, Papoian GA, (2012) Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. Proc Natl Acad Sci USA 109: 17857-17862.
14. Olausson BES, Grossfield A, Pitman MC, Brown MF, Feller SE, et al. (2012) Molecular Dynamics Simulations Reveal Specific Interactions of Post-translational Palmitoyl Modifications with Rhodopsin in Membranes. J Am Chem Soc 134: 4324-4331.
15. Marlowe AE, Singh A, Yingling YG, (2012) The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study. Mater Sci Eng C Mater Biol Appl 32: 2583-2588.
16. Seeliger D, Soeroes S, Klingberg R, Schwarzer D, Grubmuller H, et al. (2012) Quantitative Assessment of Protein Interaction with Methyl-Lysine Analogues by Hybrid Computational and Experimental Approaches. Acs Chemical Biology 7: 150-154.
17. Jorgensen WL, Maxwell DS, TiradoRives J, (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118: 11225-11236.
18. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
19. Schuler LD, Daura X, van Gunsteren WF, (2001) An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J Comput Chem 22: 1205-1218.
20. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24: 1999-2012.
21. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF, (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 25: 1656-1676.
22. Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, et al. (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J 40: 843-856.
23. Lee TY, Huang HD, Hung JH, Huang HY, Yang YSO, et al. (2006) dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res 34: D622-D627.
24. UniProt C, (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-D75.
25. Beveridge DL, DiCapua FM, (1989) Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem 18: 431-492.
26. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, et al. (2011) An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. J Chem Theory Comput 7: 4026-4037.
27. Efremov RG, Chugunov AO, Pyrkov TV, Priestle JP, Arseniev AS, et al. (2007) Molecular lipophilicity in protein modeling and drug design. Curr Med Chem 14: 393-415.
28. Polyansky AA, Chugunov AO, Vassilevski AA, Grishin EV, Efremov RG, (2012) Recent Advances in Computational Modeling of alpha-Helical Membrane-Active Peptides. Curr Protein Pept Sci 13: 644-657.
29. Vistoli G, Straniero V, Pedretti A, Fumagalli L, Bolchi C, et al. (2012) Predicting the physicochemical profile of diastereoisomeric histidine-containing dipeptides by property space analysis. Chirality 24: 566-576.
30. Hlevnjak M, Zitkovic G, Zagrovic B, (2010) Hydrophilicity Matching- A Potential Prerequisite for the Formation of Protein-Protein Complexes in the Cell. PLoS One 5: e11169 doi:10.1371/journal.pone.0011169.
31. Case DA, Darden TA, T.E. Cheatham I, Simmerling CL, Wang J, et al. (2012) AMBER, version 12. San Francisco: University of California.
32. Zoete V, Cuendet MA, Grosdidier A, Michielin O, (2011) SwissParam: A Fast Force Field Generation Tool for Small Organic Molecules. J Comput Chem 32: 2359-2368.
33. Schuttelkopf AW, van Aalten DMF, (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 60: 1355-1363.
34. Vanquelef E, Simon S, Marquant G, Garcia E, Klimerak G, et al. (2011) RED Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Res 39: W511-W517.
35. Schmid N, Christ CD, Christen M, Eichenberger AP, van Gunsteren WF, (2012) Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. Comput Phys Commun 183: 890-903.
36. Lindahl E, Hess B, van der Spoel D, (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317.
37. Margreitter C, Petrov D, Zagrovic B, (2013) Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Res doi: 10.1093/nar/gkt416.
38. Huq MDM, Tsai NP, Khan SA, Wei LN, (2007) Lysine trimethylation of retinoic acid receptor-alpha- A novel means to regulate receptor function. Mol Cell Proteomics 6: 677-688.
39. Bottomley MJ, (2004) Structures of protein domains that create or recognize histone modifications. EMBO Rep 5: 464-469.
40. Chandrasekhar I, Oostenbrink C, van Gunsteren WF, (2004) Simulating the physiological phase of hydrated DPPC bilayers: The ester moiety. Soft Mater 2: 27-45.
41. Oostenbrink C, Juchli D, van Gunsteren WF, (2005) Amine hydration: A united-atom force-field solution. Chemphyschem 6: 1800-1804.
42. Hritz J, Oostenbrink C, (2009) Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers. J Phys Chem B 113: 12711-12720.
43. Dolenc J, Oostenbrink C, Koller J, van Gunsteren WF, (2005) Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site. Nucleic Acids Res 33: 725-733.
44. Brunger A, Brooks CL, Karplus M, (1984) Stochastic boundary-conditions for molecular-dynamics simulations of ST2 water. Chem Phys Lett 105: 495-500.
45. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular Forces. Dordrecht: Reidel. pp. 331-342.
46. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR, (1984) Molecular-dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
47. Beutler TC, Mark AE, Vanschaik RC, Gerber PR, van Gunsteren WF, (1994) Avoiding singularities and numerical instabilities in free-energy calculations based on molecular simulations. Chem Phys Lett 222: 529-539.
48. Gallicchio E, Zhang LY, Levy RM, (2002) The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 23: 517-529.
49. Rizzo RC, Aynechi T, Case DA, Kuntz ID, (2006) Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial, charge models and optimization of nonpolar contributions. J Chem Theory Comput 2: 128-139.
50. Sulea T, Wanapun D, Dennis S, Purisima EO, (2009) Prediction of SAMPL-1 Hydration Free Energies Using a Continuum Electrostatics-Dispersion Model. J Phys Chem B 113: 4511-4520.