Molecular dynamics simulations of membrane proteins

Methods in Molecular Biology

Volumn 1033, Issue , 2013, Pages 85-101

  Pluhackova, Kristyna ^a   Wassenaar, Tsjerk A ^b   Böckmann, Rainer A ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

All atom force field; Backmapping; Coarse grained force field; Lipid bilayers; MARTINI; Membrane proteins; Molecular dynamics simulation

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; LIPID BILAYER; MEMBRANE COMPONENT; MEMBRANE STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION;

COMPUTER SIMULATION; DATABASES, PROTEIN; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATION;

EID: 84884181332     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-487-6_6     Document Type: Article

References (26)

1. Jensen MO, Jogini V, Borhani DW, Leffler AE, Dror RO, Shaw DE (2012) Mechanism of voltage gating in potassium channels. Science 336:229-233
2. Tieleman DP (2012) Computer simulation of membrane dynamics. In: Comprehensive biophysics, vol 5. Elsevier
3. Wolf MG, Hoefling M, Aponte-Santamaría C, Grubmüller H, Groenhof G (2010) g-membed: efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J Comput Chem 31:2169-2174
4. Kandt C, Ash WL, Tieleman DP (2007) Setting up and running molecular dynamics simulations of membrane proteins. Methods 41:475-488
5. Marrink SJ, Lindahl E, Edholm O (2001) Simulation of the spontaneous aggregation of phospholipids into bilayers. J Am Chem Soc 123:8638-8639
6. Böckmann RA, Caflisch A (2005) Formation of detergent micelles around the outer membrane protein OmpX. Biophys J 88: 3191-3204
7. Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI forcefield: coarse grained model for biomolecular simulations. J Phys Chem B 111:7812-7824
8. Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ (2008) The MARTINI coarse grained forcefield: extension to proteins. J Chem Theory Comput 4: 819-834
9. Hess B, Kutzner K, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447
10. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M (1995) Evaluation of comparative protein modelling by MODELLER. Proteins 23:318-326
11. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637
12. de Jong DH, Gurpreet S, Bennett WFD, Arnarez C, Wassenaar TA, Schäfer LV, Periole X, Tieleman DP, Marrink SJ (2013) Improved parameters for the martini coarse-grained protein force field. J Chem Theory Comput 9: 687-697
13. Wassenaar TA, Sengupta D, Tieleman DP, Marrink SJ (in preparation) INSANE: fast and versatile generation of custom membranes for molecular simulations
14. Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP (2013) Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models. (in preparation)
15. Humphrey W, Dalke A, Schulten K (1996) VMD-visual molecular dynamics. J Mol Graph 14:33-38
16. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723
17. The PyMOL molecular graphics system, Version 1.5.0.4 Schrödinger, LLC
18. Klauda JB et al (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114:7830-7843
19. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712-725
20. Jämbec JPM, Lyubartsev AP (2012) An extension and further validation of an all-atomistic force field for biological membranes. J Chem Theory Comput 8:2938-2948
21. 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
22. Poger D, Mark AE (2010) On the validation of molecular dynamics simulations of saturated and cis-mono unsaturated phosphatidylcholine lipid bilayers: A comparison with experiment. J Chem Theory Comput 6:325-336
23. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092
24. Allen WJ, Lemkul JA, Bevan DR (2009) GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics. J Comput Chem 30:1952-1958
25. Georgescu RE, Alexov EG, Gunner MR (2002) Combining conformational flexibility and continuum electrostatics for calculating pKa's in proteins. Biophys J 83:1731-1748
26. Alexov E, Gunner MR (1997) Incorporating protein conformational flexibility into pHtitration calculations: results on T4 lysozyme. Biophys J 74:2075-2093