CHARMM-GUI PACE CG builder for solution, micelle, and bilayer coarse-grained simulations

Journal of Chemical Information and Modeling

Volumn 54, Issue 3, 2014, Pages 1003-1009

  Qi, Yifei ^a   Cheng, Xi ^a   Han, Wei ^b   Jo, Sunhwan ^a   Schulten, Klaus ^b   Im, Wonpil ^a  

^a UNIVERSITY OF KANSAS   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGICAL SYSTEMS; GRAPHICAL USER INTERFACES; LIPID BILAYERS; LIPIDS; PROTEINS;

BILAYER SYSTEMS; BILAYER THICKNESS; COMPLEX BIOLOGICAL SYSTEMS; MULTI-SCALE SIMULATION; MULTIPLE COMPONENTS; RADIUS OF GYRATION; ROOT MEAN SQUARED DEVIATIONS; SIMULATION SYSTEMS;

MICELLES;

LIPID BILAYER; MICELLE; PROTEIN; SOLUTION AND SOLUBILITY;

CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; LIPID BILAYER; MICELLE; PROTEIN DATABASE; SOLUTION AND SOLUBILITY;

COMPUTER SIMULATION; DATABASES, PROTEIN; LIPID BILAYERS; MICELLES; MODELS, MOLECULAR; PROTEINS; SOFTWARE; SOLUTIONS;

EID: 84897017759     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500007n     Document Type: Article

References (51)

1. Arkhipov, A.; Freddolino, P. L.; Schulten, K. Stability and Dynamics of Virus Capsids Described by Coarse-Grained Modeling Structure 2006, 14, 1767-1777
2. Nguyen, H. D.; Reddy, V. S.; Brooks, C. L., 3rd Invariant Polymorphism in Virus Capsid Assembly J. Am. Chem. Soc. 2009, 131, 2606-2614
3. Ayton, G. S.; Voth, G. A. Multiscale Computer Simulation of the Immature Hiv-1 Virion Biophys. J. 2010, 99, 2757-2765
4. Hall, B. A.; Armitage, J. P.; Sansom, M. S. Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles PLoS Comput. Biol. 2012, 8, e1002685
5. Janosi, L.; Li, Z.; Hancock, J. F.; Gorfe, A. A. Organization, Dynamics, and Segregation of Ras Nanoclusters in Membrane Domains Proc. Natl. Acad. Sci. USA 2012, 109, 8097-8102
6. Qi, Y.; Huang, Y.; Liang, H.; Liu, Z.; Lai, L. Folding Simulations of a De Novo Designed Protein with a Betaalphabeta Fold Biophys. J. 2010, 98, 321-329
7. Zhang, Z.; Chan, H. S. Competition between Native Topology and Nonnative Interactions in Simple and Complex Folding Kinetics of Natural and Designed Proteins Proc. Natl. Acad. Sci. USA 2010, 107, 2920-2925
8. Marrink, S. J.; de Vries, A. H.; Tieleman, D. P. Lipids on the Move: Simulations of Membrane Pores, Domains, Stalks and Curves Biochim. Biophys. Acta 2009, 1788, 149-168
9. Wu, Z.; Cui, Q.; Yethiraj, A. Why Do Arginine and Lysine Organize Lipids Differently? Insights from Coarse-Grained and Atomistic Simulations J. Phys. Chem. B 2013, 117, 12145-12156
10. Yoo, J.; Jackson, M. B.; Cui, Q. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores Biophys. J. 2013, 104, 841-852
11. Marius, P.; Leung, Y. M.; Piggot, T. J.; Khalid, S.; Williamson, P. T. Probing the Oligomeric State and Interaction Surfaces of Fukutin-I in Dilauroylphosphatidylcholine Bilayers Eur. Biophys. J. 2012, 41, 199-207
12. Grubisic, I.; Shokhirev, M. N.; Orzechowski, M.; Miyashita, O.; Tama, F. Biased Coarse-Grained Molecular Dynamics Simulation Approach for Flexible Fitting of X-Ray Structure into Cryo Electron Microscopy Maps J. Struct. Biol. 2010, 169, 95-105
13. Yang, S.; Blachowicz, L.; Makowski, L.; Roux, B. Multidomain Assembled States of Hck Tyrosine Kinase in Solution Proc. Natl. Acad. Sci. USA 2010, 107, 15757-15762
14. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The Martini Force Field: Coarse Grained Model for Biomolecular Simulations J. Phys. Chem. B 2007, 111, 7812-7824
15. López, C. A.; Rzepiela, A. J.; de Vries, A. H.; Dijkhuizen, L.; Hünenberger, P. H.; Marrink, S. J. Martini Coarse-Grained Force Field: Extension to Carbohydrates J. Chem. Theory Comput. 2009, 5, 3195-3210
16. Monticelli, L.; Kandasamy, S. K.; Periole, X.; Larson, R. G.; Tieleman, D. P.; Marrink, S.-J. The Martini Coarse-Grained Force Field: Extension to Proteins J. Chem. Theory Comput. 2008, 4, 819-834
17. Han, W.; Wan, C.-K.; Jiang, F.; Wu, Y.-D. Pace Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification J. Chem. Theory Comput. 2010, 6, 3373-3389
18. Han, W.; Wan, C.-K.; Wu, Y.-D. Pace Force Field for Protein Simulations. 2. Folding Simulations of Peptides J. Chem. Theory Comput. 2010, 6, 3390-3402
19. Han, W.; Schulten, K. Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains J. Chem. Theory Comput. 2012, 8, 4413-4424
20. Jo, S.; Kim, T.; Im, W. Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations PloS One 2007, 2, e880
21. Jo, S.; Kim, T.; Iyer, V. G.; Im, W. Charmm-Gui: A Web-Based Graphical User Interface for Charmm J. Comput. Chem. 2008, 29, 1859-1865
22. Miller, B. T.; Singh, R. P.; Klauda, J. B.; Hodoscek, M.; Brooks, B. R.; Woodcock, H. L., 3rd Charmming: A New, Flexible Web Portal for Charmm J. Chem. Inf. Model 2008, 48, 1920-1929
23. Jo, S.; Lim, J. B.; Klauda, J. B.; Im, W. Charmm-Gui Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes Biophys. J. 2009, 97, 50-58
24. van Dijk, M.; Wassenaar, T. A.; Bonvin, A. M. J. J. A Flexible, Grid-Enabled Web Portal for Gromacs Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 3463-3472
25. Cheng, X.; Jo, S.; Lee, H. S.; Klauda, J. B.; Im, W. Charmm-Gui Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems J. Chem. Inf. Model 2013, 53, 2171-2180
26. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank. A Computer-Based Archival File for Macromolecular Structures Eur. J. Biochem. 1977, 80, 319-324
27. Lomize, M. A.; Lomize, A. L.; Pogozheva, I. D.; Mosberg, H. I. Opm: Orientations of Proteins in Membranes Database Bioinformatics 2006, 22, 623-625
28. Brooks, B. R.; Brooks, C. L., 3rd; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. Charmm: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-1614
29. Walsh, S. T.; Cheng, H.; Bryson, J. W.; Roder, H.; DeGrado, W. F. Solution Structure and Dynamics of a De Novo Designed Three-Helix Bundle Protein Proc. Natl. Acad. Sci. USA 1999, 96, 5486-5491
30. Weaver, L. H.; Matthews, B. W. Structure of Bacteriophage T4 Lysozyme Refined at 1.7 a Resolution J. Mol. Biol. 1987, 193, 189-199
31. Park, S. H.; Marassi, F. M.; Black, D.; Opella, S. J. Structure and Dynamics of the Membrane-Bound Form of Pf1 Coat Protein: Implications of Structural Rearrangement for Virus Assembly Biophys. J. 2010, 99, 1465-1474
32. Call, M. E.; Wucherpfennig, K. W.; Chou, J. J. The Structural Basis for Intramembrane Assembly of an Activating Immunoreceptor Complex Nat. Immunol. 2010, 11, 1023-1029
33. Arora, A.; Abildgaard, F.; Bushweller, J. H.; Tamm, L. K. Structure of Outer Membrane Protein a Transmembrane Domain by Nmr Spectroscopy Nat. Struct. Biol. 2001, 8, 334-338
34. MacKenzie, K. R.; Prestegard, J. H.; Engelman, D. M. A Transmembrane Helix Dimer: Structure and Implications Science 1997, 276, 131-133
35. Hiller, S.; Garces, R. G.; Malia, T. J.; Orekhov, V. Y.; Colombini, M.; Wagner, G. Solution Structure of the Integral Human Membrane Protein Vdac-1 in Detergent Micelles Science 2008, 321, 1206-1210
36. Steinbacher, S.; Bass, R.; Strop, P.; Rees, D. C. Structures of the Prokaryotic Mechanosensitive Channels Mscl and Mscs Curr. Top. Membr. 2007, 58, 1-24
37. Cheng, X.; Im, W. Nmr Observable-Based Structure Refinement of Dap12-Nkg2c Activating Immunoreceptor Complex in Explicit Membranes Biophys. J. 2012, 102, L27-29
38. de Jong, D. H.; Singh, G.; Bennett, W. F. D.; Arnarez, C.; Wassenaar, T. A.; Schafer, L. V.; Periole, X.; Tieleman, D. P.; Marrink, S. J. Improved Parameters for the Martini Coarse-Grained Protein Force Field J. Chem. Theory Comput. 2013, 9, 687-697
39. Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant-Pressure Molecular-Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189
40. Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant-Pressure Molecular-Dynamics Simulation-the Langevin Piston Method J. Chem. Phys. 1995, 103, 4613-4621
41. Humphrey, W.; Dalke, A.; Schulten, K. Vmd: Visual Molecular Dynamics J. Mol. Graph. 1996, 14, 33-38
42. Pronk, S.; Pall, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. Gromacs 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit Bioinformatics 2013, 29, 845-854
43. Faber, H. R.; Matthews, B. W. A Mutant T4 Lysozyme Displays Five Different Crystal Conformations Nature 1990, 348, 263-266
44. McHaourab, H. S.; Oh, K. J.; Fang, C. J.; Hubbell, W. L. Conformation of T4 Lysozyme in Solution. Hinge-Bending Motion and the Substrate-Induced Conformational Transition Studied by Site-Directed Spin Labeling Biochemistry 1997, 36, 307-316
45. Trabuco, L. G.; Villa, E.; Mitra, K.; Frank, J.; Schulten, K. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics Structure 2008, 16, 673-683
46. Marrink, S. J.; de Vries, A. H.; Mark, A. E. Coarse Grained Model for Semiquantitative Lipid Simulations J. Phys. Chem. B 2004, 108, 750-760
47. Petrache, H. I.; Dodd, S. W.; Brown, M. F. Area Per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by (2)H Nmr Spectroscopy Biophys. J. 2000, 79, 3172-3192
48. Nagle, J. F.; Tristram-Nagle, S. Structure of Lipid Bilayers Biochim. Biophys. Acta 2000, 1469, 159-195
49. Konig, B.; Dietrich, U.; Klose, G. Hydration and Structural Properties of Mixed Lipid/Surfactant Model Membranes Langmuir 1997, 13, 525-532
50. Rand, R. P.; Parsegian, V. A. Hydration Forces between Phospholipid-Bilayers Biochim. Biophys. Acta 1989, 988, 351-376
51. Rui, H.; Lee, K. I.; Pastor, R. W.; Im, W. Molecular Dynamics Studies of Ion Permeation in Vdac Biophys. J. 2011, 100, 602-610