Dynamics simulations for engineering macromolecular interactions

Chaos

Volumn 23, Issue 2, 2013, Pages

  Robinson Mosher, Avi ^a,b   Shinar, Tamar ^c   Silver, Pamela A ^a,b   Way, Jeffrey ^a  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c Riverside 900 University Ave ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MACROMOLECULE; PROTEIN BINDING;

ANIMAL; COMPUTER SIMULATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC ENGINEERING; HUMAN; MACROMOLECULE; METABOLISM; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY; ARTICLE; PROTEIN BINDING;

ANIMALS; COMPUTER SIMULATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC ENGINEERING; HUMANS; MACROMOLECULAR SUBSTANCES; PROTEIN BINDING; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY;

EID: 84880351891     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4810915     Document Type: Article

References (45)

1. Dodd I.B. Shearwin K.E. Perkins A.J. Burr T. Hochschild A. Egan J.B. Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev. 2004, 18:344-354. 10.1101/gad.1167904, ,.
2. Hochschild A. Lewis M. The bacteriophage lambda CI protein finds an asymmetric solution. Curr. Opin. Struct. Biol. 2009, 19:79-86. 10.1016/j.sbi.2008.12.008.
3. Dong G. Golden S.S. How a cyanobacterium tells time. Curr. Opin. Microbiol. 2008, 11:541-546. 10.1016/j.mib.2008.10.003.
4. Nakajima M. Imai K. Ito H. Nishiwaki T. Murayama Y. Iwasaki H. Oyama T. Kondo T. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 2005, 308:414-415. 10.1126/science.1108451, ,.
5. Li S. Schmitz K.R. Jeffrey P.D. Wiltzius J.J. W. Kussie P. Ferguson K.M. Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. Cancer Cell 2005, 7:301-311. 10.1016/j.ccr.2005.03.003, ,.
6. Garrett T.P. J. McKern N.M. Lou M. Elleman T.C. Adams T.E. Lovrecz G.O. Zhu H.-J. Walker F. Frenkel M.J. Hoyne P.A. Jorissen R.N. Nice E.C. Burgess A.W. Ward C.W. Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor alpha. Cell 2002, 110:763-773. 10.1016/S0092-8674(02)00940-6, , ,.
7. Cironi P. Swinburne I. Enhancement of cell type specificity by quantitative modulation of a chimeric ligand. J. Biol. Chem. 2008, 283(13):8469-8476. 10.1074/jbc.M708502200.
8. Taylor N.D. Way J.C. Silver P.A. Cironi P. Anti-glycophorin single-chain Fv fusion to low-affinity mutant erythropoietin improves red blood cell-lineage specificity. Protein Eng. 2010, 23:251-260. 10.1093/protein/gzp085,.
9. Stahl N. Yancopoulos G.D. The tripartite CNTF receptor complex: activation and signaling involves components shared with other cytokines. J. Neurobiol. 1994, 25:1454-1466. 10.1002/neu.480251111.
10. Suzuki M. Yagi N. DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. Proc. Natl. Acad. Sci. U.S.A. 1994, 91:12357-12361. 10.1073/pnas.91.26.12357.
11. Zhang L. Spratt S.K. Liu Q. Johnstone B. Qi H. Raschke E.E. Jamieson A.C. Rebar E.J. Wolffe A.P. Case C.C. Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene. J. Biol. Chem. 2000, 275:33850-33860. 10.1074/jbc.M005341200, ,.
12. Khalil A.S. Lu T.K. Bashor C.J. Ramirez C.L. Pyenson N.C. Joung J.K. Collins J.J. A synthetic biology framework for programming eukaryotic transcription functions. Cell 2012, 150:647-658. 10.1016/j.cell.2012.05.045, ,.
13. Garg A. Lohmueller J.J. Silver P.A. Armel T.Z. Engineering synthetic TAL effectors with orthogonal target sites. Nucl. Acids Res. 2012, 40:7584-7595. 10.1093/nar/gks404,.
14. Boch J. Scholze H. Schornack S. Landgraf A. Hahn S. Kay S. Lahaye T. Nickstadt A. Bonas U. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 2009, 326:1509-1512. 10.1126/science.1178811, ,.
15. Moscou M.J. Bogdanove A.J. A simple cipher governs DNA recognition by TAL effectors. Science 2009, 326:1501. 10.1126/science.1178817.
16. Perez-Pinera P. Ousterout D.G. Brunger J.M. Farin A.M. Glass K.A. Guilak F. Crawford G.E. Hartemink A.J. Gersbach C.A. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat. Methods 2013, 10:239-242. 10.1038/nmeth.2361, ,.
17. Blount B.A. Weenink T. Vasylechko S. Ellis T. Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS ONE 2012, 7:e33279. 10.1371/journal.pone.0033279,.
18. 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. 10.1021/jp071097f,.
19. Voth G.A. Coarse-Graining of Condensed Phase and Biomolecular Systems 2009, (CRC Press, ).
20. Frazier Z. Alber F. A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling. J. Comput. Biol. 2012, 19:606-618. 10.1089/cmb.2012.0027.
21. van Zon J. ten Wolde P. Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics. Phys. Rev. Lett. 2005, 94:128103. 10.1103/PhysRevLett.94.128103.
22. van Zon J.S. ten Wolde P.R. Green's-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space. J. Chem. Phys. 2005, 123:234910. 10.1063/1.2137716.
23. Northrup S.H. Erickson H.P. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc. Natl. Acad. Sci. U.S.A. 1992, 89:3338-3342. 10.1073/pnas.89.8.3338.
24. Phillips J.C. Braun R. Wang W. Gumbart J. Tajkhorshid E. Villa E. Chipot C. Skeel R.D. Kale L. Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26:1781-1802. 10.1002/jcc.20289, ,.
25. Shaw D. Deneroff M.M. Dror R. Kuskin J.S. Larson R.H. Salmon J.K. Young C. Batson B. Bowers K.J. Chao J.C. Anton, a special-purpose machine for molecular dynamics simulation. Commun. ACM 2008, 51:91-97. 10.1145/1364782.1364802, ,.
26. Klepeis J.L. Lindorff-Larsen K. Dror R.O. Shaw D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol. 2009, 19:120-127. 10.1016/j.sbi.2009.03.004,.
27. Gabdoulline R.R. Wade R.C. Protein-protein association: Investigation of factors influencing association rates by Brownian dynamics simulations. J. Mol. Biol. 2001, 306:1139-1155. 10.1006/jmbi.2000.4404.
28. Berg H.C. Random Walks in Biology 1993, (Princeton University Press, ).
29. Iserles A. A First Course in the Numerical Analysis of Differential Equations 2008, (Cambridge University Press, ).
30. Courant R. Variational methods for the solution of problems of equilibrium and vibrations. Bull. Am. Math. Soc. 1943, 49:1-23. 10.1090/S0002-9904-1943-07818-4.
31. Hauth M. Etzmuß O. Straßer W. Analysis of numerical methods for the simulation of deformable models. Visual Comput. 2003, 19:581-600. 10.1007/s00371-003-0206-2.
32. Kräutler V. van Gunsteren W.F. Hünenberger P.H. A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 2001, 22:501-508. 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V.
33. Hess B. Bekker H. Berendsen H.J. C. Fraaije J.G. E. M. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18:1463-1472. 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H,.
34. Izaguirre J.A. Reich S. Skeel R.D. Longer time steps for molecular dynamics. J. Chem. Phys. 1999, 110:9853. 10.1063/1.478995.
35. Lipková J. Zygalakis K.C. Chapman S.J. Erban R. Analysis of Brownian dynamics simulations of reversible bimolecular reactions. SIAM J. Appl. Math. 2011, 71:714-730. 10.1137/100794213,.
36. Kim S. Karrila S.J. Microhydrodynamics: Principles And Selected Applications 1991, and (Dover Publications, ).
37. Balay S. Gropp W.D. McInnes L.C. Smith B.F. Efficient management of parallelism in object oriented numerical software libraries. in Modern Software Tools in Scientific Computing 1997, 163-202. E. Arge, A. M. Bruaset, H. P. Langtangen, and edited by and (Birkhäuser Press, )
38. Paige C.C. Saunders M.A. Solution of sparse indefinite systems of linear equations. SIAM J. Numer. Anal. 1975, 12:617-629. 10.1137/0712047.
39. Parmar A.S. Muschol M. Hydration and hydrodynamic interactions of lysozyme: Effects of chaotropic versus kosmotropic ions. Biophys. J. 2009, 97:590-598. 10.1016/j.bpj.2009.04.045.
40. Harkness J. The viscosity of human blood plasma: its measurement in health and disease. Biorheology 1971, 8:171-193.
41. Evers T.H. van Dongen E.M. W. M. Faesen A.C. Meijer E.W. Merkx M. Quantitative understanding of the energy transfer between fluorescent proteins connected via flexible peptide linkers. Biochemistry 2006, 45:13183-13192. 10.1021/bi061288t,.
42. Hagan M.F. Chandler D. Dynamic pathways for viral capsid assembly. Biophys. J. 2006, 91:42-54. 10.1529/biophysj.105.076851.
43. Ohashi T. Galiacy S.D. Briscoe G. Erickson H.P. An experimental study of GFP-based FRET, with application to intrinsically unstructured proteins. Protein Sci. 2007, 16:1429-1438. 10.1110/ps.072845607,.
44. Berg O.G. Winter R.B. von Hippel P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 1981, 20:6929-6948. 10.1021/bi00527a028.
45. See supplementary material at E-CHAOEH-23-012393 for the video of the flexible linker simulation, flexible-linker.mp4; for the video of the chimeric activator simulation where the linker has zero bending stiffness, flexible-chimeric-video.mp4; and for the video of the chimeric activator simulation where the linker has a bending stiffness constant of 20 z-N per nm, stiff-chimeric-video.mp4.