Flexibility analysis of biomacromolecules with application to computer-aided drug design

Methods in Molecular Biology

Volumn 819, Issue , 2012, Pages 75-91

  Fulle, Simone ^a   Gohlke, Holger ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Constraint counting; FIRST; Flexibility rigidity analysis; ProFlex; Rigidity theory; Statics of biomacromolecules

Indexed keywords

LIGAND; PROTON; WATER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; DRUG DESIGN; MACROMOLECULE; PLIABILITY;

COMPUTER-AIDED DESIGN; DRUG DESIGN; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PLIABILITY; PROTONS; SOFTWARE; WATER;

EID: 84855932239     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-465-0_6     Document Type: Article

References (56)

1. Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, Emerson A, Fanelli F, Gohlke H, Kuhn LA, Morris GM, Orozco M, Pertinhez TA, Rizzi M, and Sotriffer CA. (2008) Target flexibility: An emerging consideration in drug discovery and design. J Med Chem 51:6237-6255.
2. Wlodawer A and Vondrasek J. (1998) Inhibitors of HIV-1 protease: A major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct 27:249-284. (Pubitemid 28286016)
3. Zhang Q, Sun X, Watt ED, and Al-Hashimi HM. (2006) Resolving the motional modes that code for RNA adaptation. Science 311:653-656. (Pubitemid 43191308)
4. Perez A, Noy A, Lankas F, Luque FJ, and Orozco M. (2004) The relative flexibility of B-DNA and A-RNA duplexes: Database analysis. Nucleic Acids Res 32:6144-6151. (Pubitemid 40081087)
5. Getz M, Sun X, Casiano-Negroni A, Zhang Q, and Al-Hashimi HM. (2007) NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers 86:384-402. (Pubitemid 47237806)
6. Jacobs DJ, Rader AJ, Kuhn LA, and Thorpe MF. (2001) Protein flexibility predictions using graph theory. Proteins 44:150-165.
7. Keating KS, Flores SC, Gerstein MB, and Kuhn LA. (2009) StoneHinge: Hinge prediction by network analysis of individual protein structures. Protein Sci 18:359-371.
8. Fulle S and Gohlke H. (2008) Analysing the flexibility of RNA structures by constraint counting. Biophys J 94:4202-4219.
9. Radestock S and Gohlke H. (2008) Exploiting the link between protein rigidity and thermostability for data-driven protein engineering. Eng Life Sci 8:507-522.
10. Livesay DR and Jacobs DJ. (2006) Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Proteins 62:130-143. (Pubitemid 43063011)
11. Tan HP and Rader AJ. (2009) Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120. Proteins 74:881-894.
12. Radestock S and Gohlke H. (2011) Protein rigidity and thermophilic adaptation. Proteins 79:1089-1108.
13. Gohlke H, Kuhn LA, and Case DA. (2004) Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 56:322-337. (Pubitemid 38850165)
14. Wells SA, Jimenez-Roldan JE, and Romer RA. (2009) Comparative analysis of rigidity across protein families. Phys Biol 6:46005.
15. Hespenheide BM, Rader AJ, Thorpe MF, and Kuhn LA. (2002) Identifying protein folding cores from the evolution of flexible regions during unfolding. J Mol Graphics Modell 21:195-207. (Pubitemid 35279850)
16. Rader AJ and Bahar I. (2004) Folding core predictions from network models of proteins. Polymer 45:659-668. (Pubitemid 38082199)
17. Fulle S and Gohlke H. (2009) Statics of the ribosomal exit tunnel: Implications for co-translational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol 387:502-517.
18. Rader AJ, Hespenheide BM, Kuhn LA, and Thorpe MF. (2002) Protein unfolding: Rigidity lost. Proc Natl Acad Sci U S A 99:3540-3545. (Pubitemid 34256390)
19. Hespenheide BM, Jacobs DJ, and Thorpe MF. (2004) Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J Phys: Condens Matter 16: 5055-5064.
20. Wang Y, Rader AJ, Bahar I, and Jernigan R. (2004) Global ribosome motions revealed with elastic network model. J Struct Biol 147:302-314. (Pubitemid 39140737)
21. Ahmed A and Gohlke H. (2006) Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins 63: 1038-1051. (Pubitemid 43765154)
22. Wells S, Menor S, Hespenheide B, and Thorpe MF. (2005) Constrained geometric simulation of diffusive motion in proteins. Phys Biol 2:S127-136. (Pubitemid 41609439)
23. Rader AJ. (2010) Thermostability in rubredoxin and its relationship to mechanical rigidity. Phys Biol 7:16002.
24. Fulle S and Gohlke H. (2009) Constraint counting on RNA structures: Linking flexibility and function. Methods 49:181-188.
25. Hooft RWW, Vriend G, Sander C, and Abola EE. (1996) Errors in protein structures. Nature 381:272-272.
26. Vriend G. (1990) WHAT IF: A molecular modeling and drug design program. J Mol Graph 8:52-56. (Pubitemid 20717037)
27. Word JM, Lovell SC, Richardson JS, and Richardson DC. (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1747.
28. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, andWoods RJ. (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668-1688. (Pubitemid 43076180)
29. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, and Onufriev A. (2005) H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules. Nucleic Acids Res 33:W368-W371. (Pubitemid 44529945)
30. Draper DE. (2004) A guide to ions and RNA structure. RNA 3:335-343. (Pubitemid 38240993)
31. Hashem Y and Auffinger P. (2009) A short guide for molecular dynamics simulations of RNA systems. Methods 47:187-197.
32. Ahmed A, Kazemi S, and Gohlke H. (2007) Protein flexibility and mobility in structurebased drug design. Front Drug Des Discov 3:455-476.
33. Stauffer D and Aharony A. (1994) Introduction to Percolation Theory., Taylor and Francis, London.
34. Mamonova T, Hespenheide B, Straub R, Thorpe MF, and Kurnikova M. (2005) Protein flexibility using constraints from molecular dynamics simulations. Phys Biol 2:S137-147. (Pubitemid 41609440)
35. Vaiana AC, Westhof E, and Auffinger P. (2006) A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: Conformational and hydration patterns. Biochimie 88:1061-1073. (Pubitemid 44291879)
36. Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, and Batey RT. (2010) Free State Conformational Sampling of the SAM-I riboswitch aptamer domain. Structure 18:787-797.
37. Fulle S, Christ NA, Kestner E, and Gohlke H. (2010) HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations. J Chem Inf Model 50:1489-1501.
38. Saenger W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
39. Ornstein RL, Rein R, Breen DL, and Macelroy RD. (1978) An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers 17:2341-2360. (Pubitemid 9029395)
40. Gralla J and Crothers DM. (1973) Free energy of imperfect nucleic acid helices: III. Small internal loops resulting from mismatches. J Mol Biol 78:301-319.
41. Whiteley W. (2005) Counting out to the flexibility of molecules. Phys Biol 2:S116-126. (Pubitemid 41609438)
42. Pan Y and MacKerell AD. (2003) Altered structural fluctuations in duplex RNA versus DNA: A conformational switch involving base pair opening. Nucleic Acids Res 31:7131-7140. (Pubitemid 38016159)
43. Noy A, Pérez A, Lankas F, Luque FJ, and Orozco M. (2004) Relative flexibility of DNA and RNA: A molecular dynamics study. J Mol Biol:627-638. (Pubitemid 39311610)
44. Gohlke H and Thorpe MF. (2006) A natural coarse graining for simulating large biomolecular motion. Biophys J 91:2115-2120. (Pubitemid 44352394)
45. Livesay DR, Dallakyan S, Wood GG, and Jacobs DJ. (2004) A flexible approach for understanding protein stability. FEBS Letters 576:468-476. (Pubitemid 39388647)
46. Schneidman-Duhovny D, Inbar Y, Nussinov R, and Wolfson HJ. (2005) Geometry-based flexible and symmetric protein docking. Proteins 60:224-231. (Pubitemid 40934891)
47. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, and Olson AJ. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30:2785-2791.
48. Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, and Beckmann R. (2009) Structural insight into nascent polypeptide chain-mediated translational stalling. Science 326:1412-1415.
49. Vázquez-Laslop N, Ramu H, Klepacki D, Kannan K, and Mankin A. (2010) The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide. EMBO J 29:3108-3117.
50. Lei M, Zavodszky MI, Kuhn LA, and Thorpe MF. (2004) Sampling protein conformations and pathways. J Comput Chem 25: 1133-1148.
51. Ahmed A and Gohlke H. (2009) Multiscale modeling of macromolecular conformational changes, in 1st International Conference on Computational & Mathematical Biomedical Engineering -CMBE09 (Nithiarasu P., and Löhner R., Eds.), pp 219-222, Swansea, UK.
52. Farrell DW, Speranskiy K, and Thorpe MF. (2010) Generating stereochemically acceptable protein pathways. Proteins 78:2908-2921.
53. Zavodszky MI, Ming L, Thorpe MF, Day AR, and Kuhn LA. (2004) Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins 57:243-261. (Pubitemid 39223730)
54. Totrov M and Abagyan R. (2008) Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr Opin Struct Biol 18:178-184.
55. Ahmed A, Rippmann F, Barnickel G, and Gohlke H. (2011) A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model 51:1604-1622.
56. de Amorim HLN, Netz PA, and Guimaraes JA. (2010) Thrombin allosteric modulation revisited: a molecular dynamics study. J Mol Model 16:725-735.