Performance comparison of computational methods for modeling alpha-helical structures

Journal of Molecular Modeling

Volumn 19, Issue 1, 2013, Pages 193-203

  Lupan, Alexandru ^a   Kun, Attila Zsolt ^a   Carrascoza, Francisco ^a   Silaghi Dumitrescu, Radu ^a  

^a BABE BOLYAI UNIVERSITY   (Romania)

Author keywords

Alpha helix; DFT; Hydrogen bond; Peptide; PM6; Protein

Indexed keywords

CALMODULIN; POLYPEPTIDE;

AB INITIO CALCULATION; ALPHA HELIX; ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; MATHEMATICAL MODEL; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; SOLVATION; THEORETICAL MODEL;

AMINO ACIDS; CALMODULIN; COMPUTATIONAL BIOLOGY; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY;

EID: 84872286166     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1531-z     Document Type: Article

References (49)

1. Noodleman L, Lovell T, Han WG, Li J, Himo F (2004) Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems. Chem Rev 104:459-508
2. Siegbahn PE, Blomberg MRA (2000) Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods. Chem Rev 100:421-437
3. Harris DL (2001) High-valent intermediates of heme proteins and model compounds. Curr Opin Chem Biol 5:724-735
4. Friesner RA, Dunietz BD (2001) Large-scale ab initio quantum chemical calculations on biological systems. Acc Chem Res 34:351-358
5. Gooding SR, Winn PJ, Jones GA, Ferenczy GG, Frusher MJ, Reynolds CA (2006) Classical polarization in hybrid QM/MM methods. J Phys Chem A 110:6487-6497
6. Warshel A, Parson WW (2001) Dynamics of biochemical and biophysical reactions: insight from computer simulations. Q Rev Biophys 34:563-679
7. Warshel A (2002) Molecular dynamics simulations of biological reactions. Acc Chem Res 35:385-395
8. Rosta E, Klahn M, Warshel A (2006) Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. J Phys Chem B 110:2934-2941
9. Ryde U (2003) Combined quantum and molecular mechanics calculations on metalloproteins. Curr Opin Chem Biol 7:136-142
10. Silaghi-Dumitrescu R (2004) On the performance of the PM3 semiempirical method with heme complexes relevant to dioxygen and peroxide activation. Rev Chim 55:304-307
11. Tejero I, Gonzalez-Lafont A, Lluch JM (2007) A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. J Comput Chem 28:997-1005
12. Mcnamara JP, Sundararajan M, Hillier IH, Ge J, Campbell A, Morgado C (2006) Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules? J Comput Chem 27:1307-1323
13. Mcnamara JP, Sundararajan M, Hillier IH (2005) Development of parameter sets for semi-empirical MO calculations of transition metal systems: iron parameters for iron-sulfur proteins. J Mol Graph Model 24:128-137
14. Csontos J, Palermo NY, Murphy RF, Lovas S (2008) Calculation of weakly polar interaction energies in polypeptides using density functional and local Moller-Plesset perturbation theory. J Comput Chem 29:1344-1352
15. Sulpizi M, Raugei S, Vandevondele J, Carloni P, Sprik M (2007) Calculation of redox properties: understanding short- and long-range effects in rubredoxin. J Phys Chem B 111:3969-3976
16. Jensen KP (2006) Iron-sulfur clusters: why iron? J Inorg Biochem 100:1436-1439
17. Sundararajan M, Hillier IH, Burton NA (2006) Structure and redox properties of the protein, rubredoxin, and its ligand and metal mutants studied by electronic structure calculation. J Phys Chem A 110:785-790
18. Machonkin TE, Westler WM, Markley JL (2005) Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins. Inorg Chem 44:779-797
19. Vrajmasu VV, Munck E, Bominaar EL (2004) Theoretical analysis of the three-dimensional structure of tetrathiolato iron complexes. Inorg Chem 43:4867-4879
20. Kennepohl P, Solomon EI (2003) Electronic structure contributions to electron-transfer reactivity in iron-sulfur active sites: 3. Kinetics of electron transfer. Inorg Chem 42:696-708
21. Vrajmasu VV, Bominaar EL, Meyer J, Munck E (2002) Mossbauer study of reduced rubredoxin as purified and in whole cells. Structural correlation analysis of spin Hamiltonian parameters. Inorg Chem 41:6358-6371
22. Glaser T, Rose K, Shadle SE, Hedman B, Hodgson KO, Solomon EI (2001) S K-edge X-ray absorption studies of tetranuclear iron-sulfur clusters: mu-sulfide bonding and its contribution to electron delocalization. J Am Chem Soc 123:442-454
23. Sigfridsson E, Olsson MH, Ryde U (2001) Inner-sphere reorganization energy of iron-sulfur clusters studied with theoretical methods. Inorg Chem 40:2509-2519
24. Kloiber K, Weiskirchen R, Krautler B, Bister K, Konrat R (1999) Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains. J Mol Biol 292:893-908
25. + binding sites. J Mol Biol 256:228-234
26. + polyalanine peptides (n = 5, 10, 15) in vacuo: helical or not? J Phys Chem Lett 1:3465-3470
27. 10-helical polyalanines: both electrostatic and van der Waals interactions are essential. J Phys Chem B 115:11462-11469
28. Tkatchenko A, Rossi M, Blum V, Ireta J, Scheffler M (2011) Unraveling the stability of polypeptide helices: critical role of van der Waals interactions. Phys Rev Lett 106:118102
29. Wavefunction, Inc. (1998)Spartan 5.0, Wavefunction, Inc., Irvine
30. Frisch MJ, Trucks GW, H. B. Schlegel HB, Scuseria GE, Robb, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery, Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell K, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, revision A.02. Gaussian Inc., Wallingford
31. Hypercube, Inc. (2007) HyperChem molecular modelling system, release 8.0 for Windows. Hypercube, Inc.
32. Stewart JJP (2009) MOPAC2009, version 10.153L. Stewart Computational Chemistry, Colorado Springs
33. Eckert F, Klamt A (2002) COSMO solvation model. AICHE J 48:369-385
34. Kudin KN, Scuseria GE, Cancès E (2002) A black-box self-consistent field convergence algorithm: one step closer. J Chem Phys 116:8255-8261
35. Kun ZA, Lupan A, Silaghi-Dumitrescu R (2010) PM6 modeling of alpha helical polypeptide structures. Studia Universitatis Babes-Bolyai Chemia 55:31-36
36. Korth M, Pitonak M, Rezac J, Hobza P (2010) A transferable H-bonding correction for semiempirical quantum-chemical methods. J Chem Theor Comput 6:344-352
37. Klamt A, Schüürmann G (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2:799-805
38. Baker J (1986) An algorithm for the location of transition states. J Comput Chem 7:385-395
39. Davidon WC (1991) Variable metric method for minimization. SIAM J Optim 1:1-17
40. Fletcher R (1987) Practical methods of optimization, 2nd edn. Wiley, New York
41. Broyden CG (1970) The convergence of a class of double-rank minimization algorithms. II. The new algorithm. J Inst Math Appl 6:222-231
42. Fletcher R (1970) A new approach to variable metric algorithms. Comput J 13:317-322
43. Goldfarb D (1970) A family of variable-metric methods derived by variational means. Math Comput 24:23-26
44. Shanno DF (1970) Conditioning of quasi-Newton methods for function minimization. Math Comput 24:647-656
45. Matthies H, Strang G (1979) The solution of nonlinear finite element equations. Int J Num Meth Eng 14:1613-1626
46. Nocedal J (1980) Updating quasi-Newton matrices with limited storage. Math Comput 35:773-782
47. Byrd RH, Nocedal J, Schnabel RB (1994) Representations of quasi-Newton matrices and their use in limited memory methods. Math Prog 63:129-156
48. Babu YS, Bugg CE, Cook WJ (1988) Structure of calmodulin refined at 2.2 Å resolution. J Mol Biol 204:191-204
49. Nordhoff A, Tziatzios C, Van Den Broek JA, Schott MK, Kalbitzer HR, Becker K, Schubert D, Schirmer RH (1997) Solution structure of an HGR inhibitor. Eur J Biochem 245:273-282