The importance of secondary structure in determining CO2-protein binding patterns

Journal of Molecular Modeling

Volumn 18, Issue 6, 2012, Pages 2527-2541

  Drummond, Michael L ^a   Wilson, Angela K ^a   Cundari, Thomas R ^a  

^a UNIVERSITY OF NORTH TEXAS   (United States)

Author keywords

Carbon storage; Molecular dynamics; Protein models; Protein secondary structures; Protein ligand interactions

Indexed keywords

AMINO ACID; CARBON DIOXIDE; POLYPEPTIDE;

ARTICLE; BINDING AFFINITY; BIOINFORMATICS; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE;

ARGININE; CARBON DIOXIDE; HISTIDINE; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SURFACE PROPERTIES;

EID: 84864709672     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1276-0     Document Type: Article

References (45)

1. Stickle DF, Presta LG, Dill KA, Rose GD (1992) Hydrogen bonding in globular proteins. J Mol Biol 226:1143-1159
2. Fleming PJ, Rose GD (2005) Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci 14:1911-1917 (Pubitemid 40994162)
3. Rose GD, Fleming PJ, Banavar JR, Maritan A (2006) A backbone-based theory of protein folding. Proc Natl Acad Sci USA 103:16623-16633 (Pubitemid 44737304)
4. Lu W, Randal M, Kossiakoff A, Kent S B H (1999) Probing intermolecular backbone H-bonding in serine proteinase-protein inhibitor complexes. Chem Biol 6:419-427 (Pubitemid 29311479)
5. Moreira IS, Fernandes PA, Ramos MJ (2007) Backbone importance for protein-protein binding. J Chem Theor Comput 3:885-893
6. Lazo ND, Maji SK, Fradinger EA, Bitan G, Teplow DB (2005) The amyloid beta-protein. In: Sipe JC (ed) Amyloid proteins-the beta sheet conformation and disease. Wiley-VCH, Weinheim, pp 385-492
7. Teplow DB, Lazo ND, Bitan G, Bernstein S, Wyttenbach T, Bowers MT, Baumketner A, Shea J, Urbanc B, Cruz L, Borreguero J, Stanley HE (2006) Elucidating amyloid β-protein folding and assembly: a multidisciplinary approach. Acc Chem Res 39:635-645
8. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75:333-366 (Pubitemid 44118036)
9. Laidman J, Forse GJ, Yeates TO (2006) Conformational change and assembly through edge β-strands in transthyretin and other amyloid proteins. Acc Chem Res 39:576-583
10. Richardson JS, Richardson DC (2002) Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci USA 99:2754-2759 (Pubitemid 34240533)
11. Gleitsman KR, Lester HA, Dougherty DA (2009) Probing the role of backbone hydrogen bonding in a critical β-sheet of the extracellular domain of a Cys-loop receptor. Chem Bio Chem 10:1385-1391
12. Doig AJ (1997) A three stranded β-sheet peptide in aqueous solution containing N-methyl amino acids to prevent aggregation. Chem Commun 2153-2154 (Pubitemid 127495678)
13. Das A, Mukhopadhyay C (2009) Urea-mediated protein denaturation: a consensus view. J Phys Chem B 113:12816-12824
14. Hua L, Zhou R, Thirumalai D, Berne BJ (2008) Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci USA 105:16928-16933
15. Rossky PJ (2008) Protein denaturation by urea: slash and bond. Proc Natl Acad Sci USA 105:16825-16826
16. Bartlett GJ, Porter CT, Borkakoti N, Thornton JM (2002) Analysis of catalytic residues in enzyme active sites. J Mol Biol 324:105-121 (Pubitemid 35352183)
17. Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM (1998) Protein folds and functions. Structure 6:875-884 (Pubitemid 28348650)
18. Schneider G, Lindqvist Y, Brändèn C-I (1992) RUBISCO: structure and mechanism. Annu Rev Biophys Biomol Struct 21:119-143
19. Tcherkez G G B, Farquhar GD, Andrews TJ (2006) Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc Natl Acad Sci USA 103:7246-7251 (Pubitemid 43727818)
20. 2 sequestration using the enzyme carbonic anhydrase. Energy Fuel 15:309-316
21. 2 sequestration. 1. Immobilization of carbonic anhydrase within polyurethane foam. Energy Fuel 23:5725-5730
22. Nelson DL, Cox MM (2005) Lehninger: principles of biochemistry. WH Freeman, New York
23. 2-formatics: how do proteins bind carbon dioxide? J Chem Inf Model 49:2111-2115
24. 2 binding sites in proteins. Energy Fuel 24:1464-1470
25. Costantini S, Colonna G, Facchiano AM (2006) Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Comm 342:441-451 (Pubitemid 43289012)
26. Chemical Computing Group (2008) Molecular Operating Environment (MOE). Chemical Computing Group, Montreal
27. Cornell WD, Cieplak P, Bayly CI, Gould IR, K. M. Merz J, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197
28. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 26:3219-3228
29. Bond SD, Benedict JL, Laird BB (1999) The Nosé-Poincaré method for constant temperature molecular dynamics. J Comput Phys 151:114-134
30. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21:1049-1074
31. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F T K, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616 (Pubitemid 128576688)
32. MacKerell AD Jr, Banavali N (2000) All-atom empirical force field for nucleic acids. 2. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 21:105-120
33. Foloppe N, MacKerell AD Jr (2000) All-atom empirical force field for nucleic acids. 1. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21:86-104
34. Potoff JJ, Siepmann JI (2001) Vapor-liquid equilibria of mixtures containing alkanes, carbon dioxide, and nitrogen. AICHE J 47:1676-1682
35. Breneman CM, Wiberg KB (1990) Determining atom-centered monopoles from molecular electrostatic potentials-the need for high sampling density in formamide conformational analysis. J Comput Chem 11:361-373
36. Besler BH, Merz KM Jr, Kollman PA (1990) Atomic charges derived from semiempirical methods. J Comput Chem 11:431-439
37. Montgomery JA Jr, Frisch MJ, Ochterski JW, Petersson GA (2000) A complete basis set model chemistry. VII. Use of the minimum population localization method. J Chem Phys 112:6532-6542 (Pubitemid 33638867)
38. In Het Panhuis M, Patterson CH, Lynden-Bell RM (1998) A molecular dynamics study of carbon dioxide in water: diffusion, structure and thermodynamics. Mol Phys 94:963-972 (Pubitemid 128480227)
39. Sarkhel S, Desiraju GR (2004) N-H·O, O-H·O, and C-H·O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition. Proteins Struct Func Bioinf 54:247-259 (Pubitemid 38084066)
40. Park S, Saven JG (2005) Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins Struct Func Bioinf 60:450-463. (Pubitemid 41061638)
41. Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709-713
42. Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S (1998) Analytical shape computation of macromolecules. I. Molecular area and volume through alpha shape. Proteins Struct Func Bioinf 33:1-17 (Pubitemid 28413009)
43. Morozov AV, Kortemme T, Tsemekhman K, Baker D (2004) Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci USA 101:6946-6951 (Pubitemid 38596423)
44. DeYonker NJ, Cundari TR, Wilson AK (2006) The correlation consistent composite approach (ccCA): an alternative to the Gaussian-n methods. J Chem Phys 124:114104
45. DeYonker NJ, Wilson BR, Pierpont AW, Cundari TR, Wilson AK (2009) Toward the intrinsic error of the correlation consistent composite approach (ccCA). Mol Phys 107:1107-1121