Weakly hydrated surfaces and the binding interactions of small biological solutes

European Biophysics Journal

Volumn 41, Issue 4, 2012, Pages 369-377

  Brady, John W ^a   Tavagnacco, Letizia ^b   Ehrlich, Laurent ^a   Chen, Mo ^a   Schnupf, Udo ^a   Himmel, Michael E ^c   Saboungi, Marie Louise ^d   Cesáro, Attilio ^b  

^a Department of Molecular Biology and Genetics   (United States)

^b UNIVERSITY OF TRIESTE   (Italy)

^c NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

^d Centre National de la Recherche Scientifique   (France)

Author keywords

Hydrophobic hydration; Molecular aggregation; Molecular dynamics; Serotonin

Indexed keywords

GLUCOSE; PROTEIN; SOLVENT; WATER;

ARTICLE; CHEMICAL PHENOMENA; CHEMISTRY; METABOLISM; SURFACE PROPERTY;

GLUCOSE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; PROTEINS; SOLVENTS; SURFACE PROPERTIES; WATER;

EID: 84860312311     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-011-0776-2     Document Type: Article

References (53)

1. Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Clarendon Press, Oxford
2. Ashbaugh HS, Paulaitis ME (2001) Effect of solute size and solutewater attractive interactions on hydration water structure around hydrophobic solutes. J Am Chem Soc 123:10721-10728 (Pubitemid 33015719)
3. Atwood JL, Hamada F, Robinson KD, Orr GW, Vincent RL (1991) X-ray diffraction evidence for aromatic pi hydrogen-bonding to water. Nature 349:683-684 (Pubitemid 21912134)
4. Bergenstråhle M, Wohlert J, Himmel ME, Brady JW (2010) Simulation studies of the insolubility of cellulose. Carbohydr Res 345:2060-2066
5. Blow DM, Collyer CA, Goldberg JD, Smart OS (1992) Structure and mechanism of D-xylose isomerase. Faraday Discuss 93:1-7
6. Brooks BR, Brooks CL, MacKerell AD, Nilsson J, Petrella L, Roux RJ, Won B, Archontis Y, Bartels G, Boresch CS et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545-1614
7. Cesàro A, Russo E, Crescenzi V (1976) Thermodynamics of caffeine aqueous solutions. J Phys Chem 80:335-339
8. Chandler D (2005) Interfaces and the driving force of hydrophobic assembly. Nature 437:640-647 (Pubitemid 41486526)
9. Chen M, Bomble YJ, Himmel M E, Brady JW (2011) Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution. Carbohydr Res (submitted)
10. Delbaere LTJ, Vandonselaar M, Prasad L, Quail JW, Nikrad PV, Pearlstone JR, Carpenter MR, Smillie LB, Spohr U, Lemieux RU (1989) Structures of Griffonia Simplicifolia Lectin IV and its complex with a Synthetic Lewis b Blood Group Determinant. Trans Am Crystallogr Assoc 25:65-76 (Pubitemid 21696293)
11. Einspahr H, Parks EH, Suguna K, Subramanian E, Suddath FL (1986) The crystal structure of pea lectin at 3.0-A° resolution. J Biol Chem 261:16518-16527
12. Frankel AE, Burbage C, Fu T, Tagge E, Chandler J, Willingham MC (1996) Ricin toxin contains at least three galactose-binding sites located in B chain subdomains 1a, 1b, and 2c. Biochemistry 35:14749-14756 (Pubitemid 26423807)
13. Franks F, Mathias S (eds) (1982) Biophysics of water. Wiley, Chichester
14. Geiger A, Mausbach P, Schnitker J, Blumberg RL, Stanley HE (1984) Structure and dynamics of the hydrogen bond network in water by computer simulations. Journal de Physique 45:13-31
15. Hansen JP, McDonald JR (1976) Theory of simple liquids. Academic Press, London
16. Henrissat B (1994) Cellulases and their interaction with cellulose. Cellulose 1:169-196
17. Huang DM, Chandler D (2002) The hydrophobic effect and the influence of solute-solvent attractions. J Phys Chem B 106:2047-2053 (Pubitemid 35276029)
18. Israelachvili J, Wennerstrom H (1996) Role of hydration and water structure in biological and colloidal interactions. Nature 379:219-225 (Pubitemid 26025205)
19. Kusalik PG, Svishchev IM (1994) The spatial structure in liquid water. Science 265:1219-1221 (Pubitemid 24292788)
20. Lavie A, Allen KN, Petsko GA, Ringe D (1994) X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis. Biochemistry 33:5469-5480 (Pubitemid 24162982)
21. Lee SH, Rossky PJ (1994) A comparison of the structure and dynamics of liquid water at hydrophobic and hydrophilic surfaces-a molecular dynamics simulation study. J Chem Phys 100:3334-3345
22. Lee CY, McCammon JA, Rossky PJ (1984) The structure of liquid water at an extended hydrophobic surface. J Chem Phys 80:4448-4455
23. Linse P (1990) Molecular dynamics simulation of a dilute aqueous solution of benzene. J Am Chem Soc 112:1744-1750 (Pubitemid 20217084)
24. Liu Q, Brady JW (1996) Anisotropic solvent structuring in aqueous sugar solutions. J Am Chem Soc 118:12276-12286 (Pubitemid 27006794)
25. Lounnas V, Pettitt BM (1994) A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment. Proteins Struct Funct Genet 18:133-147 (Pubitemid 24055076)
26. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616 (Pubitemid 128576688)
27. Mason PE, Neilson GW, Enderby JE, Saboungi M-L, Dempsey CE, MacKerell AD, Brady JW (2004) The structure of aqueous guanidinium chloride solutions. J Am Chem Soc 126:11462-11470 (Pubitemid 39244962)
28. Mason PE, Neilson GW, Enderby JE, Saboungi M-L, Brady JW (2005) The structure of aqueous glucose solutions as determined by neutron diffraction with isotopic substitution experiments and molecular dynamics calculations. J Phys Chem B 109:13104-13111 (Pubitemid 41048713)
29. Mason PE, Neilson GW, Price DL, Saboungi M-L, Brady JW (2010) Observation of pyridine aggregation in aqueous solution using neutron scattering experiments and MD simulations. J Phys Chem B 114:5412-5419
30. Mason PE, Lerbret A, Saboungi M-L, Neilson GW, Dempsey CE, Brady JW (2011) The interactions of glucose with a model peptide. Proteins 79:2224-2232
31. McCarter JD, Withers SG (1994) Mechanisms of enzymatic glycoside hydrolysis. Curr Opin Struct Biol 4:885-892
32. Mezei M, Beveridge DL (1984) Generic solvent sites in a crystal. J Comput Chem 5:523-527
33. Parsiegla G, Reverbel C, Tardif C, Driguez H, Haser R (2008) Structures of mutants of cellulase Cel48F of Clostridium cellulolyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J Microbiol 375:499-510 (Pubitemid 350199663)
34. Quiocho FA, Vyas KK (1984) Novel stereospecificity of the L-arabinose-binding protein. Nature 310:381-386 (Pubitemid 14051102)
35. Ramírez-Gualito K, Alonso-Ríos R, Quiroz-García B, Rojas-Aguilar A, Díaz D, Jiménez-Barbero J, Cuevas G (2009) Enthalpic nature of the CH/p interaction involved in the recognition of carbohydrates by aromatic compounds, confirmed by a novel interplay of NMR, calorimetry, and theoretical calculations. J Am Chem Soc 131:18129-18138
36. Resat H, Mezei M (1996) Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate. Biophys J 71:1179-1190 (Pubitemid 26299757)
37. Rossky PJ, Karplus M (1979) Solvation. A molecular dynamics study of a dipeptide in water. J Am Chem Soc 101:1913-1937 (Pubitemid 9454633)
38. Schmidt RK, Karplus M, Brady JW (1996) The anomeric equilibrium in D-xylose: free energy and the role of solvent structuring. J Am Chem Soc 118:541-546 (Pubitemid 126532505)
39. Sharon N, Lis H (1990) Carbohydrate-protein interactions. Chemistry in Britain, 679-682
40. Singh G, Brovchenko I, Oleinkova A, Winter R (2008) Peptide aggregation in finite systems. Biophys J 95:3208-3221
41. Stillinger FH (1980) Water revisited. Science 209:451-457
42. Stoesser PR, Gill SJ (1967) Calorimetric study of self-association of 6-methylpurine in water. J Phys Chem 71:564-567
43. Suzuki S, Green PG, Bumgarner RE, Dasgupta S, Goddard WA, Blake GA (1992) Benzene forms hydrogen bonds with water. Science 257:942-945
44. Svishchev IM, Kusalik PG (1993) Proton chemical shift of water in the liquid state: computer simulation results. J Am Chem Soc 115:8270-8274
45. Svishchev IM, Kusalik PG (1994) Structure in liquid methanol from spatial distribution functions. J Chem Phys 100:5165-5171
46. Tavagnacco L, Mason PE, Schnupf U, Pitici F, Zhong L, Himmel ME, Crowley M, Cesàro A, Brady JW (2011a) Sugar binding sites on the surface of the carbohydrate binding module of CBH I from Trichoderma reesei. Carbohydr Res 346:839-846
47. Tavagnacco L, Schnupf U, Mason PE, Saboungi M-L, Cesàro A, Brady JW (2011b) Molecular dynamics simulation studies of caffeine aggregation in aqueous solution. J Phys Chem B 115:10957-10966
48. Tavagnacco L, Schnupf U, Saboungi M-L, Cesàro A, Brady JW (2011c) Simulation studies of sugars interacting with caffeine in aqueous solution. J Phys Chem B (in preparation)
49. Teng M-K, Usman N, Frederick CA, Wang AH-J (1988) The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acid Res 16:2671-2690
50. Vasella A, Davies GJ, Böhm M (2002) Glycosidase mechanisms. Curr Opin Chem Biol 6:619-629 (Pubitemid 35284193)
51. Wilson DB (1988) Cellulases of Thermomonospora fusca. Methods Enzymol 160:314-323
52. Wohlert J, Schnupf U, Brady JW (2010) Free energy surfaces for the interaction of glucose with planar aromatic groups in aqueous solution. J Chem Phys 133:155103
53. Zangi R, Berne BJ (2008) Temperature dependence of dimerization and dewetting of large-scale hydrophobes: a molecular dynamics study. J Phys Chem B 112:8634-8644