The importance of water

Astrochemistry and Astrobiology

Volumn , Issue , 2013, Pages 169-210

  Ball, Philip ^a  

^a NONE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROPHOBICITY; SUBSTRATES;

ADAPTIVE COMPONENTS; BIOCHEMICAL REACTIONS; BIOMOLECULAR INTERACTIONS; ELECTRONIC EXCITATION ENERGY; HYDROPHOBIC INTERACTIONS; PROTON TRANSPORT; RECEPTOR SUBSTRATES; WATER SCARCITY;

PROTEINS;

EID: 84969821158     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-31730-9_6     Document Type: Chapter

References (118)

1. Henderson L (1913) The fitness of the environment. Macmillan, New York
2. Ferber D (2004) Microbes made to order. Science 303: 158-161
3. Chin JW, Cropp TA, Anderson JC, Zhang Z, Schultz PG (2003) An expanded eukaryotic genetic code. Science 301: 964-967
4. Kool ET (2002) Replacing the nucleobases in DNA with designer molecules. Acc Chem Res 35: 936-943
5. Ball P (2007) Water as an active constituent in cell biology. Chem Rev 108: 74-108
6. Katz JJ, Crespi HL (1966) Deuterated organisms: cultivation and uses. Science 151: 1187-1194
7. Benner SA, Ricardo A, Carrigan MA (2004) Is there a common chemical model for life in the universe? Curr Opin Chem Biol 8: 672-689
8. Fernández A, Scott R (2003) Dehydron: a structurally encoded signal for protein interaction. Biophys J 85: 1914-1928
9. Lynden-Bell RM, Morris SC, Barrow JD, Finney JL, Harper CL (eds) (2010) Water and life. CRC Press, Boca Raton
10. Franks F (2000) Water: a matrix of life. Royal Society of Chemistry, Cambridge
11. Wernet Ph, Nordlund D, Bergmann U, Cavalleri M, Odelius M, Ogasawara H, Näslund LÅ, Hirsch TK, Ojamäe L, Glatzel P, Pettersson LGM, Nilsson A (2004) The structure of the first coordination shell in water. Science 304: 995-999
12. Head-Gordon T, Johnson ME (2006) Tetrahedral structure or chains for liquid water. Proc Natl Acad Sci USA 103: 7973-7977
13. Luzar A, Chandler D (1996) Hydrogen-bond kinetics in liquid water. Nature 379: 55-57
14. Sciortino F, Geiger A, Stanley HE (1991) Effects of defects on molecular mobility in liquid water. Nature 354: 218-221
15. Ellis RJ, Minton AP (2003) Join the crowd. Nature 425: 27-28
16. Major RC, Houston JE, McGrath MJ, Siepmann JI, Zhu X-Y (2006) Viscous water meniscus under confinement. Phys Rev Lett 96: 177803
17. Li T-D, Gao J, Szoszkiewicz R, Landman U, Riedo E (2007) Structured and viscous water in subnanometer gaps. Phys Rev B 75: 115415
18. Henderson D (ed) (1992) Fundamentals of inhomogeneous fluids. CRC Press, Boca Raton
19. Hassan S, Steinbach P (2011) Water-exclusion and liquid-structure forces in implicit solvation. J Phys Chem B 115: 14668-14682
20. Stradner A, Sedgwick H, Cardinaux F, Poon WCK, Egelhaaf SU, Schurtenberger P (2004) Equilibrium cluster formation in concentrated protein solutions and colloids. Nature 432: 492-495
21. Gliko O, Pan W, Katsonis P, Neumaier N, Galkin O, Weinkauf S, Velikov PG (2007) Metastable liquid clusters in super- and undersaturated protein solutions. J Phys Chem B 111: 3106-3114
22. Pollack GH (2001) Cells, gels, and the engines of life. Ebner & Sons, Seattle
23. ChaplinM(2006) Do we underestimate the importance of water in cell biology? Nat Rev Mol Cell Biol 7: 861-866
24. Halle B, Persson E (2008) Cell water dynamics on multiple time scales. Proc Natl Acad Sci USA 105: 6266-6271
25. Tanford C (1980) The hydrophobic effect, 2nd edn. Wiley, New York
26. Blokzijl W, Engberts JBFN (1993) Hydrophobic effects. Opinions and facts. Angew Chem Int Ed 32: 1545-1579
27. Frank HS, Evans MW (1945) Free volume and entropy in condensed systems. III. Entropy in binary liquid mixtures; partial molal entropy in dilute solutions; structure and thermodynamics in aqueous solutions. J Chem Phys 13: 507-532
28. Kauzmann W (1969) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14: 1-63
29. Ball P (2003) How to keep dry in water. Nature 423: 25-26
30. Lum K, Chandler D, Weeks JD (1999) Hydrophobicity at small and large length scales. J Phys Chem B 103: 4570-4577
31. Wallqvist A, Berne BJ (1995) Computer simulation of hydrophobic hydration forces on stacked plates at short range. J Phys Chem 99: 2893-2899
32. ten Wolde PR, Chandler D (2002) Drying-induced hydrophobic polymer collapse. Proc Natl Acad Sci USA 99: 6539-6543
33. Li ITS, Walker GC (2011) Signature of hydrophobic hydration in a single polymer. Proc Natl Acad Sci USA 108: 16527-16532
34. Liu P, Huang X, Zhou R, Berne BJ (2005) Observation of a dewetting transition in the collapse of the melittin tetramer. Nature 437: 159-162
35. Zhou R, Huang X, Margulis CJ, Berne BJ (2004) Hydrophobic collapse in multidomain protein folding. Science 305: 1605-1609
36. Hua L, Huang X, Liu P, Zhou R, Berne BJ (2007) Nanoscale dewetting transition in protein complex folding. J Phys Chem B 111: 9069-9077
37. Giovambattista N, Lopez CF, Rossky PJ, Debenedetti PG (2008) Hydrophobicity of protein surfaces: separating geometry from chemistry. Proc Natl Acad Sci USA 105: 2274-2279
38. Patel AJ, Varrily P, Chandler D (2010) Fluctuations of water near extended hydrophobic and hydrophilic surfaces. J Phys Chem B 114: 1632-1637
39. Patel AJ, Varilly P, Jamadagni SN, Hagan MF, Chander D, Garde S (2012) Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function. J Phys Chem B. doi: 10.1021/jp2107523
40. Onuchic JN, Luthey-Schulten Z, Wolynes PG (1997) Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 48: 545-600
41. Dobson CM (2003) Protein folding and misfolding. Nature 426: 884-890
42. Zong C, Papaoian GA, Ulander J, Wolynes PG (2006) Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of a/b proteins. J Am Chem Soc 128: 5168-5176
43. Patel AJ, Varilly P, Jamadagni SN, Acharya H, Garde S, Chandler D (2011) Extended surfaces modulate hydrophobic interactions of neighboring solutes. Proc Natl Acad Sci USA 108: 17678-17683
44. Davidovic M, Mattea C, Qvist J, Halle B (2009) Protein cold denaturation as seen from the solvent. J Am Chem Soc 131: 1025-1036
45. Hua L, Zhou R, Thirumalai D, Berne BJ (2008) Urea denaturation by stronger dispersion interactions with proteins that water implies a 2-stage unfolding. Proc Natl Acad Sci USA 105: 16928-16933
46. England JL, Pande VS, Haran G (2008) Chemical denaturants inhibit the onset of dewetting. J Am Chem Soc 130: 11854-11855
47. Zangi R, Zhou R, Berne BJ (2009) Urea’s action on hydrophobic interactions. J Am Chem Soc 131: 1535-1541
48. Bennion BJ, Daggett V (2003) The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci USA 100: 5142-5147
49. Towey JJ, Soper AK, Dougan L (2011) Preference for isolated water molecules in a concentrated glycerol-water mixture. J Phys Chem B 115: 7799-7807
50. Pioliti R, Sapir L, Harries D (2009) The impact of polyols on water structure in solution: a computational study. J Phys Chem A 113: 7548-7555
51. Dougan L, Genchev GZ, Lu H, Fernández JM (2011) Probing osmolyte participation in the unfolding transition state of a protein. Proc Natl Acad Sci USA 108: 9759-9764
52. Reddy G, Straub E, Thirumalai D (2010) Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires. Proc Natl Acad Sci USA 107: 21459-21464
53. Fernández A, Kardos J, Scott LR, Goto Y, Berry RS (2003) Structural defects and the diagnosis of amyloidogenic propensity. Proc Natl Acad Sci USA 100: 6446-6451
54. Fernández A, Lynch M (2011) Non-adaptive origins of interactome complexity. Nature 474: 502-505
55. De Simone A, Dhulesia A, Soldi G, Vendruscolo M, Hsu S-TD, Chiti F, Dobson CM (2011) Experimental free energy surfaces reveal the mechanisms of maintenance of protein stability. Proc Natl Acad Sci USA 108: 21057-21062
56. Yu H, Rick S (2010) Free energy, entropy, and enthalpy of a water molecule in various protein environments. J Phys Chem B 114: 11552-11560
57. Baron R, Setny P, McCammon JA (2010) Water in cavity-ligand recognition. J Am Chem Soc 132: 12091-12097
58. Snyder PW, Mecinovic J, Moustakas DT, Thomas SW III, Harder M, Mack ET, Lockett MR, Héroux A, Sherman W, Whitesides GM (2011) Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Proc Natl Acad Sci USA 108: 17889-17894
59. Yin H, Hummer G, Rasaiah JC (2007) Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J Am Chem Soc 129: 7369-7377
60. Ahmad M, Gu W, Geyer T, Helms V (2011) Adhesive water networks facilitate binding of protein interfaces. Nat Commun 2: 261
61. Sahai MA, Biggin PC (2011) Quantifying water-mediated protein-ligand interactions in a glutamate receptor: a DFT study. J Phys Chem B 115: 7085-7096
62. Tame JRH, Sleigh SH, Wilkinson AJ, Ladbury JE (1996) The role of water in sequenceindependent ligand binding by an oligopeptide transporter protein. Nat Struct Biol 3: 998-1001
63. Grossman M, Born B, Heyden M, Tworowski D, Fields GB, Sagi I, Havenith M (2011) Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site. Nat Struct Mol Biol 18: 1102-1108
64. Gnanasekaran R, Xu Y, Leitner DM (2010) Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 114: 16989-16996
65. Rodriquez JC, Zeng Y, Wilks A, Rivera M (2007) The hydrogen-bonding network in heme oxygenase also functions as a modulator of enzyme dynamics: chaotic motions upon disrupting the H-bond network in heme oxygenase from Psuedomonas aeruginosa. J Am Chem Soc 129: 11730-11742
66. Krauss M, Gilson HSR, Gresh N (2001) Structure of the first-shell active site in metallolactamase: effect of water ligands. J Phys Chem B 105: 8040-8049
67. Wang L, Yu X, Hu P, Broyde S, Zhang Y (2007) A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. J Am Chem Soc 129: 4731-4737
68. Sicking W, Korth H-G, de Groot H, Sustmann R (2008) On the functional role of a water molecule in clade 3 catalases: a proposal for the mechanism by which NADPH prevents the formation of compound II. J Am Chem Soc 130: 7345-7356
69. Agmon N (1995) The Grotthuss mechanism. Chem Phys Lett 244: 456-462
70. Garczarek F, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR Spectroscopy. Nature 439: 109-112
71. Mathias G, Marx D (2007) Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proc Natl Acad Sci USA 104: 6980-6985
72. Chen H, Ilan B, Wu Y, Zhu F, Schulten K, Voth GA (2007) Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. Biophys J 92: 46-60
73. Brändén M, Sandén T, Brzezinski P, Widengren J (2006) Localized proton microcircuits at the biological membrane-water interface. Proc Natl Acad Sci USA 103: 19766-19770
74. Springer A, Hagen V, Cherepanov DA, Antonenko YN, Pohl P (2011) Protons migrate along interfacial water without significant contributions from jumps between ionizable groups on the membrane surface. Proc Natl Acad Sci USA 108: 14461-14466
75. Beckstein O, Biggin PC, Sansom MSPA (2001) A hydrophobic gating mechanism for nanopores. J Phys Chem B 105: 12902-12905
76. Rasaiah JC, Garde S, Hummer G (2008) Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu Rev Phys Chem 59: 713-740
77. Anishkin A, Sukharev S (2004) Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. Biophys J 86: 2883-2895
78. Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A °. Nature 473: 55-60
79. Rupley JA, Careri G (1991) Protein hydration and function. Adv Protein Chem 41: 37-172
80. Purkiss A, Skoulakis S, Goodfellow JM (2001) The protein-solvent interface: a big splash. Phil Trans R Soc Lond A Math Phys Eng Sci 359: 1515-1527
81. Olano LR, Rick SW (2004) Hydration free energies and entropies for water in protein interiors. J Am Chem Soc 126: 7991-8000
82. Okimoto N, Nakamura T, Suenaga A, Futatsugi N, Hirano Y, Yamaguchi I, Ebisuzaki T (2004) Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase. J Am Chem Soc 126: 13132-13139
83. Bizzarri AR, Cannistraro S (2002) Molecular dynamics of water at the protein-solvent interface. J Phys Chem B 106: 6617-6633
84. Russo D, Murarka RK, Copley JRD, Head-Gordon T (2005) Molecular view of water dynamics near model peptides. J Phys Chem B 109: 12966-12975
85. Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357: 423-424
86. Reat V, Dunn R, Ferrand M, Finney JL, Daniel RM, Smith JC (2000) Solvent dependence of dynamic transitions in protein solutions. Proc Natl Acad Sci USA 97: 9961-9966
87. Tarek M, Tobias DJ (2002) Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Phys Rev Lett 88: 138101
88. Chen S-H, Liu L, Fratini E, Baglioni P, Faraone A, Mamontov E (2006) Observation of fragile-to-strong dynamic crossover in protein hydration water. Proc Natl Acad Sci USA 103: 9012-9016
89. Tournier AL, Xu J, Smith JC (2003) Translational hydration water dynamics drives the protein glass transition. Biophys J 85: 1871-1875
90. Smolin N, Oleinikova A, Brovchenko I, Geiger A, Winter R (2005) Properties of spanning water networks at protein surfaces. J Phys Chem B 109: 10995-11005
91. Gallat F-X, Laganowsky A, Wood K, Gabel F, van Eijk L, Wuttke J, Moulin M, Härtlein M, Eisenberg D, Colletier J-P, Zaccai G, Weik M. (2012) Dynamical coupling of intrinsically disordered proteins and their hydration water: comparison with folded soluble and membrane proteins. Biophys J 103: 129-136
92. Magazu S, Migliardo F, Benedetto A (2011) Puzzle of protein dynamical transition. J Phys Chem B 115: 7736-7743
93. Lopez M, Kurkal-Siebert V, Dunn RV, Tehei M, Finey JL, Smith JC, Daniel RM (2010) Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions. Biophys J 99: L62-L64
94. Turner DH (2000) Conformational changes. In: Bloomfield VA, Crothers DM, Tinoco I (eds) Nucleic acids. Structure, properties and functions. University Science, Sausalito, pp 259-334
95. Rueda M, Kalko SG, Luque FJ, Orozco M (2003) The structure and dynamics of DNA in the gas phase. J Am Chem Soc 125: 8007-8014
96. Cui S, Albrecht C, Kühner F, Gaub HE (2006) Weakly bound water molecules shorten singlestranded DNA. J Am Chem Soc 128: 6636-6639
97. Kopka ML, Fratini AV, Drew HR, Dickerson RE (1983) Ordered water structure around a B-DNA dodecamer: a quantitative study. J Mol Biol 163: 129-146
98. Szyc L, Yang M, Elsaesser T (2010) Ultrafast energy exchange via water-phosphate interactions in hydrated DNA. J Phys Chem B 114: 7951-7957
99. Ha JH, Capp MW, Hohenwalter MD, Baskerville M, Record MT Jr (1992) Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA: possible thermodynamic origins of the ‘glutamate effect’ on protein-DNA interactions. J Mol Biol 228: 252-264
100. Robinson CR, Sligar SG (1993) Molecular recognition mediated by bound water: a mechanism for star activity of the restriction enzyme endonuclease EcoRI. J Mol Biol 234: 302-306
101. Fuxreiter M, Mezei M, Simon I, Osman R (2005) Interfacial water as a ‘hydration fingerprint’ in the noncognate complex of BamHI. Biophys J 89: 903-911
102. Brovchenko I, Krukau A, Oleinikova A, Mazur AK (2006) Water percolation governs polymorphic transitions and conductivity of DNA. Phys Rev Lett 97: 137801
103. Brovchenko I, Krukau A, Oleinikova A, Mazur AK (2007) Water clustering and percolation in low hydration DNA shells. J Phys Chem B 111: 3258-3266
104. Reiter GF, Senesi R, Mayers J (2010) Changes in the zero-point energy of protons as the source of the binding energy of water to A-phase DNA. Phys Rev Lett 105: 148101
105. Shui X, Sines CC, McFail-Isom L, VanDerveer D, Williams LD (1998) Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 37: 16877-16887
106. Sorin EJ, Rhee YM, Pande VS (2005) Does water play a structural role in the folding of small nucleic acids? Biophys J 88: 2516-2524
107. Tjivikua T, Ballester P, Rebek J Jr (1990) Self-replicating system. J Am Chem Soc 112: 1249-1250
108. Kunz W, Henle J, Ninham BW (2004) ‘Zur Lehre von der Wikrung der Salze’ (about the science of the effect of salts): Franz Hofmeister’s historical papers. Curr Opin Colloid Interface Sci 9: 19-37
109. Tobias D, Hemminger J (2008) Getting specific about specific ion effects. Science 319: 1197-1198
110. Jungwirth P, Tobias DJ (2006) Specific ion effects at the air/water interface. Chem Rev 106: 1259-1281
111. Petersen PB, Saykally RJ (2006) On the nature of ions at the liquid water surface. Annu Rev Phys Chem 57: 333-364
112. Zangi R, Berne BJ (2006) Aggregation and dispersion of small hydrophobic particles in aqueous electrolyte solutions. J Phys Chem B 110: 22736-22741
113. Zangi R, Hagen M, Berne BJ (2007) Effects of ions on the hydrophobic interaction between two plates. J Am Chem Soc 129: 4678-4686
114. Petersen MK, Iyengar SS, Day TJF, Voth GA (2004) The hydrated proton at the water liquid/vapor interface. J Phys Chem B 108: 14804-14806
115. Buch V, Milet A, Vácha R, Jungwirth P, Devlin JP (2007) Proc Natl Acad Sci USA 104: 7342
116. Beattie JK, Djerdjev AM, Warr GG (2009) The surface of neat water is basic. Faraday Discuss 141: 31-39
117. Creux P, Lachaise J, Graciaa A, Beattie JK, Djerdjev AM (2009) Strong specific hydroxide ion binding at the pristine oil/water and air/water interfaces. J Phys Chem B 113: 14146-14150
118. Daniel RM, Finney JL, Stoneham M (2004) The molecular basis of life: is life possible without water? Phil Trans R Soc Lond B 359: 1143-1328