Abstract
The structures of buried water molecules were studied in an ensemble of high-quality and non-redundant protein crystal structures. Buried water molecules were clustered and classified in lake-like clusters, which are completely isolated from the bulk solvent, and bay-like clusters, which are in contact with the bulk solvent through a surface water molecule. Buried water molecules are extremely common: lake-like clusters are found in 89 % of the protein crystal structures and bay-like clusters in 93 %. Clusters with only one water molecule are much more common than larger clusters. Both cluster types incline to be surrounded by loop residues, and to a minor extent by residues in extended secondary structure. Helical residues on the contrary do not tend to surround clusters of buried water molecules. One buried water molecule is found every 30–50 amino acid residues, depending on the secondary structures that are more abundant in the protein. Both main- and side-chain atoms are in contact with buried waters; they form four hydrogen bonds with the first water and 1–1.5 additional hydrogen bond for each additional water in the cluster. Consequently, buried water molecules appear to be firmly packed and rigid like the protein atoms. In this regard, it is remarkable to observe that prolines often surround water molecules buried in the protein interior. Interestingly, clusters of buried water molecules tend to be just beneath the protein surface. Moreover, water molecules tend to form a one-dimensional wire rather than more compact arrangements. This agrees with recent evidence of the mechanisms of solvent exchange between internal cavities and bulk solvent.
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References
Berman HM et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242
Bernstein FC et al (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535–542
Carugo O (2008) Amino acid composition and protein dimension. Protein Sci 17:2187–2191
Carugo O, Argos P (1997) Correlation between side chain mobility and conformation in protein structures. Prot Eng 10:777–787
Carugo O, Argos P (1998) Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors. Proteins 31:201–213
Collins G, Quillins ML, Matthews BW, Grunner SM (2005) Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci USA 102:16668–16671
Connolly ML (1985a) Atomic size packing defects in proteins. Int J Pept Protein Res 28:360–363
Connolly ML (1985b) Computation of molecular volume. J Am Chem Soc 107:1118–1124
Denisov VP, Halle B (1995) Protein hydration dynamics in aqueous solution: a comparison of bovine pancreatic trypsin inhibitor and ubiquitin by oxygen-17 spin relaxation dispersion. J Mol Biol 245:682–697
Denisov VP, Halle B, Peters J, Hoerlein HD (1995) Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant. Biochemistry 34:9046–9051
Denisov VP, Peters J, Hörlein HD, Halle B (1996) Using buried water molecules to explore the energy landscape of proteins. Nat Struct Biol 3:505–509
Denisov VP, Peters J, Hoerlein H-D, Halle B (2004) Accelerated exchange of a buried water molecule in selectively disulfide-reduced bovine pancreatic trypsin inhibitor. Biochemistry 43:12020–12027
Fischer S, Smith JC, Verma C (2001) Dissecting the vibrational entropy change on protein/ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor. J Phys Chem B 105:8050–8055
Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566–579
Griffin S, Vitello A, Wittung-Stafshede P (2002) Buried water molecules contribute to cytochrome f stability. Arch Biochem Biophys 404:335–337
Hubbard SE, Thornton JM (1993) NACCESS. University College London, Department of Biochemistry and Molecular Biology, London, Computer Program
Koellner G, Kryger G, Millard CB, Silman I, Sussman JL, Steiner T (2000) Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. J Mol Biol 296:713–735
Laage D, Hynes JT (2006) A molecular jump mechanism of water reorientation Science 311:832–835
Lauble H, Kennedy MC, Beinert H, Stout CD (1992) Crystal structures of aconitase with isocitrate and nitroisocitrate bound. Biochemistry 31:2735–2748
Likic VA, Juranic N, Macura S, Prendergast FG (2000) A “structural” water molecule in the family of fatty acid binding proteins. Prot Sci 9:497–504
Loris R et al (1999) Conserved water molecules in a large family of microbial ribonucleases. Proteins 36(36):117–134
McDonald IK, Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238:777–793
Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540
Park S, Saven JG (2005) Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 60:450–463
Pavlov MY, Fedorov BA (1983) Improved techniques for calculating X-ray scattering intensity of biopolymers in solution: evaluation of the form, volume, and surface of a particle. Biopolymers 22:1517–1522
Persson E, Halle B (2008) Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules. J Am Chem Soc 130:1774–1787
Persson F, Halle B (2013) Transient Access to the Protein Interior: simulation versus NMR. J Am Chem Soc 135:8735–8748
Pintar A, Carugo O, Pongor S (2003a) Atom depth as a descriptor of the protein interior. Biophys J 84:2553–2561
Pintar A, Carugo O, Pongor S (2003b) Atom depth in protein structure and function. Trends Biochem Sci 28:593–597
Pintar A, Carugo O, Pongor S (2003c) DPX: for the analysis of the protein core. Bioinformatics 19:313–314
Rashin AA, Iofin M, Honig B (1986) Internal cavities and buried waters in globular proteins. Biochemistry 25:3619–3625
Renthal R (2008) Buried water molecules in helical transmembrane proteins. Prot Sci 17:293–298
Roux B, Nina M, Pomès R, Smith JC (1996) Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J 71:670–681
Szep S, Park S, Boder ET, Van Duyne GD, Saven JG (2009) Structural coupling between FKBP12 and buried water. Proteins 74:603–611
Takano K, Yamagata Y, Yutano K (2003) Buried water molecules contribute to the conformational stability of a protein. Prot Eng 16(16):5–9
Teze S, Hendrickx J, Dion M, Tellier C, Woods VLJ, Tran V, Sanejouand Y-H (2013) Conserved water molecules in family 1 glycosidases: a DXMS and molecular dynamics study. Biochemistry 52:5900–5910
Vaitheeswaran S, Yin H, Rasaiah JC, Hummer G (2004) Water clusters in nonpolar cavities. Proc Natl Acad Sci USA 101:17002–17005
Vlahovicek K, Pintar A, Parthasarathi L, Carugo O, Pongor S (2005) CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures. Nucleic Acids Res 33:W252–W254
Vrielink A, Lloyd LF, Blow DM (1991) Crystal structure of cholesterol oxidase from Brevibacterium sterolicum refined at 1.8 A resolution. J Mol Biol 219:533–554
Wade RC, Mazor MH, McCammon JA, Quiocho FA (1990) Hydration of cavities in proteins: a molecular dynamics approach. J Am Chem Soc 112:7057–7059
Williams MA, Goodfellow JM, Thornton JM (1994) Buried waters and internal cavities in monomeric proteins. Prot Sci 3:1224–1235
Wuethrich K, Otting G, Liepinsh E (1992) Protein hydration in aqueous solution. Faraday Discuss 93:35–45
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Carugo, O. Statistical survey of the buried waters in the Protein Data Bank. Amino Acids 48, 193–202 (2016). https://doi.org/10.1007/s00726-015-2064-4
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DOI: https://doi.org/10.1007/s00726-015-2064-4