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Contribution of water molecules in the interior of a protein to the conformational stability.

Takano K, Funahashi J, Yamagata Y, Fujii S, Yutani K
J Mol Biol 274 132-42 (1997)
Related entries: 1oub, 1ouc, 1oud, 1oue, 1ouf, 1oug, 1ouh, 1oui, 1ouj, 1yam, 1yan, 1yao, 1yap, 1yaq, 2hea, 2heb, 2hec, 2hed, 2hef

Cited: 58 times
EuropePMC logo PMID: 9398521

Abstract

Water molecules frequently occur in the interior of globular proteins. To elucidate the contribution of buried water molecules to the conformational stability of a protein, we examined the crystal structures and the thermodynamic parameters of denaturation of six Ile to Ala/Gly mutant human lysozymes, in which a cavity is created at each mutation site by the substitution of a smaller side-chain for a larger one. One or two ordered water molecules were found in the cavities created in some mutants (I106A, I59A and I59G). The cavity volumes for these three mutants were bigger than those that remained empty in the other mutants. The stability of the mutant proteins with the newly introduced water molecules was about 8 kJ/mol higher than that expected from the change in hydrophobic surface area (DeltaDeltaASAHP) exposed upon denaturation. It was concluded that a water molecule in a cavity created in the interior of a protein contributes favorably to the stability.

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  1. A review about nothing: are apolar cavities in proteins really empty? Matthews BW, Liu L. Protein Sci 18 494-502 (2009)
  2. Slow unfolding of monomeric proteins from hyperthermophiles with reversible unfolding. Mukaiyama A, Takano K. Int J Mol Sci 10 1369-1385 (2009)

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  1. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. Guerois R, Nielsen JE, Serrano L. J Mol Biol 320 369-387 (2002)
  2. Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes. Gianese G, Bossa F, Pascarella S. Proteins 47 236-249 (2002)
  3. Binding of buried structural water increases the flexibility of proteins. Fischer S, Verma CS. Proc Natl Acad Sci U S A 96 9613-9615 (1999)
  4. Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. Tahirov TH, Oki H, Tsukihara T, Ogasahara K, Yutani K, Ogata K, Izu Y, Tsunasawa S, Kato I. J Mol Biol 284 101-124 (1998)
  5. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. Loladze VV, Ermolenko DN, Makhatadze GI. J Mol Biol 320 343-357 (2002)
  6. Statistical and molecular dynamics studies of buried waters in globular proteins. Park S, Saven JG. Proteins 60 450-463 (2005)
  7. Structural insights into the stability and flexibility of unusual erythroid spectrin repeats. Kusunoki H, MacDonald RI, Mondragón A. Structure 12 645-656 (2004)
  8. Molecular dynamics study of water penetration in staphylococcal nuclease. Damjanović A, García-Moreno B, Lattman EE, García AE. Proteins 60 433-449 (2005)
  9. Buried water molecules contribute to the conformational stability of a protein. Takano K, Yamagata Y, Yutani K. Protein Eng 16 5-9 (2003)
  10. McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. Till MS, Ullmann GM. J Mol Model 16 419-429 (2010)
  11. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins? Funahashi J, Takano K, Yutani K. Protein Eng 14 127-134 (2001)
  12. Dynamics of hydration in hen egg white lysozyme. Sterpone F, Ceccarelli M, Marchi M. J Mol Biol 311 409-419 (2001)
  13. Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme. Xu J, Baase WA, Quillin ML, Baldwin EP, Matthews BW. Protein Sci 10 1067-1078 (2001)
  14. A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme. Takano K, Yamagata Y, Yutani K. J Mol Biol 280 749-761 (1998)
  15. Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme. Funahashi J, Takano K, Yamagata Y, Yutani K. Protein Eng 12 841-850 (1999)
  16. Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. Takano K, Ota M, Ogasahara K, Yamagata Y, Nishikawa K, Yutani K. Protein Eng 12 663-672 (1999)
  17. The role of conserved waters in conformational transitions of Q61H K-ras. Prakash P, Sayyed-Ahmad A, Gorfe AA. PLoS Comput Biol 8 e1002394 (2012)
  18. Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins. Damjanović A, Schlessman JL, Fitch CA, García AE, García-Moreno E B. Biophys J 93 2791-2804 (2007)
  19. Hydration and protein folding in water and in reverse micelles: compressibility and volume changes. Valdez D, Le Huérou JY, Gindre M, Urbach W, Waks M. Biophys J 80 2751-2760 (2001)
  20. Effect of extra N-terminal residues on the stability and folding of human lysozyme expressed in Pichia pastoris. Goda S, Takano K, Yamagata Y, Katakura Y, Yutani K. Protein Eng 13 299-307 (2000)
  21. Effect of foreign N-terminal residues on the conformational stability of human lysozyme. Takano K, Tsuchimori K, Yamagata Y, Yutani K. Eur J Biochem 266 675-682 (1999)
  22. Interatomic potentials and solvation parameters from protein engineering data for buried residues. Lomize AL, Reibarkh MY, Pogozheva ID. Protein Sci 11 1984-2000 (2002)
  23. Knowledge-based potential defined for a rotamer library to design protein sequences. Ota M, Isogai Y, Nishikawa K. Protein Eng 14 557-564 (2001)
  24. Structural coupling between FKBP12 and buried water. Szep S, Park S, Boder ET, Van Duyne GD, Saven JG. Proteins 74 603-611 (2009)
  25. Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants. Fernández L, Caballero J, Abreu JI, Fernández M. Proteins 67 834-852 (2007)
  26. Hydrophobic effect on the stability and folding of a hyperthermophilic protein. Dong H, Mukaiyama A, Tadokoro T, Koga Y, Takano K, Kanaya S. J Mol Biol 378 264-272 (2008)
  27. Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies. Lu SY, Jiang YJ, Lv J, Zou JW, Wu TX. J Comput Chem 32 1907-1918 (2011)
  28. Studies of Pseudomonas aeruginosa azurin mutants: cavities in beta-barrel do not affect refolding speed. Pozdnyakova I, Guidry J, Wittung-Stafshede P. Biophys J 82 2645-2651 (2002)
  29. A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis. Hagan CL, Johnson RJ, Dhulesia A, Dumoulin M, Dumont J, De Genst E, Christodoulou J, Robinson CV, Dobson CM, Kumita JR. Protein Eng Des Sel 23 499-506 (2010)
  30. Kinetic spectroscopy of heme hydration and ligand binding in myoglobin and isolated hemoglobin chains: an optical window into heme pocket water dynamics. Esquerra RM, López-Peña I, Tipgunlakant P, Birukou I, Nguyen RL, Soman J, Olson JS, Kliger DS, Goldbeck RA. Phys Chem Chem Phys 12 10270-10278 (2010)
  31. Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme. Takano K, Yamagata Y, Yutani K. Proteins 44 233-243 (2001)
  32. Site-specific measurement of water dynamics in the substrate pocket of ketosteroid isomerase using time-resolved vibrational spectroscopy. Jha SK, Ji M, Gaffney KJ, Boxer SG. J Phys Chem B 116 11414-11421 (2012)
  33. Optical detection of disordered water within a protein cavity. Goldbeck RA, Pillsbury ML, Jensen RA, Mendoza JL, Nguyen RL, Olson JS, Soman J, Kliger DS, Esquerra RM. J Am Chem Soc 131 12265-12272 (2009)
  34. Probing the dynamic nature of water molecules and their influences on ligand binding in a model binding site. Cappel D, Wahlström R, Brenk R, Sotriffer CA. J Chem Inf Model 51 2581-2594 (2011)
  35. Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein. Takano K, Yamagata Y, Yutani K. Proteins 45 274-280 (2001)
  36. Water-protein interactions in the molten-globule state of carbonic anhydrase b: an NMR spin-diffusion study. Kutyshenko VP, Cortijo M. Protein Sci 9 1540-1547 (2000)
  37. Dynamics of a protein and water molecules surrounding the protein: hydrogen-bonding between vibrating water molecules and a fluctuating protein. Yoshioki S. J Comput Chem 23 402-413 (2002)
  38. The Significance of the Location of Mutations for the Native-State Dynamics of Human Lysozyme. Ahn M, Hagan CL, Bernardo-Gancedo A, De Genst E, Newby FN, Christodoulou J, Dhulesia A, Dumoulin M, Robinson CV, Dobson CM, Kumita JR. Biophys J 111 2358-2367 (2016)
  39. Direct determination of hydration in the interdigitated and ripple phases of dihexadecylphosphatidylcholine: hydration of a hydrophobic cavity at the membrane/water interface. Channareddy S, Janes N. Biophys J 77 2046-2050 (1999)
  40. Possible role of laccase from Fusarium incarnatum UC-14 in bioremediation of Bisphenol A using reverse micelles system. Chhaya U, Gupte A. J Hazard Mater 254-255 149-156 (2013)
  41. Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins. Chakraborty D, Taly A, Sterpone F. J Phys Chem B 119 12760-12770 (2015)
  42. Buried water molecules contribute to cytochrome f stability. Griffin S, Vitello A, Wittung-Stafshede P. Arch Biochem Biophys 404 335-337 (2002)
  43. Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site. Pujadas G, Palau J. Protein Sci 10 1645-1657 (2001)
  44. Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering. Close DW, Paul CD, Langan PS, Langan PS, Wilce MC, Traore DA, Halfmann R, Rocha RC, Waldo GS, Payne RJ, Rucker JB, Prescott M, Bradbury AR. Proteins 83 1225-1237 (2015)
  45. Minimizing frustration by folding in an aqueous environment. Mattos C, Clark AC. Arch Biochem Biophys 469 118-131 (2008)
  46. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F. J Phys Chem B 119 8939-8949 (2015)
  47. Structure of a thermophilic cyanobacterial b6f-type Rieske protein. Veit S, Takeda K, Tsunoyama Y, Rexroth D, Rögner M, Miki K. Acta Crystallogr D Biol Crystallogr 68 1400-1408 (2012)
  48. A faster way to characterize by triple-quantum-filtered (17)O NMR water molecules strongly bound to macromolecules in solution. Lehoux A, Krzystyniak M, Baguet E. J Magn Reson 148 11-22 (2001)
  49. Molecular dynamics study of naturally existing cavity couplings in proteins. Barbany M, Meyer T, Hospital A, Faustino I, D'Abramo M, Morata J, Orozco M, de la Cruz X. PLoS One 10 e0119978 (2015)
  50. Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme. Guo R, Cang Z, Yao J, Kim M, Deans E, Wei G, Kang SG, Hong H. Proc Natl Acad Sci U S A 117 22146-22156 (2020)
  51. Conserved buried water molecules enable the β-trefoil architecture. Blaber M. Protein Sci 29 1794-1802 (2020)
  52. Pressure-induced structural and hydration changes of proteins in aqueous solutions. Zhang M, Wu Y. Anal Sci 27 1139-1142 (2011)
  53. The mutational effect of Ile58 at subsite C in hen egg-white lysozyme on substrate binding, enzymatic activity, and protein stability. Kawamura S, Chijiiwa Y, Torikata T, Araki T. Biosci Biotechnol Biochem 77 560-565 (2013)
  54. Under proper control, oxidation of proteins with known chemical structure provides an accurate and absolute method for the determination of their molar concentration. Guermant C, Azarkan M, Smolders N, Baeyens-Volant D, Nijs M, Paul C, Brygier J, Vincentelli J, Looze Y. Anal Biochem 277 46-57 (2000)
  55. In silico study of effects of polymorphisms on biophysical chemical properties of oxidized N-terminal domain of X-ray cross-complementing group 1 protein. Mehrzad J, Monajjemi M, Hashemi M. Biochemistry (Mosc) 79 31-36 (2014)
  56. Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor. Kruchinin SE, Kislinskaya EE, Chuev GN, Fedotova MV. Int J Mol Sci 23 14785 (2022)


Related citations provided by authors (2)

  1. Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants.. Takano K, Yamagata Y, Fujii S, Yutani K Biochemistry 36 688-98 (1997)
  2. Contribution of hydrophobic residues to the stability of human lysozyme: calorimetric studies and X-ray structural analysis of the five isoleucine to valine mutants.. Takano K, Ogasahara K, Kaneda H, Yamagata Y, Fujii S, Kanaya E, Kikuchi M, Oobatake M, Yutani K J Mol Biol 254 62-76 (1995)

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