Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus

Journal of Molecular Biology

Volumn 284, Issue 1, 1998, Pages 101-124

  Tahirov, Tahir H ^a,b,c   Oki, Hideyuki ^a   Tsukihara, Tomitake ^a   Ogasahara, Kyoko ^a   Yutani, Katsuhide ^a   Ogata, Kazuhiro ^b,c   Izu, Yukiko ^d   Tsunasawa, Susumu ^d   Kato, Ikunoshin ^d  

^a OSAKA UNIVERSITY   (Japan)

^b Kanagawa Acad Sci Technol (KAST)   (Japan)

^c YOKOHAMA CITY UNIVERSITY   (Japan)

^d TAKARA SHUZO CO LTD   (Japan)

Author keywords

Binuclear reaction center; Cobalt dependent enzyme; Hyperthermophile; Methionine aminopeptidase; Water mediated crystal transformation

Indexed keywords

AMINOPEPTIDASE; COBALT;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PYROCOCCUS; THERMOSTABILITY;

EID: 0032553557     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2146     Document Type: Article

References (101)

1. Abola F. C., Bernstein F. C., Bryant S. H., Koetzle T. F., Weng J. Crystallographic Databases-Information Content, Software Systems, Scientific Applications. 1987;Data Commission of the International Union of Crystallography, Bonn, Cambridge, Chester. p. 107-132.
2. Adams M. W. W. The metabolism of hydrogen by extremely thermophilic, sulfur-dependent bacteria. FEMS Microbiol. Rev. 75:1990;219-238.
3. Adams M. W. W. Enzymes and proteins from organisms that grow near and above 100°C. Annu. Rev. Microbiol. 47:1993;627-658.
4. Adams M. W. W., Perler F. B., Kelly R. M. Extremozymes: expanding the limits of biocatalysis. Biotechnology. 13:1995;662-668.
5. Afrin S. M., Kendall R. L., Hall L., Weaver L. H., Stewart A. E., Matthews B. W., Bradshaw R. A. Eukaryotic methionyl aminopeptidases: two classes of cobalt-dependent enzymes. Proc. Natl Acad. Sci. USA. 92:1995;7714-7718.
6. Aguilar C. F., Sanderson I., Moracci M., Ciaramella M., Nucci R., Rossi M., Pearl L. H. Crystal structure of the β-glycosidase from the hyperthermophilic archeon Sulfolobus solfataricus: resilience as a key factor in thermostability. J. Mol. Biol. 271:1997;789-802.
7. Auerbach G., Huber R., Grattinger M., Zaiss K., Schurig H., Jaenicke R., Jacob U. Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability. Structure. 5:1997;1475-1483.
8. Barlow D. J., Thornton J. M. Ion-pairs in proteins. J. Mol. Biol. 168:1983;867-885.
9. Bazan J. F., Weaver L. H., Roderick S. L., Huber R., Matthews B. W. Sequence and structure comparison suggest that methionine aminopeptidase, prolidase, aminopeptidase P, and creatinase share a common fold. Proc. Natl Acad. Sci. USA. 91:1994;2473-2477.
10. Ben-Bassat A., Bauer K., Chang S. Y., Myambo K., Boosman A., Chang S. Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure. J. Bacteriol. 169:1987;751-757.
11. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
12. Blake P. R., Park J.-B., Zhou Z. H., Hare D. R., Adams M. W. W., Summers M. F. Solution state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium, Pyrococcus furiosus. Protein Sci. 1:1992;1508-1521.
13. Brunger A. T. X-PLOR, Version 3.1. A System for X-ray Crystallography and NMR. 1993;Yale University Press, New Haven.
14. Buehner M., Ford G. C., Moras D., Olsen K. W., Rossman M. G. Three-dimensional structure of d-glyceraldehyde-3-phosphate dehydrogenase. J. Mol. Biol. 90:1974;25-49.
15. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D., Kerlavage A. R., Dougherty B. A., Tomb J.-F., Adams M. D., Reich C. I. et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 273:1995;1058-1073.
16. Burley S. K., David P. R., Taylor A., Lipscomb W. N. Molecular structure of leucine aminopeptidase at 2.7 Å resolution. Proc. Natl Acad. Sci. USA. 87:1990;6878-6882.
17. Burley S. K., David P. R., Lipscomb W. N. Leucine aminopeptidase: bestatin inhibition and a model for enzyme-catalyzed peptide hydrolysis. Proc. Natl Acad. Sci. USA. 88:1991;6916-6920.
18. Burley S. K., David P. R., Sweet R. M., Taylor A., Lipscomb W. N. Sructure determination and refinement of leucine aminopeptidase and its complex with bestatin. J. Mol. Biol. 224:1992;113-140.
19. Cavagnero S., Zhou Z. H., Adams M. W. W., Chan S. I. Responce of rubredoxin from Pyrococcus furiosus to enviromental changes: implications for the origin of hyperthermostability. Biochemistry. 34:1995;9865-9873.
20. Chakrabartty A., Baldwin R. L. Stability of α-helices. Adv. Protein Chem. 46:1995;141-173.
21. Chan M. K., Mukund S., Kletzin A., Adams M. W. W., Rees D. C. Structure of a huperthermophilic tungstopterin enzyme, aldehyde ferrodoxin oxidoreductase. Science. 267:1995;1463-1469.
22. Chang Y.-H., Teichert U., Smith J. A. Molecular cloning, sequencing, deletion, and oveexpression of a methionine aminopeptidase from Saccharomyces cerevisiae. J. Biol. Chem. 267:1992;8007-8011.
23. Chevrier B., Schalk C., D'Orchymont H., Rondeau J.-M., Moras D., Tarnus C. Crystal structure of Aeromonas proteolytica aminopeptidase: a prototypical member of the co-catalytic zinc enzyme family. Structure. 2:1994;283-291.
24. Coll M., Knof S. H., Ohga Y., Messerschmidt A., Huber R. Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures. J. Mol. Biol. 214:1990;597-610.
25. Acta Crystallog. sect. D. 50:1994;760-763.
26. Day M. W., Hsu B. T., Joshua-Tor L., Park J.-B., Zhou Z. H., Adams M. W. W., Rees D. C. X-ray structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1:1992;1494-1507.
27. DeDecker B. S., O'Brien R., Fleming P. J., Geider J. H., Jackson S. P., Sigler P. B. The crystal structure of a hyperthermophilic archaeal TATA-box binding protein. J. Mol. Biol. 264:1996;1072-1084.
28. Dunitz J. D. The entropic cost of bound water in crystals and biomolecules. Science. 264:1994;670.
29. Edmonson S. P., Qui L., Shriver J. W. Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry. 34:1995;13289-13304.
30. Ermler U., Merckel M. C., Thauer R. K., Shima S. Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri-new insights into salt-dependence and thermostability. Structure. 5:1997;635-646.
31. Fiala G., Stetter K. O. Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotropic archaebacteria growing optimally at 100°C. Arch. Microbiol. 145:1986;56-61.
32. Flam F. The chemistry of the life at the margins. Science. 265:1994;471-472.
33. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J.-F., Dougherty B. A., Merrick J. M., McKenney K., Sutton G., FitzHugh W., Fields C., Gocayne J. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512.
34. Flinta C., Persson B., Jornvall H., von Heijne G. Sequence determinants of cytosolic N-terminal protein processing. Eur. J. Biochem. 154:1986;193-196.
35. Forterre P. A hot topic: the origin of hyperthermophiles. Cell. 85:1996;789-792.
36. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Kirkness E. F., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M., Fritchman J. L., Weidman J. F., Small K. V., Sundusky M. et al. The minimal gene complement of Mycoplasma genitalium. Science. 270:1995;397-403.
37. Gandini D., Gogioso L., Bolognesi M., Bordo D. Patterns of ionizable side-chain interactions in protein crystals. Proteins: Struct. Funct. Genet. 24:1996;439-449.
38. Greenblatt H. M., Almog O., Maras B., Spungin-Bialik A., Barra D., Blumberg S., Shoham G. Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 Å resolution. J. Mol. Biol. 265:1997;620-636.
39. Gunasekaran K., Ramakrishnan C., Balaram P. Disallowed Ramachandran conformations of amino acid residues in protein structures. J. Mol. Biol. 264:1996;191-198.
40. Haas E. S., Daniels C. J., Reeve J. N. Genes encoding 5S rRNA and tRNAs in the extremely thermophilic archaebacterium Methamothermus fervidus. Gene. 77:1989;253-263.
41. Hennig M., Darimont B., Sterner R., Kirschner K., Jansonius J. N. 2.0 Å structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability. Structure. 3:1995;1295-1306.
42. Hennig M., Sterner R., Kirschner K., Jansonius J. N. Crystal structure at 2.0 Å resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability. Biochemistry. 36:1997;6009-6016.
43. Hilbert H., Himmelreich R., Plagens H., Herrmann R. Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pnemoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes. Nucl. Acids Res. 24:1996;628-639.
44. Hoeffken H. W., Knof S. H., Bartlett P. A., Huber R., Moellering H., Schumacher G. Crystal structure determination, refinement and molecular model of creatine aminohydrolase from Pseudomonas putida. J. Mol. Biol. 204:1988;417-433.
45. Jaenicke R. Protein stability and molecular adaptation to extreme conditions. Eur. J. Biochem. 202:1991;715-728.
46. Kaneko T., Tanaka A., Sato S., Kotani H., Sazuka T., Miyajima N., Sugiura M., Tabata S. Sequence analysis of the genome of the intracellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features of the 1 Mb region from map positions 64% to 92% of the genome. DNA Res. 2:1995;153-166.
47. Kim H., Lipscomb W. N. X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state. Biochemistry. 32:1993a;8465-8478.
48. Kim H., Lipscomb W. N. Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by x-ray crystallography. Adv. Enzymol. Relat. Areas Mol. 68:1993b;153-213.
49. Kim H., Burley S. K., Lipscomb W. N. Re-refinement of the X-ray crystal structure of bovine lens leucine aminopeptidase complexed with bestatin. J. Mol. Biol. 230:1993;722-724.
50. Kishan K. V. R., Chandra N. R., Sudarsanakumar C., Suguna K., Vijayan M. Water-dependent domain motion and flexibility in ribonuclease A and invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme. Acta Crystallog. sect. D. 51:1995;703-710.
51. Kleywegt G. J., Brünger A. T. Checking your imagination: applications of the free R value. Structure. 4:1996;897-904.
52. Kodandapani R., Suresh C. G., Vijayan M. Crystal structure of low humidity tetragonal lysozyme at 2.1 Å resolution. J. Biol. Chem. 265:1990;16126-16131.
53. Korndorfer I., Steipe B., Huber R., Tomschy A., Jaenicke R. The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 Å resolution. J. Mol. Biol. 246:1995;511-521.
54. Kosa P. F., Ghosh G., DeDecker B. S., Sigler P. B. The 2.1-Å crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box. Proc. Natl Acad. Sci. USA. 94:1997;6042-6047.
55. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
56. Li X., Chang Y.-H. Amino-terminal processing in Saccharomyces cerevisiae is an essential function that requires two distinct methionine aminopeptidases. Proc. Natl Acad. Sci. USA. 92:1995a;12357-12361.
57. Li X., Chang Y.-H. Molecular cloning of a human complementary DNA encoding an initiation factor 2-associated protein (p67). Biochim. Biophys. Acta. 1260:1995b;333-336.
58. Lim J.-H., Yu Y. G., Han Y. S., Cho S., Ahn B.-Y., Kim S.-H., Cho Y. The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 Å resolution: structural basis for thermostability. J. Mol. Biol. 270:1997;259-274.
59. Luzatti P. V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallog. 5:1952;802-810.
60. Macedo-Ribeiro S., Darimont B., Sterner R., Huber R. Small structural changes account for the high thermostability of 1[4Fe-4S] ferrodoxin from hyperthermophilic bacterium Thermotoga Maritima. Structure. 4:1996;1291-1301.
61. Madhusudan A., Kodandapani R., Vijayan M. Protein hydration and water structure: X-ray analysis of a closely packed protein crystal with a very low solvent content. Acta Crystallog. sect. D. 49:1993;234-245.
62. Matthews B. W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
63. Matthews B. W., Nicholson H., Becktel W. J. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl Acad. Sci. USA. 84:1987;6663-6667.
64. Meinnel T., Mechulam Y., Blanquet S. Methionine as translation signal: a review of the enzymes of the pathway in Escherichia coli. Biochimie. 75:1993;1061-1075.
65. Morris A. L., MacArthur M. W., Hutchinson E. G., Thornton J. M. Stereochemical quality of protein structure coordinates. Proteins: Struct. Funct. Genet. 12:1992;345-364.
66. Movva N. R., Semon D., Meyer C., Kawashima E., Wingfield P., Miller J. L., Miller C. G. Cloning and nucleotide sequence of the Salmonella typhimurium pepM gene. Mol. Gen. Genet. 223:1990;345-348.
67. Nagase T., Miyajima N., Tanaka A., Sazuka T., Seki N., Sato S., Tabata S., Ishikawa K., Kawarabayasi Y., Kotani H. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1. DNA Res. 2:1995;37-43.
68. Nakamura K., Nakamura A., Takamatsu H., Yoshikawa H., Yamane K. Cloning and characterization of a Bacillus subtilis gene homologous to E. coli secY. J. Biochem. 107:1990;603-607.
69. Obermaier B., Gassenhuber J., Piravandi E., Domdey H. Sequence analysis of a 78.6 kb segment of the left end of Saccharomyces cerevisiae chromosome II. Yeast. 11:1995;1103-1112.
70. Ogasahara K., Lapshina E. A., Sakai M., Izu Y., Tsunasawa S., Kato I., Yutani K. Electrostatic stabilization of methionine aminopeptidase from hyperthermophile Pyrococcus furiosus. Biochemistry. 37:1998;5939-5946.
71. Otwinowski Z. DENZO. Sawyer L., Yssacs N., Bailey S. Proceedings of the CCP4 Study Weekend. 1993;56-62 Science and Engineer ing Research CouncilDaresbury Laboratory, Warrington.
72. Perutz M., Raidt H. Stereochemical basis of heat stability in bacterial ferredoxins and in hemoglobin A2. Nature. 255:1975;256-259.
73. Rice D. W., Yip K. S., Stillman T. J., Britton K. L., Fuentes A., Connerton I., Pasquo A., Scandurra R., Engel P. C. Insights into the molecular basis of thermal stability from the structure determination of Pyrococcus furiosus glutamate dehydrogenase. FEMS Microbiol. Rev. 18:1996;105-117.
74. Roderick S. L., Matthews B. W. Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli a new type of proteolytic enzyme. Biochemistry. 32:1993;3907-3912.
75. Russell R. J. M., Hough D. W., Danson M. J., Taylor G. L. The crystal structure of sitrate synthase from the thermophilic Archaeon, Thermoplasma acidophilum. Structure. 2:1994;1157-1167.
76. Sakabe N. X-ray diffraction data collection system for modern crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation. Nucl. Instr. Methods Phys. Res. ser. A. 303:1991;448-463.
77. Salunke D. M., Veerapandian B., Kodandapani R., Vijayan M. Water-mediated transformations in protein crystals. Acta Crystallog. sect. B. 41:1985;431-436.
78. Schueler O., Margalit H. Conservation of salt bridges in protein families. J. Mol. Biol. 248:1995;125-135.
79. Skarzynski T., Moody P. C. E., Wonnacot A. J. Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. J. Mol. Biol. 193:1987;171-187.
80. Starich M. R., Sandman K., Reeve J. N., Summers M. NMR structure of HMfB from the hyperthermophile, Methanothermus fervidus, confirms that this archaeal protein is a histone. J. Mol. Biol. 255:1996;187-203.
81. Stetter K. O. Diversity of extremely thermophilic archaebacteria. Brock T. D. The Thermophiles: General, Molecular and Applied Microbiology. 1986;39-74 John Wiley, New York.
82. Stetter K. O., Fiala G., Huber G., Huber R., Segerer G. Hyperthermophilic microorganisms. FEMS Microbiol. Rev. 75:1990;117-124.
83. Strater N., Lipscomb W. N. Transition state analogue L-leucinephosphonic acid bound to bovine lens leucine aminopeptidase: X-ray structure at 1.65 Å resolution in a new crystal form. Biochemistry. 34:1995;9200-9210.
84. Suh J. W., Boylan S. A., Oh S. H., Price C. W. Genetic and transcriptional organization of the Bacillus subtilus spc-alpha region. Gene. 168:1996;17-23.
85. Sundaralingam M., Drendel W., Greaser M. Stabilization of the central long helix of troponin C by intrahelical salt bridges between charged amino acid side chains. Proc. Natl Acad. Sci. USA. 82:1985;7944-7947.
86. Sundaralingam M., Sekharudu Y. C., Yathindra N., Ravichadran V. Ion-pairs in alpha helices. Proteins: Struct. Funct. Genet. 2:1987;64-71.
87. Tahirov T., Oki H., Tsukihara T., Ogasahara K., Izu Y., Tsunasawa S., Kato I., Yutani K. Crystallization and preliminary X-ray analysis of methionine aminopeptidase from hyperthermophilic bacterium, Pyrococcus furiosus. Acta Crystallog. sect. D. 53:1997;798-801.
88. Tahirov T., Oki H., Tsukihara T., Ogasahara K., Yutani K., Peters Libeu C., Izu Y., Tsunasawa S., Kato I. High resolution crystals of methionine aminopeptidase from Pyrococcus furiosus obtained by water-mediated transformation. J. Struct. Biol. 121:1998;68-72.
89. Takano K., Funahashi J., Yamagata Y., Fujii S., Yutani K. Contribution of water molecules in the interior of a proteinto the conformational stability. J. Mol. Biol. 274:1997;132-142.
90. Tanner J. J., Hecht R. M., Krause K. L. Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticusD-glyceraldehyde-3-phosphate dehydrogenase at 2.5 Å resolution. Biochemistry. 35:1996;2597-2609.
91. Tomb J.-F., White O., Kerlavage A. R., Clayton R. A., Sutton G., Fleischmann R. D., Ketchum K. A., Klenk H. P., Gill S., Dougherty B. A., Nelson K., Quackenbush J., Zhou L., Kirkness E. F., Peterson S. et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 388:1997;539-547.
92. Tsunasawa S., Izu Y., Miyagi M., Kato I. Methionine aminopeptidase from hyperthermophilic archaeon Pyrococcus furiosus: molecular cloning and overexpression in Escherichia coli of the gene, and characteristics of the enzyme. J. Biochem. 122:1997;843-850.
93. Vallee B. L., Auld D. S. New perspective of zinc biochemistry: co-catalytic site in multi-zinc enzymes. Biochemistry. 32:1993;6493-6500.
94. Watanabe K., Masuda T., Ohashi H., Mihara H., Suzuki Y. Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur. J. Biochem. 226:1994;277-283.
95. Watanabe K., Hata Y., Kizaki H., Katsube Y., Suzuki Y. The refined structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: structural characterization of proline-substitution sites for protein thermostabilization. J. Mol. Biol. 269:1997;142-153.
96. Williams M. A., Goodfellow J. M., Thornton J. M. Buried waters and internal cavities in monomeric proteins. Protein Sci. 3:1994;1224-1235.
97. Wilmot C. M., Thornton J. M. β-Turns and their distortions: a proposed new nomenclature. Protein Eng. 3:1990;479-493.
98. Wingfield P. T., Graber P., Turcatti G., Movva N. R., Pelletier M., Craig S., Rose K., Miller C. G. Purification and characterization of methionine-specific aminopeptidase from Salmonella typhimurium. Eur. J. Biochem. 180:1989;23-32.
99. 67). J. Biol. Chem. 268:1993;10796-10801.
100. Yip K. S. P., Stillman T. J., Britton K. L., Artymiuk P. J., Baker P. J., Sedelnikova S. E., Engel P. C., Pasquo A., Chiaraluce R., Consalvi V., Scandurra R., Rice D. W. The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pairs networks in maintaining enzyme stability at extreme temperatures. Structure. 3:1995;1147-1158.
101. Zhang L., Hermans J. Hydrophilicity of cavities in proteins. Proteins: Struct. Funct. Genet. 24:1996;433-438.