Conformational substates in enzyme mechanism: The 120 K structure of α- lytic protease at 1.5 Å resolution

Protein Science

Volumn 6, Issue 7, 1997, Pages 1375-1386

  Rader, Stephen D ^c   Agard, David A ^a,b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NONE

Author keywords

B factor; Cryocrystallography; Dynamics; Plasticity; Serine protease; Substrate specificity; Thermal expansion; lytic protease

Indexed keywords

BACTERIAL ENZYME; SERINE PROTEINASE;

ARTICLE; DYNAMICS; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; NONHUMAN; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS);

EID: 0030877587     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060701     Document Type: Article

References (42)

1. Alber T. Gilbert WA, Ponzi DR, Petsko GA. 1983. The role of mobility in the substrate binding and catalytic machinery of enzymes. Ciba Found Symp 93:4-24.
2. Bone R, Frank D, Kettner CA, Agard DA. 1989a. Structural analysis of specificity: Alpha-lytic protease complexes with analogs of reaction intermediates. Biochemistry 28(19):7600-7609.
3. Bone R, Fujishige A, Kettner CA, Agard DA. 1991a. Structural basis for broad specificity in alpha-lytic protease mutants. Biochemistry 30(43):10388-10398.
4. Bone R, Sampson NS, Bartlett PA, Agard DA. 1991b. Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate esters. Biochemistry 30(8):2263-2272.
5. Bone R, Shenvi AB, Kettner CA, Agard DA. 1987. Serine protease mechanism: Structure of an inhibitory complex of alpha-lytic protease and a tightly bound peptide boronic acid. Biochemistry 26(24):7609-7614.
6. Bone R, Silen JL, Agard DA. 1989b. Structural plasticity broadens the specificity of an engineered protease. Nature 339(6221):191-195.
7. Brayer GD, Delbaere LT, James MN. 1979. Molecular structure of the alphalytic protease from Myxobacter 495 at 2.8 Ångstroms resolution. J Mol Biol 131(4):743-775.
8. Brunger AT. 1992. X-PLOR: A system for X-ray crystallography and NMR. New Haven, Connecticut: Yale University Press.
9. Burling FT, Weis WI, Flaherty KM, Brünger AT. 1996. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 271(5245):72-77.
10. Caspar DL, Clarage J, Salunke DM, Clarage M. 1988. Liquid-like movements in crystalline insulin. Nature 332(6165):659-662.
11. CCP4. 1979. Collaborative Computing Project No. 4. A suite of programs for protein crystallography. Warrington, UK: SERC Daresbury Laboratory.
12. Chen H, Hughes DD, Chan TA, Sedat JW, Agard DA. 1996. IVE (Image Visualization Environment) - A software platform for all three-dimensional microscopy applications. J Struct Biol 116(1):56-60.
13. Cusack S, Doster W. 1990. Temperature dependence of the low frequency dynamics of myoglobin. Measurement of the vibrational frequency distribution by inelastic neutron scattering. Biophys J 58(1):243-251.
14. Doucet J, Benoit JP. 1987. Molecular dynamics studied by analysis of the X-ray diffuse scattering from lysozyme crystals. Nature 325(6105):643-646.
15. Earnest T, Fauman E, Craik CS, Stroud R. 1991. 1.59 Å structure of trypsin at 120 K: Comparison of low temperature and room temperature structures. Proteins Struct Funct Genet 10(3):171-187.
16. Frauenfelder H, Hartmann H, Karplus M, Kuntz ID Jr, Kuriyan J, Parak F, Petsko GA, Ringe D, Tilton RF Jr, Connolly ML et al. 1987. Thermal expansion of a protein. Biochemistry 26(1):254-261.
17. Frauenfelder H, Petsko GA, Tsernoglou D. 1979. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280(5723):558-563.
18. Frauenfelder H, Sligar SG, Wolynes PG. 1991. The energy landscapes and motions of proteins. Science 254(5038):1598-1603.
19. Fujinaga M, Delbaere LT, Brayer GD, James MN. 1985. Refined structure of alpha-lytic protease at 1.7 Å resolution. Analysis of hydrogen bonding and solvent structure. J Mol Biol 184(3):479-502.
20. Hartmann H, Parak F, Steigemann W, Petsko GA, Ponzi DR, Frauenfelder H. 1982. Conformational substates in a protein: Structure and dynamics of metmyoglobin at 80 K. Proc Natl Acad Sci USA 79(16):4967-4971.
21. Hayward S, Kitao A, Go N. 1995. Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis. Proteins Struct Funct Genet 23(2):177-186.
22. Jones TA. 1982. FRODO. In: Sayre D., ed. Computational crystallography. Oxford, UK: Oxford University. pp 303-317.
23. Kettner CA, Bone R, Agard DA, Bachovchin WW. 1988. Kinetic properties of the binding of alpha-lytic prolease to peptide boronic acids. Biochemistry 27(20):7682-7688.
24. Kleywegt GJ. 1994. A super position. In: ESF/CCP4 Newsletter, pp 9-14.
25. Kleywegt GJ. 1995. Dictionaries for heteros. In: ESF/CCP4 Newsletter. pp 45-50.
26. Kossiakoff AA, Randal M, Guenot J, Eigenbrot C. 1992. Variability of conformations at crystal contacts in bpti represent true low-energy structures: Correspondence among lattice packing and molecular dynamics structures. Proteins Struct Funct Genet 14:65-74.
27. Kurinov IV, Harrison RW. 1995. The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water Acta Crystallogr D 51:98-109.
28. Kuriyan J, Osapay K, Burley SK, Brünger AT, Hendrickson WA, Karplus M. 1991. Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins Struct Funct Genet 10(4):340-358.
29. Leeson DT, Berg O, Wiersma DA. 1994. Low-temperature protein dynamics studied by the long-lived stimulated photon echo. J Phys Chem 98:3913-3916.
30. Leeson DT, Wiersma DA. 1995. Looking into the energy landscape of myoglobin. Nature Struct Biol 2(10):848-851.
31. Mace JE, Agard DA. 1995. Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protcase: A new target for engineering substrate specificity. J Mol Biol 254(4):720-736.
32. Mace JE, Wilk BJ, Agard DA. 1995. Functional linkage between the active site of alpha-lytic protease and distant regions of structure: Scanning alanine mutagenesis of a surface loop affects activity and substrate specificity J Mol Biol 251(1):116-134.
33. Rasmussen BF, Stock AM, Ringe D, Petsko GA. 1992. Crystalline ribonuclease A loses function below the dynamical transition at 220 K [see comments]. Nature 357(6377):423-424.
34. Richards FM. 1977. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 6:151-176.
35. Ringe D, Petsko GA. 1986. Study of protein dynamics by X-ray diffraction. Methods Enzymol 131:389-433.
36. Schlechter I, Berger A. 1967. On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun 27(2):157-162.
37. Smith JL, Hendrickson WA, Honzatko RB, Sheriff S. 1986. Structural heterogeneity in protein crystals. Biochemistry 25(18):5018-5027.
38. Thune T, Badger J. 1995. Thermal diffuse X-ray scattering and its contribution to understanding protein dynamics. Prog Biophys Mol Biol 65(3):251-276.
39. Tilton RF Jr, Dewan JC, Petsko GA. 1992. Effects of temperature on protein structure and dynamics: X-ray cryslallographic studies of the protein ribonuelease-A at nine different temperatures from 98 to 320 K. Biochemistry 31(9):2469-2481.
40. Whitaker DR, Jurasek L, Roy C. 1966. The nature of the bacteriolytic proteases of Sorangium sp. Biochem Biophys Res Commun 24(2):173-178.
41. Willis BTM, Pryor AW. 1975. Thermal vibrations in crystallography. Cambridge, UK: Cambridge University Press.
42. Young AC, Tilton RF, Dewan JC. 1994. Thermal expansion of hen egg-white lysozyme. Comparison of the 1.9 Å resolution structures of the tetragonal form of the enzyme at 100 K and 298 K. J Mol Biol 235(1): 302-317.