Lysozyme structural analysis

From crystal-structure analysis of hen-egg lysozyme and of its complex with the competitive inhibitor tri-Af-acetylchitotriose, the following conclusions were drawn the active site consists of a cleft containing six sub-sites, A to F, of which each could accommodate a) -( 1 — 4)-linked A-acetylglucosa-... 

Crystal-structure analysis of Taka amylase A gave similar results, in that it showed that it had an extended cleft which could accommodate six, or possibly seven, a-( 1 — 4)-linked glucose units and two oppositely placed acidic amino acids (Asp-206 and Glu-230) which could interact with the bound substrate similarly to Asp-52 and Glu-35 in lysozyme. 

No sequence homologies can be detected. This is, perhaps, not surprising. The X-ray structure analysis of lysozyme by Phillips has shown that the polypeptide chain is folded in a way which puts none of the amino acids in sequential vicinity of the catalytic Asp-52 and Glu-37 that are near to the bound substrate. Comparable folding patterns can probably be realized with widely differing arrangements of amino acids, and thus the apparent lack of homologies. 

In any event it was the analysis of baboon a-lactalbumin crystals for which the first X-ray crystal structure was produced, initially at 0.6 nm (6 A) and 0.45 nm (4.5 A) (Phillips etal., 1987 Smith etal., 1987). More recently, the structure has been refined at 0.17-nm (1.7-A) resolution, enabling comparison with the high-resolution c-type lysozyme structure (Acharya et al., 1989) (see Fig. 7). 

In conclusion, attention is drawn to several puzzling features the differences found in the cleft region suffice to predict that a-lactalbumin would have no cell lytic activity. It remains an anomaly, however, that weak activity has been demonstrated for a-lactalbumin from various sources by McKenzie and White (1987) (Section X), and it is an unresolved problem as to how such activity could be explained, except by the possible involvement of His-32 in a-lactalbumin as an active site residue, in place of Glu-35, which appears in lysozyme (for further discussion see Section X). In addition, there are numerous discrepancies between the reactivities of a-lactalbumin and lysozyme. The former is generally a more reactive protein (Section IX), and these differences could not have been predicted by consideration of the above models, nor from the X-ray structural analysis. 

Hurley JH, Baase WA, Matthews BW. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J. Mol. Biol. 1992 224 1143-1159. 44. 

Ijeucine aminopeptidase has been applied in many ways to particular problems in structural analysis of peptides and proteins. Sequences in the amino-terminal portion of a peptide can often be established by measurement of the order of appearance of amino acids that are released during hydrolysis. The procedure has been used with a variety of proteins and peptides, including ribonuclease (Hirs et al., 1960), hemoglobin (Konigsberg and Hill, 1962, 1963 Schroeder et al., 1963), cytochrome c (Margoliash, 1962 Matsubara and Smith, 1963), and lysozyme (Canfield, 1963). 

Sternberg, M. J. E., Grace, D. E. P., and Phillips. D. C. Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure. J. Molec. Biol. 130, 231-253 (1979). 

With the interest in glycosidase inhibitors, compounds lending insight to the structures and mechanisms of these enzymes have received much attention. Recently, Lehmann, et al.,27 prepared a series of diastereotopic C-glycosides designed to be substrates for p-D-galactosidase. The premise was that in order to confirm this enzyme s mechanism of action, proposed from an extrapolation of lysozyme activity,28 31 the structural analysis of products resulting from the enzyme s effect on its substrates would be helpful. Therefore, the structures... 

Makin OS, Serpell LC (2005) Structures for amyloid fibrils. FEBS J 272 5950-5961 Malinchik SB, Inouye H, Szumowski KE, Kirschner DA (1998) Structural analysis of Alzheimer s beta(l O) amyloid protofilament assembly of tubular fibrils. Biophys J 74 537-545 Malisauskas M, Zamotin V, Jass J, Noppe W, Dobson CM, Morozova-Roche LA (2003) Amyloid protofilaments from the calcium-binding protein equine lysozyme formation of ring and linear structures depends on pH and metal ion concentration. J Mol Biol 330 879-890 Mantuano E, Veneziano L, Jodice C, ErontaU M (2003) Spinocerebellar ataxia type 6 and episodic ataxia type 2 differences and similarities between two allelic disorders. Cytogenet Genome Res 100 147-153 Markesbery WR(1997) Oxidative stress hypothesis in Alzheimer s disease. Free Radic Biol Med 23 134-147 Marks MS, Seabra MC (2001) The melanosome membrane dynamics in black and white. Nat Rev Mol Cell Biol 2 738-748... 

Remmele, R. L., Stushoff, Carpenter, J. F. Real-time spectroscopy analysis of lysozyme during Lyophilization structure-hydration behavior and influence of sucrose. American Chemical Society Symposium, Ser. 567 (Formulation and delivery of proteins and peptides) 1994. 1994 American Chemical Society... 

Tello, D., E. Eisenstein, F.P. Schwarz, F.A. Goldbaum, B.A. Fields, R.A. Mariuzza, and R.J. Poljak. 1994. Structural and physicochemical analysis of the reaction between the anti-lysozyme antibody D1.3 and the anti-idiotopic antibodies E225 and E5.2. J Mol Recognit 7 57-62. 

T4 lysozyme 33,497 helix stability of 528, 529 hydrophobic core stability of 533, 544 Tanford j8 value 544, 555, 578, 582-Temperature jump 137, 138, 541 protein folding 593 Terminal transferase 408,410 Ternary complex 120 Tertiary structure 22 Theorell-Chance mechanism 120 Thermodynamic cycles 125-131 acid denaturation 516,517 alchemical steps 129 double mutant cycles 129-131, 594 mutant cycles 129 specificity 381, 383 Thermolysin 22, 30,483-486 Thiamine pyrophosphate 62, 83 - 84 Thionesters 478 Thiol proteases 473,482 TNfn3 domain O-value analysis 594 folding kinetics 552 Torsion angle 16-18 Tbs-L-phenylalanine chloromethyl ketone (TPCK) 278, 475 Transaldolase 79 Tyransducin-o 315-317 Transit time 123-125 Transition state 47-49 definition 55... 

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