Modeling of solvent effects in the activation of the lipase from Rhizomucor miehei

Bioorganic and Medicinal Chemistry Letters

Volumn 6, Issue 7, 1996, Pages 839-844

  Benedetti, Fabio ^a   Berti, Federico ^a   Linda, Paolo ^a   Miertus, Stanislav ^b   Sabot, Andrea ^a  

^a UNIVERSITY OF TRIESTE   (Italy)

^b Polybios   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

TRIACYLGLYCEROL LIPASE;

ARTICLE; ENZYME ACTIVATION; ENZYME STABILITY; ENZYME STRUCTURE; FUNGUS; MOLECULAR MODEL; THERMODYNAMICS;

EID: 84962440453     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/0960-894X(96)00123-0     Document Type: Article

References (14)

1. Derewenda, Z. S., Sharp, A.M. TIBS, 1993, 18, 20.
2. Brady, L., Brzozowski, A.M., Derewenda, Z.S., Dodson, E., Dodson, G., Tolley, S., Turkenburg, J.P., Christiansen, L., Huge-Jensen, B., Norskov, L., Thim, L., Menge, U. Nature, 1990, 343, 767.
3. Brzozowski, A.M., Derewenda, Z.S., Derewenda, U., Dodson, G., Lawson, D.M., Turkenburg, J.P., Björkling, F., Huge-Jensen, B., Patkar, S.A., Thim, L. Nature, 1991, 351, 491.
4. Derewenda, U., Brzozowski, A.M., Lawson, D.M., Derewenda, Z.S. Biochemistry, 1992, 31, 1532.
5. Norin, M., Olsen, O., Svendsen, A., Edholm, O., Hult, K. Prot. Eng., 1993, 6, 855.
6. The CVFF force field was used (Dauber-Osguthorpe, P., Roberts, V.A., Osguthorpe, D.J., Wolff, J., Genest, M., Hagler, A.T. Proteins: Structure, Function & Genetics 1988, 4, 31), as implemented in Discover 2.7, Insight II, Biosym Technologies 1990
7. a: Frecer, V., Miertus, S., Int. J. Quant. Chem., 1992, 42, 1449.
8. b: Miertus, S., Scrocco, E., Tomasi, J. Chem.Phys. 1981, 55, 117
9. Biopolymer module of Insight II, Biosym Technologies.
10. The simple scaling electrostatic model can not distinguish between solvent accessible and non-accessible regions This inadequacy is, to some extent, corrected by the arbitrary choice of an intermediate value of the effective dielectric constant ε for the polar medium (ε = 10), corresponding approximately to a 90% reduction of all intramolecular electrostatic interactions, which mimicks the concurrence of solute-solvent interactions. The use of the macroscopic value of the dielectric constant for water (ε = 78.5) leads to a further reduction of electrostatic interactions, but leaves the overall picture unchanged.
11. ij were obtained from ref. 6.
12. The assumption is based on the observation that the structural differences between the two forms, in areas remote from the lid, are negligible both in the crystal structures and in the minimized structures of this work (r.m.s.= 0.42 Å, excluding the lid (residues 80 to 97)).
13. Sixty-four residues were considered for direct solvation: 27 to 33, 57 to 63, 79 to 98 (lid), 106 to 114, 143 to 146, 117, 204 to 215, 254 to 258, 266.
14. Handbook of Chemistry and Physics, R.C. West, Ed.; CRC Press, Boca Raton, 67th Edition, 1989.