Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1994 Sep;3(9):1493–1503. doi: 10.1002/pro.5560030915

Computer modeling of substrate binding to lipases from Rhizomucor miehei, Humicola lanuginosa, and Candida rugosa.

M Norin 1, F Haeffner 1, A Achour 1, T Norin 1, K Hult 1
PMCID: PMC2142940  PMID: 7833809

Abstract

The substrate-binding sites of the triacyl glyceride lipases from Rhizomucor miehei, Humicola lanuginosa, and Candida rugosa were studied by means of computer modeling methods. The space around the active site was mapped by different probes. These calculations suggested 2 separate regions within the binding site. One region showed high affinity for aliphatic groups, whereas the other region was hydrophilic. The aliphatic site should be a binding cavity for fatty acid chains. Water molecules are required for the hydrolysis of the acyl enzyme, but are probably not readily accessible in the hydrophobic interface, in which lipases are acting. Therefore, the hydrophilic site should be important for the hydrolytic activity of the enzyme. Lipases from R. miehei and H. lanuginosa are excellent catalysts for enantioselective resolutions of many secondary alcohols. We used molecular mechanics and dynamics calculations of enzyme-substrate transition-state complexes, which provided information about molecular interactions important for the enantioselectivities of these reactions.

Full Text

The Full Text of this article is available as a PDF (3.1 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bachovchin W. W., Kaiser R., Richards J. H., Roberts J. D. Catalytic mechanism of serine proteases: reexamination of the pH dependence of the histidyl 1J13C2-H coupling constant in the catalytic triad of alpha-lytic protease. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7323–7326. doi: 10.1073/pnas.78.12.7323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., 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. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Brady L., Brzozowski A. M., Derewenda Z. S., Dodson E., Dodson G., Tolley S., Turkenburg J. P., Christiansen L., Huge-Jensen B., Norskov L. A serine protease triad forms the catalytic centre of a triacylglycerol lipase. Nature. 1990 Feb 22;343(6260):767–770. doi: 10.1038/343767a0. [DOI] [PubMed] [Google Scholar]
  4. Brzozowski A. M., Derewenda U., Derewenda Z. S., Dodson G. G., Lawson D. M., Turkenburg J. P., Bjorkling F., Huge-Jensen B., Patkar S. A., Thim L. A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature. 1991 Jun 6;351(6326):491–494. doi: 10.1038/351491a0. [DOI] [PubMed] [Google Scholar]
  5. Derewenda U., Brzozowski A. M., Lawson D. M., Derewenda Z. S. Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase. Biochemistry. 1992 Feb 11;31(5):1532–1541. doi: 10.1021/bi00120a034. [DOI] [PubMed] [Google Scholar]
  6. Derewenda U., Swenson L., Green R., Wei Y., Dodson G. G., Yamaguchi S., Haas M. J., Derewenda Z. S. An unusual buried polar cluster in a family of fungal lipases. Nat Struct Biol. 1994 Jan;1(1):36–47. doi: 10.1038/nsb0194-36. [DOI] [PubMed] [Google Scholar]
  7. Derewenda Z. S., Derewenda U., Dodson G. G. The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution. J Mol Biol. 1992 Oct 5;227(3):818–839. doi: 10.1016/0022-2836(92)90225-9. [DOI] [PubMed] [Google Scholar]
  8. Derewenda Z. S., Sharp A. M. News from the interface: the molecular structures of triacylglyceride lipases. Trends Biochem Sci. 1993 Jan;18(1):20–25. doi: 10.1016/0968-0004(93)90082-x. [DOI] [PubMed] [Google Scholar]
  9. Goodford P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 1985 Jul;28(7):849–857. doi: 10.1021/jm00145a002. [DOI] [PubMed] [Google Scholar]
  10. Grochulski P., Bouthillier F., Kazlauskas R. J., Serreqi A. N., Schrag J. D., Ziomek E., Cygler M. Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. Biochemistry. 1994 Mar 29;33(12):3494–3500. doi: 10.1021/bi00178a005. [DOI] [PubMed] [Google Scholar]
  11. Grochulski P., Li Y., Schrag J. D., Bouthillier F., Smith P., Harrison D., Rubin B., Cygler M. Insights into interfacial activation from an open structure of Candida rugosa lipase. J Biol Chem. 1993 Jun 15;268(17):12843–12847. [PubMed] [Google Scholar]
  12. Kossiakoff A. A., Spencer S. A. Direct determination of the protonation states of aspartic acid-102 and histidine-57 in the tetrahedral intermediate of the serine proteases: neutron structure of trypsin. Biochemistry. 1981 Oct 27;20(22):6462–6474. doi: 10.1021/bi00525a027. [DOI] [PubMed] [Google Scholar]
  13. Ollis D. L., Cheah E., Cygler M., Dijkstra B., Frolow F., Franken S. M., Harel M., Remington S. J., Silman I., Schrag J. The alpha/beta hydrolase fold. Protein Eng. 1992 Apr;5(3):197–211. doi: 10.1093/protein/5.3.197. [DOI] [PubMed] [Google Scholar]
  14. Porubcan M. A., Westler W. M., Ibañez I. B., Markley J. L. (Diisopropylphosphoryl)serine proteinases. Proton and phosphorus-31 nuclear magnetic resonance-pH titration studies. Biochemistry. 1979 Sep 18;18(19):4108–4116. doi: 10.1021/bi00586a008. [DOI] [PubMed] [Google Scholar]
  15. SARDA L., DESNUELLE P. Action de la lipase pancréatique sur les esters en émulsion. Biochim Biophys Acta. 1958 Dec;30(3):513–521. doi: 10.1016/0006-3002(58)90097-0. [DOI] [PubMed] [Google Scholar]
  16. Schrag J. D., Cygler M. 1.8 A refined structure of the lipase from Geotrichum candidum. J Mol Biol. 1993 Mar 20;230(2):575–591. doi: 10.1006/jmbi.1993.1171. [DOI] [PubMed] [Google Scholar]
  17. Wade R. C., Goodford P. J. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J Med Chem. 1993 Jan 8;36(1):148–156. doi: 10.1021/jm00053a019. [DOI] [PubMed] [Google Scholar]
  18. van Tilbeurgh H., Sarda L., Verger R., Cambillau C. Structure of the pancreatic lipase-procolipase complex. Nature. 1992 Sep 10;359(6391):159–162. doi: 10.1038/359159a0. [DOI] [PubMed] [Google Scholar]
  19. von Itzstein M., Wu W. Y., Kok G. B., Pegg M. S., Dyason J. C., Jin B., Van Phan T., Smythe M. L., White H. F., Oliver S. W. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature. 1993 Jun 3;363(6428):418–423. doi: 10.1038/363418a0. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES