Abstract
Molecular constraints for the localization of active site directed ligands (competitive inhibitors and substrates) in the active site of phospholipase A2 (PLA2) are characterized. Structure activity relationships with known inhibitors suggest that the head group interactions dominate the selectivity as well as a substantial part of the affinity. Theab initio fitting of the amide ligands in the active site was carried out to characterize the head group interactions. Based on a systematic coordinate space search, formamide is docked with known experimental constraints such as coordination of the carbonyl group to Ca2+ and hydrogen bond between amide nitrogen and ND1 of His48. An optimal position for a bound water molecule is identified and its significance for the catalytic mechanism is postulated. Unlike the traditional “pseudo-triad” mechanism, the “Ca-coordinated-oxyanion” mechanism proposed here invokes activation of the catalytic water to form the oxyanion in the coordination sphere of calcium. As it attacks the carbonyl carbon of the ester, a near-tetrahedral intermediate is formed. As the second proton of the catalytic water is abstracted by the ester oxygen, its reorientation and simultaneous cleavage form hydrogen bond with ND1 of His48. In this mechanism of esterolysis, a catalytic role for the water co-ordinated to Ca2+ is recognised.
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Abbreviations
- cmc:
-
critical micelle concentration
- PLA2:
-
14 kD secreted phospholipase A2
- ND1 of His48:
-
nitrogen at the delta position of the imidazole ring of histidine-48
- NE2:
-
nitrogen at the epsilon position of histidine-48
References
Balaji P V 1991Specificity and mechanism of action of ribonuclease Tl-A computer modelling study, PhD thesis, Indian institute of Science, Bangalore
Berg O G, Yu B -Z, Rogers J and Jain M K 1991Biochemistry 30 7283
Goldstein H 1980Classical mechanics (Reading, MA: Addison-Wesley) p, 143
Jain M K 1988Introduction to biomembranes 2nd edn (New York: John Wiley) p. 423
Jain M K and Berg O 1989Biochim. Biophys. Acta 1002 127
Jain M K, de Haas G H, Marecek J F and Ramirez F 1986Biochim. Biophys. Acta 860 475
Jain M K, Gelb M H, Rogers J and Berg O G 1994Methods in enzymology (in press)
Jain M K, Ghomashchi F, Yu B-Z, Bayburt T, Murphy D, Houck D, Brownell J, Reid J C, Solwiej J E, Wong S M, Mocek U, Jarrell R, Sasser M and Gelb M H 1992J. Med. Chem. 35 3584
Jain M K, Rogers J and de Haas G H 1988Biochim. Biophys. Acta 940 51
Jain M K, Rogers J, Hendrickson H S and Berg O G 1993aBiochemistry 32 8360
Jain M K, Tao W, Rogers J, Arenson C, Eibl H and Yu B-Z 1991Biochemistry 30 10256
Jain M K, Yu B-Z and Berg O G 1993bBiochemistry 32 11319
Jain M K, Yuan W and Gelb M H 1989Biochemistry 28 4135
Ramachandran G N and Sasisekharan V 1968Adv. Protein Chem. 23 283
Scott D L, White S P, Otwinowski Z, Yuan W, Gelb M H and Sigler P B 1990Science 250 1541
Sekharudu Y C 1985The modes of binding of carbohydrates to concanavalin A: A computer modelling approach, Ph D thesis, Indian Institute of Science, Bangalore
Thunnissen M M G M, Eiso A B, Kalk K H, Drenth J, Dijkstra B W, Kuipers O P, Dikjkman R, de Haas G H and Verheij H M 1990Nature (London) 347 689
Verheij H M, Volwerk J J, Jansen E H J M, Puyk W C, Dijkstra B W, Drenth J and de Haas G H 1980Biochemistry 19 743
Yu B -Z, Berg O G and Jain M K 1993Biochemistry 32 6485
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Seshadri, K., Vishveshwara, S. & Jain, M.K. Binding of active site directed ligands to phospholipase A2: Implications on the molecular constraints and catalytic mechanism. Proc. Indian Acad. Sci. (Chem. Sci.) 106, 1177–1189 (1994). https://doi.org/10.1007/BF02841925
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DOI: https://doi.org/10.1007/BF02841925