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Monte Carlo simulation of multiple attack mechanism of β‐amylase‐catalyzed reaction
Author(s) -
Nakatani Hiroshi
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(199712)42:7<831::aid-bip8>3.0.co;2-u
Subject(s) - chemistry , tetramer , amylopectin , monte carlo method , dimer , maltose , substrate (aquarium) , molecule , stereochemistry , enzyme , amylose , computational chemistry , organic chemistry , mathematics , statistics , oceanography , starch , geology
β‐Amylase (EC 3.2.1.2) produces maltose (dimer) from the nonreducing ends of α‐1,4 glucosidic bonds of substrates like maltooligosaccharides, amylose, and amylopectin. The enzyme releases several maltose molecules from a single enzyme‐substrate complex without dissociation by multiple or repetitive attack containing many branching reaction paths. The Monte Carlo method was applied to the simulation of the β‐amylase‐catalyzed reaction including the multiple attack mechanism. The simulation starts from a single enzyme molecule and a finite number of substrate molecules. The selection of the substrate by the enzyme and degree of multiple attack proceeds by random numbers produced from a computer. The simulation was carried out until the whole substrate and the intermediate molecules were consumed. The simulated data were compared with experimental data of sweet potato β‐amylase using heptamer, octamer, nanomer, and 11‐mer as substrates. The only adjustable parameter for odd‐numbered substrates was the probability of multiple attack, while an additional adjustable parameter (a correction factor due to low reactivity of tetramer) was needed for even‐numbered substrates. © 1997 John Wiley & Sons, Inc. Biopoly 42: 831–836, 1997