Enzymology: simulation

Maximum (maximized) likelihood is a statistical term that refers to the probability of randomly drawing a particular sample from a population, maximized over the possible values of the population parameters. Selected entries from Methods in Enzymology [vol, page(s)] Theory, 210, 203 testing by simulations, 210, 225 computer applications for, 210, 233 fitting of sums of exponentials to dwell-time distributions, 207, 772 fluorescence data analysis, 210,... 

Selected entries from Methods in Enzymology [vol, page(s)] Theory, 63, 159-162 activation effect, 63, 174, 175 analysis, 63, 140, 159-183 burst, 64, 20, 203, 215 enzyme concentration, 63, 175-177 hysteresis, 64, 197, 200-204 limitations, 63, 181-183 plotting, 63, 177-180 practical methods, 63, 175-177 reversible inhibitor action, 63, 163-175 reversible reaction, 63, 171-175 simulation of, 63, 180 advantages and disadvantages, 249, 61-62 analysis, in kinetic models of inhibition, 249, 168-169 concave-down, 249, 156 concave-up, 249, 156 with enzyme-product complex instability, 249, 88 with enzyme-substrate instabil-... 

Fanelli, F., Menziani, C., Scheer, A., Cotecchia, S., De Benedetti, P. G. Ab Initio modelling and molecular dynamics simulation of the aib-adrenergic receptor activation. Methods A companion to methods in enzymology, 1998, 14,302-317. 

We hope to apply this method in the near future for enzymatic active centres. Replacement of the polar solvent with a fluctuating macromolecular environment, such as an enzyme, is methodologically a straightforward step but requires a lot of coding efforts. Quantum treatment of the nuclear motion is essential for calculation of the kinetic isotope effects that are of vital importance for enzymology. Very recently the H/D kinetic isotope effect h/ d = 80 was simulated with what is in excellent agreement with the experiment [36]. 

There has been significant recent development in the application of QM/MM methods for computational enzymology, whereby both the detail of the physical model of the enzyme system, and the quality of conformational sampling have improved dramatically. This has now led to computational simulations of certain enzyme systems that are sufficiently accurate to allow direct comparison with experiment. Computer simulations have now reached a level of accuracy, for some systems, that permits their use as a means of verifying or dismissing proposed... 

The approach and analysis presented in this article enable the regulatory characteristics of any metabolic system to be described, analyzed, and computed. This therefore provides a bridge between conventional enzymology and sophisticated computer simulations of metabolism. 

Marti, M. A., Capece, L., Bidon-Chanal, A., Crespo, A., Guallar, V., Luque, F. J., 8c Estrin, D. A. (2008). Nitric oxide reactivity with globins as investigated through computer simulation. Methods in Enzymology, 437, 477. 

Paci, E. (2002). High pressure simulations of biomolecules. BBA-Protein Structure and Molecular Enzymology, 1595,185. 

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