Hi
I want to calculate the enzyme activities of a wild type (structure determined using x-ray crystallography) and a mutant protein (the structure of this protein was determined by homology modelling). I would like to measure the differences in enzyme activities for a particular substrate using any computational methods without any experimental procedures. Please tell me any methods or studies regarding the same.
Thank you.
Dear Murthy,
You can use the following molecular dynamics methods: GOLD (genetic optimization for ligand docking) and GLIDE (gridbased ligand docking with energetics). The two programs employ different methods in placing and evaluating the molecules into the binding site.
GOLD is a docking program provided by the Cambridge Crystallographic Data Centre (CCDC). It uses a genetic search algorithm (GA) based on Mendelian genetics for finding possible binding modes. In the implementation of genetic algorithms to the docking problem, the process of evolution is mimicked by applying genetic operators to a pool of docking poses generated for the ligand, which are described by sets of 3D variables (“genes”). The first generation of conformations are generated and allowed to “evolve” by crossbreeding and mutation of the 3D variables (defining position, orientations, state of each rotatable bond, etc.). There is also the possibility of migrating an individual from one pool of conformations to another pool in order to introduce larger diversity. The fitness of the resulting docking poses is evaluated at each evolutionary operation with a scoring function (see below). The new conformation will replace an earlier generation conformation in the pool of breeding conformations if the fitness improves. This cycle is then repeated until there is no more or only marginal improvement in fitness in the final
generation of conformations
GLIDE is a docking program provided with the Schrödinger Suite. It tries to mimic a full systematic search of the conformational, orientational and positional space of the docked ligand by using a series of hierarchical filters for determining the location of the ligand in the binding pocket. This is then followed by ligand torsion-angle minimization and a minimization of the ligand inside the binding pocket using the OPLS-AA force field. The lowest energy poses are then selected for a Monte Carlo procedure that examines nearby torsional minima and the poses are finally scored using a combination of a scoring function and the MM interaction energy while taking into account the ligand strain energy.
Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J. Improved Protein–Ligand Docking
Using GOLD. Proteins: Struct., Funct., Genet. 2003, 609–623.
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz,
D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.;
Francis, P.; Shenkin, P. S. Glide: a New Approach for Rapid, Accurate Docking
and Scoring. 1. Method and Assessment of Docking Accuracy. J. Med. Chem.
2004, 47, 1739–1749.
For more on these methods, please use the following link:
https://uu.diva-portal.org/smash/get/diva2:723674/FULLTEXT01.pdf
The following link contains all available docking software including free down load programs.
https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software
Hoping this will be helpful,
Rafik
Dear Murthy
I purpose you some approach:
Current computational studies of enzyme activity as measured by the activation free energy generally restrict their focus to the wild type enzyme and, perhaps, one or two mutants described with a comparatively high or moderately hig level of theory. The agreements with experimental results are often impressive and these studies can provide valuable insight into the catalytic mechanism. However, the computational demands of these methods makes it difficult to apply them to the actual design of new enzymatic catalysts where the activity of hundreds of mutants has to be evaluated.
You can get more details in the following publication:
Hediger MR, De Vico L, Svendsen A, Besenmatter W, Jensen JH (2012) A Computational Methodology to Screen Activities of Enzyme Variants. PLoS ONE 7(12): e49849. doi:10.1371/journal.pone.0049849.
Good luck
Marius
Warshel & Weiss (1980) An empirical valence bond approach for comparing reactions in solutions and in enzymes. J Am Chem Soc 102: 6218-6226.
http://dx.doi.org/10.1021/ja00540a008
According to the standard definition of Enzyme activity, it could be calculated as moles of substrate converted into product per unit time. So definitely one can not measure it computationally. What people do is to calculate relative interaction of different substrate molecules and the residues of active site in wild type and mutant enzymes. This could give an indirect indication of potential enzyme activities in different settings. Therefore, for real enzyme activities one must perform a biochemical assay and computational studies may just give a preliminary idea about it. For computational analysis you may refer to our recent paper:
Article Structural and mechanistic analysis of engineered trichodien...
From another perspective . . . "Enzyme activity" is conversion of substrates into products by enzyme. The activity (phenomenon) can be quantified (activation barrier & reaction rate) according to the transition state theory [Eyring (1935) Chemical Reviews 17: 65-77]. Enzyme catalysis is then the difference in the reaction rate between the reaction carried out by the enzyme and the model reaction in solution. And this can be done with the empirical valence bond (EVB) approach. One can then compare, e.g., different substrates, different enzyme variants and different possible reaction mechanisms.
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