Computational Approaches to Enzyme Structure and Function -

Rational design, the earliest approach applied to the modification of enzymes [ 3 – 5 ], requires the availability of detailed structural information and catalytic mechanism of the targets. Computational tools have been developed to deal with a large number of data produced in rational enzyme design. Enzyme design is an important area of ongoing research with a broad range of applications in protein therapeutics, biocatalysis, bioengineering, and other biomedical areas; however, significant challenges exist in the design of enzymes to catalyze specific reactions of interest. Here, we develop a computational protocol using an approach that combines molecular dynamics, docking, and MM. Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences.

Various approaches like homology-based function transfer and machine learning methods have been utilized for in silico enzyme functional classifications in terms of Enzyme Commission number EC number for a protein. May 19, 2008 · Computational Design and Optimization of Novel Enzyme Activities A model for the proposed active site is created initially based upon the geometric constraints dictated by the expected transition state structure for the reaction to be catalyzed. Oct 23, 2001 · Techniques used to predict function from sequence or function from structure are in their infancy and rely either on analogies to related proteins of known function 2 – 8 or on computational searches for binding sites by docking 9 of selected sets of small molecules onto the structure.

Computational Approaches to Enzyme Structure and Function

The International Union of Pure and Applied Chemistry IUPAC Enzyme Classification EC system was an early approach to identifying molecular function. The Gene Ontology GO system of classifying function recognizes ways of defining function, using distinct cellular components, molecular function, and biological process hierarchies [ 1 ]. The application of computational protein design methods to the design of enzyme active sites offers potential routes to new catalysts and new reaction specificities. Computational design methods have typically treated the protein backbone as a rigid structure for the sake of computational tractability.

Ø In simple term, the minimum energy required to start a chemical reaction. Ø For a chemical reaction to proceed at a reasonable rate, there should exist an appreciable number of molecules with energy equal to or greater than the activation energy. Ø The activation energy of a reaction is denoted as Ea. As the demand grows for a more holistic understanding of enzymatic processes it is likely that computational methods of tunnel prediction and evaluation will become increasingly instrumental to gain new insight into structure-function relationships in proteins with buried active sites. Aug 23, 2011 · Alternatively, computational methods can be used to annotate the enormous amount of unannotated enzyme sequences. For function prediction and classification of enzymes, features based on amino acid composition, sequence and structural properties, domain composition and specific peptide information have been widely used by different.

COMPUTATIONAL APPROACHES TO DESIGN SYNTHETIC METABOLIC PATHWAYS. The design of a synthetic metabolic pathway begins with specification of the metabolic function to be achieved by engineering. In the case of improving nutritional value of a crop, the metabolic function corresponds to the production of a target compound e.g. vitamin C.

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