A Computational Methodology to Screen Activities of Enzyme Variants
نویسندگان
چکیده
We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors. The methodology is based on the PM6 and MOZYME methods as implemented in MOPAC2009, and is tested on the first step of the amide hydrolysis reaction catalyzed by the Candida Antarctica lipase B (CalB) enzyme. The barrier heights are estimated using adiabatic mapping and shown to give barrier heights to within 3 kcal/mol of B3LYP/6-31G(d)//RHF/3-21G results for a small model system. Relatively strict convergence criteria (0.5 kcal/(molÅ)), long NDDO cutoff distances within the MOZYME method (15 Å) and single point evaluations using conventional PM6 are needed for reliable results. The generation of mutant structures and subsequent setup of the semiempirical calculations are automated so that the effect on barrier heights can be estimated for hundreds of mutants in a matter of weeks using high performance computing.
منابع مشابه
Comprehensive Computational Analysis of Protein Phenotype Changes Due to Plausible Deleterious Variants of Human SPTLC1 Gene
Genetic variations found in the coding and non-coding regions of a gene are known to influence the structure as well as the function of proteins. Serine palmitoyltransferase long chain subunit 1 a member of α-oxoamine synthase family is encoded by SPTLC1 gene which is a subunit of enzyme serine palmitoyltransferase (SPT). Mutations in SPTLC1 have been associated with hereditary sensory and auto...
متن کاملComputational Approach for Rational Design of Fusion Uricase with PAS Sequences
Tumor lysis syndrome is a life-threatening condition for humans due to the lack of urate oxidase. In this study, several variants of PASylateduricasefrom the Aspergillus flavus species were analyzed computationally to find the appropriate fusions to solve short half-life and stability concerns. The Ab initio method was performed using Rosetta software to structurally characterize the PAS sequen...
متن کاملComputational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta
Amelogenin gene (AMEL-X) encodes an enamel protein called amelogenin, which plays a vital role in tooth development. Any mutations in this gene or the associated pathway lead to developmental abnormalities of the tooth. The present study aims to analyze functional missense mutations in AMEL-X genes and derive an association with amelogenesis imperfecta. The information on miss...
متن کاملMolecular Surveying of the Common Variants of Glucose 6-Phosphate Dehydrogenase Gene in Deficient Patients
Glucose 6-phoshphate dehydrogenase is X-chromosome linked that expressed in all tissues. This is the first enzyme of pentose phosphate pathway were 5-carbon sugar Ribose and NADPH were synthesized by coupled oxidation /reduction reactions and this enzyme is a highly polymorphic enzyme in humans. G6PD deficiency are shown to be the cause of haemolytic effect of Fava beans and primaquine. It soon...
متن کاملDetermination of Optimum Conditions for the Production of Peptides with Antioxidant and Nitric-Oxide Inhibition Properties from Protein Hydrolysis of Pumpkin Seed Meals Using Pepsin Enzyme
Background and Objectives: In this study, hydrolysis condition optimization of the pumpkin (Cucurbita pepo) seed proteins was carried out achieve maximum DPPH radical scavenging and nitric-oxide inhibition properties using Design Expert Software and response surface methodology. Materials & Methods: In general, 1–3% concentrations of pepsin enzyme, 30–40 °C temperature and 120–100 min time we...
متن کامل