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How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.

ABSTRACT: Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.

SUBMITTER: Cui P

PROVIDER: S-EPMC4264029 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.

Cui Peixin P Wang Yu Y Chu Wangsheng W Guo Xiaoyun X Yang Feifei F Yu Meijuan M Zhao Haifeng H Dong Yuhui Y Xie Yaning Y Gong Weimin W Wu Ziyu Z

Scientific reports 20141212

Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations ...[more]

PMID: 25503313

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Project description:BackgroundIn order to regulate water flow, hydraulic structures such as weirs or checks, frequently equipped with gates, are used. Water can flow below or over the gate or, simultaneously, over and below the gate. Both diversifications of hydraulic gradient, being an effect of damming up a river by the structure and shear stresses at the bed, which exceeds the critical shear stress value, invoke the local scouring downstream the structure. This phenomenon has been studied in laboratory and field conditions for many years, however Researchers do not agree on the parameters that affect the size of the local scour and the intensity of its formation. There are no universal methods for estimating its magnitude However, solutions are sought in the form of calculation formulas typical for the method of flow through the structure, taking into account the parameters that characterize a given structure. These formulas are based on factors that affect the size of the local scours, that is, their dimensions and location. Examples of such formulas are those contained in this article: Franke (1960), Straube (1963), Tarajmovič (1966), Rossinski & Kuzmin (1969) equations. The need to study this phenomenon results from the prevalence of hydrotechnical structures equipped with gates (from small gated checks to large weirs) and from potential damage that may be associated with excessive development of local erosion downstream, including washing of foundations and, consequently, loss of stability of the structure.MethodsThis study verifies empirical formulas applied to estimate the geometry parameters of a scour hole on a laboratory model of a structure where water is conducted downstream the gate with bottom reinforcements of various roughness. A specially designed remote-controlled measuring device, equipped with laser scanner, was applied to determine the shape of the sandy bottom. Then the formula optimization is conducted, using Monte Carlo sampling method, followed by verification of field conditions.ResultsThe suitability of a specially designed device, equipped with laser scanner for measuring the bottom shape in laboratory conditions was demonstrated. Simple formula describing local scour geometry in laboratory conditions was derived basing on the Straube formula. The optimized formula was verified in field conditions giving very good comparative results. Therefore, it can be applied in engineering and designing practices.

Dataset Information

How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.

Publications

How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.

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