Irreversible site-directed labeling of the 4-aminobutyrate binding site by tritiated meta-sulfonate benzene diazonium . Contribution of a nucleophilic amino acid residue of the alpha1 subunit

The active site of an enzyme performs the twofold function of binding a substrate and catalysing a reaction. The efficiency of these actions determines the overall activity of the enzyme towards the particular substrate, i.e. determines the specificity of the enzyme. It is therefore possible to obtain information on the active site by the kinetics of the enzyme’s reactions with different substrates and inhibitors. An important feature of the active site is its size. It should be possible to 'measure’ this by using substrates or inhibitors large enough to show up the interactions of the furthermost parts of the binding site. In the present series of investigations on proteolytic enzymes, our approach is to compare the activity of the enzyme towards ( a ) peptides of increasing length, ( b ) diastereoisomeric pairs of peptides in which a particular amino acid residue has been replaced by its antipode, and ( c ) pairs of substrates in which a particular side chain (say a methyl group) has been replaced by another (say an aromatic group). The influence of these changes on reaction rates as a function of distance from the point of cleavage indicates the extent of the active site (Schechter, Abramowitz & Berger 1965; Abramowitz, Schechter & Berger 1967).

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Contribution of amino acid residue 208 in the hydrophobic binding site to the catalytic mechanism of human glutathione transferase A1-1

Biochemistry ◽

10.1021/bi00205a007 ◽

1994 ◽

Vol 33 (39) ◽

pp. 11717-11723 ◽

Cited By ~ 23

Author(s):

Mikael Widersten ◽

Robert Bjoernestedt ◽

Bengt Mannervik

Keyword(s):

Amino Acid ◽

Binding Site ◽

Amino Acid Residue ◽

Catalytic Mechanism ◽

Glutathione Transferase ◽

Hydrophobic Binding

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Characterization of Met-139 as the photolabeled amino acid residue in the steroid binding site of sex hormone binding globulin using .DELTA.6 derivatives of either testosterone or estradiol as unsubstituted photoaffinity labeling reagents

Biochemistry ◽

10.1021/bi00148a024 ◽

1992 ◽

Vol 31 (33) ◽

pp. 7609-7621 ◽

Cited By ~ 30

Author(s):

Catherine Grenot ◽

Arnaud De Montard ◽

Thierry Blachere ◽

Marc Rolland De Ravel ◽

Elisabeth Mappus ◽

...

Keyword(s):

Amino Acid ◽

Binding Site ◽

Amino Acid Residue ◽

Photoaffinity Labeling ◽

Sex Hormone ◽

Sex Hormone Binding Globulin ◽

Hormone Binding ◽

Steroid Binding ◽

Derivatives Of

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Mutagenesis of an Amino Acid Residue in the Activator-Binding Site of Cyanobacterial ADP-Glucose Pyrophosphorylase Causes Alteration in Activator Specificity

Archives of Biochemistry and Biophysics ◽

10.1006/abbi.1995.1256 ◽

1995 ◽

Vol 318 (2) ◽

pp. 476-480 ◽

Cited By ~ 6

Author(s):

Y.Y. Charng ◽

J. Sheng ◽

J. Preiss

Keyword(s):

Amino Acid ◽

Binding Site ◽

Amino Acid Residue ◽

Adp Glucose Pyrophosphorylase

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Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

Current Computer - Aided Drug Design ◽

10.2174/1573409915666190708103132 ◽

2020 ◽

Vol 16 (4) ◽

pp. 451-459 ◽

Cited By ~ 1

Author(s):

Fortunatus C. Ezebuo ◽

Ikemefuna C. Uzochukwu

Keyword(s):

Molecular Dynamics ◽

Amino Acid ◽

Binding Energy ◽

Binding Site ◽

Conformational Dynamics ◽

Side Chain ◽

Amino Acid Residues ◽

Conformational Selection ◽

Hybrid Mechanism ◽

Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

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