scholarly journals Determination of Ligand-Binding Sites on Proteins Using Long-Range Hydrophobic Potential

2008 ◽  
Vol 31 (8) ◽  
pp. 1552-1558 ◽  
Author(s):  
Noriyuki Yamaotsu ◽  
Akifumi Oda ◽  
Shuichi Hirono
Keyword(s):  
Ligand Binding ◽  
Long Range ◽  
Binding Sites ◽  
Ligand Binding Sites

scholarly journals A quantitative study of the biospecific desorption of rat liver (M4) lactate dehydrogenase from 10-carboxydecylamino-Sepharose. Determination of the number of ligand-binding sites blocked on adsorption

1982 ◽  
Vol 207 (3) ◽  
pp. 549-556 ◽  
Author(s):  
P Kyprianou ◽  
R J Yon
Keyword(s):  
Lactate Dehydrogenase ◽  
Ligand Binding ◽  
Rat Liver ◽  
Binding Sites ◽  
Free Ligand ◽  
Factors Affecting ◽  
Adsorption Sites ◽  
Ligand Binding Sites ◽  
Chromatographic Parameters

1. The theory of Nichol, Ogston, Winzor & Sawyer [(1974) Biochem. J. 143, 435-443] for quantitative affinity chromatography, when adapted for use with a non-specific column from which a multi-site protein can be specifically desorbed by its free ligand, permits determination of the concentration of adsorption sites on the column, their adsorptive affinity (as an association constant) and either the intrinsic (site) constant for ligand-binding to the protein or an ‘occlusion coefficient’ (defined as the number of ligand-binding sites blocked on adsorption), one of which must be known. 2. The theory has been applied to the NADH-specific desorption of rat liver M4 lactate dehydrogenase from 10-carboxydecylamino-Sepharose. It suggests that most of the enzyme molecules are adsorbed with at least two NADH-binding sites blocked, indicating an extensive adsorption interface in relation to the protein surface. Other chromatographic parameters were also determined for the system. 3. Among topics discussed are (a) factors affecting the experimentally determined value for the number of blocked sites, (b) the nature of the adsorption sites on the column and (c) the similarity of the analysis to that for determining Hill coefficients, and other possible applications.

scholarly journals In SilicoDetermination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Fatemeh Sefid ◽  
Iraj Rasooli ◽  
Abolfazl Jahangiri
Keyword(s):  
Ligand Binding ◽  
Homology Modeling ◽  
Binding Sites ◽  
Tertiary Structure ◽  
Outer Membrane Proteins ◽  
3D Structure ◽  
Essential Element ◽  
Nosocomial Pathogen ◽  
Ligand Binding Sites

Acinetobacter baumanniiis a deadly nosocomial pathogen. Iron is an essential element for the pathogen. Under iron-restricted conditions, the bacterium expresses iron-regulated outer membrane proteins (IROMPs). Baumannii acinetobactin utilization (BauA) is the most important member of IROMPs inA. baumannii. Determination of its tertiary structure could help deduction of its functions and its interactions with ligands. The present study unveils BauA 3D structure viain silicoapproaches. Apart fromab initio, other rational methods such as homology modeling and threading were invoked to achieve the purpose. For homology modeling, BLAST was run on the sequence in order to find the best template. The template was then served to model the 3D structure. All the models built were evaluated qualitatively. The best model predicted by LOMETS was selected for analyses. Refinement of 3D structure as well as determination of its clefts and ligand binding sites was carried out on the structure. In contrast to the typical trimeric arrangement found in porins, BauA is monomeric. The barrel is formed by 22 antiparallel transmembraneβ-strands. There are short periplasmic turns and longer surface-located loops. An N-terminal domain referred to either as the cork, the plug, or the hatch domain occludes theβ-barrel.

scholarly journals Non-catalytic binding sites induce weaker long-range evolutionary rate gradients than catalytic sites in enzymes

2019 ◽  
Author(s):  
Avital Sharir-Ivry ◽  
Yu Xia
Keyword(s):  
Ligand Binding ◽  
Long Range ◽  
Binding Sites ◽  
Evolutionary Rate ◽  
Functional Sites ◽  
Interaction Sites ◽  
Catalytic Sites ◽  
Ligand Binding Sites ◽  
Different Types ◽  
Rate Gradient

AbstractEnzymes exhibit a strong long-range evolutionary constraint that extends from their catalytic site and affects even distant sites, where site-specific evolutionary rate increases monotonically with distance. While protein-protein sites in enzymes was previously shown to induce only a weak conservation gradient, a comprehensive relationship between different types of functional sites in proteins and the magnitude of evolutionary rate gradients they induce has yet to be established. Here, we systematically calculate the evolutionary rate (dN/dS) of sites as a function of distance from different types of binding sites on enzymes and other proteins: catalytic sites, non-catalytic ligand binding sites, allosteric binding sites, and protein-protein interaction sites. We show that catalytic binding sites indeed induce significantly stronger evolutionary rate gradient than all other types of non-catalytic binding sites. In addition, catalytic sites in enzymes with no known allosteric function still induce strong long-range conservation gradients. Notably, the weak long-range conservation gradients induced by non-catalytic binding sites on enzymes is nearly identical in magnitude to those induced by ligand binding sites on non-enzymes. Finally, we show that structural determinants such as local solvent exposure of sites cannot explain the observed difference between catalytic and non-catalytic functional sites. Our results suggest that enzymes and non-enzymes share similar evolutionary constraints only when examined from the perspective of non-catalytic functional sites. Hence, the unique evolutionary rate gradient from catalytic sites in enzymes is likely driven by the optimization of catalysis rather than ligand binding and allosteric functions.

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