How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

2007 ◽  
Vol 365 (1) ◽  
pp. 257-273 ◽  
Author(s):  
Kannan Gunasekaran ◽  
Ruth Nussinov
Keyword(s):  
Ligand Binding ◽  
Conformational Change ◽  
Binding Sites ◽  
Structural Features

scholarly journals Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change

1992 ◽  
Vol 285 (2) ◽  
pp. 419-425 ◽  
Author(s):  
U Christensen ◽  
L Mølgaard
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Conformational Change ◽  
Conformational Changes ◽  
Binding Sites ◽  
High Specificity ◽  
Stopped Flow ◽  
Protein Fluorescence ◽  
Lysine Residues ◽  
Kinetics Of

The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.

Recognition of ion ligand binding sites based on amino acid features with the fusion of energy, physicochemical and structural features

2020 ◽  
Vol 26 ◽  
Author(s):  
Shan Wang ◽  
Xiuzhen Hu ◽  
Zhenxing Feng ◽  
Liu Liu ◽  
Kai Sun ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Metal Ion ◽  
Structural Features ◽  
Support Vector ◽  
Sequence Information ◽  
Ligand Binding Site ◽  
Ligand Binding Sites

Background: Rational drug molecular design based on virtual screening requires the ligand binding site to be known. Recently, the recognition of ion ligand binding site has become an important research direction in pharmacology. Methods: In this work, we selected the binding residues of 4 acid radical ion ligands(NO2 - , CO3 2- , SO4 2- and PO4 3- ) and 10 metal ion ligands (Zn2+,Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+ , K+ and Co2+) as research objects. Based on the protein sequence information, we extracted amino acid features, energy, physicochemical and structure features. Then we incorporating the above features and input them into the MultilayerPerceptron (MLP) and support vector machine (SVM) algorithms. Results: In the independent test, the best accuracy was higher than 92.5%, which was better than the previous result on Conclusion: Finally, we set up a free web server for the prediction of protein-ion ligand binding sites (http://39.104.77.103:8081/lsb/HomePage/HomePage.html). This study is helpful for molecular drug design.

Role of Urokinase Receptor and Caveolin in Regulation of Integrin Signaling

1999 ◽  
Vol 82 (08) ◽  
pp. 291-297 ◽  
Author(s):  
Ying Wei ◽  
Daniel Simon ◽  
David Waltz ◽  
Harold Chapman
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Structural Features ◽  
Conformational State ◽  
Structural Proteins ◽  
Dynamic Regulation ◽  
Β2 Integrin ◽  
Cytoplasmic Tails ◽  
Β1 Integrins ◽  
Α Chain

Introduction: Integrin-Associated ProteinsIntegrins are a group of heterodimeric adhesion receptors that mediate attachment of cells to extracellular matrices and other cells. These receptors serve as a major site of information flow from the immediate pericellular environment to the cellular interior and, in reverse, as effectors of the cellular responses to such information in biological processes as diverse as inflammation, tissue remodeling, growth, and tumorigenesis.1-3 The binding specificities of integrin receptors are determined by interactions of ligands with both the α and β chains that comprise integrins. Diversity of ligand binding is promoted by the fact that a single α chain may partner with numerous distinct β chains, and cells may express more than one and, sometimes, many α and β chains. Thus, as a family, integrins have the capacity to interact with a large set of cellular and extracellular matrix ligands. The structural features of integrin heterodimers that underlie their interactive potential and ligand specificity have been the subject of several recent reviews and will not be discussed here.4,5 A fundamental feature of integrins is that their function is determined not simply by their expression on the cell surface but by their dynamic regulation through activating events that amplify, sometimes only transiently, the adhesive capacity of integrins for their counter-ligands and the signals that follow.1-3,6,7 These dynamic aspects of integrin function are dependent on integrin interactions with its neighbors in the cell membrane and inside the cell, a structural consequence of the fact that integrins contain only short cytoplasmic tails without intrinsic signaling capacity. Three major sites of dynamic regulation of integrin function, indicated schematically in Figure 1, are as follows: ligand binding, association of cytoplasmic signaling elements with integrin cytoplasmic tails, and regulation of integrin binding and signaling by association with non-integrin “membrane adaptors.” Ligand binding by integrins is a function of their conformational state (Fig. 1a). Recent molecular modeling suggests that integrin α and β chains may exist in a relatively weak binding or “inactive state,” in which α and β chains extensively overlap and the β chain obscures binding sites on the α chain.5,8 In this model “activation” of integrins results from an altered conformation in which there is less overlap and more extensive availability of binding sites for ligand engagement. Such changes in conformational state may occur as a consequence of integrin clustering (following initially weak ligand binding).The capacity of integrins to cluster and connect with the cytoskeleton (Fig. 1b) in a manner promoting adhesion and migration is also regulated by complex interactions of kinases, phosphatases, and various structural proteins that bind to and assemble around integrin cytoplasmic tails. Signals derived from G-protein-coupled chemotactic receptors or generated by engagement of integrin extracellular ligand domains and clustering promote the activation of Src-family kinases, generation of lipid mediators, and in some cases, Ca2+ transients. These membrane proximate signals initiate and then propagate the accumulation of kinases and structural proteins surrounding a cluster of integrins. These events may also, in effect, be “insideout signals” affecting the conformational state of integrin extracellular domains1 (Fig. 1a). The assembly of cytoplasmic signaling elements on or near integrin cytoplasmic tails appears fundamental to the capacity of integrins to mediate adhesion and to impart, by signaling to the cellular interior, the nature of the immediate extracellular milieu.More recently, evidence has emerged that integrin function is also regulated by non-integrin membrane proteins that associate with integrins outside or within the plasma membrane (Fig. 1c). These include the tetraspan family of membrane proteins (CD9, CD63, CD81, CD82, and others), integrin-associated protein (CD47), and CD98.9-11 In addition, we and others have previously reported that β1 integrin function is regulated by its association with the glycosylphosphatidyl-inositol (GPI)-linked non-integrin receptor, the urokinase receptor (u-PAR, CD87), and a cholesterol-binding membrane protein called caveolin.12,13 As with ligand binding, structural features of the integrin heterodimers appear to dictate their association with these different membrane adaptors. For example, CD47 is reported to specifically interact with and promote the signaling function of αv/β3.10 The tetraspan family of proteins predominantly interacts with β1 integrins, but reportedly, only with certain α chain/β1 pairs.9 The functional effects of tetraspan proteins on integrin function is uncertain, though it is remarkable that at least two of these proteins (CD81 and 82) have been reported to inhibit tumor cell motility and act as tumor suppressors.14, 15 Caveolin and u-PAR also exhibit preferences for integrin interactions. Wary et al reported α-chain specificity for the association of β1 integrins with caveolin-1.12 The u-PAR receptor physically binds to the purified β2 integrin Mac-1 (CD11b/CD18), though no binding is observed in similar experiments with the β2 integrin CD11a/CD18 (LFA-1).16 Thus, like extracellular ligand interactions and intracellular cytoplasmic interactions, the capacity of integrins to interact with non-integrin membrane adaptors appears to be determined by amino acid sequences within the integrin heterodimers. The exact molecular basis for these interactions remains uncertain and is being actively investigated. This brief review will focus on the functional consequences of interaction of β1integrins with two of these membrane adaptors, u-PAR and caveolin.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

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