scholarly journals Cation-π bonding and amino-aromatic interactions in the biomolecular recognition of substituted ammonium ligands

1996 ◽  
Vol 319 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Nigel S. SCRUTTON ◽  
Andrew R.C. RAINE
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Biologically Active ◽  
Biomolecular Recognition ◽  
Structure Based Drug Design ◽  
Protein Architecture ◽  
Aromatic Interactions ◽  
Ligand Binding Sites ◽  
Amine Ligands

Cation-π bonds and amino-aromatic interactions are known to be important contributors to protein architecture and stability, and their role in ligand-protein interactions has also been reported. Many biologically active amines contain substituted ammonium moieties, and cation-π bonding and amino-aromatic interactions often enable these molecules to associate with proteins. The role of organic cation-π bonding and amino-aromatic interactions in the recognition of small-molecule amines and peptides by proteins is an important topic for those involved in structure-based drug design, and although the number of structures determined for proteins displaying these interactions is small, general features are beginning to emerge. This review explores the role of cation-π bonding and amino-aromatic interactions in the biological molecular recognition of amine ligands. Perspectives on the design of ammonium-ligand-binding sites are also discussed.

scholarly journals Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site

2021 ◽  
Author(s):  
Shiran Lacham-Hartman ◽  
Yulia Shmidov ◽  
Evette S. Radisky ◽  
Ronit Bitton ◽  
David B. Lukatsky ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Protein Interactions ◽  
Protein Complex ◽  
Binding Sites ◽  
Biological Interactions ◽  
Protein Protein Interactions ◽  
Regulatory Pathways ◽  
Multiple Binding Sites ◽  
Ligand Binding Sites

AbstractAlthough myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.Impact statementLacham-Hartman et al. demonstrate enhancement of binding affinity through avidity in a complex between a bivalent ligand and a soluble monomeric target with a single binding site. Avidity effects have previously been demonstrated only for clustered receptor molecules presenting multiple binding sites. Our model may explain how polyvalent ligands can agonize or antagonize biological interactions involving nonclustered target molecules that are crucial for intra- and extracellular structural, metabolic, signaling, and regulatory pathways.

Ligand binding to integrin αvβ3requires tyrosine 178 in the αv subunit

Blood ◽  
2001 ◽  
Vol 97 (1) ◽  
pp. 175-182 ◽  
Author(s):  
Shigenori Honda ◽  
Yoshiaki Tomiyama ◽  
Nisar Pampori ◽  
Hirokazu Kashiwagi ◽  
Teruo Kiyoi ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Integrin Αvβ3 ◽  
Alanine Scanning Mutagenesis ◽  
Α Subunit ◽  
Fibrinogen Binding ◽  
293 Cells ◽  
Ligand Binding Sites ◽  
Arginine Glycine Aspartic Acid

Abstract Integrin αvβ3 has been implicated in angiogenesis and other biological processes. However, the ligand-binding sites in αv, a non–I-domain α subunit, remain to be identified. Recently in αIIb, the other partner of the β3 subunit, several discontinuous residues important for ligand binding were identified in the predicted loops between repeats 2 and 3 (W3 4-1 loop) and within repeat 3 (W3 2-3 loop). Based on these findings, alanine-scanning mutagenesis in 293 cells was used to investigate the role of these loops (cysteine [C]142-C155 and glycine [G]172-G181) of αv in ligand binding. Wild-type αvβ3 was able to bind soluble fibrinogen following integrin activation either by 0.5 mM manganese dichloride (MnCl2) or a mutation of β3 threonine (T)562 to asparagine. However, mutation of tyrosine (Y)178 to alanine in the predicted G172-G181 loop of αv abolished fibrinogen binding, and alanine (A) substitutions at adjacent residues phenylalanine (F)177 and tryptophan (W)179 had a similar effect. Cells expressing Y178Aαvalso failed to bind to immobilized fibrinogen. Moreover, the Y178A mutation abolished the binding of WOW-1 Fab, a monovalent ligand-mimetic anti-αvβ3 antibody, and the expression of β3 ligand–induced binding sites (LIBS) induced by arginine-glycine-aspartic acid-tryptophan (RGDW). In sharp contrast to the data obtained with αIIb, none of the mutations in the predicted W3 4-1 loop in αv impaired ligand binding. These results implicate αv Y178 in ligand binding to αvβ3, and they suggest that there are key structural differences in the adhesive ligand-binding sites of αvβ3 and αIIbβ3.

scholarly journals Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium

2020 ◽  
Vol 6 (40) ◽  
pp. eabd0480
Author(s):  
Yumiko Mizukoshi ◽  
Koh Takeuchi ◽  
Yuji Tokunaga ◽  
Hitomi Matsuo ◽  
Misaki Imai ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Protein Interactions ◽  
Binding Sites ◽  
Drug Targets ◽  
Conformational Equilibrium ◽  
Wild Type ◽  
Protein Protein Interactions ◽  
Hit Rate ◽  
Open Conformation ◽  
Ligand Binding Sites

Cryptic ligand binding sites, which are not evident in the unligated structures, are beneficial in tackling with difficult but attractive drug targets, such as protein-protein interactions (PPIs). However, cryptic sites have thus far not been rationally pursued in the early stages of drug development. Here, we demonstrated by nuclear magnetic resonance that the cryptic site in Bcl-xL exists in a conformational equilibrium between the open and closed conformations under the unligated condition. While the fraction of the open conformation in the unligated wild-type Bcl-xL is estimated to be low, F143W mutation that is distal from the ligand binding site can substantially elevate the population. The F143W mutant showed a higher hit rate in a phage-display peptide screening, and the hit peptide bound to the cryptic site of the wild-type Bcl-xL. Therefore, by controlling the conformational equilibrium in the cryptic site, the opportunity to identify a PPI inhibitor could be improved.

scholarly journals Two independent domains of hDlg are sufficient for subcellular targeting: the PDZ1-2 conformational unit and an alternatively spliced domain.

1996 ◽  
Vol 135 (4) ◽  
pp. 1125-1137 ◽  
Author(s):  
R A Lue ◽  
E Brandin ◽  
E P Chan ◽  
D Branton
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Subcellular Targeting ◽  
Erm Proteins ◽  
Permeabilized Cells ◽  
Protein 4.1 ◽  
Alternatively Spliced

hDlg, a human homologue of the Drosophila Dig tumor suppressor, contains two binding sites for protein 4.1, one within a domain containing three PSD-95/Dlg/ZO-1 (PDZ) repeats and another within the alternatively spliced I3 domain. Here, we further define the PDZ-protein 4.1 interaction in vitro and show the functional role of both 4.1 binding sites in situ. A single protease-resistant structure formed by the entirety of both PDZ repeats 1 and 2 (PDZ1-2) contains the protein 4.1-binding site. Both this PDZ1-2 site and the I3 domain associate with a 30-kD NH2-terminal domain of protein 4.1 that is conserved in ezrin/radixin/moesin (ERM) proteins. We show that both protein 4.1 and the ezrin ERM protein interact with the murine form of hDlg in a coprecipitating immune complex. In permeabilized cells and tissues, either the PDZ1-2 domain or the I3 domain alone are sufficient for proper subcellular targeting of exogenous hDlg. In situ, PDZ1-2-mediated targeting involves interactions with both 4.1/ERM proteins and proteins containing the COOH-terminal T/SXV motif. I3-mediated targeting depends exclusively on interactions with 4.1/ERM proteins. Our data elucidates the multivalent nature of membrane-associated guanylate kinase homologue (MAGUK) targeting, thus beginning to define those protein interactions that are critical in MAGUK function.

scholarly journals Chromatin Opening and Transactivator Potentiation by RAP1 in Saccharomyces cerevisiae

1999 ◽  
Vol 19 (8) ◽  
pp. 5279-5288 ◽  
Author(s):  
Liuning Yu ◽  
Randall H. Morse
Keyword(s):  
Binding Site ◽  
Protein Interactions ◽  
Binding Sites ◽  
Accessory Protein ◽  
Dna Binding Domain ◽  
Transcriptional Activators ◽  
Protein Protein Interactions ◽  
Chromatin Opening

ABSTRACT Transcriptional activators function in vivo via binding sites that may be packaged into chromatin. Here we show that whereas the transcriptional activator GAL4 is strongly able to perturb chromatin structure via a nucleosomal binding site in yeast, GCN4 does so poorly. Correspondingly, GCN4 requires assistance from an accessory protein, RAP1, for activation of the HIS4 promoter, whereas GAL4 does not. The requirement for RAP1 for GCN4-mediated HIS4activation is dictated by the DNA-binding domain of GCN4 and not the activation domain, suggesting that RAP1 assists GCN4 in gaining access to its binding site. Consistent with this, overexpression of GCN4 partially alleviates the requirement for RAP1, whereas HIS4activation via a weak GAL4 binding site requires RAP1. RAP1 is extremely effective at interfering with positioning of a nucleosome containing its binding site, consistent with a role in opening chromatin at the HIS4 promoter. Furthermore, increasing the spacing between binding sites for RAP1 and GCN4 by 5 or 10 bp does not impair HIS4 activation, indicating that cooperative protein-protein interactions are not involved in transcriptional facilitation by RAP1. We conclude that an important role of RAP1 is to assist activator binding by opening chromatin.

scholarly journals Structural dynamics of the β-coronavirus Mpro protease ligand binding sites

2021 ◽  
Author(s):  
Eunice Cho ◽  
Margarida Rosa ◽  
Ruhi Anjum ◽  
Saman Mehmood ◽  
Mariya Soban ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Protein Interactions ◽  
Binding Sites ◽  
Adaptive Sampling ◽  
Conformational Dynamics ◽  
Current Crisis ◽  
Ligand Binding Sites ◽  
Structural Conservation ◽  
State Models ◽  
Viral Components

Abstractβ-coronaviruses alone have been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a back-up against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensible role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all non-redundant ligand-binding sites available for SARS-CoV2, SARS-CoV and MERS-CoV Mpro. Extensive adaptive sampling has been used to explore conformational dynamics employing convolutional variational auto encoder-based deep learning, and investigates structural conservation of the ligand binding sites using Markov state models across β-coronavirus homologs. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-coronavirus homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

scholarly journals Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0249616
Author(s):  
Shiran Lacham-Hartman ◽  
Yulia Shmidov ◽  
Evette S. Radisky ◽  
Ronit Bitton ◽  
David B. Lukatsky ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Protein Interactions ◽  
Protein Complex ◽  
Binding Sites ◽  
Protein Protein Interactions ◽  
Multiple Receptors ◽  
Ligand Binding Sites ◽  
Multiple Ligands ◽  
Multiple Ligand

Although myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.

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