Laminar Distribution of Putative Neurotransmitter Amino Acids and Ligand Binding Sites in the Dog Olfactory Bulb

Several secondary structures, such asπ-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-preferϕ/ψbox residues are exposed more to solvents, whereas amino acids following ligand-preferϕ/ψbox residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.

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DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity

10.1101/2021.08.22.456843 ◽

2021 ◽

Author(s):

Felix M Quintana ◽

Zhaoming Kong ◽

Lifang He ◽

Brian Y Chen

Keyword(s):

Neural Networks ◽

Amino Acids ◽

Ligand Binding ◽

Electrostatic Potential ◽

Binding Sites ◽

Binding Specificity ◽

Ligand Binding Sites ◽

Salient Regions ◽

Biochemical Mechanisms ◽

Activation Mapping

Amino acids that play a role in binding specificity can be identified with many methods, but few techniques identify the biochemical mechanisms by which they act. To address a part of this problem, we present DeepVASP-E, an algorithm that can suggest electrostatic mechanisms that influence specificity. DeepVASP-E uses convolutional neural networks to classify an electrostatic representation of ligand binding sites into specificity categories. It also uses class activation mapping to identify regions of electrostatic potential that are salient for classification. We hypothesize that electrostatic regions that are salient for classification are also likely to play a biochemical role in achieving specificity. Our findings, on two families of proteins with electrostatic influences on specificity, demonstrate that large salient regions can identify amino acids that have an electrostatic role in binding, and that DeepVASP-E is an effective classifier of ligand binding sites.

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Faculty Opinions recommendation of Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1044116.497853 ◽

2006 ◽

Author(s):

Wolfgang Jahnke

Keyword(s):

Ligand Binding ◽

Binding Sites ◽

Hot Spots ◽

Ligand Binding Sites

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Faculty Opinions recommendation of LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725748869.793514601 ◽

2016 ◽

Author(s):

Jeffrey Skolnick

Keyword(s):

Ligand Binding ◽

Binding Sites ◽

Ligand Binding Sites ◽

Connolly Surface

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Usefulness of Molecular Modeling in Characterizing the Ligand-Binding Sites of Proteins: Experience with Human PDI, PDIp and COX

Current Medicinal Chemistry ◽

10.2174/09298673113209990207 ◽

2013 ◽

Vol 20 (31) ◽

pp. 3840-3854 ◽

Cited By ~ 2

Author(s):

Pan Wang ◽

Bao-Ting Zhu

Keyword(s):

Molecular Modeling ◽

Ligand Binding ◽

Binding Sites ◽

Ligand Binding Sites

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Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

Biochemical Journal ◽

10.1042/bj20150068 ◽

2015 ◽

Vol 471 (3) ◽

pp. 403-414 ◽

Cited By ~ 19

Author(s):

M. Florencia Rey-Burusco ◽

Marina Ibáñez-Shimabukuro ◽

Mads Gabrielsen ◽

Gisela R. Franchini ◽

Andrew J. Roe ◽

...

Keyword(s):

Fatty Acid ◽

Ligand Binding ◽

Tissue Distribution ◽

Binding Sites ◽

Binding Proteins ◽

Retinol Binding Protein ◽

Internal Cavity ◽

Binding Characteristics ◽

Necator Americanus ◽

Ligand Binding Sites

Necator americanus fatty acid and retinol-binding protein-1 (Na-FAR-1) is an abundantly expressed FAR from a parasitic hookworm. The present work describes its tissue distribution, structure and ligand-binding characteristics and shows that Na-FAR-1 expands to transport multiple FA molecules in its internal cavity.

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Adenosine Receptors of Cerebral Microvessels and Choroid Plexus

Journal of Cerebral Blood Flow & Metabolism ◽

10.1038/jcbfm.1986.80 ◽

1986 ◽

Vol 6 (4) ◽

pp. 463-470 ◽

Cited By ~ 33

Author(s):

Rajesh N. Kalaria ◽

Sami I. Harik

Keyword(s):

Cerebral Cortex ◽

Ligand Binding ◽

Choroid Plexus ◽

Adenosine Receptors ◽

Binding Sites ◽

Specific Binding ◽

Cerebral Microvessels ◽

High Affinity ◽

Receptor Sites ◽

Ligand Binding Sites

We studied, by ligand binding methods, the two adenosine receptors, A, and A2, in rat and pig cerebral microvessels and pig choroid plexus. Ligand binding to cerebral microvessels was compared with that to membranes of the cerebral cortex. [3H]Cyclohexyladenosine and [3H]l-phenylisopropyladenosine were the ligands used for A1-receptors, and [3H]5'- N-ethylcarboxamide adenosine ([3H]NECA) was used to assess A2-receptors. We report that cerebral microvessels and choroid plexus exhibit specific [3H]NECA binding, but have no appreciable A1-receptor ligand binding sites. Specific binding of [3H]NECA to cerebral microvessels, choroid plexus, and cerebral cortex was saturable and suggested the existence of two classes of A2-receptor sites: high-affinity ( Kd ∼ 250 n M) and low-affinity ( Kd ∼ 1–2 μ M) sites. The Kd and Bmax of NECA binding to cerebral microvessels and cerebral cortex were similar within each species. Our results, indicating the existence of A2-receptors in cerebral microvessels, are consistent with results of increased adenylate cyclase activity by adenosine and some of its analogues in these microvessels.

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A naturally occurring Tyr143HisαIIb mutation abolishes αIIbβ3 function for soluble ligands but retains its ability for mediating cell adhesion and clot retraction: comparison with other mutations causing ligand-binding defects

Blood ◽

10.1182/blood-2002-07-2144 ◽

2003 ◽

Vol 101 (9) ◽

pp. 3485-3491 ◽

Cited By ~ 17

Author(s):

Teruo Kiyoi ◽

Yoshiaki Tomiyama ◽

Shigenori Honda ◽

Seiji Tadokoro ◽

Morio Arai ◽

...

Keyword(s):

Cell Adhesion ◽

Ligand Binding ◽

Binding Sites ◽

Clot Retraction ◽

Naturally Occurring ◽

Binding Function ◽

293 Cells ◽

Ligand Binding Sites ◽

Functional Defect ◽

And Function

The molecular basis for the interaction between a prototypic non–I-domain integrin, αIIbβ3, and its ligands remains to be determined. In this study, we have characterized a novel missense mutation (Tyr143His) in αIIb associated with a variant of Glanzmann thrombasthenia. Osaka-12 platelets expressed a substantial amount of αIIbβ3(36%-41% of control) but failed to bind soluble ligands, including a high-affinity αIIbβ3-specific peptidomimetic antagonist. Sequence analysis revealed that Osaka-12 is a compound heterozygote for a single 521T>C substitution leading to a Tyr143His substitution in αIIb and for the null expression of αIIb mRNA from the maternal allele. Given that Tyr143 is located in the W3 4-1 loop of the β-propeller domain of αIIb, we examined the effects of Tyr143His or Tyr143Ala substitution on the expression and function of αIIbβ3 and compared them with KO (Arg-Thr insertion between 160 and 161 residues of αIIb) and with the Asp163Ala mutation located in the same loop by using 293 cells. Each of them abolished the binding function of αIIbβ3 for soluble ligands without disturbing αIIbβ3 expression. Because immobilized fibrinogen and fibrin are higher affinity/avidity ligands for αIIbβ3, we performed cell adhesion and clot retraction assays. In sharp contrast to KO mutation and Asp163AlaαIIbβ3, Tyr143HisαIIbβ3-expressing cells still had some ability for cell adhesion and clot retraction. Thus, the functional defect induced by Tyr143HisαIIb is likely caused by its allosteric effect rather than by a defect in the ligand-binding site itself. These detailed structure–function analyses provide better understanding of the ligand-binding sites in integrins.

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