Mapping the Ligand-binding Sites and Disease-associated Mutations on the Most Abundant Protein in the Human, Type I Collagen

Osteogenesis imperfecta (OI) is a rare genetic disorder demonstrating considerable phenotypic and genetic heterogeneity. The extensively studied genotype–phenotype correlation is a crucial issue for a reliable counseling, as the disease is recognized at increasingly earlier stages of life, including prenatal period. Based on population studies, clusters in COL1A1 and COL1A2 genes associated with the presence of glycine substitutions leading to fatal outcome have been distinguished and named as “lethal regions.” Their localization corresponds to the ligand-binding sites responsible for extracellular interactions of collagen molecules, which could explain high mortality associated with mutations mapping to these regions. Although a number of non-lethal cases have been identified from the variants located in lethal clusters, the mortality rate of mutations has not been updated. An next generation sequencing analysis, using a custom gene panel of known and candidate OI genes, was performed on a group of 166 OI patients and revealed seven individuals with a causative mutations located in the lethal regions. Patients’ age, ranging between 3 and 25 years, excluded the expected fatal outcome. The identification of non-lethal cases caused by mutations located in lethal domains prompted us to determine the actual mortality caused by glycine substitutions mapping to lethal clusters and evaluate the distribution of all lethal glycine mutations across collagen type I genes, based on records deposited in the OI Variant Database. Finally, we identified six glycine substitutions located in lethal regions of COL1A1 and COL1A2 genes, of which four are novel. The review of all mutations in the dedicated OI database, revealed 33 distinct glycine substitutions in two lethal domains of COL1A1, 26 of which have been associated with a fatal outcome. Similarly, 109 glycine substitutions have been identified in eight lethal clusters of COL1A2, of which 51 have been associated with a fatal manifestation. An analysis of all glycine substitutions leading to fatal phenotype, showed that their distribution along collagen type I genes is not regular, with 17% (26 out of 154) of mutations reported in COL1A1 and 64% (51 out of 80) in COL1A2 corresponding to localization of the lethal regions.

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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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Functional analysis of cis-acting DNA sequences controlling transcription of the human type I collagen genes.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)38305-x ◽

1990 ◽

Vol 265 (22) ◽

pp. 13351-13356

Author(s):

S Boast ◽

M W Su ◽

F Ramirez ◽

M Sanchez ◽

E V Avvedimento

Keyword(s):

Functional Analysis ◽

Dna Sequences ◽

Type I Collagen ◽

Type I ◽

Cis Acting ◽

Human Type ◽

Collagen Genes

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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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