Sandbox Reserved 1493

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This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.

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Integrin αIIbβ3 (2VDL)

Integrin αIIbβ3 (or glycoprotein IIb/IIIa) is a complex present on the membrane of platelets that intervenes in the activation, adherence and aggregation of platelets during clotting. It is a cation-dependant heterodimeric transmembrane receptor containing a large extracellular headpiece and short intracellular tails. It is synthesized in megakaryocytes.

Its particular shape and localisation on the membrane allows both ligand binding and transduction of the activation signal. It is the dominant integrin on platelets with 70,000 to 90,000 receptors expressed on each platelet in the resting state.

The headpiece (2VDL) of integrin αIIbβ3 enables cation-facilitated ligand binding with multiple ligands (most known being fibrinogen, fibronectin, von Willebrand factors, thrombospondin and vitronectin). Binding affinity is dynamic and depends on the conformational status of the receptor.

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1 Structure
- 1.1 αIIb subunit
- 1.2 β3 subunit
2 Function
3 Activity modulation
- 3.1 Activation of the headpiece: inside-out signaling
- 3.2 Responses: outside-in signaling from the headpiece
4 Disease
5 Relevance
6 Structural highlights

Structure

αIIbβ3 belongs to the integrin family: it is a bidirectional information mediator between the interior of the cell and its external environment. It has the ability to receive intracellular signals via the cytoplasmic tail and to bind ligands at the extracellular headpiece.

It is composed of adjacent αIIb and β3 subunits that are not covalently linked. Both have a small intracellular cytoplasmic tail domain and a single transmembrane domain which links the first one to a large N-terminal extracellular domain. The latter far exceeds the cytoplasmic domain in size, which can be related to its role in binding high molecular weight ligands (fibrinogen is approximately 340 kDa).

Ligands bind in a groove between the integrin subunits, at the intersection of the integrin extracellular β-propeller of the αIIb subunit and the β I domain of the β3 subunit. There are multiple binding sites in both subunits.

αIIb subunit

The αIIb subunit (glycoprotein IIb) is composed of 1008 amino acids unevenly distributed over 2 chains. A part forms a light chain which comports a cytoplasmic tail of 20 amino acids and a transmembrane helix. An extracellular disulfide segment links this chain to the heavy extracellular domain which is part of the headpiece of the integrin.

The extracellular N-Terminus forms a cap over the β-propeller domain which is folded by seven successive blades of aminoterminal repeats. Each blade is composed of 4 antiparallel β strands located in each repeat and connected by loops located on the surface. This β-propeller is linked to a thigh and two calf domains, which form the leg structure that supports the heavy head. The total forms the stalk of the αIIb subunit. The region between the thigh and the first calf domain is the site at which the head region bends (in the inactivated form of the integrin) is called the knee of the subunit.

The β-propeller hosts multiple cation biding sites. The last 3 or 4 blades bind Ca2+ ions which influence ligand binding on the lower side of the blades. The I domain inserted between blades 2 and 3 in the β-propeller follows a Rossman fold with five β-sheets surrounded by seven α-helices. Ligand binding occurs between the β-propeller and the β I domain of the β3 subunit via a coordinating Mg2+ ion in the MIDAS of the β3 subunit.

The RGD binding site (Arg-Gly-Asp) is in a crevice in this region, inserted between the β-propeller and β I domains. The Arg side chain is located in a groove on the upper surface of the propeller and the Asp carboxylate protruding into a cleft on the β I surface.

β3 subunit

The β3 subunit (glycoprotein IIIa) is a 762 amino acids polypeptide chain.

Its head is composed of a β I domain which has a fold similar to the I domains of the head of the α subunit. It has a Mg2+ coordinating metal ion dependent adhesion site (MIDAS) motif and a site adjacent to MIDAS (ADMIDAS) which coordinate ions.

Its stalk is mainly composed of a plexin-sempahorin-integrin (PSI) domain and

A cysteine-rich core occupies the extracellular part of β3 from residues 400 to 650. It is linked to the N-terminal of the protein thanks to a long-range disulfide bond. As the globular head is part of the ligand-binding headpiece (1 cation binding site, RGD and KGD binding sites), the cysteine-rich region is thought to have a role in the activation of the headpiece.

The cytoplasmic tail of the β3 subunit has a NPLY domain which bind proteins with phosphotyrosine binding (PTB) domains.

Function

4 principal ligand binding domains involved in clotting have been characterized on the extracellular headpiece of the integrin at the interface between the αIIb subunit β propeller and the β3 subunit I domain.

Most ligands of integrin αIIbβ3 share the particularity of having at least one RGD pattern in their protein sequence that can be recognized by the RGD binding site in the β3 subunit.

Cation binding sites

Multiple cation binding sites of integrin are located in the head of both subunits and are indirectly involved in ligand binding. Calcium ion in the β-propeller of αIIb coordinate EF-hand patterns (helix-loop-helix calcium binding patterns) which contribute to the structure of the active site.

The β I domain which also interacts with the ligand includes 3 metal ion binding sites: a Mg2+ ion in MIDAS surrounded by 2 Ca2+ ions (including one from AMIDAS). MIDAS Mg2+ ion coordinates the Asp side chain of ligands containing RGD.

AMIDAS binds an inhibitory Ca2+ ion and an activating Mn2+ ion resulting in conformational changes. It shows the importance of cation binding sites in activity modulation.

KQAGDV binding site

On stimulated platelets, αIIbβ3 has a highly specific receptor for the plasma protein fibrinogen. The KQAGDV binding site interacts with the fibrinogen γ-chain C terminus at the γHHLGGAKQAGDV sequence (residues 400 to 411 of γC). KQAGD is the minimal binding motif for αIIbβ3. The Asp side chain interacts with Mg2+ (MIDAS) and the Gly residue is in a pocket between the two subunits. The peptide ligand interacts with an extended binding site on the integrin and has a turn in the backbone that leads the Lys side chain into a pocket, so that its ammonium group is involved in hydrogen bonding with the αIIb subunit.

RGD binding site

αIIbβ3 can also recognize and bind to the Arg-Gly-Asp (RGD) sequence. This pattern is present within flexible loop regions of fibrinogen α-subunit as well as in other ligands. Indeed, fibronectin binds to αIIbβ3 thanks an Arg-Gly-Asp-Ser-Pro sequence (which is located at the apex of a flexible loop between two β-strands) and von Willebrand factor thanks to the Arg-Gly-Asp sequence in the C1 domain.

RGD binding present similar features to binding of the γC domain of fibrinogen to the KQAGDV binding site: the Asp side chain coordinates the Mg2+ ion in MIDAS and the Gly residue is in the same pocket between the two subunits. The side chain of Arg (along the same pocket as the Lys side chain of the KQAGDV motif of γC) enables to position its guanidinium group for hydrogen bonding to Asp 224.

Structural data revealed the HHLGGAKQAGDV peptide of the γC domain of fibrinogen binds to an extended site on the receptor that includes the RGD binding site. There is thus competing between he HHLGGAKQAGDV peptide and RGD patterns.

The RGD motif can be recognized by eight other integrins such as αvβ3. This enables different integrins to be complementary (rather than competitive) in the mechanisms involved in hemostasis.

KGD binding site

Unlike fibrinogen or von Willebrand factors, some proteins such as collagen have hidden RGD sequences which are only exposed after cleavage or protein denaturation. Still, collagen contains multiple KGD motifs (12 KGD motifs in the α-chains of the COL15 domain of collagen XVII). This pattern can be recognized by the KGD binding site of the β3 subunit

Activity modulation

Activation of the headpiece: inside-out signaling

The resting state

On circulating platelets, integrin αIIbβ3 is maintained in a resting state by intramolecular interactions of the transmembrane and the cytoplasmic domains of its subunits. The transmembrane helices of αIIb and β3 form a complex specifically packed with an inclined geometry. The membrane-proximal regions of the cytoplasmic tails interact thanks to a salt bridge between αIIb-Arg995 and β3-Asp723. The low-affinity compact bent conformation of the inactivated protein allows the platelet to circulate in blood without clotting.

Initiation of activation

Affinity modulation is initiated at the cytoplasmic tails. It is induced by various agonists (such as ADP, thrombin, collagen, and epinephrine) which constitute intracellular signals for the binding of cytoskeletal proteins (talin and kindlin-3) to the cytoplasmic tail of the β3 subunit. For instance, once unmasked, the PTB domain of talin binds the NPLY motif of the β3 subunit, which breaks the salt bridge linking the cytoplasmic tails together. The result is the dissociation of the transmembrane α-helices of the two subunits.

Propagation of activation

It opens a hinge in the integrin which triggers a very quick succession of subunit shifts that are transmitted from the tail to the extracellular headpiece across the transmembrane domain (inside-out signaling). Movements of helices, loops and swing out of the hybrid domain around the active site switches the protein to an extended conformation which facilitates binding to ligands. The active site is at its higher affinity state.

The precise mechanisms of activation which occurs in the extracellular part of the integrin remain a mystery. Still, the conformational difference of a disulfide-bonded knot localised in the cysteine-rich core of the β3 subunit between inactivation and activation suggests that this region plays a part in activation. It is thought that the cysteine core of the β3 subunit linked to its N-terminal extremity apply a conformational constraint on the ligand binding site. It includes a few cysteines that remain unpaired and which redox state influence the activation of the integrin, which supposed this region could host a redox site.

Activated headpiece

Once the ligand binding site has been activated, ligand binding can gradually occur. The initial contact with the ligand is reversible, but then irreversible binding prevents ligand from dissociating. Binding also changes the conformation of the ligand and may unmask new binding regions on it.

Extracellular proteins such as fibrinogen enables platelets aggregation and clotting. Integrin αIIbβ3 also bridges to other αIIbβ3 of adjacent platelets.

Responses: outside-in signaling from the headpiece

Signals transmitted from the ligand-occupied receptor to the inside of the cell (outside-in signaling) triggers the stability of clots and cellular processes such as: - membrane fluidification - reorganization of cytoskeleton with platelets - mobilisation of intracellular calcium - granules secretion: α-granules contained in the membrane of platelets release integrins on platelets to increase the surface expression of αIIbβ3 by 25% to 50%. - increased expression of new receptor sites: ligand-induced binding site (LIBS)

Also, as clotting advances, interactions between αIIbβ3 and the ligand evolve. The new contacts appearing between the integrin and bound soluble fibrin makes the ligand appear like an insoluble fibrinogen matrix which progressively provokes clot retraction.

Disease

Relevance

Structural highlights

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References

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

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@@ Line 50: / Line 50: @@
 === Cation binding sites ===
-Multiple cation binding sites of integrin are located in the head of both subunits and are indirectly involved in ligand binding. Calcium ion in the β-propeller of αIIb coordinate EF-hand patterns (helix-loop-helix calcium-binding motif) which contributes to the structure of the active site.
+Multiple cation binding sites of integrin are located in the head of both subunits and are indirectly involved in ligand binding. Calcium ion in the β-propeller of αIIb coordinate EF-hand patterns (helix-loop-helix calcium binding patterns) which contribute to the structure of the active site.
 The β I domain which also interacts with the ligand includes 3 metal ion binding sites: a Mg2+ ion in MIDAS surrounded by 2 Ca2+ ions (including one from AMIDAS). MIDAS Mg2+ ion coordinates the Asp side chain of ligands containing RGD.
@@ Line 93: / Line 93: @@
 Extracellular proteins such as fibrinogen  enables platelets aggregation and clotting. Integrin αIIbβ3 also bridges to other αIIbβ3 of adjacent platelets.
-=== RESPONSES: outside-in signaling from the headpiece ===
+=== Responses: outside-in signaling from the headpiece ===
 Signals transmitted from the ligand-occupied receptor to the inside of the cell (outside-in signaling) triggers the stability of clots and cellular processes such as: