In silico analysis of Glanzmann variants of Calf-1 domain of \u03b1IIb\u03b23 integrin revealed dynamic allosteric effect

Matthieu Goguet,Alexandre G. de Brevern,Vincent Jallu,Rachel Petermann,Tarun Jairaj Narwani

doi:10.1038/s41598-017-08408-w

Abstract

Integrin αIIbβ3 mediates platelet aggregation and thrombus formation. In a rare hereditary bleeding disorder, Glanzmann thrombasthenia (GT), αIIbβ3 expression / function are impaired. The impact of deleterious missense mutations on the complex structure remains unclear. Long independent molecular dynamics (MD) simulations were performed for 7 GT variants and reference structure of the Calf-1 domain of αIIb. Simulations were analysed using a structural alphabet to describe local protein conformations. Common and flexible regions as well as deformable zones were observed in all the structures. The most flexible region of Calf-1 (with highest B-factor) is rather a rigid region encompassed into two deformable zones. Each mutated structure barely showed any modifications at the mutation sites while distant conformational changes were observed. These unexpected results question the relationship between molecular dynamics and allostery; and the role of these long-range effects in the impaired αIIbβ3 expression. This method is aimed at studying all αIIbβ3 sub-domains and impact of missense mutations at local and global structural level.

Highlights

In humans, the Integrins protein superfamily consists of 24 heterodimeric receptors resulting from different combination of 18 α and 8 β subunits
Defective primary haemostasis leads to two severe life-threatening bleeding disorders: (1) Glanzmann thrombasthenia (GT), a rare autosomal recessive genetic disease associated with impaired αIIbβ[3] expression and/or function[7]; and (2) Fetal/neonatal alloimmune thrombocytopenia (FNAIT) results from fetal/neonatal platelet destruction by maternal antibodies in mothers lacking an alloantigen inherited from the father
Root mean square deviations (RMSD) from all molecular dynamics (MD) simulations reach a steady state at 50 nsec (Figure S1) that is maintained in longer runs of 100 nsec indicating stable and reproducible independent dynamics

Summary

Introduction

The Integrins protein superfamily consists of 24 heterodimeric receptors resulting from different combination of 18 α and 8 β subunits. Upon activation the integrin αIIbβ[3] binds plasmatic fibrinogen leading to platelet aggregation and thrombus formation (Primary haemostasis). The β-I domain of β3 mainly consists of α helices and loops with coordinated metal ions Ca2+ and Mg2+ constituting a MIDAS (Metal Ion Dependent Adhesion Sites) with an ADMIDAS (Adjacent to MIDAS) and SyMBS (Synergistic Metal Binding Site) These sites play critical role in opening the αIIbβ[3] binding site and helps in ligand binding[2]. The short loop of αIIb Genu coordinates with a divalent calcium[3] This metal ion might help in stabilizing Calf-1 and Thigh domains interface during the opening of the structure following the activation process (angular shift at Genu). FNAIT clinical consequences range from no symptoms to intracranial haemorrhages with a risk of neurological sequel and/or fetal/neonatal death[8]

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Conclusion