Conformational Plasticity-Rigidity Axis of the Coagulation Factor VII Zymogen Elucidated by Atomistic Simulations of the N-Terminally Truncated Factor VIIa Protease Domain

Abstract

The vast majority of coagulation factor VII (FVII), a trypsin-like protease, circulates as the inactive zymogen. Activated FVII (FVIIa) is formed upon proteolytic activation of FVII, where it remains in a zymogen-like state and it is fully activated only when bound to tissue factor (TF). The catalytic domains of trypsin-like proteases adopt strikingly similar structures in their fully active forms. However, the dynamics and structures of the available corresponding zymogens reveal remarkable conformational plasticity of the protease domain prior to activation in many cases. Exactly how ligands and cofactors modulate the conformational dynamics and function of these proteases is not entirely understood. Here, we employ atomistic simulations of FVIIa (and variants hereof, including a TF-independent variant and N-terminally truncated variants) to provide fundamental insights with atomistic resolution into the plasticity-rigidity interplay of the protease domain conformations that appears to govern the functional response to proteolytic and allosteric activation. We argue that these findings are relevant to the FVII zymogen, whose structure has remained elusive despite substantial efforts. Our results shed light on the nature of FVII and demonstrate how conformational dynamics has played a crucial role in the evolutionary adaptation of regulatory mechanisms that were not present in the ancestral trypsin. Exploiting this knowledge could lead to engineering of protease variants for use as next-generation hemostatic therapeutics.

Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures

“…Encouraged by the observed differences in H‐bond stability for agonist and antagonist‐bound structures, we complemented the H‐bond analysis with PCA on the ER structures obtained for the two receptor systems considered above. PCA is a useful technique for reducing the dimensionality of general applicability, case in point being analysis of MD simulations and ER data 76–83 . Since the H‐bond analysis indicated different stability in the upper and lower parts of the receptors, PCA was performed separately on the upper (extracellular) and the lower half (intracellular) of the TM region of the receptors.…”

“…PCA is a useful technique for reducing the dimensionality of general applicability, case in point being analysis of MD simulations and ER data. [76][77][78][79][80][81][82][83] Since the H-bond analysis indicated different stability in the upper and lower parts of the receptors, PCA was performed separately on the upper (extracellular) and the lower half (intracellular) of the TM region of the receptors. The selection of upper and lower half was based on the TM definitions in GPCRdb 84 by dividing each TM in two equal-sized halves with only minor modifications (see Table S2 for the exact definitions).…”

Resolving Protein Conformational Plasticity and Substrate Binding Through the Lens of Machine-Learning

“…As a result,judicious introduction of supervised classifiers within ML based protocols are gaining tractions in biomolecular and chemical sciences. 32,33,44–46 Towards this end, the current investigation offers an effective solution in resolving underlying mechanism of ligand binding in conformationally plastic receptors 16–18…”

“…This has given rise to the theme of conformational plasticity in protein. 13,16–18 Figure 1 provides a schematic illustration of the theme of conformational plasicity.…”

A systematic approach for evaluating the role of surface-exposed loops in trypsin-like serine proteases applied to the 170 loop in coagulation factor VIIa

“…For coagulation factor VIIa (FVIIa), the 170 loop has proven itself to be of predominant importance in the co-factor-mediated initiating of coagulation and as such has received considerable attention 16 – 20 . Several crystal structures are available which 21 – 26 , in combination with extensive molecular dynamics simulations, has been used to explore the TLP domain ensemble and different loop conformations 27 – 35 , shedding light on allostery, substrate recognition and co-factor interaction. Past work has substantiated that the conformation of the 170 loop 1) plays a central role in co-factor mediated allosteric regulation of FVIIa activity by Tissue Factor (TF) 2) is involved in maintaining free FVIIa in its low activity state and 3) influences the initiation of coagulation upon TF binding 16 .…”