Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2

TL;DR

This paper explores how a nematode protein called NAPc2 stabilizes its structure when binding to a blood coagulation factor, offering insights into natural anticoagulants.

Contribution

The study reveals a conserved internal salt bridge in NAPc2 that stabilizes its bound conformation, a novel mechanism for protease inhibitors.

Findings

Molecular dynamics simulations show NAPc2 becomes more rigid upon binding factor Xa.

Two conserved residues form an internal salt bridge that stabilizes the bound conformation.

Clotting assays confirm the salt bridge's role in stabilizing protease inhibitors.

Abstract

Abnormal blood coagulation is a major health problem and natural anticoagulants from blood-feeding organisms have been investigated as novel therapeutics. NAPc2, a potent nematode-derived inhibitor of coagulation, has an unusual mode of action that requires coagulation factor Xa but does not inhibit it. Molecular dynamics simulations of NAPc2 and factor Xa were generated to better understand NAPc2. The simulations suggest that parts of NAPc2 become more rigid upon binding factor Xa and reveal that two highly conserved residues form an internal salt bridge that stabilises the bound conformation. Clotting time assays with mutants confirmed the utility of the salt bridge and suggested that it is a conserved mechanism for stabilising the bound conformation of secondary structure-poor protease inhibitors.

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