Lactaderhin's C1 domain restricts protein's ensemble as it binds to charged membranes.

Abstract

Lactadherin's (Lact) binding to phosphotidylserine (PS) enriched cell surfaces is critical for controlling our blood coagulation. Although structural and mutagenesis studies indicate important binding regions of this protein, they are not sufficient to construct a detailed, membrane-bound model especially since they mainly consider only one of its two globular domains, namely C2. We thus use molecular dynamics (MD) simulations and the AlphaFold program to generate an ensemble of Lact encounter complexes with a negatively charged bilayer consistent with biochemical studies. This was accomplished by first using the highly mobile membrane mimetic (HMMM) to efficiently simulate its C2 domain binding to PS lipids. We then converted the HMMM model to standard full-tail lipid membranes to further sample and obtain converged bound structures that we call the “vertical” and “side-lying” ensembles. From these bilayer-bound poses, we infer which one allows for attachment of its other C1 domain and use AlphaFold to reconstruct it and further simulate to capture equilibrium complexes. Modeling revealed that C1 domain restricts the dynamics structural ensemble of Lact bound to membranes. We also report Lact's full dynamic structure in the presence of negatively charged lipids and compare them with other homologous blood coagulation proteins to provide a rationale for its competitive binding. These results shed light on the structural mechanism of blood coagulation by considering its binding in a membrane environment which can serve as a general framework for studying these critical protein-membrane interactions. They also provide a structural basis for further understanding the significance that PS lipids play in regulating blood coagulation processes.