Browsing by Author "Madsen, Jesper J."

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Citation - WoS: 4
Citation - Scopus: 4
Elucidating the Complex Membrane Binding of a Protein With Multiple Anchoring Domains Using extHMMM
(Public Library Science, 2024) Madsen, Jesper J.; Ohkubo, Y. Zenmei
Membrane binding is a crucial mechanism for many proteins, but understanding the specific interactions between proteins and membranes remains a challenging endeavor. Coagulation factor Va (FVa) is a large protein whose membrane interactions are complicated due to the presence of multiple anchoring domains that individually can bind to lipid membranes. Using molecular dynamics simulations, we investigate the membrane binding of FVa and identify the key mechanisms that govern its interaction with membranes. Our results reveal that FVa can either adopt an upright or a tilted molecular orientation upon membrane binding. We further find that the domain organization of FVa deviates (sometimes significantly) from its crystallographic reference structure, and that the molecular orientation of the protein matches with domain reorganization to align the C2 domain toward its favored membrane-normal orientation. We identify specific amino acid residues that exhibit contact preference with phosphatidylserine lipids over phosphatidylcholine lipids, and we observe that mostly electrostatic effects contribute to this preference. The observed lipid-binding process and characteristics, specific to FVa or common among other membrane proteins, in concert with domain reorganization and molecular tilt, elucidate the complex membrane binding dynamics of FVa and provide important insights into the molecular mechanisms of protein-membrane interactions. An updated version of the HMMM model, termed extHMMM, is successfully employed for efficiently observing membrane bindings of systems containing the whole FVa molecule. Understanding the intricacies of protein-membrane interaction is essential for fleshing out the functional roles of membrane proteins. Substantial evidence indicates that the binding of some proteins, such as coagulation factor Va, proceeds in a multi-step manner requiring some form of rearrangements within the structure and dynamics of the protein, as well as in the protein's orientation relative to the membrane surface. In the case of factor Va, the intricate binding process can be attributed to the presence of multiple membrane-anchoring domains. In order to feasibly study the dynamics of these mechanisms, we employ an enhanced membrane-mimetic model, HMMM, capable of capturing such processes and rearrangements and making new discoveries possible using the molecular dynamics technique. The successful execution of these studies demanded several modifications to the original implementation of the HMMM. Our exploration not only improves our understanding of FVa's membrane binding dynamics but also contributes to the broader molecular mechanisms governing protein-membrane interactions.
Citation - WoS: 2
Citation - Scopus: 2
Membrane Binding and Lipid-Protein Interaction of the C2 Domain From Coagulation Factor V
(Elsevier, 2024) Ohkubo, Y. Zenmei; Radulovic, Peter W.; Kahira, Albert N.; Madsen, Jesper J.
Anchoring of coagulation factors to anionic regions of the membrane involves the C2 domain as a key player. The rate of enzymatic reactions of the coagulation factors is increased by several orders of magnitude upon membrane binding. However, the precise mechanisms behind the rate acceleration remain unclear, primarily because of a lack of understanding of the conformational dynamics of the C2-containing factors and corresponding complexes. We elucidate the membrane-bound form of the C2 domain from human coagulation factor V (FV-C2) by characterizing its membrane binding the specific lipid -protein interactions. Employing all-atom molecular dynamics simulations and leveraging the highly mobile membrane-mimetic (HMMM) model, we observed spontaneous binding of FV-C2 to a phosphatidylserine (PS)-containing membrane within 2-25 ns across twelve independent simulations. FV-C2 interacted with the membrane through three loops (spikes 1-3), achieving a converged, stable orientation. Multiple HMMM trajectories of the spontaneous membrane binding provided extensive sampling and ample data to examine the membrane-induced effects on the conformational dynamics of C2 as well as specific lipid -protein interactions. Despite existing crystal structures representing presumed "open" and "closed" states of FV-C2, our results revealed a continuous distribution of structures between these states, with the most populated structures differing from both "open" and "closed" states observed in crystal environments. Lastly, we characterized a putative PS-specific binding site formed by K23, Q48, and S78 located in the groove enclosed by spikes 1-3 (PS-specificity pocket), suggesting a different orientation of a bound headgroup moiety compared to previous proposals based upon analysis of static crystal structures.
Citation - WoS: 12
Citation - Scopus: 13
Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches
(Georg Thieme verlag Kg, 2021) Ohkubo, Y. Zenmei; Madsen, Jesper J.
In the life sciences, including hemostasis and thrombosis, methods of structural biology have become indispensable tools for shedding light on underlying mechanisms that govern complex biological processes. Advancements of the relatively young field of computational biology have matured to a point where it is increasingly recognized as trustworthy and useful, in part due to their high space-time resolution that is unparalleled by most experimental techniques to date. In concert with biochemical and biophysical approaches, computational studies have therefore proven time and again in recent years to be key assets in building or suggesting structural models for membrane-bound forms of coagulation factors and their supramolecular complexes on membrane surfaces where they are activated. Such endeavors and the proposed models arising from them are of fundamental importance in describing and understanding the molecular basis of hemostasis under both health and disease conditions. We summarize the body of work done in this important area of research to drive forward both experimental and computational studies toward new discoveries and potential future therapeutic strategies.