Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis
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Recently, a 3.65 angstrom resolution structure of the transporter, NorM from the multidrug and toxic compound extrusion family has been determined in the outward-facing conformation. This antiporter uses electrochemical gradients to drive substrate export ...
Simulation is a key issue in the design of control electrical systems. Simulation packages using component library, such as PSIM®, are very useful to achieve this goal. The simulation model is thus easily built from the system topology (structural model). ...
Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...
Experiments and molecular simulations have shown that the hydrophobic mismatch between proteins and membranes contributes significantly to lipid-mediated protein-protein interactions. In this article, we discuss the effect of cholesterol on lipid-mediated ...
During mild heat-stress, a native thermolabile polypeptide may partially unfold and transiently expose water-avoiding hydrophobic segments that readily tend to associate into a stable misfolded species, rich in intra-molecular non-native beta-sheet structu ...
The molecular chaperone Hsp104 plays a central role in the clearance of aggregates after heat shock and the propagation of yeast prions. Hsp104's disaggregation activity and prion propagation have been linked to its ability to resolubilize or remodel prote ...
We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of proteins. This term mimics the backbone dipole−dipole interactions and accounts for the needed directionality to form stable folded secondary structure elements. We sh ...
PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry, and dynamics with the PDZ function repres ...
In this paper, we present a coarse-grained model of a hydrated saturated phospholipid bilayer (dimyristoylphosphatidylcholine, DMPC) containing cholesterol that we study using a hybrid dissipative particle dynamics-Monte Carlo method. This approach allows ...
Background: Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is therefore becoming critical. We previous ...