ABSTRACT
Molecular simulations are carried out on the Immunoglobulin 27 domain of the titin protein. The energy landscape is mapped out using an implicit solvent model, and molecular dynamics simulations are run with the solvent explicitly modeled. Stretching a protein is shown to produce a dynamic energy landscape in which the energy minima move in configuration space, change in depth, and are created and destroyed. The connections of these landscape changes to the mechanical unfolding of the Immunoglobulin 27 domain are addressed. Hydrogen bonds break upon stretching by either intrabasin processes associated with the movement of energy minima, or interbasin processes associated with transitions between energy minima. Intrabasin changes are reversible and dominate for flexible interactions, whereas interbasin changes are irreversible and dominate for stiff interactions. The most flexible interactions are Glu-Lys salt bridges, which can act like tethers to bind strands even after all backbone interactions between the strands have been broken. As the protein is stretched, different types of structures become the lowest energy structures, including structures that incorporate nonnative hydrogen bonds. Structures that have flat energy versus elongation profiles become the lowest energy structures at elongations of several Angstroms, and are associated with the unfolding intermediate state observed experimentally.
Subject(s)
Energy Transfer , Immunoglobulins/chemistry , Immunoglobulins/ultrastructure , Models, Chemical , Models, Molecular , Muscle Proteins/chemistry , Muscle Proteins/ultrastructure , Protein Kinases/chemistry , Protein Kinases/ultrastructure , Computer Simulation , Connectin , Elasticity , Protein Conformation , Protein Structure, Tertiary , Stress, MechanicalABSTRACT
Over the past decade or more, contradictory evidence of Martian climate, indicating that surface temperatures seldom if ever approach the melting point of water at midlatitudes, and geomorphic features, consistent with liquid flows at these same latitudes, have proven difficult to reconcile. In this article, we demonstrate that several features of liquid-erosional flows can be produced by dry granular materials when individual particle settling is slower than characteristic debris flow speeds. Since the gravitational acceleration on Mars is about one-third that on Earth, and since particle settling speeds scale with gravity, we propose that some (although perhaps not all) Martian geomorphological features attributed to liquid flows may in fact be associated with dry granular flows in the presence of reduced gravity.
