Folding and stretching in a Go‐like model of titin

Abstract

Mechanical stretching of the I27 domain of titin and of its double and triple repeats are studied through molecular dynamics simulations of a Go-like model with Lennard-Jones contact interactions. We provide a thorough characterization of the system and correlate the sequencing of the folding and unraveling events with each other and with the contact order. The roles of cantilever stiffness and pulling rate are studied. Unraveling of tandem titin structures has a serial nature. The force-displacement curves in this coarse-grained model are similar to those obtained through all atom calculations.

Optimal allocation of replicas in parallel tempering simulations

“…1BDD͔͒. 15 Very briefly, the protein a͒ model is coarse grained so that each amino acid is represented by individual beads located at the C ␣ atoms. Consecutive beads along the chain interact through an anharmonic potential given by…”

Thermal unfolding of proteins

“…Its scenario is defined in terms of the last average distance, d u , at which contacts are still holding when the C-terminus is moving at a constant speed and the N-terminus is attached to an elastic anchor. We have already established that stretching at "room temperature" proceeds in a way that is unrelated to folding [16,9]. It is only in the entropic limit, when stretching is governed exclusively by the sequential distance that stretching is approximately reverse to folding at optimality [23].…”

“…Mechanical stretching of this protein has been extensively studied in experiments involving atomic force microscopy [11][12][13] and there is also some information about its folding [14,15]. Furthermore, we have already studied it undergoing both processes through molecular dynamics simulations within the topology based model [9,[16][17][18].…”

“…The broken line corresponds to the distance of 1.5σ ij that is considered as a qualitative treshold for the amino acids staying or not staying in a contact [8,16]. It is seen that the treshold line is being crossed repeatedly due to thermal fluctuations.…”

Elasticity of Semiflexible Polymers with and without Self-Interactions

“…In the following we will present and discuss Molecular Dynamics (MD) simulation results in which we can perform a quasi-fixed stretch treatment. In these simulations (similar to what has been done for protein-like polymers [27,28]) the two ends of the polymer are tethered by springs to two fixed points in space so its end-to-end vector can vary only little. The two fixed points are chosen such that a line connecting them is along the z-direction.…”