相关论文: Role of pulling direction in understanding the ene…
We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost…
Based on large-scale Monte Carlo simulations on lattice the energy probability distribution functions are investigated for a large set of primary sequences in distinct models of copolymers at low temperatures below transitions to compacted…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
An evolution partial differential equation for the surface of a non-wetting single-crystal film in an attractive substrate potential is derived and used to study the dynamics of a pinhole for the varying initial depth of a pinhole and the…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the…
We study the unfolding of a single polymer chain due to an external force. We use a simplified model which allows to perform all calculations in closed form without assuming a Boltzmann-Gibbs form for the equilibrium distribution.…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…