Related papers: Internal protein dynamics shifts the distance to t…
The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein…
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…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale…
Unfolding, in the context of high-energy particle physics, refers to the process of removing detector distortions in experimental data. The resulting unfolded measurements are straightforward to use for direct comparisons between…
The calculation of Euclidean distance between points is generalized to one-dimensional objects such as strings or polymers. Necessary and sufficient conditions for the minimal transformation between two polymer configurations are derived.…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible…
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…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
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…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…