Related papers: Single-domain protein folding: a multi-faceted pro…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
A simple statistical mechanical model proposed by Wako and Sait$\hat{\rm o}$ has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Mu$\tilde{\rm n}$oz and Eaton and has…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
Motivated by claims about the nature of the observed timescales in protein systems said to fold downhill, we have studied the finite, linear master equation which is a model of the downhill process. By solving for the system eigenvalues, we…
Folding protein dynamics has been an area of high interest for quite some time, especially given the increased focus on the field of Biophysics. Because folding dynamics occur on such short time scales, empirical techniques developed for…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has…
Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic behavior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized,…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics…
Many proteins undergo conformational changes during their activity. A full understanding of the function of these proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution,…