Related papers: Machinery of Functional Dynamics in Native Protein…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. To date, many theories for the prevalence of two-state kinetics have been…
The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
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…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same…
Proteins often exhibit subdiffusive configurational dynamics. The origins of this subdiffusion are still unresolved. We investigate the impact of non-Markovian friction and the free energy landscape on the dynamics of fast-folding proteins…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We examine temperature dependent picosecond dynamics as a function of structure and function for lysozyme and cytochrome c using temperature dependent terahertz permittivity measurements. A double Arrhenius temperature dependence with…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…