Related papers: Theoretical Perspectives on Protein Folding
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…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved…