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Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
An increasing number of proteins are being discovered with a remarkable and somewhat surprising feature, a knot in their native structures. How the polypeptide chain is able to knot itself during the folding process to form these highly…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and…
A small-world topology characterizes many complex systems including the structural and functional organization of brain networks. The topology allows simultaneously for local and global efficiency in the interaction of the system…
The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…