Related papers: Why does a protein fold?
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
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…
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…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native…
Metamorphic proteins like Lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three dimensional structure. In particular, the human chemokine lymphotactin protein (Ltn) exists in…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Chaperonins are biological nanomachines that help newly translated proteins to fold by rescuing them from kinetically trapped misfolded states. Protein folding assistance by the chaperonin machinery is obligatory in vivo for a subset of…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…