相关论文: Molecular origin of constant m-values, denatured s…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size…
A model which treats the denatured and native conformers of spontaneously-folding fixed two-state systems as being confined to harmonic Gibbs energy-wells has been developed.Within the assumptions of this model the Gibbs energy functions of…
The molecular evolution that occurs in collapsing prestellar cores is investigated. To model the dynamics, we adopt the Larson-Penston (L-P) solution and analogues with slower rates of collapse. For the chemistry, we utilize the new…
Pattern formation in drying protein droplets continues to attract considerable research attention because it can be linked to specific protein-protein interactions. An extensive study of the drying evolution and the final crack patterns are…
We have developed a new simulation method to estimate the distance between the native state and the first transition state, and the distance between the intermediate state and the second transition state of a protein which mechanically…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
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…
A major challenge in molecular simulations is to describe denaturant-dependent folding of proteins order to make direct comparisons with {\it in vitro} experiments. We use the molecular transfer model, which is currently the only method…
A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst-phase) or simultaneously with the protein folding transition. Single molecule fluorescence…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, $N$, using lattice models with side chains,off-lattice Go models and the…
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding transition…
The asymmetry in the shapes of folded and unfolded states are probed using two parameters, one being a measure of the sphericity and the other that describes the shape. For the folded states, whose interiors are densely packed, the radii of…