We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal dipoles that are ordered around the unfolded surfaces, where the influence of these surfaces, covered with an "ice-like" shell of water, is represented by a...

A thorough understanding of protein structure and stability requires that we elucidate the molecular basis for the effects of both temperature and pressure on protein conformational transitions. While temperature effects are relatively well understood and the change in heat capacity upon unfolding has been reasonably well parameterized, the state of understanding of pressure effects is much les...

Introduction: Unfolding X-ray spectrum is a powerful tool for quality control of X-ray tubes. Generally, the acquisition of the X-ray spectrum in diagnostic radiology departments is complicated and difficult due to high photon flux. Measurement of x ray spectra using radiation detectors could not be performed accurately, because of the pulse pile up. Therefore, indirect methods...

We use single-molecule force spectroscopy to study the kinetics of unfolding of the small protein ubiquitin. Upon a step increase in the stretching force, a ubiquitin polyprotein extends in discrete steps of 20.3 +/- 0.9 nm marking each unfolding event. An average of the time course of these unfolding events was well described by a single exponential, which is a necessary condition for a memory...

Hydrogen exchange experiments show that cytochrome c and other proteins under native conditions reversibly unfold in a multi-step manner. The step from one intermediate to the next is determined by the intrinsically cooperative nature of secondary structural elements, which is retained in the native protein. Folding uses the same pathway in the reverse direction, moving from the unfolded to the...

In this review, I discuss the various methods researchers use to unfold proteins in the lab in order to understand protein folding both in vitro and in vivo. The four main techniques, chemical-, heat-, pressure- and force-denaturation, produce distinctly different unfolded conformational ensembles. Recent measurements have revealed different folding kinetics from different unfolding mechanisms....

We study the stability of globular proteins as a function of temperature and pressure through NPT simulations of a coarse-grained model. We reproduce the elliptical stability of proteins and highlight a unifying microscopic mechanism for pressure and cold denaturations. The mechanism involves the solvation of nonpolar residues with a thin layer of water. These solvated states have lower volume ...

The kinetics of folding and unfolding underlie protein stability and quantification of these rates provides important insights into the folding process. Here, we present a simple high throughput protein unfolding kinetic assay using a plate reader that is applicable to the studies of the majority of 2-state folding proteins. We validate the assay by measuring kinetic unfolding data for the SH3 ...

The failure to appreciate that the hydration of polar groups is a major contribution to the entropy of protein unfolding has led to considerable underestimates for the loss of configurational freedom when a protein chain folds.

The relaxation of long-lived states (LLS) corresponds to the slow return to statistical thermal equilibrium between symmetric and antisymmetric proton spin states. This process is remarkably sensitive to the presence of external spins and can be used to obtain information about partial unfolding of proteins. We detected the appearance of a destabilized conformer of ubiquitin when urea is added ...