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....

Previous hydrogen exchange (HX) studies of the spontaneous reversible unfolding of Cytochrome c (Cyt c) under native conditions have led to the following conclusions. Native Cyt c (104 residues) is composed of five cooperative folding units, called foldons. The high-energy landscape is dominated by an energy ladder of partially folded forms that differ from each other by one cooperative foldon ...

Repeat proteins contain tandem arrays of a simple structural motif. In contrast to globular proteins, repeat proteins are stabilized only by interactions between residues that are relatively close together in the sequence, with no "long-range" interactions. Our work focuses on the tetratricopeptide repeat (TPR), a 34 amino acid helix-turn-helix motif found in tandem arrays in many natural prote...

GroE, the chaperonin system of Escherichia coli, prevents the aggregation of partially folded or misfolded proteins by complexing them in a form competent for subsequent folding to the native state. We examined the exchange of amide protons of cyclophilin A (CypA) interacting with GroEL, using NMR spectroscopy. We have applied labeling pulses in H2O to the deuterated GroEL-CypA-complex. When AT...

In this paper, we investigate the variational problem for a sequence of 3-dimensional domains with highly oscillating boundaries. Using the unfolding method and the averaging method, we obtain the result of the homogenization problem, that is, a sequence of solutions of Eq. (3.1) converges to the solution of Eq. (3.4) as the periodic length approaches zero. It is noteworthy that the convergence...

ATP-dependent proteases are responsible for most energy-dependent protein degradation across all species. Proteases initially bind an unstructured region on a substrate and then translocate along the polypeptide chain, unfolding and degrading protein domains as they are encountered. Although this process is normally processive, resulting in the complete degradation of substrate proteins to smal...

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 ...