PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “PROTEIN DENATURATION”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed1993

Circular dichroic analysis of denatured proteins: inclusion of denatured proteins in the reference set.

We hypothesize that inclusion of denatured proteins in the set of reference native proteins may better represent the unordered form in the current circular dichroism (CD) analyses of proteins involving unfolding ones. Adding three denatured-protein spectra and one oligopeptide spectrum to 16 reference protein spectra markedly improved the correlation coefficients (r) between CD calculations and X-ray determinations for the unordered form and, to a lesser extent, for beta-turn, but the r-values for alpha-helix and beta-sheet decreased slightly. With 20 reference proteins the estimates of the unordered form of denatured proteins were significantly improved. Thus, we suggest that as a compromise the new set of reference proteins be used for estimating the changes in conformation for unfolding proteins. However, the current use of 16 reference native proteins appears to be adequate for CD analysis of native proteins and the expansion to 20 reference proteins including denatured ones may not enhance the analysis of native proteins.

Amino Acid Sequence↗
PubMed1995

Thermal protein denaturation and protein aggregation in cells made thermotolerant by various chemicals: role of heat shock proteins.

Thermotolerance (TT) induced by sodium arsenite (A-TT: 100 microM, 1 h, 37 degrees C) was compared to heat-induced thermotolerance (H-TT: 15 min, 44 degrees C) using HeLa S3 cells. All four pretreatments led to comparable levels of thermotolerance and also induced resistance to arsenite-, ethanol-, and diamide-induced toxicity (clonogenic ability). Stress-induced expression of the major heat shock proteins (hsp27, hsc70(p73), hsp70(p72), and hsp90) was generally highest in H-TT cells and lowest in A-TT cells. Interestingly, the four types of TT cells showed distinct differences in certain aspects of resistance against thermal protein damage. Thermal protein denaturation and aggregation determined in isolated cellular membrane fractions was found to be attenuated when they were isolated from H-TT and A-TT cells but not when isolated from E-TT and D-TT cells. The heat resistance in the proteins of the membrane fraction corresponded with elevated levels of hsp70(p72) associated with the isolated membrane fractions. In the nuclear fraction, only marginal (not significant) attenuation of the formation of protein aggregates (as determined by TX-100 (in)solubility) was observed. However, the postheat recovery from heat-induced protein aggregation in the nucleus was faster in H-TT, E-TT, and D-TT cells, but not in A-TT cells. Despite the fact that elevated levels of hsp27, hsp70(p73), and hsp70(p72) were found in the TX-100 insoluble nuclear fraction derived from all TT cells, no correlation was found with the degree of resistance in terms of the accelerated recovery from nuclear protein aggregation. The only correlation between accelerated recovery from nuclear protein aggregates was that with total cellular levels of hsp27. The data indicate that heat-induced loss of clonogenic ability may be a multitarget rather than a single target event. A threshold of damage may exist in cells after exposure to heat; multiple sets of proteins in (different compartments of) the cell need to be damaged before this threshold is exceeded and the cell dies. As a consequence, stabilization of only one of these sets of proteins is already sufficient to render cells thermotolerant at the clonogenic level.

Arsenites↗
PubMedDate not supplied

Effect of additives on refolding of a denatured protein.

Denatured lysozyme was refolded by a dilution method. The refolding yield depended greatly on the lysozyme concentration in the refolding mixture. When the concentration of denatured lysozyme was 0.02 g/L, the refolding yield was as high as 60%. However, when the concentration of denatured lysozyme was 0.2 g/L, the refolding yield was as low as 10% due to the formation of aggregates. To prevent the formation of aggregates and to increase the refolding yield at a low cost, inexpensive additives were screened. The addition of acetone, acetoamide, or urea derivatives was very effective for improving the refolding yield. To clarify why the addition of acetoamide in the refolding mixture improved the refolding yield at the high lysozyme concentration, the time courses of the concentration and the average diameter of the aggregates in the refolding mixture were monitored by the dynamic light scattering method. The experimental results showed that acetoamide played a role in preventing the formation and growth of aggregates and secondary aggregation between the lysozyme aggregates.

Acetamides↗
PubMed2001

Chemical shifts in denatured proteins: resonance assignments for denatured ubiquitin and comparisons with other denatured proteins.

Chemical shift assignment is reported for the protein ubiquitin denatured in 8M urea at pH 2. The variations in 15N chemical shifts of three different proteins (ubiquitin, disulfide reduced, carboxymethylated lysozyme, all-Ala-alpha-lactalbumin), all without disulfides and denatured in 8M urea at pH 2 are compared to 'random coil shifts' of small model peptides (Braun et al., 1994) and to the averaged native chemical shifts taken from the BMRB database. Both parameterizations show a remarkable agreement with the averaged measured 15N chemical shifts in the three denatured proteins. Detailed analysis of these experimental 15N chemical shifts provides an estimate of the influence of nearest neighbors and conformational preferences on the chemical shift and provides a direct means to identify non-random structural preferences in denatured proteins.

Animals↗
PubMed2005

Urea promotes polyproline II helix formation: implications for protein denatured states.

It is commonly assumed that urea denatures proteins by promoting backbone disorder, resulting in random-coil behavior. Indeed, it has been demonstrated that highly denatured proteins obey random-coil statistics. However, the random-coil model is specified by the global geometric properties of a polymeric chain and does not preclude locally ordered backbone structure. While urea clearly disfavors a compact native structure, it is not clear that the resulting backbone conformations are disordered. Using circular dichroism (CD) spectroscopy, we demonstrate that urea promotes formation of left-handed polyproline II (P(II)) helical structures in both short peptides and denatured proteins. The observed increase in P(II) content is sequence-dependent. These data indicate that denatured states possess significant amounts of locally ordered backbone structure. It is time for the formulation of new denatured-state models that take into account the presence of significant local backbone structure. Criteria for such models are outlined.

Amino Acid Sequence↗
PubMed2001

ATP causes small heat shock proteins to release denatured protein.

Small heat-shock proteins (sHSPs) are a ubiquitous family of low molecular mass (15-30 kDa) stress proteins that have been found in all organisms. Under stress, sHSPs such as alpha-crystallin can act as chaperones binding partially denatured proteins and preventing further denaturation and aggregation. Recently, it has been proposed that the function of sHSPs is to stabilize stress-denatured protein and then act cooperatively with other HSPs to renature the partially denatured protein in an ATP-dependent manner. However, the process by which this occurs is obscure. As no significant phosphorylation of alpha-crystallin was observed during the renaturation, the role of ATP is not clear. It is now shown that ATP at normal physiological concentrations causes sHSPs to change their confirmation and release denatured protein, allowing other molecular chaperones such as HSP70 to renature the protein and renew its biological activity. In the absence of ATP, sHSPs such as alpha-crystallin are more efficient than HSP70 in preventing stress-induced protein aggregation. This work also indicates that in mammalian systems at normal cellular ATP concentrations, sHSPs are not effective chaperones.

Adenosine Triphosphate↗
PubMed1999

The cytoplasmic chaperone hsp104 is required for conformational repair of heat-denatured proteins in the yeast endoplasmic reticulum.

Severe heat stress causes protein denaturation in various cellular compartments. If Saccharomyces cerevisiae cells grown at 24 degrees C are preconditioned at 37 degrees C, proteins denatured by subsequent exposure to 48-50 degrees C can be renatured when the cells are allowed to recover at 24 degrees C. Conformational repair of vital proteins is essential for survival, because gene expression is transiently blocked after the thermal insult. Refolding of cytoplasmic proteins requires the Hsp104 chaperone, and refolding of lumenal endoplasmic reticulum (ER) proteins requires the Hsp70 homologue Lhs1p. We show here that conformational repair of heat-damaged glycoproteins in the ER of living yeast cells required functional Hsp104. A heterologous enzyme and a number of natural yeast proteins, previously translocated and folded in the ER and thereafter denatured by severe heat stress, failed to be refolded to active and secretion-competent structures in the absence of Hsp104 or when an ATP-binding site of Hsp104 was mutated. During recovery at 24 degrees C, the misfolded proteins persisted in the ER, although the secretory apparatus was fully functional. Hsp104 appears to control conformational repair of heat-damaged proteins even beyond the ER membrane.

Carboxypeptidases↗
PubMed1992

Disulfide containing proteins denatured in 6 mol/L guanidinium chloride are not completely unfolded.

The unfolded states of serum albumin, lysozyme and ribonuclease denatured in GuHCl with their disulfide bridges intact or reduced and carboxyamidomethylated have been compared by their circular dichroism, second-derivative and difference spectra in the ultraviolet region. Results obtained indicate that although the secondary structures of denatured proteins with intact disulfides are largely destroyed, they still have considerable ordered conformation even in 6 mol/L guanidinium chloride as indicated by the differences in the extents of exposure of the aromatic residues compared to the denatured proteins without the native disulfide bonds.

Albumins↗
PubMed2000

Structure and dynamics of an acid-denatured protein G mutant.

NMR studies of protein denatured states provide insights into potential initiation sites for folding that may be too transient to be observed kinetically. We have characterized the structure and dynamics of the acid-denatured state of protein G by using a F30H mutant of G(B1) which is on the margin of stability. At 5 degrees C, F30H-G(B1) is greater than 95% folded at pH 7.0 and is greater than 95% unfolded at pH 4.0. This range of stability is useful because the denatured state can be examined under relatively mild conditions which are optimal for folding G(B1). We have assigned almost all backbone (15)N, H(N), and H(alpha) resonances in the acid-denatured state. Chemical shift, coupling constant, and NOE data indicate that the denatured state has considerably more residual structure when studied under these mild conditions than in the presence of chemical denaturants. The acid-denatured state populates nativelike conformations with both alpha-helical and beta-hairpin characteristics. To our knowledge, this is the first example of a denatured state with NOE and coupling constant evidence for beta-hairpin character. A number of non-native turn structures are also detected, particularly in the region corresponding to the beta1-beta2 hairpin of the folded state. Steady-state ¿(1)H-(15)N¿ NOE results demonstrate restricted backbone flexibility in more structured regions of the denatured protein. Overall, our studies suggest that regions of the helix, the beta3-beta4 hairpin, and the beta1-beta2 turn may serve as potential initiation sites for folding of G(B). Furthermore, residual structure in acid-denatured F30H-G(B1) is more extensive than in peptide fragments corresponding to the beta1-beta2, alpha-helix, and beta3-beta4 regions, suggesting additional medium-to-long-range interactions in the full-length polypeptide chain.

Amino Acid Sequence↗
PubMed1992

Heat shock gene regulation by nascent polypeptides and denatured proteins: hsp70 as a potential autoregulatory factor.

Heat shock genes encode proteins (hsp's) that play important structural roles under normal circumstances and are essential to the cells' ability to survive environmental insults. Evidence is presented herein that transcriptional regulation of hsp gene expression is linked with the regulation of overall protein synthesis as well as with the accumulation of proteins denatured by stressful events. The factor that connects the three processes appears to be one of the hsp's, presumably a member(s) of the hsp70 family. Biochemical experiments demonstrate that complexes containing hsp70 and heat shock transcription factor, the specific regulator of hsp gene activity, are formed in the cells.

Base Sequence↗
PubMed2002

The Escherichia coli small heat-shock proteins IbpA and IbpB prevent the aggregation of endogenous proteins denatured in vivo during extreme heat shock.

The roles of the Escherichia coli IbpA and IbpB chaperones in protection of heat-denatured proteins against irreversible aggregation in vivo were investigated. Overproduction of IbpA and IbpB resulted in stabilization of the denatured and reversibly aggregated proteins (the S fraction), which could be isolated from E. coli cells by sucrose gradient centrifugation. This finding is in agreement with the present model of the small heat-shock proteins' function, based mainly on in vitro studies. Deletion of the ibpAB operon resulted in almost twofold increase in protein aggregation and in inactivation of an enzyme (fructose-1,6-biphosphate aldolase) in cells incubated at 50 degrees C for 4 h, decreased efficiency of the removal of protein aggregates formed during prolonged incubation at 50 degrees C and affected cell viability at this temperature. IbpA/B proteins were not needed for removal of protein aggregates or for the enzyme protection/renaturation in cells heat shocked at 50 degrees C for 15 min. These results show that the IbpA/B proteins are required upon an extreme, long-term heat shock. Overproduction of IbpA but not IbpB caused an increase of the level of beta-lactamase precursor, which was localized in the S fraction, together with the IbpA protein, which suggests that the unfolded precursor binds to IbpA but not to IbpB. Although in the wild-type cells both E. coli small heat-shock proteins are known to localize in the S fraction, only 2% of total IbpB co-localized with the aggregated proteins in the absence of IbpA, while in the absence of IbpB, the majority of IbpA was present in the aggregates fraction.

Escherichia coli↗
PubMed1984

Liquid-like state of side chains at the intermediate stage of protein denaturation.

We propose a model for a conformational state of a partially denatured protein molecule which we call CMG (Compact Molten Globule) state. The CMG state is one where the freedom of motion of side chains is released while that of the backbone chain is restricted as in the native state; In other words, it is the state of fixed psi and phi, but of free chi in terms of the dihedral angles of the polypeptide chain. Experimental results of our study on the denatured state of cytochrome c in pH 2, 0.5 M KCl (IIb state) and those in the report of Dolgikh et al. (1981) on acid denatured state (A state) of alpha-lactalbumin support the present model. In IIb state, the 360 MHz 1H-NMR spectrum is similar to that of the fully denatured state, while intrinsic viscosity and diffusion coefficient are close to the native state. A diagram of the internal phase of cytochrome c in the course of acid denaturation is given, and discussions are presented as to whether this molten globule state might be comprehensively applied to other proteins.

Animals↗
PubMed2000

alpha-crystallin prevents irreversible protein denaturation and acts cooperatively with other heat-shock proteins to renature the stabilized partially denatured protein in an ATP-dependent manner.

alpha-Crystallin, a major lens protein of approximately 800 kDa with subunits of approximately 20 kDa has previously been shown to act as a chaperone protecting other proteins from stress-induced aggregation. Here it is demonstrated that alpha-crystallin can bind to partially denatured enzymes at 42-43 degrees C and prevent their irreversible aggregation, but cannot prevent loss of enzyme activity. However, the alpha-crystallin-bound enzymes regain activity on interaction with other chaperones. The data indicate that the re-activated enzymes are no longer associated with the alpha-crystallin, and ATP is required for re-activation. When inactive luciferase bound to alpha-crystallin was treated with reticulocyte lysate, a rich source of chaperones, up to 60% of the original luciferase activity could be recovered. Somewhat less re-activation was observed when the alpha-crystallin-bound enzyme was treated with heat-shock protein (HSP)70, HSP40, HSP60 and an ATP-generating system. Similar results were also obtained with citrate synthase. The overall results suggest that alpha-crystallin acts to stabilize denaturing proteins so that they can later be re-activated by other chaperones.

Adenosine Triphosphate↗
PubMed1998

Folding under inequilibrium conditions as a possible reason for partial irreversibility of heat-denatured proteins: computer simulation study.

Using computer simulations we have studied possible effects of heating and cooling at different scan rates on unfolding and refolding of macromolecules. We have shown that even the simplest two-state reversible transition can behave irreversibly when an unfavorable combination of cooling rate, relaxation time and activation energy of refolding occurs. On the basis of this finding we suppose that apparent irreversibility of some proteins denatured by heat may result from slow relaxation on cooling rather than thermodynamic instability and/or irreversible alterations of the polypeptide chain. Using this kinetic reversible two-state model, we estimated the effects of the scan rate and kinetic parameters of the macromolecule on its unfolding-refolding process. A few recommendations are suggested on how to reach maximal possible recovery after denaturation if refolding appears to be under kinetic control.

Journal Article↗