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Results for “Protein Stability”

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PubMed2005

The mating pair stabilization protein, TraN, of the F plasmid is an outer-membrane protein with two regions that are important for its function in conjugation.

F plasmid TraN (602 aa, processed to 584 aa with 22 conserved cysteines), which is essential for F plasmid conjugation, is an outer-membrane protein involved in mating pair stabilization (MPS). Unlike R100 TraN, F TraN requires OmpA in the recipient cell for efficient MPS. The authors have identified three external loops (aa 172-187, 212-220 and 281-284) in the highly divergent region from aa 164 to aa 333 as candidates for interaction with OmpA. These loops were identified using both site-directed and random TnphoA/in mutagenesis to insert epitopes (31-aa or c-myc) into TraN and monitor their effect on sensitivity to external proteases and on mating ability. TraN is a hallmark protein of F-type IV secretion systems as demonstrated by blast searches of the databases. The C-terminal region is highly conserved and contains five of the six completely conserved cysteines. Mutation of these residues to serine demonstrated their importance in TraN function. TraN appears to require both intra- and intermolecular disulfide bond formation for its stability and structure as demonstrated by its instability in a dsbA mutant and its aberrant migration on SDS-polyacrylamide gels under non-reducing conditions or by cross-linking with bis(sulfosuccinimidyl)suberate (BS3). Thus, F TraN appears to have two domains: the N-terminal region is involved in OmpA interaction with OmpA during MPS; and the C-terminal region, which is rich in conserved cysteine residues, is essential for conjugation.

Amino Acid Sequence↗

PubMed1999

Protein stabilization: a common consequence of mutations in independently derived v-Myc alleles.

Myc is overexpressed in many cancers as a result of gene rearrangement or amplification, but coding sequence changes which cluster in the N-terminal transactivation domain also appear to play a role in tumour progression. The prototypic v-Myc gene of MC29 virus differs from avian c-Myc by a series of mutations, including a change at a regulatory phosphorylation site within the mutational hotspot (thr-61) which is known to potentiate transformation in vitro. We now show that the mutation at thr-61 stabilizes the v-Myc protein (turnover difference) and that this single mutation is both necessary and sufficient for the phenotype. A major involvement of the proteasome in Myc degradation was confirmed, but surprisingly, a dilysine motif adjacent to thr-61 proved not to be the ubiquitin target. Two other v-Myc genes which carry a mutation at thr-61 (avian MH2) or a large deletion encompassing this domain (feline T17) were found to be stabilized to a similar extent as MC29, showing that stabilization is a common feature of independently derived Myc oncogenes. These results suggest a common selective process in the genesis of these three viral oncoproteins and a mechanistic link with Jun, Fos and Myb oncoproteins which are also stabilized relative to their cellular counterparts.

Alleles↗

PubMed1998

Volatile anesthetics alter protein stability.

1. We have used differential scanning calorimetry to measure the halothane induced change in stability of five lipid-free proteins in aqueous solution. 2. The temperature at peak heat capacity (Tm) as the sample is heated provides a measure of stability. 3. Addition of halothane increases Tm for bovine and human serum albumin, but decreases Tm for hen egg white lysozyme, bovine pancreatic ribonuclease A, and horse skeletal muscle myoglobin. 4. A shift of Tm in either direction may model the action of inhaled anesthetics on relevant proteins in the central nervous system.

Anesthetics, Inhalation↗

PubMed2006

Domain:domain interactions within Hop, the Hsp70/Hsp90 organizing protein, are required for protein stability and structure.

The major heat shock protein (Hsp) chaperones Hsp70 and Hsp90 both bind the co-chaperone Hop (Hsp70/Hsp90 organizing protein), which coordinates Hsp actions in folding protein substrates. Hop contains three tetratricopeptide repeat (TPR) domains that have binding sites for the conserved EEVD C termini of Hsp70 and Hsp90. Crystallographic studies have shown that EEVD interacts with positively charged amino acids in Hop TPR-binding pockets (called carboxylate clamps), and point mutations of these carboxylate clamp positions can disrupt Hsp binding. In this report, we use circular dichroism to assess the effects of point mutations and Hsp70/Hsp90 peptide binding on Hop conformation. Our results show that Hop global conformation is destabilized by single point mutations in carboxylate clamp positions at pH 5, while the structure of individual TPR domains is unaffected. Binding of peptides corresponding to the C termini of Hsp70 and Hsp90 alters the global conformation of wild-type Hop, whereas peptide binding does not alter conformation of individual TPR domains. These results provide biophysical evidence that Hop-binding pockets are directly involved with domain:domain interactions, both influencing Hop global conformation and Hsp binding, and contributing to proper coordination of Hsp70 and Hsp90 interactions with protein substrates.

Binding Sites↗

PubMed1998

Use of propensities of amino acids to the local structural environments to understand effect of substitution mutations on protein stability.

Advances in site-directed mutagenesis and other genetic engineering techniques have made it possible to create novel proteins of interest. A challenging aspect of these studies is to understand the effect of substitution mutations on folding and stability of natural proteins. We present an analysis of protein structure data, available from the literature, for which substitution mutations have been made and changes in stability characteristics are reported. Amino acid structural environment parameters have been computed for a set of 304 non-homologous best resolved protein structures. The structural environment parameters were used to calculate each of the 20 amino acid propensities to a given structural environment. The observed increase or decrease in stability upon mutation was found to be correlated with the average residue structural environment propensity of wild-type residue versus mutant residue. The analysis presented here helps identification of less optimally placed residues in a given protein structure, and suggests possible substitution mutations to a residue with higher propensity to the corresponding local structural environment. We propose that such substitution mutations, suggested based on amino acid propensities to local structural environments, should bestow higher stability to the protein structure.

Amino Acid Substitution↗

PubMed1996

Perturbations of the denatured state ensemble: modeling their effects on protein stability and folding kinetics.

By considering the denatured state of a protein as an ensemble of conformations with varying numbers of sequence-specific interactions, the effects on stability, folding kinetics, and aggregation of perturbing these interactions can be predicted from changes in the molecular partition function. From general considerations, the following conclusions are drawn: (1) A perturbation that enhances a native interaction in denatured state conformations always increases the stability of the native state. (2) A perturbation that promotes a non-native interaction in the denatured state always decreases the stability of the native state. (3) A change in the denatured state ensemble can alter the kinetics of aggregation and folding. (4) The loss (or increase) in stability accompanying two mutations, each of which lowers (or raises) the free energy of the denatured state, will be less than the sum of the effects of the single mutations, except in cases where both mutations affect the same set of partially folded conformations. By modeling the denatured state as the ensemble of all non-native conformations of hydrophobic-polar (HP) chains configured on a square lattice, it can be shown that the stabilization obtained from enhancement of native interactions derives in large measure from the avoidance of non-native interactions in the D state. In addition, the kinetic effects of fixing single native contacts in the denatured state or imposing linear gradients in the HH contact probabilities are found, for some sequences, to significantly enhance the efficiency of folding by a simple hydrophobic zippering algorithm. Again, the dominant mechanism appears to be avoidance of non-native interactions. These results suggest stabilization of native interactions and imposition of gradients in the stability of local structure are two plausible mechanisms involving the denatured state that could play a role in the evolution of protein folding and stability.

Kinetics↗

PubMed2002

Mutational studies of protein stability and folding of the hyperstable MYL Arc repressor variant.

The Arc-MYL variant is hyperstable and has an earlier transition state than wild type as a consequence of replacing the wild-type salt-bridge triad formed by R31, E36 and R40 with hydrophobic interactions formed by M31, Y36 and L40. Amino acid substitution mutations were constructed at 16 positions in the Arc-MYL background and the equilibrium stabilities of the corresponding mutant proteins were determined. At three positions, mutations were found to be less destabilizing in MYL than in wild-type Arc, and, at one position, the opposite result was obtained. The kinetics of refolding and unfolding were determined for a subset of the Arc-MYL core mutants. Three mutations--VA18, LA19 and LA40--had their major energetic effects on the refolding rate. The interactions perturbed by these mutations appear to be substantially formed in the transition state. V18 and L19 are in the N-terminal turn of helix A and L40 is in the center of helix B. The remaining mutations--VA22, MA31, VA33, YA36, VA41, MA42 and FA45--had some effects on refolding but exerted their major effects on the unfolding rate. Approximately 30% of the energetic interactions mediated by these latter side chains seem to be present in the transition state of Arc-MYL.

Kinetics↗

PubMed2003

Determination of membrane protein stability via thermodynamic coupling of folding to thiol-disulfide interchange.

Although progress has been made in understanding the thermodynamic stability of water-soluble proteins, our understanding of the folding of membrane proteins is at a relatively primitive level. A major obstacle to understanding the folding of membrane proteins is the discovery of systems in which the folding is in thermodynamic equilibrium, and the development of methods to quantitatively assess this equilibrium in micelles and bilayers. Here, we describe the application of disulfide cross-linking to quantitatively measure the thermodynamics of membrane protein association in detergent micelles. The method involves initiating disulfide cross-linking of a protein under reversible redox conditions in a thiol-disulfide buffer and quantitative assessment of the extent of cross-linking at equilibrium. The 19-46 alpha-helical transmembrane segment of the M2 protein from the influenza A virus was used as a model membrane protein system for this study. Previously it has been shown that transmembrane peptides from this protein specifically self-assemble into tetramers that retain the ability to bind to the drug amantadine. We used thiol-disulfide exchange to quantitatively measure the tetramerization equilibrium of this transmembrane protein in dodecylphosphocholine (DPC) detergent micelles. The association constants obtained agree remarkably well with those derived from analytical ultracentrifugation studies. The experimental method established herein should provide a broadly applicable tool for thermodynamic studies of folding, oligomerization and protein-protein interactions of membrane proteins.

Chromatography, High Pressure Liquid↗

PubMed2006

Tyrosine phosphorylation controls PCNA function through protein stability.

The proliferating cell nuclear antigen (PCNA) is an essential protein for DNA replication and damage repair. How its function is controlled remains an important question. Here, we show that the chromatin-bound PCNA protein is phosphorylated on Tyr 211, which is required for maintaining its function on chromatin and is dependent on the tyrosine kinase activity of EGF receptor (EGFR) in the nucleus. Phosphorylation on Tyr 211 by EGFR stabilizes chromatin-bound PCNA protein and associated functions. Consistently, increased PCNA Tyr 211 phosphorylation coincides with pronounced cell proliferation, and is better correlated with poor survival of breast cancer patients, as well as nuclear EGFR in tumours, than is the total PCNA level. These results identify a novel nuclear mechanism linking tyrosine kinase receptor function with the regulation of the PCNA sliding clamp.

Cell Nucleus↗

PubMed2003

A novel function of Rad54 protein. Stabilization of the Rad51 nucleoprotein filament.

Homologous recombination is important for the repair of double-stranded DNA breaks in all organisms. Rad51 and Rad54 proteins are two key components of the homologous recombination machinery in eukaryotes. In vitro, Rad51 protein assembles with single-stranded DNA to form the helical nucleoprotein filament that promotes DNA strand exchange, a basic step of homologous recombination. Rad54 protein interacts with this Rad51 nucleoprotein filament and stimulates its DNA pairing activity, suggesting that Rad54 protein is a component of the nucleoprotein complex involved in the DNA homology search. Here, using physical criteria, we demonstrate directly the formation of Rad54-Rad51-DNA nucleoprotein co-complexes that contain equimolar amounts of each protein. The binding of Rad54 protein significantly stabilizes the Rad51 nucleoprotein filament formed on either single-stranded DNA or double-stranded DNA. The Rad54-stabilized nucleoprotein filament is more competent in DNA strand exchange and acts over a broader range of solution conditions. Thus, the co-assembly of an interacting partner with the Rad51 nucleoprotein filament represents a novel means of stabilizing the biochemical entity central to homologous recombination, and reveals a new function of Rad54 protein.

Adenosine Triphosphatases↗

PubMed2005

Functional implication of p73 protein stability in neuronal cell survival and death.

p73, a newly identified member of p53 family, locates at human chromosome 1p36.2-3, a region which is frequently deleted in a wide variety of human tumors including neuroblastoma. p73 is induced to be accumulated in response to a subset of DNA damaging agents such as cisplatin, and thereby promoting G1/S cell cycle arrest and/or apoptosis. Since the expression levels of p73 are kept extremely low under normal conditions, stabilization of p73 is critical for its effects on cell growth inhibition and apoptosis. Indeed, p73 is induced at protein level in SH-SY5Y neuroblastoma cells exposed to cisplatin. Several lines of evidence indicate that stress-induced post-translational modifications of p73 such as phosphorylation and acetylation lead to a marked extension of its half-life. p73 stability is regulated at least in part by proteasome-dependent degradation pathway, however, MDM2 which mediates ubiquitination and subsequent degradation of p53 by the 26S proteasome, does not promote the proteolytic degradation of p73, implying that the protein stability of p73 is regulated through a pathway distinct from that of p53. Although little is known about the regulation of p73 turnover, we are now beginning to understand the regulatory mechanisms by which p73 is induced to be stabilized in response to apoptotic stimuli, and exerts its pro-apoptotic activity. In this review, we discuss about the cellular proteins implicated in the stability control of p73.

Cell Death↗

PubMed1991

Regulation of PGI2 activity by serum proteins: serum albumin but not high density lipoprotein is the PGI2 binding and stabilizing protein in human blood.

Although previous studies have shown that serum albumin binds PGI2 and protects it from rapid degradation, it remains debatable whether it is physiologically important due to its low binding affinity for PGI2. We were intrigued by the observations of Yui et al. (J. Clin. Invest. 82 (1988) 803-807) which suggested that apo A-I of the high density lipoprotein (HDL) is the "serum PGI2 stabilizing factor". To clarify this, we carried out experiments to determine the binding kinetics and parameters of HDL and albumin purified from normal pooled human serum. Despite the use of multiple binding assays, we could not detect any binding activity in HDL2, HDL3 or nascent HDL preparations, nor could we demonstrate any PGI2 protecting activity by these molecules. By contrast, purified albumin exhibited essentially identical binding parameters as the native serum from which the albumin was purified. The binding activity of various albumin preparations was not due to the contamination of apo A-I. Computer simulation analysis also failed to provide evidence to support the notion that HDL bound and prolonged PGI2 activity. To determine whether physiological concentrations of albumin influence PGI2 binding to platelet receptors, we measured PGI2 binding to platelet membrane in the absence and presence of albumin. Albumin at 40 mg/ml increased the KD of PGI2 binding to the receptors by 2-3 fold. These findings indicate that albumin plays a major role in protecting PGI2 activity and regulating its availability for platelet PGI2 receptors.

Apolipoprotein A-I↗

PubMed2006

Protein stability in the presence of polymer degradation products: consequences for controlled release formulations.

When encapsulating proteins in polymer microspheres for sustained drug delivery there are three stages during which the stability of the protein must be maintained: (1) the fabrication of the microspheres, (2) the storage of the microspheres, and (3) the release of the encapsulated protein. This study focuses on the effects of polymer degradation products on the primary, secondary, and tertiary structure of tetanus toxoid, ovalbumin (Ova), and lysozyme after incubation for 0 or 20 days in the presence of ester (lactic acid and glycolic acid) and anhydride (sebacic acid and 1,6-bis(p-carboxyphenoxy)hexane) monomers. The structure and antigenicity or enzymatic activity of each protein in the presence of each monomer was quantified. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, circular dichroism, and fluorescence spectroscopy were used to assess/evaluate the primary, secondary, and tertiary structures of the proteins, respectively. Enzyme-linked immunosorbent assay was used to measure changes in the antigenicity of tetanus toxoid and Ova and a fluorescence-based assay was used to determine the enzymatic activity of lysozyme. Tetanus toxoid was found to be the most stable in the presence of anhydride monomers, while Ova was most stable in the presence of sebacic acid, and lysozyme was stable when incubated with all of the monomers studied.

Animals↗

PubMed2000

Influence of process parameters on the protein stability encapsulated in poly-DL-lactide-poly(ethylene glycol) microspheres.

Glucose oxidase (GOD) has been encapsulated as a model protein within poly-DL-lactide-poly(ethylene glycol) (PELA) microspheres to evaluate the activity retention during microencapsulation process. This paper was aimed to investigate the effect of process parameters, such as the preparation method, the used matrix polymer with different compositions, the solvent system and the addition of stabilizer on the structural integrity and activity retention of encapsulated protein. The stability of the protein released during in vitro assay was also assessed. The obtained results showed that the solvent extraction/evaporation method based on the formation of double emulsion w(1)/o/w(2) benefited the activity retention compared with the phase separation method based on the formation of w/o(1)/o(2). And in the emulsion-evaporation system most of the protein activity was lost during the first emulsification procedure to form primary emulsion w(1)/o (ca. 28%) and the second emulsification procedure to form the double emulsion w(1)/o/w(2) (ca. 20%), in contrast to other processes occurring during microspheres preparation. The matrix polymer and the solvent system in the oil phase had an impressive impact on the activity retention, while the addition of gelatin in the internal aqueous phase resulted in no major reduction of activity loss. GOD release from PELA microspheres exhibited a triphasic profile, that is, the initial burst release during the first day, the gradual release over about 1 month, and then the second burst release. The encapsulation of GOD in PELA microspheres was effective in reducing its specific activity loss. Sixty-seven per cent of the initial specific activity retention was detected for the released GOD from microspheres formulation during 1 week of incubation, but nearly all the activity was lost for GOD in solution incubated under the same condition. SDS-PAGE results showed that, although the activity loss was detected, no rough changes of molecular weight of GOD was observed during encapsulation procedure and the initial days of incubation into the in vitro release medium.

Absorbable Implants↗

PubMed2005

Influence of the 33 kDa manganese-stabilizing protein on the structure and substrate accessibility of the oxygen-evolving complex of photosystem II.

The 33 kDa manganese-stabilizing extrinsic protein binds to the lumenal side of photosystem II (PS II) close to the Mn(4)Ca cluster of the oxygen-evolving complex, where it limits access of small molecules to the metal site. Our previous finding that the removal of this protein did not alter the magnetic coupling regime within the manganese cluster, measured by electron spin-echo envelope modulation [Gregor, W., and Britt, R. D. (2000) Photosynth. Res. 65, 175-185], prompted us to examine whether this accessibility control is also true for substrate water, using the same pulsed EPR technique. Comparing the deuteron modulation of the S(2)-state multiline signal of PS II membranes, equilibrated with deuterated water (D(2)O) after removal or retention of the 33 kDa protein, we observed no change in the number and the distance of deuterons magnetically coupled to manganese, indicating that the number and distance of water molecules bound to the manganese cluster are independent of bound 33 kDa protein in the S(1) state, in which the sample was poised prior to cryogenic illumination. A simple modulation depth analysis revealed a distance of 2.5-2.6 A between the closest deuteron and manganese. These results are in agreement with our refined X-ray absorption analysis. The manganese K-edge positions, reflecting their oxidation states, and the extended X-ray absorption fine structure amplitudes and distances between the manganese ions and their oxygen and nitrogen ligands (1.8, 2.7, and 3.3-3.4 A) were independent of bound 33 kDa protein.

Binding Sites↗

PubMed1997

Protein stability; optimization of electrostatic contributions by partially neutralizing surface ionic charges.

'Partial Charge-Neutralization Method' is developed to study influence of the relative amount of positive and negative charges in proteins on their structural stability. A given number of either positively or negatively charged groups are neutralized in all of their possible combinations to generate a whole set of distinct species. The Coulomb energy of each species is calculated by numerically solving the Poisson-Boltzmann equation for aqueous solutions. Partial neutralization of lysine residues of tuna cytochrome c in aqueous solution at neutral pH with the Debye-Hückel screening parameter kappa = 1 nm-1 reproduces qualitatively well the destabilization of acetylated cytochrome c observed in physicochemical measurements at pH 7. The stabilization of its molten globule state at pH 2 is also studied with the present method. It is shown that the electrostatic contribution to the structural stability of natural proteins can be optimized by changing the difference in number of their positive and negative charges.

Cytochrome c Group↗

PubMed2005

Coalescence of protein-stabilized bubbles undergoing expansion at a simultaneously expanding planar air-water interface.

A novel design of apparatus is described that allows observation of the coalescence stability of bubbles at a planar interface when the planar interface and the bubble surface both expand. Bubbles are introduced beneath the planar air-water interface contained within a square barrier made of perfluorocarbon rubber. The bubbles are then expanded by reducing the air pressure above the interface, while at the same time the rubber barrier is mechanically expanded, maintaining its square shape, to give the same rate and extent of expansion of the planar interface. The area can typically be increased by a factor of three over time scales as short as 0.2 s. This arrangement has been designed to mimic the behavior of aerated products when they exit from a pressurized aeration unit or product dispenser. Compared to results obtained via a previous technique, where it was only possible to expand the bubbles but not the planar interface, the bubbles are less stable. The apparatus has been used to compare the stabilizing effects of ovalbumin, beta-lactoglobulin, whey protein isolate, and sodium caseinate, in a model aqueous food system thickened with 40% invert sugar. Stability improved with increasing concentration of all the proteins and with a decrease in expansion rate, but considerable instability remained even at protein concentrations as high as 4 to 6 wt % and also at very low expansion rates, though the systems were stable in the absence of expansion. However, the stability was greatly improved by the replacement of the above proteins by the hydrocolloids gelatine or polypropylene glycol alginate. Detailed analysis revealed that the coalescence of individual bubbles in clusters of bubbles were not strongly correlated in distance or time, but larger bubbles and bubbles toward the outside of a cluster were found to be, on average, less stable than smaller bubbles and bubbles located more toward the interior of a cluster. The different degrees of stability are discussed in terms of local deformation, fracture behavior, and time-dependent composition of the adsorbed layers.

Air↗

PubMed2001

Pegylation enhances protein stability during encapsulation in PLGA microspheres.

During encapsulation of proteins in biodegradable microspheres, a significant amount of the protein reportedly undergoes denaturation to form irreversible insoluble aggregates. Incomplete in vitro release of proteins from the microspheres is a common observation. An attempt was made to overcome this problem by pegylation of the protein to be encapsulated. Lysozyme, a model protein, was conjugated with methoxy polyethylene glycol (mPEG, MW 5000). The conjugate was characterized by SDS-PAGE, SE-HPLC, and MALDI-TOF mass spectroscopy. The pegylated lysozyme (Lys-mPEG) consisted of different isomers of mono-, di- and tri-pegylated with about 15% as native lysozyme. The specific activity of the protein was retained after pegylation (101.3+/-10.4%). The microsphere encapsulation process was simulated for pegylated and native lysozyme. Pegylated lysozyme exhibited much better stability than native lysozyme against exposure to organic solvent (dichloromethane), homogenization, and showed reduced adsorption onto the surface of blank PLGA microspheres. Release profiles of the two proteins from microspheres were very different. For native lysozyme, it was high initial release (about 50%) followed by a nearly no release (about 10% in 50 days). In contrast, Lys-mPEG conjugate showed a triphasic and near complete release over 83 days. This study shows that the pegylation of protein can provide substantial protection against the destabilization of protein during encapsulation.

Adsorption↗