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PubMed2005

Downregulation of Bax mRNA expression and protein stability by the E6 protein of human papillomavirus 16.

Previous studies have shown that human papillomavirus (HPV) 16 E6 inhibits apoptosis induced during terminal differentiation of primary human keratinocytes (PHKs) triggered by serum and calcium. E6 inhibition of apoptosis was accompanied with prolonged expression of Bcl-2 and reduced elevation of Bax levels. In the present study, the effect of E6 on Bax mRNA expression and protein stability was investigated. These studies indicate that stable E6 expression in differentiating keratinocytes reduced the steady-state levels of Bax mRNA and shortened the half-life of Bax protein. These results were confirmed in transiently transfected 293T cells where E6 degraded Bax in a dose-dependent manner. Bax degradation was also exhibited in Saos-2 cells that lack p53, indicating its p53 independence. E6 did not form complexes with Bax and did not induce Bax degradation in vitro under experimental conditions where p53 was degraded. Finally, E6 aa 120-132 were shown to be necessary for Bax destabilization and, more importantly, for abrogating the ability of Bax to induce cellular apoptosis, highlighting the functional consequences of the E6-induced alterations in Bax expression.

Down-Regulation↗
PubMed1992

Structural organization of proteins on the oxidizing side of photosystem II. Two molecules of the 33-kDa manganese-stabilizing proteins per reaction center.

The 33-kDa manganese-stabilizing protein stabilizes the manganese cluster in the oxygen-evolving complex. There has been, however, a considerable amount of controversy concerning the stoichiometry of this photosystem II (PS II) component. In this paper, we have verified the extinction coefficient of the manganese-stabilizing protein by amino acid analysis, determined the manganese content of oxygen-evolving photosystem II membranes and reaction center complex using inductively coupled plasma spectrometry, and determined immunologically the amount of the manganese-stabilizing protein associated with photosystem II. Oxygen-evolving photosystem II membranes and reaction center complex preparations contained 258 +/- 11 and 67 +/- 3 chlorophyll, respectively, per tetranuclear manganese cluster. Immunoquantification of the manganese-stabilizing protein using mouse polyclonal antibodies on "Western blots" demonstrated the presence of 2.1 +/- 0.2 and 2.0 +/- 0.3 molecules of the manganese-stabilizing protein/tetranuclear manganese cluster in oxygen-evolving PS II membranes and highly purified PS II reaction center complex, respectively. Since the manganese-stabilizing protein co-migrated with the D2 protein in our electrophoretic system, accurate immunoquantification required the inclusion of CaCl2-washed PS II membrane proteins or reaction center complex proteins in the manganese-stabilizing protein standards to compensate for the possible masking effect of the D2 protein on the binding of the manganese-stabilizing protein to Immobilon-P membranes. Failure to include these additional protein components in the manganese-stabilizing protein standards leads to a marked underestimation of the amount of the manganese-stabilizing protein associated with these photosystem II preparations.

Chloroplasts↗
PubMed1999

In silico design for protein stabilization.

Newly developed in silico protein design methods have recently been applied to problems in protein stabilization. Stabilized protein sequences can be designed by combining potential functions that model a protein sequence's compatibility with a structure and fast optimization tools that can search the enormous number of sequence possibilities. The experimental testing of several sequence-design strategies has demonstrated that a wide range of protein structures can be stabilized. The primary advantage of in silico design is the vast number of sequences that can be rapidly screened in the search for an optimal design, far exceeding non-computational methods. This feature allows very large changes in protein properties to be discovered.

Biotechnology↗
PubMed1997

Towards a molecular level understanding of protein stabilization: the interaction between lysozyme and sorbitol.

The paper is investigating the mechanism of stabilization of proteins by polyols at the molecular level. It is addressing the interactions of sorbitol, a polyol commonly used as a protein stabilizing agent, with hen egg white lysozyme, a well studied protein. Differential scanning calorimetry shows an increase in denaturation temperature of lysozyme upon addition of sorbitol at a concentration of 250 mM and above. Increasing sorbitol concentration also caused an increase in signal intensity of the CD spectrum of lysozyme in the wavelength region of 280-300 nm. Two-dimensional nuclear magnetic resonance spectroscopy was used to examine interactions between lysozyme and sorbitol. Most significant changes are manifest in the anomalous relaxation properties of Ala and Thr methyl groups indicating modifications of local motions and possibly compression of the entire structure. This is further corroborated by new intra-protein nuclear Overhauser effects in the presence of sorbitol. There is also evidence that water is displaced from the enzyme surface close to Ile-88 upon addition of sorbitol. In combination these results reveal a complex interplay of different interactions. Comparison to NMR-spectra of lysozyme with a bound inhibitor (tri-N-acetyl-glucosamine) shows that the interaction with sorbitol affects spatially disparate regions of the protein.

Calorimetry, Differential Scanning↗
PubMed2002

Selection of mutations for increased protein stability.

There are many ways to select mutations that increase the stability of proteins, including rational design, functional screening of randomly generated mutant libraries, and comparison of naturally occurring homologous proteins. The protein engineer's toolbox is expanding and the number of successful examples of engineered protein stability is increasing. Still, the selection of thermostable mutations is not a standard process. Selection is complicated by lack of knowledge of the process that leads to thermal inactivation and by the fact that proteins employ a large variety of structural tricks to achieve stability.

Bacillus↗
PubMed2006

Knowledge acquisition and development of accurate rules for predicting protein stability changes.

Knowing the mechanisms by which protein stability change is one of the most important and valuable tasks in molecular biology. The conventional methods of predicting protein stability changes mainly focus on improving prediction accuracy. However, it is desirable to extract domain knowledge from large databases that is beneficial to accurate prediction of the protein stability change. This paper presents an interpretable prediction tree method (named iPTREE) that produces explanatory rules to explore hidden knowledge accompanied with high prediction accuracy and consequently analyzes the factors influencing the protein stability changes. To evaluate iPTREE and the knowledge upon protein stability changes, a thermodynamic dataset consisting of 1615 mutants led by single point mutation from ProTherm is adopted. Being as a predictor for protein stability changes, the rule-based approach can achieve a prediction accuracy of 87%, which is better than other methods based on artificial neural networks (ANN) and support vector machines (SVM). Besides, these methods lack the ability in biological knowledge discovery. The human-interpretable rules produced by iPTREE reveal that temperature is a factor of concern in predicting protein stability changes. For example, one of interpretable rules with high support is as follows: if the introduced residue type is Alanine and temperature is between 4 degrees C and 40 degrees C, then the stability change will be negative (destabilizing). The present study demonstrates that iPTREE can easily be used in the application of protein stability changes where one requires more understandable knowledge.

Algorithms↗
PubMed1998

Protein stability function relations: beta-lactoglobulin-A sulphydryl group reactivity and its relationship to protein unfolding stability.

The effect of protein stability on the reactivity of the free sulphydryl (SH) group in beta-lactoglobulin-A (beta-LgA) provides a model for the study of protein stability-function relations (PSFR). The free energy change for protein unfolding (delta G(o)) and SH group exposure (delta GSH) were determined from (i) the urea unfolding curve for beta-LgA and (ii) the kinetics of beta-LgA SH/disulphide exchange with 2-pyridine disulphide (2-PDS) in 0-8 M urea (pH 3). Protein unfolding profiles determined from extrinsic fluorescence and SH-group reactivity measurements were not coincident. beta-LgA formed a stable intermediate (X) state in the presence of 4 M urea with delta G(o) = 20 (+/- 0.03) kJ/mol. From the low rate of SH/disulphide exchange in 4 M urea, the SH-group within beta-LgA was efficiently masked within the X-state. SH reactivity increased after beta-LgA was unfolded in 6-8 M urea with, delta GSH = 43(+/- 6.4) kJ/mol. Such results are discussed in terms of possible interrelationships between protein unfolding stability and SH reactivity in beta-LgA.

Drug Stability↗
PubMed2004

SUMO-1 modification regulates the protein stability of the large regulatory protein Rep78 of adeno associated virus type 2 (AAV-2).

The large Rep proteins Rep78 and Rep68 of the helper-dependent adeno associated virus type 2 (AAV-2) are essential for both site-specific integration of AAV DNA in the absence of helpervirus and productive AAV replication in the presence of helpervirus. We have identified UBC9, the E2 conjugating enzyme for the small ubiquitin-related polypeptide SUMO-1, as binding partner of the large Rep proteins in yeast two-hybrid analysis and in GST pulldown assays. Modification of the large Rep proteins with SUMO-1 could be demonstrated in immunoblot analysis and in immunoprecipitations, with the lysine residue at amino acid position 84 serving as the major attachment site. The largely sumolation-deficient Rep78 lysine to arginine point mutant showed a strongly reduced half-life as compared to the wild-type protein. This finding implicates a role for sumolation in the regulation of Rep78 protein stability that is assumed to be critical for the establishment and maintenance of AAV latency.

Cloning, Molecular↗
PubMed1999

Leucine 245 is a critical residue for folding and function of the manganese stabilizing protein of photosystem II.

In solution, Manganese Stabilizing Protein, the polypeptide which is responsible for the structural and functional integrity of the manganese cluster in photosystem II, is a natively unfolded protein with a prolate ellipsoid shape [Lydakis-Simantiris et al. (1999) Biochemistry 38, 404-414; Zubrzycki et al. (1998) Biochemistry 37, 13553-13558]. The C-terminal tripeptide of Manganese Stabilizing Protein was shown to be critical for binding to photosystem II and restoration of O(2) evolution activity [Betts et al. (1998) Biochemistry 37, 14230-14236]. Here, we report new biochemical, hydrodynamic, and spectroscopic data on mutants E246K, E246STOP, L245E, L245STOP, and Q244STOP. Truncation of the final dipeptide (E246STOP) or substitution of Glu246 with Lys resulted in no significant changes in secondary and tertiary structures of Manganese Stabilizing Protein as monitored by CD spectroscopy. The apparent molecular mass of the protein remained unchanged, both mutants were able to rebind to photosystem II, and both proteins reactivate O(2) evolution. Manganese Stabilizing Protein lacking the final tripeptide (L245STOP), or substitution of Glu for Leu245 dramatically modified the protein's solution structure. The apparent molecular masses of these mutants increased significantly, which might indicate unfolding of the protein in solution. This was verified by CD spectroscopy. Both mutant proteins rebound to photosystem II with lower affinities, and activation of O(2) evolution was decreased dramatically. Enhancement of these defects was observed upon removal of the final tetrapeptide (Q244STOP). These results indicate that Leu245 is essential to maintaining Manganese Stabilizing Protein's solution structure in a conformation that promotes efficient binding to photosystem II and/or for the subsequent steps that lead to enzyme activation. Based on an analysis of the properties of C-terminal mutations, a hypothesis for structural requirements for functional binding of Manganese Stabilizing Protein to photosystem II is presented. Effects of C-terminal mutations on the UV spectrum of Manganese Stabilizing Protein were also examined. Mutations that alter solution structure also affect a 293 nm absorption shoulder which is assigned to the only tryptophan residue, Trp241, in the protein, and this absorbance feature is shown to be a useful indicator of alterations to the Trp241 environment.

Circular Dichroism↗
PubMed2004

White wine continuous protein stabilization by packed column.

Protein stabilization is an important stage in the production of white wine. This paper studies white wine protein stabilization using a continuous process with zirconium oxide (powder and pellets) packed in a column. The results show that the total proteins decrease by 50 and 70% for the pellet and powdered zirconium oxides, respectively. Treatment with all zirconium oxides improves wine stability. The effect of the heat regeneration process on both zirconium oxide forms is to increase the adsorption capacity. The wine treated with powdered zirconium oxide after the regeneration is the most effective for preventing protein haze. The protein profile of wine after treatment shows that the 20-50 kDa and 50-70 kDa fractions are the ones removed preferentially, while the 15 kDa fraction and the ones higher than 70 kDa are removed the least. The results show that the protein fraction with a molecular weight of 15 kDa does not affect the protein instability of the wines studied. The protein fraction with a molecular weight higher than 70 kDa seems to influence protein instability. The physicochemical properties of wine after treatment were not affected, and the values obtained were like those of the standardized range.

Adsorption↗
PubMed1997

Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability.

The anomalous temperature dependence of protein folding has received considerable attention. Here we show that the temperature dependence of the folding of protein L becomes extremely simple when the effects of temperature on protein stability are corrected for; the logarithm of the folding rate is a linear function of 1/T on constant stability contours in the temperature-denaturant plane. This convincingly demonstrates that the anomalous temperature dependence of folding derives from the temperature dependence of the interactions that stabilize proteins, rather than from the super Arrhenius temperature dependence predicted for the configurational diffusion constant on a rough energy landscape. However, because of the limited temperature range accessible to experiment, the results do not rule out models with higher order temperature dependences. The significance of the slope of the stability-corrected Arrhenius plots is discussed.

Kinetics↗
PubMed2006

Protein stability and surface electrostatics: a charged relationship.

Engineering proteins to withstand a broad range of conditions continues to be a coveted objective, holding the potential to advance biomedicine, industry, and our understanding of disease. One way of achieving this goal lies in elucidating the underlying interactions that define protein stability. It has been shown that the hydrophobic effect, hydrogen bonding, and packing interactions between residues in the protein interior are dominant factors that define protein stability. The role of surface residues in protein stability has received much less attention. It has been believed that surface residues are not important for protein stability particularly because their interactions with the solvent should be similar in the native and unfolded states. In the case of surface charged residues, it was sometimes argued that solvent exposure meant that the high dielectric of the solvent will further decrease the strength of the charge-charge interactions. In this paper, we challenge the notion that the surface charged residues are not important for protein stability. We computationally redesigned sequences of five different proteins to optimize the surface charge-charge interactions. All redesigned proteins exhibited a significant increase in stability relative to their parent proteins, as experimentally determined by circular dichroism spectroscopy and differential scanning calorimetry. These results suggest that surface charge-charge interactions are important for protein stability and that rational optimization of charge-charge interactions on the protein surface can be a viable strategy for enhancing protein stability.

Acid Anhydride Hydrolases↗
PubMed2000

The BtpA protein stabilizes the reaction center proteins of photosystem I in the cyanobacterium Synechocystis sp. PCC 6803 at low temperature.

Specific inhibition of photosystem I (PSI) was observed under low-temperature conditions in the cyanobacterium Synechocystis sp. strain PCC 6803. Growth at 20 degrees C caused inhibition of PSI activity and increased degradation of the PSI reaction center proteins PsaA and PsaB, while no significant changes were found in the level and activity of photosystem II (PSII). BtpA, a recently identified extrinsic thylakoid membrane protein, was found to be a necessary regulatory factor for stabilization of the PsaA and PsaB proteins under such low-temperature conditions. At normal growth temperature (30 degrees C), the BtpA protein was present in the cell, and its genetic deletion caused an increase in the degradation of the PSI reaction center proteins. However, growth of Synechocystis cells at 20 degrees C or shifting of cultures grown at 30 degrees C to 20 degrees C led to a rapid accumulation of the BtpA protein, presumably to stabilize the PSI complex, by lowering the rates of degradation of the PsaA and PsaB proteins. A btpA deletion mutant strain could not grow photoautotrophically at low temperature, and exhibited rapid degradation of the PSI complex after transfer of the cells from normal to low temperature.

Bacterial Proteins↗
PubMed1981

Globular protein stability: aspects of interest in protein turnover.

The conformational stability of globular proteins is remarkably low. Under physiological conditions, the native globular conformation is only from 5 to 15 kcal/mole more stable than unfolded conformations. In addition, small changes in the structure of a protein such as removing one terminal residue or cleaving a single peptide bond frequently lead to a substantial decrease in the stability. Likewise, single substitutions in the amino acid sequence can increase or decrease the stability by several kilocalories per mole. The low conformational stability of globular proteins and the sensitivity to small changes in structure suggest a possible role for conformational stability in the intracellular degradation of proteins. Several lines of evidence from in vivo studies of protein degradation are consistent with this idea.

Cytochrome c Group↗
PubMed2006

Six specific lysine residues are crucial in maintaining the structure and function of soluble manganese stabilizing protein.

When manganese stabilizing protein (MSP) was treated with 0.5 mM N-succinimidyl propionate (NSP), the rebinding ability and oxygen-releasing capabilities of the modified MSP were not altered, in spite of changes of MSP surface Lys residues. Furthermore, far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed that 0.5 mM NSP-modified MSP retained most of its native secondary and tertiary structure. Mapping of the sites of NSP modification by Staphylococcus V(8) protease digestion of the modified protein, as well as analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry, indicated that seven Lys residues were modified. The results suggested that these residues are not absolutely essential to the structure and function of MSP. However, when the NSP concentration was increased to 4 mM, the modified MSP was unable to bind photosystem II and completely lost its reactivating capability. Both far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed a clear conformational change in MSP after 4 mM NSP treatment, suggesting that some Lys residues are involved in maintaining the structure and function of MSP. Analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry indicated that another six Lys residues, namely Lys20, Lys101, Lys196, Lys207, Lys130 (or Lys137) and Lys66 (or Lys76), were modified by 4 mM NSP. Therefore, these six Lys residues are crucial in maintaining the structure and function of soluble MSP.

Binding Sites↗
PubMed2004

Effects of naturally occurring osmolytes on protein stability and solubility: issues important in protein crystallization.

Protein solubility and stability are issues of consideration in attempts to crystallize proteins. These two properties of proteins are also at issue in the cells of organisms that have adapted to water stress conditions that could ordinarily denature or inactivate some proteins. Most organisms that have adapted to environmental stresses have done so by production and accumulation of certain small organic molecules, known as osmolytes, that arose by natural selection and have the ability to stabilize intracellular proteins against the environmental stress. Here, concepts developed to understand the special properties of the naturally occurring osmolytes in effecting protein stability and solubility, and the principles that have come from studies of these compounds have been presented. Along with excluded volume and preferential interaction parameters, identification of the osmophobic effect and the attenuation of this effect by favorable interactions of solute with side-chains appear to contribute to the full set of effects protecting osmolytes have on protein stability and solubility. With these concepts in mind and the fact that urea interacts favorably with the peptide backbone we note that: (1) osmolyte-induced effects on protein stability ranging from denaturation to forcing proteins to fold can be achieved experimentally and the underlying principles understood at near molecular-level detail, and (2) osmolyte-mediated solubility effects ranging from protein precipitation to protein solubilization are predictable based on these principles. These effects are contrasted and compared with effects of 2-methyl-2,4-pentanediol and polyethylene glycol on proteins, and how the principles found for the naturally occurring osmolytes can be applied to these two commonly used protein crystallizing agents.

Amino Acids↗
PubMed2005

Effect of sorbitol and residual moisture on the stability of lyophilized antibodies: Implications for the mechanism of protein stabilization in the solid state.

PURPOSE: To investigate the effect of plasticizers on the stability of protein formulations in the solid state and to apply these results to a study of mechanisms of protein stabilization by sugars in the solid sate. METHODS: The IgG1 antibody was formulated with either sucrose or trehalose alone or a mixture of sorbitol with sucrose or trehalose. After lyophilization, the pure protein and sucrose formulations were equilibrated at different relative humidities giving residual moistures from less than 1% to 5% for sucrose systems and up to 17% for pure protein systems. All the samples were stored at 50 degrees C for up to1 month and at 40 and 25 degrees C for up to 6 months. Aggregation and chemical degradation were monitored by size exclusion chromatography (SEC) and ion exchange chromatography (IEX), respectively. The secondary structure was characterized by FTIR using second derivative analysis of Amide I region. Structural relaxation times, tau, an indication of molecular mobility in the glassy matrix, were characterized using the thermal activity monitor (TAM). The tau values of the recombinant human monoclonal antibody (rhuMab) formulation with various water contents were also measured in this study and compared with stability data taken from the literature (Breen ED, Curley JG, Overcashier DE, Hsu CC, Shire SJ, 2001, Pharm Res 18:1345-1353). RESULTS: The structural relaxation time, tau, decreased sharply with increasing water content. However, the stability data suggest a minimum in degradation rate at 2%-3% water content. Addition of a small amount of sorbitol to a sucrose-based formulation resulted in greater retention of native structure, smaller relaxation time, but improved stability. However, with the trehalose-based formulations, addition of sorbitol had no effect on protein structure (FTIR), but the decrease in relaxation time and the improvement in stability were qualitatively similar to the corresponding data obtained with the sucrose-based formulation. CONCLUSION: Glass dynamics as measured by tau could not explain the stability results. Stability correlated best with the preservation of native structure for sucrose-based formulations, but with the trehalose-based formulation, neither structural relaxation time nor extent of native structure was predictive of stability. However, it is possible that the beta-relaxations rather than the alpha-relaxation (i.e., the tau we measured) is critical to the stability. Plasticizers like glycerol may decrease tau for "alpha-motion" but increase tau for "beta-motion" and stabilize proteins (Cicerone MT, Tellington A, Trost L, Sokolov A, 2003, BioProcess Inter 1:1-9).

Absorption↗
PubMed2003

Comparing protein stabilities during zebrafish embryogenesis.

The stabilities of many key proteins are regulated, e.g. via ubiquitination and proteasomal degradation, with important biological consequences. We present a convenient method that allows the analysis and comparison of protein stabilities during embryogenesis using early zebrafish development as a model system. Basically, this method involves ectopic overexpression of epitope-tagged proteins via mRNA injections in one-to-four-cell stage embryos and subsequent protein detection after various time points. Indeed, the protein stability of the ubiquitin ligase RLIM, which is able to autoubiquitinate and target itself for proteasomal degradation, was much shorter when compared to a protein consisting of a Myc epitope-tag and a nuclear localization domain. Thus, this method may be used more widely for the study of developmental protein stability.

Animals↗