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PubMed2007

Influence of the Hofmeister anions on protein stability as studied by thermal denaturation and chemical shift perturbation.

The influence of external cosolutes on the thermal stability of the B1 domain of protein L (ProtL) has been studied by circular dichroism, fluorescence spectroscopy, and differential scanning calorimetry. The thermal denaturation midpoint is effectively modulated by the addition of a suite of anions and follows the Hofmeister series. The maximum increase in thermostability (corresponding to 14 degrees C) was observed in the presence of 1 M sodium sulfate. After conversion of the experimental data into the change in the virial coefficient, a mechanistic model was used to estimate the relative contributions from excluded volume and preferential anion solvation for each anion. As expected, the excluded volume term stabilizes the native conformation of ProtL for all the cosolutes, but opposite effects on protein stability arise from the anion's solvation depending on their tendency to interact with or to become excluded from the protein surface. This behavior is in agreement with the results of independent NMR experiments: the anions that strongly interact with the protein surface produce significant perturbations in the amide protein chemical shift (delta d23(HN)). A correlation obtained between delta d23(HN) and the temperature coefficients for the different amide protons provides qualitative information about the structural determinants for the interaction between the protein surface and the cosolute.

Anions↗

PubMed2006

Analysis of the temperature-sensitive mutation of Escherichia coli pantothenate kinase reveals YbjN as a possible protein stabilizer.

Pantothenate kinase (PanK), a key regulatory enzyme in the coenzyme A (CoA) biosynthetic pathway, catalyzes the rate-limiting phosphorylation of pantothenic acid to form phosphopantothenate during CoA biosynthesis. Escherichia coli ts9 strain manifests temperature-sensitive phenotype on LB media due to its mutation in the coaA gene (coaA1). Sequencing analysis revealed that coaA1 arises from a single base pair mutation that results in an amino acid change, L236F. This change, located proximate to the ATP binding site of CoaA, destabilizes both enzymatic activity and structural integrity or stability of the mutant protein in vitro. Spontaneously, revertants of ts9 were occasionally found on LB medium plates. Two groups of revertants were isolated: for those that can grow at 40 degrees C, a reversion of the original amino acid mutation L236F to L236L or other amino acid (such as L236C) occurs; for those that can grow at 37 degrees C but not 40 degrees C, a mutation at another gene or intergenic suppression is strongly indicated. Towards genetic identification of genes that might interact with coaA1, ybjN, which encodes a putative sensory transduction regulator protein, and whose over-expression is capable of ameliorating the temperature-sensitive phenotype of the structurally unstable CoaA1 or CoaA[L236F], was isolated. Over-expression of ybjN appears to suppress the temperature-sensitive phenotype of several other temperature-sensitive mutations, including coaA14 (carried by DV51 strain), coaA15 (carried by DV70 strain), and ilu-1, suggesting it not only helps CoaA1, but possibly works as a general stabilizer for some other unstable proteins.

Adenosine Triphosphate↗

PubMed1990

Measuring and increasing protein stability.

Recently, it has become possible to construct proteins to order and this has promoted interest in learning how to increase their stability. This article describes recent developments in the methods used to measure the conformational stability of globular proteins, and discusses the approaches being used to increase their stability.

Globulins↗

PubMed2002

Postmortem RNA and protein stability in perinatal human lungs.

The availability of fetal and neonatal lung tissue is an invaluable resource to elucidate the molecular regulation of human lung development. In this study, we have investigated the mRNA and protein stability of perinatal lung tissues treated with RNA (Ambion Inc., Austin, TX) or snap frozen in liquid nitrogen (LN ). Lung samples were obtained from 25 consecutive perinatal autopsies of live-born and stillborn infants (median gestational age, 23 weeks) with various clinical presentations. Treatment of lung tissue with RNA yielded more total RNA and protein than LN freezing. The integrity of RNA, assessed by spectrophotometry and gel electrophoresis, was equivalent between both tissue preservation methods, and both methods produced RNA suitable for reverse transcriptase-polymerase chain reaction analysis of representative genes (beta-actin and surfactant protein-B [SP-B]). Similarly, the protein integrity of RNA -treated tissues was equivalent to that of LN -frozen tissues, as judged by Western blot analysis of SP-B/actin protein expression. Although the total yield was similar in live-born, nonmacerated stillborn and macerated stillborn infants, only RNA and protein from live-born or nonmacerated stillborn infants was suitable for subsequent molecular analyses. Within the 41-hour range studied, the duration of the postmortem interval did not affect the yield or integrity of RNA and protein with either tissue preservation method. In summary, high-quality RNA and protein, suitable for routine molecular analyses, can be obtained from postmortem lung tissue from live-born and nonmacerated stillborn infants, even with prolonged postmortem intervals. RNA is equivalent, if not superior, to LN for preservation of postmortem RNA and protein in developing human lungs.

Autolysis↗

PubMed2003

Binding of manganese stabilizing protein to photosystem II: identification of essential N-terminal threonine residues and domains that prevent nonspecific binding.

The N-terminus of spinach photosystem II manganese stabilizing protein (MSP) contains two amino acid sequences, (4)KRLTYD(10)E and (15)TYL(18)E, that are necessary for binding of two copies of this subunit to the enzyme [Popelkova et al. (2002) Biochemistry 41, 10038-10045]. To better understand the basis of MSP-photosystem II interactions, the role of threonine residues in the highly conserved motifs T(Y/F)DE and TY has been characterized. Deletion mutants lacking the first 5, 6, 7, and 15 amino acid residues at the N-terminus of the protein were examined for their ability to reconstitute activity in MSP-depleted photosystem II. The results reported here show that truncations of five and six amino acid residues (mutants DeltaR5M and DeltaL6M mutants) have no negative effect on recovery of oxygen evolution activity or on binding of MSP to photosystem II. Deletion of seven residues (mutant DeltaT7M) decreases reconstitution activity to 40% of the control value and reduces functional binding of the mutant protein to photosystem II from two to one copy. Deletion of 15 amino acid residues (mutant DeltaT15M) severely impairs functional binding of MSP, and lowers O(2) evolution activity to less than 20% of the control. DeltaT7M is the only mutant that exhibited neither nonspecific binding to photosystem II nor changes in tertiary structure. These, and previous results, show that the highly conserved Thr7 and Thr15 residues of MSP are required for functional binding of two copies of the eukaryotic protein to photosystem II. Although the N-terminal domains, (1)EGGKR(6)L, (8)YDEIQS(14)K, and (16)YL(18)E of spinach MSP are unnecessary for specific, functional binding interactions, these sequences are necessary to prevent nonspecific binding of the protein to photosystem II.

Amino Acid Sequence↗

PubMed2000

Transcriptional repressor CopR: the structured acidic C terminus is important for protein stability.

The transcriptional repressor CopR is one of the two copy-number control components of plasmid pIP501. CopR binds as a dimer at two consecutive major grooves on the same face of the DNA. Previously, equilibrium dissociation constants of CopR dimers and the CopR-DNA complex and the intracellular CopR concentration were calculated. Amino acid residues involved in DNA binding and dimerization were determined. Here, we provide a detailed analysis of the acidic C terminus of CopR. A series of C-terminally truncated CopR mutants were analysed with regard to activity and half-life in vivo and DNA binding, dimerization, structure and stability in vitro. The last 29 amino acid residues of CopR were not essential for DNA binding and dimerization but for protein stability. However, whereas CopDelta20 was, in spite of drastically shortened half-life, still 100 % active in vivo, CopDelta24 and CopDelta27 retained only 20 % activity. In vivo stability could be restored only partially by adding a C-terminal tail previously shown to stabilize the lambda repressor N terminus. However, substitution of seven Glu residues by Lys within the last 20 residues drastically reduced half-life. Our results clearly demonstrate that the acidic C terminus is important for the stability of CopR. Using CD-measurements we show that the C terminus of CopR is structured.

Amino Acid Sequence↗

PubMed2005

Binding of PTEN to specific PDZ domains contributes to PTEN protein stability and phosphorylation by microtubule-associated serine/threonine kinases.

The tumor suppressor phosphatase PTEN is a key regulator of cell growth and apoptosis that interacts with PDZ domains from regulatory proteins, including MAGI-1/2/3, hDlg, and MAST205. Here we identified novel PTEN-binding PDZ domains within the MAST205-related proteins, syntrophin-associated serine/threonine kinase and MAST3, characterized the regions of PTEN involved in its interaction with distinctive PDZ domains, and analyzed the functional consequences on PTEN of PDZ domain binding. Using a panel of PTEN mutations, as well as PTEN chimeras containing distinct domains of the related protein TPTE, we found that the PTP and C2 domains of PTEN do not affect PDZ domain binding and that the C-terminal tail of PTEN (residues 350-403) provides selectivity to recognize specific PDZ domains from MAGI-2, hDlg, and MAST205. Binding of PTEN to the PDZ-2 domain from MAGI-2 increased PTEN protein stability. Furthermore, binding of PTEN to the PDZ domains from microtubule-associated serine/threonine kinases facilitated PTEN phosphorylation at its C terminus by these kinases. Our results suggest an important role for the C-terminal region of PTEN in the selective association with scaffolding and/or regulatory molecules and provide evidence that PDZ domain binding stabilizes PTEN and targets this tumor suppressor for phosphorylation by microtubule-associated serine/threonine kinases.

Adaptor Proteins, Signal Transducing↗

PubMed1992

Correlation of co-ordinated amino acid changes at the two-domain interface of cysteine proteases with protein stability.

The engineering of a protein containing an alternative local residue packing for a set of side-chains has proven to be a major challenge because compositional, volumetric and steric constraints must be respected. Homologous proteins should provide examples of alternative groups of residues leading to a similar functional result. The functional significance of a pair of co-ordinated changes that are observed in the cysteine proteases family has been investigated by comparing the effect of individual or double changes on secretion, stability and activity of papain. The two changes are not independent. Detrimental effects of single mutations at one of the two positions can be partly suppressed by the co-ordinated mutation that reproduces naturally occurring contacts, indicating that these changes are concerted. Single mutations at the other position produce milder effects, suggesting a pathway for evolution.

Amino Acids↗

PubMed2000

Protein stability and domain topology determine the transcriptional activity of the mammalian glial cells missing homolog, GCMb.

The glial cells missing (GCM) family of transcription factors consists of Drosophila GCM and the mammalian proteins GCMa and GCMb. They are expressed in a highly restricted manner during development and are known or assumed to be important regulators of developmental fate decisions. As the biochemical properties of GCMb have not been studied so far, we have undertaken a detailed structure-function analysis of the mouse GCMb (mGCMb) protein. DNA-binding specificity was very similar to that of other GCM proteins. Nevertheless, mGCMb was only a weak transcriptional activator in a number of different tissue culture systems. Interestingly, this was not due to an intrinsic absence of transactivation potential. In effect, we were able to identify two separate transactivation domains within mGCMb, one carboxyl-terminally adjacent to the DNA-binding domain and the second within the extreme carboxyl terminus. Activity of both transactivation domains was, however, modulated by an inhibitory region unique to mGCMb and located between the two transactivation domains. Furthermore, pulse-chase experiments proved that the mGCMb protein has a half-life approximately four times shorter than mGCMa. Introduction of the above mentioned inhibitory domain of mGCMb into mGCMa shortened the half-life of mGCMa to a value typical of mGCMb with a concomitant reduction in transactivation potential. Given the strong correlation between protein stability and transactivation potential, functional differences between the two mammalian GCM homologs are likely due to differences in stability with a single inhibitory region in mGCMb being involved in the reduction of both.

Amino Acid Sequence↗

PubMed2004

Down-regulation of soluble guanylyl cyclase expression by cyclic AMP is mediated by mRNA-stabilizing protein HuR.

We analyzed whether the cyclic AMP induced down-regulation of the nitric oxide (NO) receptor soluble guanylyl cyclase (sGC) is mediated by the mRNA-protecting protein HuR. Exposure (up to 24 h) of isolated rat aortic segments to the activator of adenylyl cyclase, forskolin (10 microM), and to both activators of cAMP-stimulated protein kinase (PKA), 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole-3',5'-cyclic monophosphorothioate, Spisomer (Sp-5,6-DCl-cBIMPS; 400 nM), and N6-phenyl-cAMP (10 microM), strongly reduced sGCalpha1beta1 and HuR protein and mRNA expression in a time-dependent and actinomycin D (10 microM)-sensitive fashion. In vitro degradation of sGCalpha1 and beta1 poly(A)+ mRNA by native rat aortic protein was markedly increased by pretreatment of intact aortas with forskolin. Native protein extract from rat aorta shifted the electrophoretic mobility of biotin-labeled riboprobes from the 3'-untranslated region of sGCalpha1 and beta1 mRNA, and these bands was supershifted by a monoclonal antibody directed against the mRNA-stabilizing protein HuR. Forskolin decreased the HuR-sGCalpha1 and beta1 mRNA interaction and HuR protein expression in rat aorta, and this was prevented by the PKA inhibitory cAMP analog 3',5'-cyclic monophosphorothioate, Rp-isomer (Rp-cAMPS). In cultured smooth muscle cells from rat aorta, forskolin induced a rapid increase in Fos/p-Fos protein levels and activator protein 1 (AP-1) binding activity. Inhibition of this transcription factor by an AP-1 decoy prevented the forskolin-induced down-regulation of HuR. We conclude that forskolin/cAMP decrease the expression of heterodimeric sGC in rat aortic smooth muscle cells via activation of Fos/AP-1, which decreases the expression of HuR and thus destabilizes the sGCalpha1 and beta1 mRNA.

3' Untranslated Regions↗

PubMed2004

Smad4 protein stability is regulated by ubiquitin ligase SCF beta-TrCP1.

Smad4 is a key intracellular mediator for the transforming growth factor-beta (TGF-beta) superfamily of growth factors and is also an important tumor suppressor. The receptor-regulated Smad (R-Smad) proteins are regulated by ubiquitin-mediated degradation, yet the precise control of Smad4 protein stability is unclear. We have identified SCF(beta-TrCP1), a ubiquitin (E3) ligase, as a critical determinant for the protein degradation of Smad4 protein. F-box protein beta-TrCP1 in this E3 ligase interacts with Smad4 both in yeast and in mammalian cells, but has no interaction with Smad2 and has weak interaction with Smad3. The beta-TrCP1/Smad3 interaction was abolished by Smad4 gene silencing, indicating the interaction is indirect and is through Smad4. Ectopic expression of SCF complex containing beta-TrCP1 is sufficient to induce the ubiquitination and degradation of Smad4. Furthermore, small interfering RNA-triggered endogenous beta-TrCP1 suppression increases the expression of Smad4 protein. Consistent with these results, cells that overexpress the SCF complex display an inhibited TGF-beta-dependent transcriptional activity and an impaired cell cycle arrest function. Thus, SCF(beta-TrCP1) abrogates TGF-beta function in vivo by decreasing Smad4 stability.

Blotting, Western↗

PubMed1995

Halophilic protein stabilization by the mild solubilizing agents nondetergent sulfobetaines.

In this work, experiments performed on pig heart and halophilic malate dehydrogenase as well as halophilic elongation factor Tu demonstrate a protein stabilization property from the recently described mild solubilizing agents nondetergent sulfobetaines. A practical application is given by the separation of halophilic bacteria elongation factor Tu and halophilic malate dehydrogenase by high-performance ion-exchange chromatography achieved at reduced salt levels without significant loss of activity.

Animals↗

PubMed2003

Comparative studies on the properties of the extrinsic manganese-stabilizing protein from higher plants and of a synthetic peptide of its C-terminus.

The present study describes a comparative analysis on the fluorescence properties of the manganese-stabilizing protein (MSP), a synthetic peptide corresponding to its C terminus and a 7:1 (molar ratio) mixture of N-acetyl-tyrosine and N-acetyl-tryptophan, respectively, together with reconstitution experiments of oxygen evolution in MSP-depleted photosystem II (PS II) membrane fragments. It is found: (i) at neutral pH, the fluorescence from Trp(241) is strongly diminished in MSP solutions, whereas it highly dominates the overall emission from the C-terminus peptide; (ii) at alkaline pH, the emission of Tyr and Trp is quenched in both, MSP and C-terminus peptide, with increasing pH but the decline curve is shifted by about two pH units towards the alkaline region in MSP; (iii) a drastically different pattern emerges in the 7:1 mixture where the Trp emission even slightly increases at high pH; (iv) the anisotropy of the fluorescence emission is wavelength-independent (310-395 nm) and indicative of one emitter type (Trp) in the C-terminus peptide and of two emitter types (Tyr, Trp) in MSP; and (v) in MSP-depleted PS II membrane fragments the oxygen evolution is restored (up to 85% of untreated control) by rebinding of MSP but not by the C-terminus peptide, however, the presence of the latter diminishes the restoration effect of MSP. A quenching mechanism of Trp fluorescence by a next neighbored tyrosinate in the peptide chain is proposed and the relevance of the C terminus of MSP briefly discussed.

Amino Acid Sequence↗

PubMed1991

Protein stability: electrostatics and compact denatured states.

Globular proteins can be denatured by changing pH and ionic strength. Much recent evidence has led to the surprising conclusion that there are two acid-denatured states: one highly unfolded and the other more compact, sometimes called the "molten globule." Here we describe a molecular theory for electrostatic stability of globular proteins based on the properties of the constituent amino acids: oil/water partition coefficients, pK values of the titratable groups, and their temperature dependences. Predicted denaturation temperatures vs. pH are in good agreement with experiments of other workers on myoglobin. The theory also predicts two populations of denatured species, one open and the other more compact, with densities in the range found experimentally for molten globular states. In addition, it predicts a phase diagram (stability vs. pH, ionic strength) in good agreement with experiments of Goto and Fink [Goto, Y. & Fink, A. L. (1989) Biochemistry 28, 945-952; and Goto, Y. & Fink, A. L. (1990) J. Mol. Biol. 214, 803-805]. The well-known salt destabilization of myoglobin has been generally considered evidence for ion pairing, but the present theory, based on smeared charge repulsion, explains the salt destabilization at low pH without ion pairing. In addition, for myoglobin the theory predicts salt stabilization at high pH, as observed for beta-lactamase by Goto and Fink.

Drug Stability↗

PubMed1998

Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability.

We study the fluctuations of native proteins by exact enumeration using the HP lattice model. The model fluctuations increase with temperature. We observe a low-temperature point, below which large fluctuations are frozen out. This prediction is consistent with the observation by Tilton et al. [R. F. Tilton, Jr., J. C. Dewan, and G. A. Petsko, Biochemistry 31, 2469 (1992)], that the thermal motions of ribonuclease A increase sharply above about 200 K. We also explore protein "flexibility" as defined by Debye-Waller-like factors and solvent accessibilities of core residues to hydrogen exchange. We find that proteins having greater stability tend to have fewer large fluctuations, and hence lower flexibilities. If flexibility is necessary for enzyme catalysis, this could explain why proteins from thermophilic organisms, which are exceptionally stable, may be catalytically inactive at normal temperatures.

Enzymes↗

PubMed2006

Effects of novel maturity-onset diabetes of the young (MODY)-associated mutations on glucokinase activity and protein stability.

Glucokinase acts as the pancreatic glucose sensor and plays a critical role in the regulation of insulin secretion by the beta-cell. Heterozygous mutations in the glucokinase-encoding GCK gene, which result in a reduction of the enzymatic activity, cause the monogenic form of diabetes, MODY2 (maturity-onset diabetes of the young 2). We have identified and functionally characterized missense mutations in the GCK gene in diabetic families that result in protein mutations Leu165-->Phe, Glu265-->Lys and Thr206-->Met. The first two are novel GCK mutations that co-segregate with the diabetes phenotype in their respective families and are not found in more than 50 healthy control individuals. In order to measure the biochemical effects of these missense mutations on glucokinase activity, we bacterially expressed and affinity-purified islet human glucokinase proteins carrying the respective mutations and fused to GST (glutathione S-transferase). Enzymatic assays on the recombinant proteins revealed that mutations Thr206-->Met and Leu165-->Phe strongly affect the kinetic parameters of glucokinase, in agreement with the localization of both residues close to the active site of the enzyme. In contrast, mutation Glu265-->Lys, which has a weaker effect on the kinetics of glucokinase, strongly affects the protein stability, suggesting a possible structural defect of this mutant protein. Finally, none of the mutations tested appears to affect the interaction of gluco-kinase with the glucokinase regulatory protein in the yeast two-hybrid system.

Adult↗

PubMed1991

The Zta trans-activator protein stabilizes TFIID association with promoter DNA by direct protein-protein interaction.

Eukaryotic transcriptional activators are believed to stimulate transcription through direct and/or indirect interactions with one or more of the general transcription factors. We show here that the Zta transcriptional activator protein encoded by the Epstein-Barr virus makes direct physical contact with the basic transcription factor TFIID. Both Zta and TFIID were expressed in and purified from Escherichia coli. Zta stabilized the binding of TFIID to Zta-responsive promoters as assayed by gel electrophoresis mobility-shift and immunoprecipitation of radiolabeled promoter DNA. A deletion mutant of Zta that failed to activate transcription failed to stabilize TFIID binding. DNase I footprinting showed that Zta reduced the dissociation rate of TFIID bound to the TATA element. Protein blotting and immunoprecipitation experiments demonstrated that TFIID and Zta also interact in the absence of promoter DNA. The amino acid residues 25-86 of Zta were essential for the stable association with TFIID and were shown to be required for trans-activation in vivo. We propose that Zta stimulates transcription, in part, by direct physical contact with the conserved domain of TFIID and the formation of a stable Zta-TFIID-promoter complex.

Amino Acid Sequence↗

PubMed1998

Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme.

The substitution of methionines with leucines within the interior of a protein is expected to increase stability both because of a more favorable solvent transfer term as well as the reduced entropic cost of holding a leucine side chain in a defined position. Together, these two terms are expected to contribute about 1.4 kcal/mol to protein stability for each Met --> Leu substitution when fully buried. At the same time, this expected beneficial effect may be offset by steric factors due to differences in the shape of leucine and methionine. To investigate the interplay between these factors, all methionines in T4 lysozyme except at the amino-terminus were individually replaced with leucine. Of these mutants, M106L and M120L have stabilities 0.5 kcal/mol higher than wild-type T4 lysozyme, while M6L is significantly destabilized (-2.8 kcal/mol). M102L, described previously, is also destabilized (-0.9 kcal/mol). Based on this limited sample it appears that methionine-to-leucine substitutions can increase protein stability but only in a situation where the methionine side chain is fully or partially buried, yet allows the introduction of the leucine without concomitant steric interference. The variants, together with methionine-to-lysine substitutions at the same sites, follow the general pattern that substitutions at rigid, internal sites tend to be most destabilizing, whereas replacements at more solvent-exposed sites are better tolerated.

Bacteriophage T4↗