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PubMed1993

[Effects of ethanol on Gi protein function in rat cerebral cortex of Wistar and Fischer 344 rats: evaluation by low pH treatment].

The present study was designed to provide further information regarding the effect of ethanol on the function of inhibitory GTP-binding (Gi) protein. To eliminate the Gs function in the regulation of adenylyl cyclase, cerebral cortex membranes from Wistar or Fischer 344 rats were pretreated at pH 4.5 ("low pH"), whereupon Gpp(NH)p-dependent inhibition of forskolin-stimulated adenylyl cyclase was examined. In the membranes from Wistar rats, ethanol (100 or 250 mM) resulted in left-shifted Gpp(NH)p inhibition curves and reduced IC50 values for Gpp(NH)p in an ethanol dose-dependent manner. In contrast, ethanol exhibited no effect on the Gpp(NH)p-dependent inhibition of the enzyme or on IC50 values for Gpp(NH)p in the membranes from Fischer 344 rats. These results are consistent with the idea that ethanol, in vitro, enhances the Gi function in the cerebral cortex of Wistar rats, and that ethanol's effect on Gi protein in the cerebral cortex is different in Wistar and Fischer 344 rats.

Animals↗

PubMed1996

Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5.

Transcriptional adaptor proteins are required for full function of higher eukaryotic acidic activators in the yeast Saccharomyces cerevisiae, suggesting that this pathway of activation is evolutionarily conserved. Consistent with this view, we have identified possible human homologs of yeast ADA2 (yADA2) and yeast GCN5 (yGCN5), components of a putative adaptor complex. While there is overall sequence similarity between the yeast and human proteins, perhaps more significant is conservation of key sequence features with other known adaptors. We show several functional similarities between the human and yeast adaptors. First, as shown for yADA2 and yGCN5, human ADA2 (hADA2) and human GCN5 (hGCN5) interacted in vivo in a yeast two-hybrid assay. Moreover, hGCN5 interacted with yADA2 in this assay, suggesting that the human proteins form similar complexes. Second, both yADA2 and hADA2 contain cryptic activation domains. Third, hGCN5 and yGCN5 had similar stabilizing effects on yADA2 in vivo. Furthermore, the region of yADA2 that interacted with yGCN5 mapped to the amino terminus of yADA2, which is highly conserved in hADA2. Most striking, is the behavior of the human proteins in human cells. First, GAL4-hADA2 activated transcription in HeLa cells, and second, either hADA2 or hGCN5 augmented GAL4-VP16 activation. These data indicated that the human proteins correspond to functional homologs of the yeast adaptors, suggesting that these cofactors play a key role in transcriptional activation.

Adaptor Proteins, Signal Transducing↗

PubMed1989

The role of oligosaccharides in modifying protein function.

It has been proposed that protein-bound oligosaccharides interact with the protein to which they are attached to up- or down-regulate the bioactivity of the 'composite' glycoprotein. Oligosaccharide analyses of the glycoproteins Thy-1, tissue plasminogen activator and immunoglobulin G are presented. Correlations between particular glycoforms and enzymic activities are demonstrated for tissue plasminogen activator. The change in the prevalence of particular immunoglobulin G glycoforms is shown to correlate with disease activity in rheumatoid activity.

Animals↗

PubMed1986

Pharmacological modulation of cardiac and vascular contractile protein function.

The Ca2+-dependent regulation of contractile protein interactions in cardiac and vascular smooth muscle involves structurally related but distinct Ca2+ binding proteins. In vascular smooth muscle, Ca2+ binds to calmodulin, and Ca2+-calmodulin activates myosin light chain (MLC) kinase with ultimate stimulation of MLC phosphorylation and actin-myosin interactions. The largest class of inhibitors of vascular contractile protein interactions are the calmodulin antagonists which include certain Ca2+ entry blockers. Pharmacologically, some of these agents can be distinguished from pure Ca2+ entry blockers by being more effective vs. vasoconstrictor agents in vitro, less cardiac depressant, and more effective as platelet aggregation inhibitors. An even greater distinction from Ca2+ entry blockers is evident with another series of agents, isoquinolinesulfonamides, which directly inhibit protein kinase activity. Cardiac muscle myofibrillar regulation involves Ca2+ binding to troponin C (TnC). Some cardiotonics, such as Vardax and APP 201-533, increase the Ca2+ sensitivity of cardiac myofibrillar ATPase activity with a concomitant increase in Ca2+ binding to TnC. Several calmodulin antagonists, Ca2+ blockers, and structurally related agents differentially affect cardiac myofibrillar ATPase activity. Potency and efficacy of some of these stimulating agents is markedly greater than Vardax or APP 201-533. Mechanistically, all agents do not affect cardiac MLC phosphorylation, but directly enhance the Ca2+ sensitivity of ATPase activity. However, differential effects on basal and maximum ATPase activity by some agents suggest more complex or additional effects which are related to the type of agent as well as the species (dog vs. hamster). A major subcellular defect in congestive heart failure in various small animal models is a depressed maximum ATPase activity. Thus, a desired goal would be a pharmacological modulator which increases maximum ATPase activity, not necessarily Ca2+ sensitivity. In sum, it is possible to identify agents, Ca2+ binding protein modulators, which directly inhibit vascular smooth muscle and stimulate cardiac muscle contractile protein interactions. The potential advantages/disadvantages of this approach for vasodilator/cardiotonic drug development will have to await future development of novel compounds targeted specifically for these cellular regulatory processes.

Animals↗

PubMed2025

Properties Governing Native State Entanglements and Relationships to Protein Function.

Non-covalent lasso entanglements are structural motifs found in a majority of globular proteins, and their misfolding has been linked to a range of biological consequences. Here, we characterize these motifs' structural and physicochemical properties, sequence biases, functional site correlations, and universal features across E. coli, S. cerevisiae, and H. sapiens. We find that the crossing residues, which pierce the plane of the entanglement loop, are 11-times more likely to be a β-strand than an α-helix or random coil, and that around this position the protein sequence is 2.5-times more likely to be composed of a stretch of all hydrophobic residues (most often Val, Ile, or Phe) compared to other sequence motifs. Functionally, crossing residues are enriched at enzyme active sites in S. cerevisiae and small molecule binding residues across all species to degrees greater than expected by random chance. Metal binding residues are enriched in these entanglements in H. sapiens. Increasing statistical power by pooling together these species data, we find RNA-binding residues are enriched in these entanglement components. On the other hand, there is a spatial depletion of crossing residues at sites involved in protein binding. Using machine learning, we identified eight robust features predictive of these entanglements, achieving AUROC scores of 0.8 across species. These results are significant because they suggest a direct role for components of native entanglements in particular protein functions, as well as identifying strong secondary structure and sequence preferences in native entanglements.

Humans↗

PubMed1993

SAC1p is an integral membrane protein that influences the cellular requirement for phospholipid transfer protein function and inositol in yeast.

Mutations in the SAC1 gene exhibit allele-specific genetic interactions with yeast actin structural gene defects and effect a bypass of the cellular requirement for the yeast phosphatidylinositol/phosphatidylcholine transfer protein (SEC14p), a protein whose function is essential for sustained Golgi secretory function. We report that SAC1p is an integral membrane protein that localizes to the yeast Golgi complex and to the yeast ER, but does not exhibit a detectable association with the bulk of the yeast F-actin cytoskeleton. The data also indicate that the profound in vivo effects on Golgi secretory function and the organization of the actin cytoskeleton observed in sac1 mutants result from loss of SAC1p function. This cosuppression of actin and SEC14p defects is a unique feature of sac1 alleles as mutations in other SAC genes that result in a suppression of actin defects do not result in phenotypic suppression of SEC14p defects. Finally, we report that sac1 mutants also exhibit a specific inositol auxotrophy that is not exhibited by the other sac mutant strains. This sac1-associated inositol auxotrophy is not manifested by measurable defects in de novo inositol biosynthesis, nor is it the result of some obvious defect in the ability of sac1 mutants to utilize inositol for phosphatidylinositol biosynthesis. Thus, sac1 mutants represent a novel class of inositol auxotroph in that these mutants appear to require elevated levels of inositol for growth. On the basis of the collective data, we suggest that SAC1p dysfunction exerts its pleiotropic effects on yeast Golgi function, the organization of the actin cytoskeleton, and the cellular requirement for inositol, through altered metabolism of inositol glycerophospholipids.

Actins↗

PubMed1988

Egg-white and blood-serum proteins functioning by noncovalent interactions: studies by chemical modification and comparative biochemistry.

Some of the more interesting and important proteins are those that function by forming associations or complexes with other substances. The structure-function relationships of three of these with very different substances are transferrins, which chelate metal ions; avian ovomucoids, which form complexes with proteolytic enzymes; and antifreeze glycoproteins, which interact at the ice-solution interface. Interrelating studies on the comparative biochemistry with studies using chemical modification have helped identify the side-chain groups of the proteins involved in function as well as to be useful for studies on general protein chemistry. The most strongly associated interaction is the chelation of iron by transferrin, with an association constant of approximately 10(21); tyrosines, histidines, and sometimes aspartate are involved. For ovomucoids, individual substratelike residues such as lysine are involved in a Michaelis-like complex, and association constants are as high as 10(10). By contrast, the antifreeze glycoproteins appear to function by a polymeric interaction at the surface of ice, with a much weaker association.

Amino Acid Sequence↗

PubMed1984

Prediction of protein function from sequence properties. Discriminant analysis of a data base.

The protein superfamilies in the National Biomedical Research Foundation sequence data base cluster into six groups that can be distinguished on the basis of four variables characterizing amino acid composition and local sequence properties. The variables are average hydrophobicity, net charge, sequence length and periodic variation in hydrophobic residues along the chain. The clusters they distinguish are: globins; chromosomal proteins; contractile system proteins and respiratory proteins other than cytochromes; enzyme inhibitors and toxins; enzymes except hydrolases; and all other proteins. The overall probability of correctly allocating a given protein to one of these functional groups is 0.76, with the allocation reliability being highest for globins (0.97) and for chromosomal proteins (0.93).

Amino Acid Sequence↗

PubMed1993

Heat shock proteins functioning as molecular chaperones: their roles in normal and stressed cells.

In response to either elevated temperatures or several other metabolic insults, cells from all organisms respond by increasing the expression of so-called heat shock proteins (hsp or stress proteins). In general, the stress response appears to represent a universal cellular defence mechanism. The increased expression and accumulation of the stress proteins provides the cell with an added degree of protection. Studies over the past few years have revealed a role for some of the stress proteins as being intimately involved in protein maturation. Members of the hsp 70 family, distributed throughout various intracellular compartments, interact transiently with other proteins undergoing synthesis, translocation, or higher ordered assembly. Although not yet proven, it has been suggested that members of the hsp 70 family function to slow down or retard the premature folding of proteins in the course of synthesis and translocation. Yet another family of stress proteins, the hsp 60 or GroEL proteins (chaperonins), appear to function as catalysts of protein folding. Here I discuss the role of those stress proteins functioning as molecular chaperones, both within the normal cell and in the cell subjected to metabolic stress.

Animals↗

PubMed1994

Signal transduction during cannibalistic sexual phagocytosis: calcium is not the trigger but GTP-binding protein function is essential.

After fertilization, the zygote giant cell of Dictyostelium discoideum chemoattracts and subsequently engulfs hundreds of amoebae of the same species and strains from which it was derived. A pharmacological approach indicates that, while it may have some role, calcium is not the trigger for this cannibalistic phagocytic process. Of several agents that perturb intracellular calcium levels [A23187, LaCl, 8-diethylamino-octyl-3,4,5-trimethoxylbenzoate (TMB-8), and chlorotetracycline], only A23187 had an effect in reducing amoebal ingestion. In keeping with this, agents which interfered with downstream effectors of calcium function did not alter sexual phagocytosis. Calmidazolium and trifluoperazine, which inhibit calmodulin function, were ineffective, as were a protein kinase C inhibitor (staurosporine) and activator (phorbol 12-myristate 13-acetate). On the other hand, the nucleotide analogues GTP gamma S and GDP beta S both inhibited sexual phagocytosis indicating a role for GTP-binding protein activity at some stage in the process. Sub-fractionation of cells from non-phagocytic and phagocytic stage cell cultures followed by immunolocalization after SDS-PAGE and western blotting revealed a number of GTP-binding proteins in both the cell membrane and intracellular membrane fractions that might function during the events of sexual phagocytosis.

Animals↗

PubMed1984

The first exon of region E1a genes of adenoviruses 5 and 12 encodes a separate functional protein domain.

The transforming E1 regions of human adenoviruses Ad5 and Ad12 differ from each other in the frequency by which they can transform primary baby rat kidney cells, and in their ability to modulate expression of class I major histocompatibility (MHC) genes. We have investigated whether these two properties, which are determined by region E1a, can be assigned to one of the two protein segments encoded by the E1a exons. To that end, we have constructed chimaeric E1a regions, in which the 5' E1a exon of Ad5 was linked to the 3' E1a exon of Ad12, and vice versa. It was found that, although there is only a limited degree of homology between Ad5 and Ad12 E1a (approximately 40% at the protein level), the hybrid E1a products are functional in transformation. Furthermore, both the frequency of transformation and the modulation of class I MHC gene expression appeared to be determined by the first E1a exon. These results indicate that the first E1a exon encodes a separate functional domain in the E1a proteins.

Adenoviruses, Human↗

PubMed1990

Diagnosis of protein C deficiency in patients on oral anticoagulant treatment: comparison of three different functional protein C assays.

The efficacy of three different protein C activity assays and of protein C antigen determination for the diagnosis of protein C deficiency was studied in 13 protein C deficient patients (11 with type I, 2 with type II deficiency) and in 51 presumably non-deficient patients (control group), both groups being on oral anticoagulant (OAC) treatment. For protein C activity measurement (1) the assay according to Francis (slightly modified) with thrombin activation and measurement of activated protein C in the aPTT system, (2) an assay using Protac activation and chromogenic substrate (Protac-CS) and (3) an assay using Protac activation and the aPTT system (Protac-PTT) were used. Protein C antigen was determined by Laurell immunoelectrophoresis. The three activity assays gave different results, with the highest values obtained by the Protac-CS assay and the lowest values by the Protac-PTT assay. The Francis assay gave intermediate results. Protein C activity and antigen values were significantly lower in protein C deficient patients compared to the control group. Protein C activity tests had a higher discriminative power than the antigen determination. After taking into account the intensity of treatment, by the Francis assay all deficient and non-deficient patients were correctly classified, by the Protac-CS and the Protac-PTT assay 2 and 4 patients, respectively, were misclassified and by the antigen assay 8 patients were misclassified. Calculation of the ratios of protein C activity to factor II activity was of high discriminative power. We conclude that for diagnosis of protein C deficiency protein C activity tests are superior to antigen determination not only in type II but also in type I deficient patients.(ABSTRACT TRUNCATED AT 250 WORDS)

4-Hydroxycoumarins↗

PubMed1993

Presence of serum antibodies to coagulation protein C in patients with systemic lupus erythematosus is not associated with antigenic or functional protein C deficiencies.

Antibodies directed to immunopurified coagulation protein C (PC) were investigated in serum samples from 108 patients with systemic lupus erythematosus (SLE) and found in 12 of them. However, their presence was not associated with antigenic or functional deficiencies of PC, which were documented in 6 and 17 patients, respectively.

Antibodies↗

PubMed1986

Protons, osmolytes, and fitness of internal milieu for protein function.

The composition of the intracellular milieu shows striking similarities among widely different species. Only certain values of intracellular pH, values that generally reflect alphastat regulation, and only narrow ranges of inorganic ion concentrations are found in the cytoplasm of the cells of most animals, plants, and microorganisms. In water-stressed organisms only a few types of low-molecular-weight organic molecules (osmolytes) are accumulated. These highly conserved characteristics of the intracellular fluids reflect the need to maintain critical features of macromolecules within narrow ranges optimal for life. For proteins these features include maintaining adequate rates of catalysis, a high level of regulatory responsiveness, and a precise balance between stability and lability of structure (tertiary conformation, subunit assembly, and multiprotein complexes). The optimal values for these functional and structural features of proteins often lie near the midrange of possible values for these properties, and only under specific conditions of intracellular pH, ionic strength, and osmolyte composition are these optimal midrange values conserved. In dormant cells the departure of solution conditions from values that are optimal for protein function and structure may be instrumental in reducing or shutting down metabolic functions. Seen from a broad evolutionary perspective, the evolution of the intracellular milieu is an important complement to macromolecular evolution. In certain instances appropriate modifications of the internal milieu may reduce the need for adaptive amino acid replacements in proteins.

Acid-Base Equilibrium↗

PubMed1993

Regulation of G protein function by an effector in GTP-dependent signal transduction. An inhibitory subunit of cGMP phosphodiesterase inhibits GTP hydrolysis by transducin in vertebrate rod photoreceptors.

The regulation of cGMP phosphodiesterase in vertebrate rod photoreceptors is a typical G protein-dependent signal transduction mechanism. The interaction of P gamma, an inhibitory subunit of cGMP phosphodiesterase, with transducin alpha subunit (T alpha) is essential for the activation of cGMP phosphodiesterase. It has been shown that, in a homogenized preparation of frog (Rana catesbeiana) rods, P gamma interacts with GTP.T alpha and remains tightly bound to GDP.T alpha after GTP hydrolysis on T alpha. Association of this complex with beta gamma subunits of transducin (T beta gamma) triggers the release of P gamma from the complex and the subsequent inactivation of cGMP phosphodiesterase. In a system reconstituted with purified components, both GTP- and GDP-bound forms of T alpha were found to interact with P gamma. Under these conditions, P gamma inhibited GTP hydrolysis by transducin in a noncompetitive manner with a Ki of 92 nM. Binding of an hydrolysis-resistant GTP analog to T alpha was also inhibited by P gamma. These inhibitions of transducin function were resulted from the inhibition of both hydrolysis of GTP bound to T alpha and interaction of GDP.T alpha with membrane-bound T beta gamma. However, after GDP.T alpha reassociated with membrane-bound T beta gamma, the inhibitory effect of P gamma on the binding of an hydrolysis-resistant GTP analog to T alpha was greatly diminished, suggesting that the GTP/GDP exchange on T alpha was not inhibited by P gamma. These data indicate that the T alpha function is altered during complexing with P gamma. G protein functions may be modified by interacting with an effector in the G protein-dependent signal transduction.

3',5'-Cyclic-GMP Phosphodiesterases↗

PubMed1979

Purification of cytoplasmic tubulin and microtubule organizing center proteins functioning in microtubule initiation from the alga Polytomella.

Cytoplasmic tubulin and the microtubule organizing centers (MTOCs) for the cytoskeletal microtubule system of the flagellate Polytomella have been isolated. The isolated MTOCs serve as sites for the in vitro assembly of the purified tubulin protein. The major proteins (four polypeptides of molecular weights 190,000-210,000) functioning in this assembly have been extracted from the MTOCs and purified. Kinetic studies and experiments with in vivo 35S-labeled MTOC proteins (or 35S-labeled tubulin) demonstrate that these proteins function specifically in microtubule initiation and do not contribute to microtubule elongation. The results indicate that microtubule assembly in vivo is controlled by microtubule initiating proteins associated with the organelles termed MTOCs.

Carrier Proteins↗

PubMed1994

Microtubule-associated protein function: lessons from expression in Spodoptera frugiperda cells.

The phenotypes induced by the expression of neuronal microtubule-associated proteins (MAPs) in Sf9 cells have provided data on the in situ function of these proteins. Both MAP2 and tau can induce long processes in Sf9 cells, and the processes contain bundles of microtubules. In both cases the microtubules are aligned with their plus ends distal. Tau expression usually induces a single process that is unbranched and of uniform caliber. Processes can form even when the cells are grown in suspension. Microtubules do not extend all the way to the tip; instead the terminal region contains an actin-rich meshwork. Taxol treatment of Sf9 cells also induces the assembly of microtubules into bundles but does not induce process formation in Sf9 cells. Therefore the in vitro properties of tau as a molecule capable of assembling, stabilizing, and bundling microtubules do not fully account for the in vivo ability of tau alone to transduce microtubule assembly into a change in cell shape. The morphological features of the processes induced by MAP2 differ in highly informative ways.

Animals↗

PubMed1995

Ligand-induced changes in the conformational stability of bovine trypsinogen and their implications for the protein function.

Bovine trypsinogen was used as a model protein for studying changes in the conformational stability induced by pH or binding of the calcium ion. Spectrophotometrically monitored thermal unfolding of trypsinogen and beta-trypsin in the acidic pH range yielded substantial differences in the stability parameters. Compared to beta-trypsin, trypsinogen exhibits lower enthalpy of denaturation delta Hden, higher denaturational heat capacity change delta Cp,den, but very similar temperature of denaturation Tden. pH-dependence of the conformational stability of the ligand-free trypsinogen, measured also by GdnCl-induced unfolding, is bell shaped with the maximum free energy of unfolding delta Gden = 10.9 kcal/mole at pH 5.5 (4.5 pH units below its isoelectric point). At pH 8.3 the conformational stability of the zymogen drops to delta Gden = 3.2 kcal/mole, but increases by delta delta Gden = 6.1 kcal/mole in the presence of Ca2+. This significant stabilization of the zymogen by the calcium ion is also pH-dependent. To assess the effect of Ca2+ on the trypsinogen molecule, the spectrophotometric titrations and NOESY spectra were carried out. Based on the structural analysis, the long range effects between Ca2+-->Ile73-->Trp141 and the interdomain His40-Asp194 ion pair are proposed to be partially responsible for trypsinogen stabilization. Additionally, the steady-state parameters for hydrolysis of the oligopeptide amide substrate catalysed by free trypsinogen, its complexes with Ca2+ and the IleVal dipeptide and by beta-trypsin were measured. It appears that in the pH range 5.5 to 8.3 the stability and the catalytic activity/ligand binding properties are fully separated. Whereas the deprotonation of His57 accounts for the increase of kcat/km parameter, deprotonation of His40 is involved in the huge decrease of the conformational stability. Similarly, a large stabilization by the calcium ion is not accompanied by changes in enzymatic activity. Presented data are encouraging for an enzyme design directed toward improved stability.

Animals↗