Large systematic errors compromise quantitation of intrinsically unstructured proteins.
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Colorimetry↗
Biomedical subjects
P Tompa
Publications and source records attributed to P Tompa.
Protein-water and protein-buffer interactions in the aqueous solution of an intrinsically unstructured plant dehydrin: NMR intensity and DSC aspects.
Proton NMR intensity and differential scanning calorimetry measurements were carried out on an intrinsically unstructured late embryogenesis abundant protein, ERD10, the globular BSA, and various buffer solutions to characterize water and ion binding of proteins by this novel combination of experimental approaches. By quantifying the number of hydration water molecules, the results demonstrate the interaction between the protein and NaCl and between buffer and NaCl on a microscopic level. The findings overall provide direct evidence that the intrinsically unstructured ERD10 not only has a high hydration capacity but can also bind a large amount of charged solute ions. In accord, the dehydration stress function of this protein probably results from its simultaneous action of retaining water in the drying cells and preventing an adverse increase in ionic strength, thus countering deleterious effects such as protein denaturation.
Arabidopsis Proteins↗
The phosphorylation state of threonine-220, a uniquely phosphatase-sensitive protein kinase A site in microtubule-associated protein MAP2c, regulates microtubule binding and stability.
Phosphorylation of microtubule-associated protein 2 (MAP2) has a profound effect on microtubule stability and organization. In this work a consensus protein kinase A (PKA) phosphorylation site, T(220), of juvenile MAP2c is characterized. As confirmed by mass spectrometry, this site can be phosphorylated by PKA but shows less than average reactivity among the 3.5 +/- 0.5 phosphate residues incorporated into the protein. In contrast, T(220) is uniquely sensitive to dephosphorylation: three major Ser/Thr protein phosphatases, in the order of efficiency PP2B > PP2A(c) > PP1(c), remove this phosphate group first. MAP2c specifically dephosphorylated at this site binds and stabilizes microtubules stronger than either fully phosphorylated or nonphosphorylated MAP2c. Phosphorylation of this site also affects proteolytic sensitivity of MAP2c, which might represent a further level of control in this system. Thus, the phosphorylation state of T(220) may be a primary determinant of microtubule function.
Amino Acid Sequence↗
Prion protein: evolution caught en route.
The prion protein displays a unique structural ambiguity in that it can adopt multiple stable conformations under physiological conditions. In our view, this puzzling feature resulted from a sudden environmental change in evolution when the prion, previously an integral membrane protein, got expelled into the extracellular space. Analysis of known vertebrate prions unveils a primordial transmembrane protein encrypted in their sequence, underlying this relocalization hypothesis. Apparently, the time elapsed since this event was insufficient to create a "minimally frustrated" sequence in the new milieu, probably due to the functional constraints set by the importance of the very flexibility that was created in the relocalization. This scenario may explain why, in a structural sense, the prion protein is still en route toward becoming a foldable globular protein.
Evolution, Molecular↗
Domain III of calpain is a ca2+-regulated phospholipid-binding domain.
The X-ray structure of m-calpain shows that domain III of the large subunit is structurally related to C2 domains, Ca2+-regulated lipid binding modules in many enzymes. To address whether this structural similarity entails functional analogy, we have characterized recombinant domain III from rat micro- and m-calpain and Drosophila CALPB. In a Ca2+ overlay assay domain III displays a large capacity for Ca2+ binding, commensurable with that of domain IV, the principal Ca2+-binding domain of calpains. The amount of Ca2+ bound to domain III increases 2- to 10-fold upon the addition of liposomes containing 20-40% di- and triphosphoinositides. Conversely, phospholipid-binding in spin-column size-exclusion chromatography is significantly promoted by Ca2+, in a manner similar to known C2 domains. These results suggest that domain III might be the primary lipid binding site of calpain and may play a decisive role in orchestrating Ca2+- and lipid activation of the enzyme.
Amino Acid Sequence↗
Frequency decoding of fast calcium oscillations by calpain.
We report the development of a novel procedure for generating fast, high-frequency Ca2+ oscillations in vitro and the frequency-dependent activation of m-calpain, the Ca2+-activated intracellular cysteine protease. The procedure is based upon liberating Ca2+ from a cage, DM-Nitrophen, by repetitive UV laser pulses and its concomitant binding by a 'slow' chelator, 1,4,7,10-tetraazacyclododecane-N,N',N",N"'-tetraacetate (DOTA). It is shown that a full control over the pattern of oscillations can be readily achieved because the half-life of individual spikes is determined by DOTA concentration and pH, whereas peak amplitude can be adjusted by light intensity. Frequency is only limited by the physical parameters of the light source. The sensitivity of calpain activation to the frequency of Ca2+ oscillations was monitored by the cleavage of microtubule-associated protein 2, a very sensitive physiological substrate of the enzyme. One hundred transients at a peak Ca2+ concentration of 10 microM were presented at various pH values and frequencies ranging from 1 to 50 Hz. At pH 6.0 and 7.0 significant activation occurred at high frequencies (20 and 50 Hz), but here Ca2+ accumulated due to the overlap of transients; at low frequencies (1 and 3 Hz) where Ca2+ accumulation was negligible, there was no calpain activation. At pH 8.0, where individual transients do not overlap even at 50 Hz, frequency-dependence of activation is seen when calpain is sensitized to Ca2+ by autolysis and by the addition of a phospholipid, phosphatidylinositol-4,5-bisphosphate. Our results show that calpain is sensitive to the frequency of fast Ca2+ oscillations in vitro, which is of potential physiological significance.
Calcium↗
Inhibitory effect of a brain derived peptide preparation on the Ca++-dependent protease, calpain.
Overactivated calpain might be a key factor in destruction of cytoskeletal proteins involved in the pathophysiology of ischemia and disorders like Alzheimer's disease. Therapeutic effects imply the possible interference of Cerebrolysin (Ebewe Arzneimittel, Austria) with these molecular events. In this work several in vitro methods have been applied to investigate the interaction between Cerebrolysin and calpain [Enzyme Commission (EC) number: 3.4.22.17]. A conventional caseinolytic assay beside two flourimetric assays using a synthetic peptide substrate and a fluorescence labelled cytoskeletal protein [microtubule-associated protein 2 labelled with 5-([4,6-dichlorotriazin-2-yl]amino) fluorescein (MAP2-DTAF)] respectively for a highly sensitive fluorimetric calpain activity assay were applied for kinetic analysis. The caseinolytic assay showed that the drug inhibits both mu- and m-calpain and to a significantly lower extent also trypsin [Enzyme Commission (EC) number: 3.4.21.1] and papain [Enzyme commission (EC) number: 3.4.22.6]. Dialysis experiments revealed Cerebrolysin mediated calpain inhibition to be reversible. Kinetic analysis exhibited a non-competitive, or tight-binding competitive, mode of inhibition. This latter mode, substantiated by serial dilution experiments, and the likely existence of calpastatin in a brain derivative suggests the occurrence of calpastatin fragments or calpastatin-like fragments in Cerebrolysin. The clearly competitive inhibition of trypsin by the drug indicates distinct mechanisms and active components against different proteases.
Amino Acids↗
Kinetic analysis of human mu-calpain autolysis.
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Autolysis↗
A sensitive and continuous fluorometric activity assay using a natural substrate. Microtubule-associated protein 2.
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Animals↗
Synaptic metaplasticity and the local charge effect in postsynaptic densities.
Synaptic plasticity might be one of the elementary processes that underlies higher brain functions, such as learning and memory. Intriguingly, the capacity of a synapse for plastic changes itself displays marked variation or plasticity. This higher-order plasticity, or metaplasticity, appears to depend on the same macromolecules as plasticity, most notably the NMDA receptor and Ca2+/calmodulin kinase II; yet we do not understand metaplasticity in molecular terms. Metaplasticity has a feedback-inhibition character that confers stability to synaptic patterns, whereas in plasticity, the molecular events implicated tend to have an opposite effect. As a resolution to this difference, we suggest that metaplasticity be considered in a biophysical context. It has been shown that autophosphorylation of Ca2+/calmodulin kinase II in postsynaptic densities generates changes in the local electrostatic potential sufficient to affect the direction of synaptic plasticity. We propose that this finding could help explain both the puzzling abundance of Ca2+/calmodulin kinase II in the postsynaptic density and the metaplasticity of synaptic transmission.
Calcium-Calmodulin-Dependent Protein Kinase Type 2↗
Prion proteins as memory molecules: an hypothesis.
Prions are infectious agents widely implicated in a variety of mammalian neurodegenerative diseases generally referred to as transmissible spongiform encephalopathies. Their infectivity is primarily associated with an aberrant conformation of a host-encoded protein, the prion protein, induced by the prion itself in an autocatalytic reaction. The physiological function of this protein is not known. In this paper we suggest that alternative conformations of the prion protein, other than its pathological scrapie state, exist and that the self-sustaining autocatalytic propagation of these states underlies its normal cellular function. In kinetic model calculations we show that the prion protein may constitute a bi-stable molecular switch that can structurally encode and stably store information. A number of cases of prion involvement in normal cellular function and ample molecular detail of pathological prion propagation are cited and correlated to substantiate the implications of this tenet. Our contention is that the prion hypothesis should be extended to a wide variety of physiological processes. We propose that prion proteins are stable determinants of phenotype, operating in diverse functions possibly including memory.
Animals↗
The calpain cascade. Mu-calpain activates m-calpain.
m-Calpain, which usually requires near-millimolar Ca2+ for activation, undergoes autolysis at 25 microM Ca2+ in the presence of mu-calpain. m-Calpain in itself exhibits no sign of autolysis around this Ca2+ concentration. Half-maximal rate of the reaction occurs at 30 microM Ca2+, showing that it is mu-calpain that catalyzes the limited proteolysis of m-calpain in an intermolecular reaction ("heterolysis"). This heterolytic step is accompanied by the activation of m-calpain: mu- and m-calpain preincubated together at 25 microM Ca2+ show significantly higher activity than the sum of activities of mu- and m-calpains preincubated separately. m-Calpain is sensitized to Ca2+ by mu-calpain-mediated activation: the half-maximal value of 160 microM for activation is lowered to 64 microM, which is similar to the shift found in m-calpain autoactivation. We suggest that these in vitro observations are relevant in vivo and the calpain cascade may play an important role in coordinating the functioning of calpains in living cells.
Animals↗
Phosphorylation and dephosphorylation in the proline-rich C-terminal domain of microtubule-associated protein 2.
The C-terminal domain of microtubule-associated protein 2 (MAP2) contains a proline-rich region and the tubulin-binding domain. We have generated antibodies to follow the phosphorylation state of the proline-rich domain. One of these antibodies (no. 305) has been raised against a synthetic peptide P (sequence RTPGTPGTPSY) phosphorylated at the threonine residues. This sequence is present in the proline-rich region of MAP2 and is phosphorylated in vitro by at least three different proline-directed protein kinases: p42mpk, p34cdc2, and GSK3 (glycogen-synthase kinase 3) alpha/beta. The MAP2 sites phosphorylated by these kinases are different, although all of them phosphorylate the C-terminal domain of MAP2 as determined by Staphylococcus aureus V8 protease mapping. Nonphosphorylated peptide P can be phosphorylated in vitro by all three kinases studied with similar efficiency. In high-molecular-mass MAP2, this sequence is highly phosphorylated in vivo at the late stages of rat development. This motif can be rapidly dephosphorylated in vitro by protein-phosphatase 1 (PP1) and 2A (PP2A) catalytic subunits but not by PP2B.
Animals↗
Autolysis parallels activation of mu-calpain.
The kinetics of autolysis and activation of mu-calpain were measured with microtubule-associated protein 2 (MAP2) as a very sensitive substrate. The initial rate of MAP2 hydrolysis was found to be a linear function of the autolysed 76 kDa form of mu-calpain large subunit at both 10 and 300 microM Ca2+, and both straight lines intersected the origin. This finding supports the view that native mu-calpain is an inactive proenzyme and that activation is accompanied by autolysis. The first-order rate constant of autolysis, K1(aut), was determined at different Ca2+ concentrations: the half-maximal value was at pCa2+ = 3.7 (197 microM Ca2+), whereas the maximal value was 1.52 s-1, at 30 degrees C. The Ca(2+)-induced activation process was then monitored by using our novel, continuous fluorimetric assay with labelled MAP2 as substrate. The first-order rate constant of activation, k1(act), was derived as the reciprocal of the lag phase ('transit time') at the initial part of the progress curve: half-maximum was at pCa2+ = 3.8 (158 microM Ca2+) and the maximum value was 2.15 s-1. The good agreement between the kinetic parameters of mu-calpain autolysis and activation is remarkable. We claim that this is the first kinetically correct determination of the rate constant of autolysis of mu-calpain. Pre-activated mu-calpain has a Ca2+ requirement that is almost three orders of magnitude smaller [half-maximal activation at pCa2+ = 6.22 (0.6 microM Ca2+)]. We cannot exclude the possibility that the activation process involves other mechanistic steps, e.g. the rapid dissociation of the mu-calpain heterodimer, but we state that in our conditions in vitro autolysis and activation run in close parallel.
Autolysis↗
Mutual protection of microtubule-associated protein 2 (MAP2) and cyclic AMP-dependent protein kinase II against mu-calpain.
Phosphorylation by adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA), but not by Ca(++)-calmodulin-dependent protein kinase II (CaMK II), was shown earlier to protect microtubule-associated protein 2 (MAP2) from cleavage by m-calpain (Johnson and Foley: J Neurosci Res 34: 642-647, 1993). We reinvestigated this phenomenon with the physiologically more relevant mu-calpain and found a qualitatively similar but quantitatively different picture. We further demonstrate that 1) protection is biphasically dependent on the degree of phosphorylation; 2) Ca(++)-phospholipid-dependent protein kinase (PKC) has about the same effect as PKA; 3) the effects of kinases A and C are not additive; and 4) stripping of native MAP2 from its phosphate content (17.8 +/- 2.3 mol/mol) enhances calpainolysis 3.6-fold. A reciprocal effect between kinase A and MAP2 was found: the RII, but not the RI, regulatory subunit of kinase A, which was shown to bind specifically to MAP2, is protected by MAP2 from mu-calpain attack. It is suggested that the specific anchoring of kinase A-II on MAP2 may serve not only kinase targeting in the dendrites, but also protection from calpainolytic degradation.
Animals↗
An ultrasensitive, continuous fluorometric assay for calpain activity.
A rapid, continuous assay for calcium-activated neutral protease activity is described. This assay is based on monitoring the elevation in fluorescence intensity that occurs upon calpainolytic digestion of dichlorotriazinylamino-fluorescein-labeled microtubule-associated protein 2. Tedious separation of peptide products from the protein substrate in this rapid assay is unnecessary, which thus offers two remarkable advantages over conventional caseinolytic assay procedures: (i) it raises sensitivity of detection by about three orders of magnitude, allowing the quantitative determination of calpain in the high picogram range in 10 min; and (ii) it permits a continuous detection of activity, which may prove invaluable in enzyme-mechanism studies that require pre-steady-state measurements. Other features and advantages of the assay, along with its limitations, are discussed in detail.
Animals↗
Interaction of rabbit muscle enolase and 3-phosphoglycerate mutase studied by ELISA and by batch gel filtration.
The interaction of rabbit skeletal muscle enolase and 3-phosphoglycerate mutase was detected by an ELISA test, a batch gel-filtration technique, and fluorescence anisotropy measurements, and the activity of enolase was determined to be a function of mutase concentration. The apparent dissociation constant of this enzyme complex is approximately 1 microM. This value seems to be independent of the presence (in fluorescence anisotropy measurements) or the absence (in activity as well as in ELISA experiments) of fluorescein isothiocyanate used widely as a label for determining the complex formation between enzymes in fluorescence anisotropy measurements.
Animals↗
A possible in vivo mechanism of intermediate transfer by glycolytic enzyme complexes: steady state fluorescence anisotropy analysis of an enzyme complex formation.
Rate constants of dissociation (k(off)) and association (k(on)) of the bienzyme complex yeast glyceraldehyde-3-phosphate dehydrogenase--yeast alcohol dehydrogenase have been determined in the absence and presence of NAD or NADH by fluorescence anisotropy measurements. We found that dissociation of the complex is considerably slower than catalytic turnover of either of the enzymes (that is k(off) much less than kcat) irrespective of the presence of coenzymes. A perusal of the literature reveals that this relation invariably applies to all systems studied so far. These observations all taken together constitute compelling evidence that direct metabolite transfer in enzyme complexes cannot be satisfactorily described by invoking the dynamic model but requires a model assuming more lasting complexes. This seems to support the case of the temporary-stationary model suggested by one of us. Implications of this conclusion are treated in depth and further evidence is cited under Discussion.
Alcohol Dehydrogenase↗