Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.31.1 (micrococcal nuclease)
2,818 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Heat capacity, intrinsic viscosity and ellipticity of a number of globular proteins (pancreatic ribonuclease A, staphylococcal nuclease, hen egg-white lysozyme, myoglobin and cytochrome c) and a fibrillar protein (collagen) in various states (native, denatured, with and without disulfide crosslinks or a heme) have been studied experimentally over a broad range of temperatures. It is shown that the partial heat capacity of denatured protein significantly exceeds the heat capacity of native protein, especially in the case of globular proteins, and is close to the value calculated for an extended polypeptide chain from the known heat capacities of individual amino acid residues. The significant residual structure that appears at room temperature in the denatured states of some globular proteins (e.g. myoglobin and lysozyme) at neutral pH results in a slight decrease of the heat capacity, probably due to partial screening of the protein non-polar groups from water. The heat capacity of the unfolded state increases asymptotically, approaching a constant value at about 100 degrees C. The temperature dependence of the heat capacity of the native state, which can be determined over a much shorter range of temperature than that of the denatured state and, correspondingly, is less certain, appears to be linear up to 80 degrees C. Therefore, the denaturational heat capacity increment seems to be temperature-dependent and is likely to decrease to zero at about 140 degrees C.
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PMID:Heat capacity and conformation of proteins in the denatured state. 253 36

The T cell response to a soluble protein requires the processing of the native antigen by an antigen-presenting cell (APC) to a peptide containing an antigenic determinant, which is transported to and bound on the antigen-presenting cell surface, where it is subsequently recognized by the specific T cell in the context of the appropriate Ia molecule. Investigating the response of a pigeon cytochrome c-specific, I-Ek-restricted T cell hybrid, which recognizes a determinant present within a 10-amino acid C-terminal fragment of the protein, it was previously demonstrated that peptides homologous to the peptide from pigeon cytochrome c, but which were not stimulatory, blocked the T cell response to pigeon cytochrome c as processed and presented by APC. In this report the ability of a series of fourteen, 20-amino acid overlapping peptides, representing the entire length of staphylococcal nuclease (Nase), were assessed for their ability to block the response of a pigeon cytochrome c-specific T cell hybrid to antigen-pulsed presenting cells. Only three Nase peptides blocked the I-Ek-restricted pigeon cytochrome c-specific T cell response. Two of these, Nase 61-80 and Nase 91-110, function as T cell antigens in the I-Ad and I-Ab-restricted response to Nase. The third blocking peptide, Nase 101-120, has not been shown to be a T cell antigen. Two other peptides, Nase 51-70 and Nase 81-100, which are recognized by Nase-specific T cells in the context of I-Ek, have no effect on the I-Ek-restricted cytochrome c-specific T cell response. None of these peptides block the higher affinity, heteroclitic response of pigeon cytochrome c-specific T cells to tobacco hornworm moth cytochrome c. Moreover, the response of an I-Ak-restricted T cell to ovalbumin was blocked by the I-Ek-restricted cytochrome c peptides from three different species. Thus, peptides with no obvious primary amino acid sequence homology, and which are not capable of being recognized in the context of the same Ia, compete with one another for the sites on the APC necessary for presentation of processed antigen to T cells. These results suggest that there are structures on the APC surface in addition to Ia, which are necessary for effective antigen presentation following processing. One suitable candidate for such a cell surface material is the recently identified peptide-binding protein, PBP72/74 (Lakey et al., Proc. Natl. Acad. Sci. USA 1987. 84: 1659).
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PMID:T cell activation by processed antigen is equally blocked by I-E and I-A-restricted immunodominant peptides. 350 65

Production of 10-base multiple DNA ladder fragments during DNase I digestion of chromatin is explained by a model which does not involve site-specific nicking by the DNase I. This model was tested because it explains why 10-base (actually 10.4 base) multiple-related fragments are paradoxically generated by both endonucleolytic (DNase I) and exonucleolytic (exonuclease III) mechanisms. This new model also explains the phenomenon of substantial single-stranded DNA production during DNase I digestion of chromatin. The latter phenomenon has been widely observed but is not explained by previous models. The single-stranded gap model to be presented makes testable predictions. Primarily, these are that DNase I produces single-stranded gaps in chromatin DNA and that the termini of 10-base multiple ladder fragments are separated by single-stranded gaps. Single-stranded gap production by DNase I was confirmed by a number of methods. Sensitivity of ladder band components (from DNase I but not staphylococcal nuclease digests) to S1 nuclease suggested that the ladder fragments themselves may compose a significant portion of these gaps. Separation of ladder fragment termini by single-stranded gaps was verified by demonstrating both resistance to the nick-specific NAD+-dependent ligase and sensitivity to T4 ligase which can ligate across gaps. Many single-stranded gaps, occurring both individually and clusters, were observed by electron microscopy using either cytochrome c labeling (where the gaps) are thinner than duplex) or gene 32 protein labeling (gaps thicker than duplex). Gap sizes were estimated by protecting them with gene 32 protein and digesting away unprotected duplexes. By this method, gap sizes fall into a ladder distribution (from 10 or 20 bases up to 120 bases), which, at least in the region of the shorter sizes, clearly indicates the sizes of single-stranded gaps formed in chromatin by DNase I.
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PMID:Deoxyribonuclease I generates single-stranded gaps in chromatin deoxyribonucleic acid. 624 43

Until recently, the energetics of protein-folding intermediates eluded direct measurement by high-sensitivity microcalorimetric techniques. But during the past year, the direct measurement of thermodynamic parameters for folding intermediates of alpha-lactalbumin, apomyoglobin, cytochrome c, and staphylococcal nuclease has provided new insights on the nature of the forces involved in the stabilization of nascent protein structures. In this review, I summarize those results and discuss the structural implications of the observed thermodynamic behavior.
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PMID:Thermodynamics of partly folded intermediates in proteins. 766 12

The induction of contact sensitivity in mice by hapten reagents such as trinitrochlorobenzene (TNCB) involves the activation of class II major histocompatibility complex (MHC)-restricted, hapten-specific, CD4+ T cells. Reports from different laboratories have indicated that the relevant antigenic epitopes in such reactions might include hapten-conjugated, MHC class II-associated peptides. This study for the first time directly demonstrates that hapten-peptides account for the majority of determinants recognized by trinitrophenyl (TNP)-specific CD4+ T lymphocytes. The sequences of those TNP carrier peptides do not have to be related to mouse proteins. Thus, we show that TNP-modified peptides derived from mouse IgG, pigeon cytochrome c or staphylococcal nuclease known to bind to I-Ab or from lambda repressor with specificity to I-Ad as well as TNP-proteins such as bovine serum albumin, ovalbumin or keyhole limpet hemocyanin all create class II-restricted hapten determinants for a number of TNP-specific T cell clones and hybridomas. All of these cells were induced with cells modified by trinitrobenzene sulfonic acid (TNBS). In addition, we present arguments indicating that individual TNP-specific helper T cells may cross-react with different TNP-peptides bound to identical class II molecules. Chemical treatment of antigen-presenting cells with TNCB or TNBS may thus result in a limited number of particularly repetitive immunodominant hapten epitopes. Immunodominant epitopes were also indicated by an overrepresentation of the TCR elements V beta 2 and V alpha 10 in I-Ab/TNP-specific T cells. Most importantly, however, we demonstrate that TNP attached to lysine 97 in the staphylococcal nuclease peptide 93-105 (i.e. a clearly "non-self" sequence) is able to prime mice for subsequent elicitation of contact sensitivity by TNCB in the absence of foreign protein. We take this to indicate that those TNP-peptide determinants defined by us as immuno-dominant are responsible for the induction of contact sensitivity to haptens.
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PMID:Cross-reactive trinitrophenylated peptides as antigens for class II major histocompatibility complex-restricted T cells and inducers of contact sensitivity in mice. Limited T cell receptor repertoire. 784 58

The product of the RAD6 (UBC2) gene of Saccharomyces cerevisiae is a ubiquitin-conjugating enzyme (Rad6) which is implicated in DNA repair, induced mutagenesis, retrotransposition, sporulation and the degradation of proteins with destabilizing N-terminal amino acid residues. Deletion of the 23-residue acidic C-terminus of Rad6 impairs sporulation and N-end rule protein degradation in vivo but does not affect other functions such as DNA repair and induced mutagenesis. We have investigated the role of the C-terminus of Rad6 in in vitro interactions with various substrates and with a putative ubiquitin-protein ligase, E3-R. The removal of the Rad6 C-terminus had significant different effects on enzyme activity for individual substrates. Although the 23-residue truncated Rad6-149 protein had markedly impaired activity for histone H2B and micrococcal nuclease, the activity for cytochrome c was the same as that of the intact Rad6 protein. Similarly, truncation of Rad6 had no effect on its activity for several poor substrates, namely, beta-casein, beta-lactoglobulin and oxidized RNase. E3-R stimulated the activities of both Rad6 and Rad6-149 for the latter three substrates to similar degrees. E3-R appears to act by enhancing the low intrinsic affinity of Rad6 and Rad6-149 for these substrates. Thus Rad6 can act in three different modes in vitro depending on the substrate, namely unassisted C-terminus-dependent, unassisted C-terminus-independent and E3-R-assisted C-terminus-independent modes. We also examined the results of removing the C-terminal acidic region of Cdc34 (Ubc3), a ubiquitin-conjugating enzyme closely related to Rad6. Truncation of Cdc34 like that of Rad6 had no effect on activity for beta-casein, beta-lactoglobulin or oxidized RNase in the presence or absence of E3-R.
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PMID:Role of the C-terminus of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in substrate and ubiquitin-protein-ligase (E3-R) interactions. 816 12

Cooperative unfolding penalties are calculated by statistically evaluating an ensemble of denatured states derived from native structures. The ensemble of denatured states is determined by dividing the native protein into short contiguous segments and defining all possible combinations of native, i.e., interacting, and non-native, i.e., non-interacting, segments. We use a novel knowledge-based scoring function, derived from a set of non-homologous proteins in the Protein Data Bank, to describe the interactions among residues. This procedure is used for the structural identification of cooperative folding cores for four globular proteins: bovine pancreatic trypsin inhibitor, horse heart cytochrome c, French bean plastocyanin, and staphylococcal nuclease. The theoretical folding units are shown to correspond to regions that exhibit enhanced stability against denaturation as determined from experimental hydrogen exchange protection factors. Using a sequence similarity score for related sequences, we show that, in addition to residues necessary for enzymatic function, those amino acids comprising structurally important folding cores are also preferentially conserved during evolution. This implies that the identified folding cores may be part of an array of fundamental structural folding units.
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PMID:Identification of cooperative folding units in a set of native proteins. 926 Feb 76

Recently, we developed a simple analytical model based on local residue packing densities and the distribution of tertiary contacts for describing the conformational fluctuations of proteins in their folded state. This so-called Gaussian network model (GNM) is applied here to the interpretation of experimental hydrogen exchange (HX) behavior of proteins in their native state or under weakly denaturing conditions. Calculations are performed for five proteins: bovine pancreatic trypsin inhibitor, cytochrome c, plastocyanin, staphylococcal nuclease, and ribonuclease H. The results are significant in two respects. First, a good agreement is reached between calculated fluctuations and experimental measurements of HX despite the simplicity of the model and within computational times 2 or 3 orders of magnitude faster than earlier, more complex simulations. Second, the success of a theory, based on the coupled conformational fluctuations of residues near the native state, to satisfactorily describe the native-state HX behavior indicates the significant contribution of local, but cooperative, fluctuations to protein conformational dynamics. The correlation between the HX data and the unfolding kinetics of individual residues further suggests that local conformational susceptibilities as revealed by the GNM approach may have implications relevant to the global dynamics of proteins.
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PMID:Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. 945 98

Molten globules are partially structured protein folding intermediates that adopt a native-like overall backbone topology in the absence of extensive detectable tertiary interactions. It is important to determine the extent of specific tertiary structure present in molten globules and to understand the role of specific side-chain packing in stabilizing and specifying molten-globule structure. Previous studies indicate that a small degree of specific side-chain packing stabilizes the structures of the cytochrome c, apomyoglobin, and staphylococcal nuclease molten globules. Here we investigate the extent of specific side-chain packing in the molten globule of alpha-lactalbumin (alpha-LA), a highly fluctuating, non-cooperatively formed molten globule. By analyzing a set of point mutations in the helical domain of alpha-LA, we have identified a stabilizing hydrophobic core. Moreover, this core corresponds to a previously identified structural subdomain and likely contains some native-like packing interactions. Our results suggest that native-like packing of core amino acids helps stabilize molten globules and that some specific interactions can exist in even highly dynamic, fluctuating species.
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PMID:A specific hydrophobic core in the alpha-lactalbumin molten globule. 965 40

The fact that cleavage of single peptide linkages in proteins often leads to extensive conformational alteration, including regions far removed from the cleavage site is not fully understood. We propose, based on the work of Linderstrom-Lang and Schellman, that disruption primarily occurs within protein structural domains that are stabilized by cooperative interactions and that cleavage of single peptide linkages of the domain perturbs the entire cooperative interaction. For this model we review experimental observations: on fragment complexation (ribonuclease A, staphylococcal nuclease and cytochrome c), destabilized N-terminal large fragments (ribonuclease A and nuclease), cooperative folding and stabilization of proteins (ribonuclease A, nuclease and cytochrome c), the close relationship of the three-dimensional structure between fragment complexes and the original protein (ribonuclease A and nuclease), ligand induced stabilization (nuclease), 3D domain swapping, circular permutation (dihydrofolate reductase), evolutionary conservation (cytochrome c fold). Based on analysis of these observations, we conclude that the cooperative interactions of domains are important for the mechanism of 3D domain swapping as well as for stabilization and thereby, determination of the ground state of native proteins. Furthermore, analysis of the observations reveals that domains generally contain a hydrophobic core. Further, based on studies of cytochrome c and the Tsao, Evans and Wennerstrom model of electrostatic interactions between two hydrophobic monolayers, we propose the model that the hydrophobic core of a domain is polarizable and responds to the surface charges through its polarizability to stabilize the domain, explaining in part the nature of the cooperative interactions.
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PMID:Linderstrom-Lang-Schellman's model for protein stabilization revisited. 1532 Jul 34


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