Biomedical subjects

C Frömmel

Publications and source records attributed to C Frömmel.

At least 37 records · Page 2Linked to original sources

PubMed1996

Analysis of mammalian 20S proteasome biogenesis: the maturation of beta-subunits is an ordered two-step mechanism involving autocatalysis.

Maturation of eukaryotic 20S proteasomes involves the processing of beta-subunits by limited proteolysis. To study the processing mechanism we analysed different point mutations of the beta-subunit LMP2 in transfected human T2 cells. Here we show that the presence of the intact Gly-1Thr1 consensus motif and Lys33 are essential for correct processing. Mutation of Thr1, the active site residue in mature subunits, or of Lys33, results in complete inhibition of processing at the consensus site. In addition, proprotein processing in vitro of wild-type LMP2, incorporated in immature 16S precursor complexes, can be blocked by a proteasome-specific inhibitor. While the processing of inhibitor-treated wild-type proprotein was completely prevented, the site-directed mutagenesis of LMP2 results in processing intermediates carrying an extension of 8-10 residues preceding Thr1, suggesting an additional cleavage event within the prosequence. Furthermore, exchange of mammalian prosequences interferes with processing efficiency and suggests subunit specificity. Based on our data we propose a model for self-activation of proteasomal beta-subunits in which residue Thr1 serves as nucleophile and Lys33 as proton donor/acceptor. We provide evidence that subunit processing of mammalian beta-subunits proceeds via a novel ordered two-step mechanism involving autocatalysis.

Amino Acid Sequence↗

PubMed1996

Comparison of proline and N-methylnorleucine induced conformational equilibria in cyclic pentapeptides.

The cyclic, imido acid containing pentapeptides cyclo(Asp-Trp-(NMe)Nle-Asp-Phe) (cpp[NMeNle(3)]) and cyclo(Asp-Trp-Pro-Asp-Phe) (cpp[Pro(3)]) have been investigated by 1H-NMR spectroscopy in DMSO and by restrained molecular dynamics methods. The spectra indicate the existence of at least four cis/trans isomers for cpp[NMeNle(3)] and two cis/trans isomers for cpp[Pro(3)]. In addition to the imido peptide bonds, cpp[NMeNle(3)] shows cis/trans isomerization of the Asp4-Phe5 and Phe5-Asp1 peptide bonds whereas only the Phe5-Asp1 peptide bond isomerizes in the Pro-containing peptide. In cpp[Pro(3)] all cis bonds are centred in betaVIb turns. Also, cpp[NMeNle(3)] prefers backbone angles around the cis bonds which are rather similar to the angles of a betaVIb turn. The higher number of cis/trans isomers and slight deviations in the backbone angles of comparable isomers of both peptides are caused by an enhanced flexibility of cpp[NMeNle(3)] due to the possibility of the phi-(NMe)Nle rotation.

Amino Acid Sequence↗

PubMed1996

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

The biological function of a protein typically depends on the structure of specific binding sites. These sites are located at the surface of the protein molecule and are determined by geometrical arrangements and physico-chemical properties of tens of non-hydrogen atoms. In this paper we describe a new algorithm called APROPOS, based purely on geometric criteria for identifying such binding sites using atomic co-ordinates. For the description of the protein shape we use an alpha-shape algorithm which generates a whole family of shapes with different levels of detail. Comparing shapes of different resolution we find cavities on the surface of the protein responsible for ligand binding. The algorithm correctly locates more than 95% of all binding sites for ligands and prosthetic groups of molecular mass between about 100 and 2000 Da in a representative set of proteins. Only in very few proteins does the method find binding sites of single ions outside the active site of enzymes. With one exception, we observe that interfaces between subunits show different geometric features compared to binding sites of ligands. Our results clearly support the view that protein-protein interactions occur between flat areas of protein surface whereas specific interactions of smaller ligands take place in pockets in the surface.

Algorithms↗

PubMed1996

Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods.

The predictive limits of the amino acid composition for the secondary structural content (percentage of residues in the secondary structural states helix, sheet, and coil) in proteins are assessed quantitatively. For the first time, techniques for prediction of secondary structural content are presented which rely on the amino acid composition as the only information on the query protein. In our first method, the amino acid composition of an unknown protein is represented by the best (in a least square sense) linear combination of the characteristic amino acid compositions of the three secondary structural types computed from a learning set of tertiary structures. The second technique is a generalization of the first one and takes into account also possible compositional couplings between any two sorts of amino acids. Its mathematical formulation results in an eigenvalue/eigenvector problem of the second moment matrix describing the amino acid compositional fluctuations of secondary structural types in various proteins of a learning set. Possible correlations of the principal directions of the eigenspaces with physical properties of the amino acids were also checked. For example, the first two eigenvectors of the helical eigenspace correlate with the size and hydrophobicity of the residue types respectively. As learning and test sets of tertiary structures, we utilized representative, automatically generated subsets of Protein Data Bank (PDB) consisting of non-homologous protein structures at the resolution thresholds < or = 1.8A, < or = 2.0A, < or = 2.5A, and < or = 3.0 A. We show that the consideration of compositional couplings improves prediction accuracy, albeit not dramatically. Whereas in the self-consistency test (learning with the protein to be predicted), a clear decrease of prediction accuracy with worsening resolution is observed, the jackknife test (leave the predicted protein out) yielded best results for the largest dataset (< or = 3.0A, almost no difference to the self-consistency test!), i.e., only this set, with more than 400 proteins, is sufficient for stable computation of the parameters in the prediction function of the second method. The average absolute error in predicting the fraction of helix, sheet, and coil from amino acid composition of the query protein are 13.7, 12.6, and 11.4%, respectively with r.m.s. deviations in the range of 8.6 divided by 11.8% for the 3.0 A dataset in a jackknife test. The absolute precision of the average absolute errors is in the range of 1 divided by 3% as measured for other representative subsets of the PDB. Secondary structural content prediction methods found in the literature have been clustered in accordance with their prediction accuracies. To our surprise, much more complex secondary structure prediction methods utilized for the same purpose of secondary structural content prediction achieve prediction accuracies very similar to those of the present analytic techniques, implying that all the information beyond the amino acid composition is, in fact, mainly utilized for positioning the secondary structural state in the sequence but not for determination of the overall number of residues in a secondary structural type. This result implies that higher prediction accuracies cannot be achieved relying solely on the amino acid composition of an unknown query protein as prediction input. Our prediction program SSCP has been made available as a World Wide Web and E-mail service.

Amino Acids↗

PubMed1996

Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class.

The success rates reported for secondary structural class prediction with different methods are contradictory. On one side, the problem of recognizing the secondary structural class of a protein knowing only its amino acid composition appears completely solved by simply applying jury decision with an elliptically scaled distance function. Chou and coworkers repeatedly (see Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995) published prediction accuracies near 100%. On the other hand, traditional secondary structure prediction techniques achieve success rates of about 70% for the secondary structural state per residue and about 75% for structural class only with extensive input information (full sequence of the query protein, its amino acid composition and length, multiple alignments with homologous sequences). In this article, we resolve the paradox and consider (1) the question of the secondary structural class definition, (2) the role of the representativity of the test set of protein tertiary structure for the current state of the Protein Data Bank (PDB); and (3) we estimate the real impact of amino acid composition on secondary structural class. We formulate three objective criteria for a reasonable definition of secondary structural classes and show that only the criterion of Nakashima et al. (J. Biochem. 99:153-162, 1986) complies with all of them. Only this definition matches the distribution of secondary structural content in representative PDB subsets, whereas other criteria leave many proteins (up to 65% of all PDB entries) simply unassigned. We review critically specialized secondary-structural class prediction methods, especially those of Chou and coworkers, which claim almost 100% accuracy using only amino acid composition, and resolve the paradox that these prediction accuracies are better than those from secondary structure predictions from multiple alignments. We show (i) that these techniques rely on a preselection of test sets which removes irregular proteins and other proteins without any class assignment (about 35% of all PDB entries); and (ii) that even for preselected representative test sets, the success rate drops to 60% and lower for a 4-type classification (alpha, beta, alpha + beta, alpha/beta). The prediction accuracies fall to about 50% if the secondary structural class definition of Nakashima et al. is applied and only few irregular proteins are preselected and removed from automatically generated, representative subsets of the PDB. We have applied two new vector decomposition methods for secondary structural content prediction from amino acid composition alone, with and without consideration of amino acid compositional coupling in the learning set of tertiary structures respectively, to the problem of class prediction and achieve about 60% correct assignment among four classes (alpha, beta, mixed, irregular) as well as single sequence-based secondary structure prediction methods like GORIII and COMBI. Our results demonstrate that 60% correctness is the upper limit for a 4-type class prediction from amino acid composition alone for an unknown query protein and that consideration of compositional coupling does not improve the prediction success. The prediction program SSCP offering secondary structural class assignment for query compositions and sequences has been made available as a World Wide Web and E-mail service.

Amino Acids↗

PubMed1996

A novel mutation in the coding region for neurophysin-II is associated with autosomal dominant neurohypophyseal diabetes insipidus.

OBJECTIVE: Autosomal dominant neurohypophyseal diabetes insipidus (ADNDI) is a rare cause of diabetes insipidus, in which AVP serum levels are insufficient. AVP is synthesized along with neurophysin-II (NPII) as an AVP-NPII precursor polypeptide in the hypothalamus. After proteolytic cleavage during axonal transport, AVP and NPII are reassembled and stored loosely bound to each other in the posterior pituitary until both are released into the circulation. In this study, we investigated the genetic basis of ADNDI in a German kindred with 10 affected members spanning three generations. DESIGN: Genomic DNA was isolated from peripheral blood leucocytes. The entire coding region of the AVP-NPII gene of one of the affected persons was amplified by polymerase chain reaction (PCR) and subjected to nucleotide sequence analysis. Sequencing results were confirmed by restriction enzyme analysis of PCR products. PATIENTS: Six affected and two unaffected members of a family with ADNDI and 54 unrelated healthy control subjects were studied. RESULTS: The index patient was found by direct sequencing to be heterozygous for a G to T transversion at nucleotide position 1884 (exon 2) of the AVP-NPII gene. This mutation introduced a new recognition site for the restriction enzyme Ava II, which was used to test for the presence of the mutation in other family members and in control subjects. The mutation was detected in all family members with ADNDI, but was not found in unaffected family members or in control subjects. The mutation encodes a valine in place of the normal glycine at amino acid 65 of NPII, which is known to be highly conserved during evolution. CONCLUSIONS: In this family, the autosomal dominant neurohypophyseal diabetes insipidus phenotype cosegregates with a point mutation in a region of the AVP-neurophysin-II gene which codes for the carboxy-terminal domain of neurophysin-II. Although the altered amino acid is not directly involved in AVP binding, the mutation might lead to conformational changes that impair the dimerization of neurophysin-II molecules. This could in turn affect the AVP binding affinity of neurophysin-II or might interfere with the transport of the AVP-neurophysin-II precursor in the AVP-producing cells of the hypothalamus.

Base Sequence↗

PubMed1995

Novel disulfide-constrained pentapeptides as models for beta-VIa turns in proteins.

The conformational behavior of cyclic peptides of the amino acid sequence Cys-Phe/Ala-Pro-Ala-Cys has been investigated through the combined use of molecular simulation methods and NMR experiments to find models for beta-VIa turns of proteins. Both oxidized (cyclic) peptides and reduced (linear) forms were investigated. At least 95% of the cyclic peptides show a cis conformation of the Xaa-Pro bond in solution in DMSO or water, whereas all other peptide bonds are trans. Furthermore, we observed a hydrogen bond between the NH group of residue Ala4 and the C = O group of residue Cys1. Both properties are indicative of beta-VIa turns. After reduction of the disulfide bridge, the all-trans form of the peptide bonds predominates.

Base Sequence↗

PubMed1994

Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models.

The evaluation of calculated protein structures is an important step in the protein design cycle. Known criteria for this assessment of proteins are the polar and apolar, accessible and buried surface area, electrostatic interactions and other interactions between the protein atoms (e.g. H..O, S..S), atomic packing, analysis of amino acid environment and surface charge distribution. We show that a powerful test of accuracy of protein structure can be derived by analysing the water contact of atoms and additionally taking into account their polarity. On the basis of estimated reference values of the polar fraction of typical globular proteins with known structure (mean, SD and distribution), the evaluation of misfolded structures can be improved significantly. The reference values are derived by moving windows of different length (3-99 amino acid residues) over the amino acid sequence. Model proteins, which are included in the Brookhaven protein structure databank, deliberately misfolded proteins, hypothetical proteins and predicted protein structures are diagnosed as at least partially incorrectly folded. The local fault, mostly observed, is that polar groups are buried too frequently in the interior of the protein. The database-derived quantities are useful in screening the designed proteins prior to experimentation and may also be useful in the assessment of errors in the experimentally determined protein structures.

Chemical Phenomena↗

PubMed1990

Prediction of prolyl residues in cis-conformation in protein structures on the basis of the amino acid sequence.

In proteins most peptide bonds are in trans-conformation: the torsion angle omega = 180 degrees. Only few show cis-conformation in known protein structures (omega = 0 degrees). Most of them are prolyl residues. About 6% of about 4000 prolyl residues are in cis-conformation. Between trans- and cis-prolyl residues significant differences are observed in the surrounding sequences. E.g. there are large amounts of aromatic residues N-terminally in case of cis-prolyl residues, but in the case of trans-prolyl residues more aromatic amino acids occur C-terminally. But in all cases there are only complex patterns which are indicative of cis- and trans-conformation, respectively. Considering the neighbours (+/- 6 residues) of prolyl residues and their physicochemical properties we find 6 different patterns which allow one to assign correctly about 75% of known cis-structured prolyl residues, whereby no false positive one is predicted.

Crystallography↗

PubMed1990

Crystal structure of thermitase at 1.4 A resolution.

The crystal structure of thermitase, a subtilisin-type serine proteinase from Thermoactinomyces vulgaris, was determined by X-ray diffraction at 1.4 A resolution. The structure was solved by a combination of molecular and isomorphous replacement. The starting model was that of subtilisin BPN' from the Protein Data Bank, determined at 2.5 A resolution. The high-resolution refinement was based on data collected using synchrotron radiation with a Fuji image plate as detector. The model of thermitase refined to a conventional R factor of 14.9% and contains 1997 protein atoms, 182 water molecules and two Ca ions. The tertiary structure of thermitase is similar to that of the other subtilisins although there are some significant differences in detail. Comparison with subtilisin BPN' revealed two major structural differences. The N-terminal region in thermitase, which is absent in subtilisin BPN', forms a number of contacts with the tight Ca2+ binding site and indeed provides the very tight binding of the Ca ion. In thermitase the loop of residues 60 to 65 forms an additional (10) beta-strand of the central beta-sheet and the second Ca2+ binding site that has no equivalent in the subtilisin BPN' structure. The observed differences in the Ca2+ binding and the increased number of ionic and aromatic interactions in thermitase are likely sources of the enhanced stability of thermitase.

Amino Acid Sequence↗

PubMed1990

Mapping mutations in influenza A virus resistant to norakin.

To elucidate the mode of action of norakin against influenza A virus we sequenced the hemagglutinin gene of 11 norakin-resistant mutants. Resistance was coupled with 1-3 amino acid exchanges. The majority of mutations was localized in the HA2 polypeptide and was mostly associated with changes in charge or polarity of the amino acids. The amino acid substitutions are discussed in the context of the 3D structure of X31 hemagglutinin considered to be representative of the influenza hemagglutinins. Most of the mutations appear to destabilize the pH 7.0 structure by distorting or destroying hydrogen bonds as well as salt-bridges which are responsible for intra- and intersubunit contacts, while others destabilize the location of the fusion peptide, facilitating conformational changes in the presence of the inhibitor.

Amino Acids↗

PubMed1990

[Crystal structure of thermitase and stability of subtilisins].

Crystal structure of thermitase, a serine proteinase from Thermoactinomyces vulgaris, has been determined by X-ray diffraction at 1.4 A resolution. The atomic model of thermitase refined to an R-factor of 0.149 contains 1997 protein atoms, 182 water molecules and 2 Ca2+ ions. The tertiary structure of thermitase is similar to that of subtilisin BPN'. The greatest variations are connected with insertions and deletions in the amino acid sequence, which are located on the surface of the molecule. Higher thermostability of thermitase can be explained in terms of the three-dimensional structure. The Ca2+ ions, bound to the protein molecule, as well as the ionic and hydrophobic interactions are supposed to give the main contribution to the stabilization of the structure.

Amino Acid Sequence↗

PubMed1989

Crystal structure of thermitase from Thermoactinomyces vulgaris at 2.2 A resolution.

The crystal structure of thermitase from Thermoactinomyces vulgaris has been determined by x-ray diffraction at 2.2 A resolution. The structure was solved by a combination of single isomorphous replacement and molecular replacement methods. The structure was refined to a conventional R factor of 0.24 using restrained least square procedures CORELS and PROLSQ. The tertiary structure of thermitase is similar to that of subtilsin BPN'. The greatest differences between these structures are related to the insertions and deletions in the sequence.

Actinomycetales↗

PubMed1989

Thermitase, a thermostable subtilisin: comparison of predicted and experimental structures and the molecular cause of thermostability.

The subtilisin family of proteases has four members of known sequence and structure: subtilisin Carlsberg, subtilisin novo, proteinase K, and thermitase. Using thermitase as a test case, we ask two questions. How good are methods for model building a three-dimensional structure of a protein based on sequence homology to a known structure? And what are the molecular causes of thermostability? First, we compare predicted models of thermitase, refined by energy minimization and varied by molecular dynamics, with the preliminary crystal structure. The predictions work best in the conserved structural core and less well in seven loop regions involving insertions and deletions relative to subtilisin. Here, variation of loop regions by molecular dynamics simulation in vacuo followed by energy minimization does not improve the prediction since we find no correlation between in vacuo energy and correctness of structure when comparing local energy minima. Second, in order to identify the molecular cause of thermostability we confront hypotheses derived by calculation of the details of interatomic interactions and estimates of hydrophobic interactions with inactivation experiments. As a result, we can exclude salt bridges and hydrophobic interactions as main causes of thermostability. Based on a combination of theoretical and experimental evidence, the unusually tight binding of calcium by thermitase emerges as the most likely single influence responsible for its increased thermostability.

Actinomycetales↗

PubMed1989

Polarity as a criterion in protein design.

Hypothetical proteins can be tested computationally by determining whether or not the designed sequence-structure pair has the characteristics of a typical globular protein. We have developed such a test by deriving quantities with approximately constant value for all globular proteins, based on empirical analysis of the exposed and buried surfaces of 128 structurally known proteins. The characteristic quantities that best appear to segregate badly designed or deliberately misfolded proteins from their properly folded natural relatives are the polar fraction of side chains on the protein surface and, independently, in the protein interior. Three of the seven hypothetical structures tested here can be rejected as having too many polar side-chain groups in the interior or too few on the protein surface. In addition, a recently designed nutritional protein is identified as being very much unlike globular proteins. These database-derived characteristic quantities are useful in screening designed proteins prior to experiment and may be useful in screening experimentally determined (X-ray, NMR) protein structures for possible errors.

Electric Conductivity↗

PubMed1988

Use of the averaged mutation rate in pieces of protein sequences to predict the location of antigenic determinants.

Antigenic determinants in proteins show properties, which can be used to their prediction: high degree of accessibility, mobility, polarity etc. Furthermore, there is a remarkable correlation between the location of antigenic determinants and regions with high frequency of accepted mutations during the evolution. Consequently, it is possible to predict successfully the location of antigenic epitopes in proteins using the averaged mutation rate of protein sequence pieces.

Amino Acid Sequence↗

PubMed1988

Oxidation of a methionine residue in subtilisin-type proteinases by the hydrogen peroxide/borate system--an active site-directed reaction.

Subtilisin-type proteinases (thermitase, subtilisin Carlsberg, alkaline proteinase ZIMET 10911, proteinase K) are partially inactivated by hydrogen peroxide in the alkaline pH range only in the presence of boric acid or phenylboronic acid. A model is presented to describe the inactivation mechanism. Both boric acid and perboric acid existing in equilibrium in the presence of hydrogen peroxide bind competitively at the active site of the enzyme. The inactivation, which is known to be caused by sulfoxide formation from the methionine residue in the active site (Stauffer, C.E. and Etson, D. (1969) J. Biol. Chem. 244, 5333-5338), is due to the enzyme-bound perboric acid species. The dissociation constants for the boric acid-thermitase and perboric acid-thermitase complexes are 36 +/- 7 and 4 +/- 1 mM, respectively. The first-order rate constant of inactivation is k = 0.63 +/- 0.14 min-1. The same mechanism of inactivation holds true for phenylboronic acid in alkaline hydrogen peroxide solutions.

Bacillus↗

PubMed1987

[Long-term stability of enzymes in solution].

Two proteases (thermitase, a thermostable serine protease from Thermoactinomyces vulgaris and subtilisin Carlsberg) and one non-proteolytic enzyme (urate oxidase from Penicillium spp.) were used for revealing the main influences leading to the inactivation of enzyme preparations during their long-time storage at low temperatures. The temperature dependences (0 degree C-60 degrees C) of inactivation resulted in a linear Arrhenius-plot for each of the three native enzymes as well as in the presence of all stabilizing substances tested. Therefore, a method is available which shortens the time considerably needed for the experiments aimed at the discovery of substances stabilizing enzymes under storage conditions (i.e. long time at low temperatures). Because of the linear Arrhenius-plots potential stabilizers can be tested experimentally at suitable higher temperatures and one can extrapolate on their influence on the enzyme at storage temperatures (0 degree C-10 degrees C). By using this method effective combinations of stabilizers for urate oxidase were found, and possible reasons of their stabilizing influence on the enzyme are discussed.

Cold Temperature↗