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Biomedical subjects

M J Sippl

Publications and source records attributed to M J Sippl.

16 recordsLinked to original sources
PubMed1996

Helmholtz free energy of peptide hydrogen bonds in proteins.

We estimate the Helmholtz free energy of peptide hydrogen bonds in native protein structures as a function of spatial separation between donor and acceptor atoms. The resulting potential function has a deep narrow well at H-bond contact but bond formation is hindered by a barrier and the net change in free energy is close to zero. The barrier provides a molecular lock mechanism acting as a kinetic trap. Once formed, H-bonds keep protein chains in a precise orientation. However, bond formation requires energy input and opposes protein folding. In contrast, the free energy functions of most side-chain interactions have no energy barriers. They lack spatial precision but free energy differences of contact formation are substantial. These interactions drive folding and stabilize structures but precision is mediated and maintained by H-bonds.

Arginine↗
PubMed1995

Progress in fold recognition.

The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition.

Algorithms↗
PubMed1995

Knowledge-based potentials for proteins.

Knowledge based potentials and energy functions are extracted from a number of databases of known protein structures. Recent developments have shown that this type of potential is successful in many areas of protein structure research. Among these are quality assessment and error recognition of folds and the prediction of unknown structures by fold-recognition techniques.

Databases, Factual↗
PubMed1993

Recognition of errors in three-dimensional structures of proteins.

A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X-ray crystallography and nuclear magnetic resonance spectroscopy have accelerated the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the C alpha trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds.

Models, Molecular↗
PubMed1993

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.

The data base of known protein structures contains a tremendous amount of information on protein-solvent systems. Boltzmann's principle enables the extraction of this information in the form of potentials of mean force. The resulting force field constitutes an energetic model for protein-solvent systems. We outline the basic physical principles of this approach to protein folding and summarize several techniques which are useful in the development of knowledge-based force fields. Among the applications presented are the validation of experimentally determined protein structures, data base searches which aim at the identification of native-like sequence structure pairs, sequence structure alignments and the calculation of protein conformations from amino acid sequences.

Amino Acid Sequence↗
PubMed1992

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.

We present a model for the hydrophobic interaction in globular proteins that is based entirely on an analysis of known X-ray structures. This structure-derived hydrophobic force is identified as the strongest among the non-covalent interactions that stabilize native folds. The functional form of the hydrophobic interaction is found to be linear, corresponding to a constant force along the observable distance range (5 to 70 A). The parameters of the hydrophobic amino acid pair potentials yield a structure-derived hydrophobicity scale that correlates strongly with scales derived by a variety of complementary approaches. We demonstrate that the structure-derived hydrophobic interaction alone is able to distinguish a substantial number of native conformations from a large pool of misfolded structures.

Amino Acid Sequence↗
PubMed1992

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4.

Recently we developed methods for the construction of knowledge-based mean fields from a data base of known protein structures. As shown previously, this approach can be used to calculate ensembles of probable conformations for short fragments of polypeptide chains. Here we develop procedures for the assembly of short fragments to complete three-dimensional models of polypeptide chains. The amino acid sequence of a given protein is decomposed into all possible overlapping fragments of a given length, and an ensemble of probable conformations is calculated for each fragment. The fragments are assembled to a complete model by choosing appropriate conformations from the individual ensembles and by averaging over equivalent angles. Finally a consistent model is obtained by rebuilding the conformation from the average angles. From the average angles the local variability of the structure can be calculated, which is a useful criterion for the reliability of the model. The procedure is applied to the calculation of the local backbone conformations of myoglobin and lysozyme whose structures have been solved by X-ray analysis and thymosin beta 4, a polypeptide of 43 amino acid residues whose structure was recently investigated by NMR spectroscopy. We demonstrate that substantial fractions of the calculated local backbone conformations are similar to the experimentally determined structures.

Amino Acid Sequence↗
PubMed1992

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.

Algorithms↗
PubMed1991

Molecular basis of lipoprotein lipase deficiency in two Austrian families with type I hyperlipoproteinemia.

To determine the molecular basis for type I hyperlipoproteinemia in two Austrian families, the lipoprotein lipase (LPL) gene of two patients exhibiting LPL deficiency was analyzed by Southern blotting and by direct genomic sequencing of DNA amplified by polymerase chain reaction (PCR). All exons of the LPL gene except part of the noncoding region of exon 10, all splice donor and acceptor sites, as well as 430 basepairs of the 5'-region including the promotor were sequenced. A homozygous substitution of adenine for guanine in the fifth exon at cDNA position 818 of the LPL gene was found in both patients. Our sequencing strategy largely ruled out a linkage disequilibrium of the identified nucleotide change with another defect potentially causing the clinical phenotype. The base change described abolishes a normally present AvaII restriction site allowing the identification of carriers of the mutant allele by AvaII digestion of PCR fragments of exon 5; three members of the two families were homozygous for this mutation and ten members were heterozygous. The activity of LPL in postheparin plasma was almost completely absent in homozygotes and about half normal in heterozygotes. The loss of activity was related to LPL protein structure. This mutation alters the amino acid sequence at residue 188 from Gly to Glu. The conformational preferences of the protein chain around position 188 were calculated with the use of a knowledge-based computerized method. The most probable conformation is a beta-turn formed by residues 189-192. The mutation seems to destabilize the beta-turn and/or a yet larger domain critical for substrate alignment.

Adult↗
PubMed1990

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force.

We present an approach that is able to detect native folds amongst a large number of non-native conformations. The method is based on the compilation of potentials of mean force of the interactions of the C beta atoms of all amino acid pairs from a database of known three-dimensional protein structures. These potentials are used to calculate the conformational energy of amino acid sequences in a number of different folds. For a substantial number of proteins we find that the conformational energy of the native state is lowest amongst the alternatives. Exceptions are proteins containing large prosthetic groups, Fe-S clusters or polypeptide chains that do not adopt globular folds. We discuss briefly potential applications in various fields of protein structural research.

Animals↗
PubMed1990

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

We present a prototype of a new approach to the folding problem of polypeptide chains. This approach is based on the analysis of known protein structures. It derives the energy potentials for the atomic interactions of all amino acid residue pairs as a function of the distance between the involved atoms. These potentials are then used to calculate the energies of all conformations that exist in the data base with respect to a given sequence. Then, by using only the most stable conformations, clusters of the most probable conformations for the given sequence are obtained. To discuss the results properly we introduce a new classification of segments based on their conformational stability. Special care is taken to allow for sparse data sets. The use of the method is demonstrated in the discussion of the identical oligopeptide sequences found in different conformations in unrelated proteins. VNTFV, for example, adopts a beta-strand in ribonuclease but it is found in an alpha-helical conformation in erythrocruorin. In the case of VNTFV the ensemble obtained consists of a single cluster of beta-strand conformations, indicating that this may be the preferred conformation for the pentapeptide. When the flanking residues are included in the calculation the hepapeptide P-VNTFV-H (ribonuclease) again yields an ensemble of beta-strands. However, in the ensemble of D-VNTFV-A (erythrocruorin) the major cluster is of alpha-helical type. In the present study we concentrate on the local aspects of protein conformations. However, the theory presented is quite general and not restricted to oligopeptides. We indicate extensions of the approach to the calculation of global conformations of proteins as well as conceivable applications to a number of molecular systems.

Amino Acid Sequence↗
PubMed1989

Analysis of the cDNA for phospholipase A2 from honeybee venom glands. The deduced amino acid sequence reveals homology to the corresponding vertebrate enzymes.

A cDNA expression library was constructed from worker bee venom glands and screened with an antibody against phospho lipase A2. The nucleotide sequence of a positive clone with the largest insert showed an open reading frame that codes for part of the signal peptide, the pro-region and the entire mature enzyme of the bee venom phospholipase A2 precursor. This sequence differs in the central region from the one determined by Shipolini et al. [FEBS Lett. 17, 39-40 (1971)] in showing, among other exchanges, two additional cysteines. The revised sequence of bee venom phospholipase is similar to the pancreatic enzyme in the spacing of cysteines and the presence of several amino acids known to be part of the active site or the Ca2+-binding region in identical positions. Moreover, these parts of the bee protein can be fitted into the three-dimensional structure determined for the bovine pancreatic phospholipase A2 [Dijkstra et al. (1981) Nature 289, 604-606]. Contrary to earlier suggestions, we therefore conclude that the bee venom enzyme shows some homology to phospholipases from mammalian pancreas and snake venoms.

Amino Acid Sequence↗
PubMed1986

Cayley-Menger coordinates.

A major obstacle in applying distance geometry techniques is the analytical complexity of the Cayley-Menger determinants that are used to characterize euclidian spaces in terms of distances between points. In this paper we show that, with the aid of a theorem of Jacobi, the complex Cayley-Menger determinants can be replaced by simpler determinants, and we derive the concept of Cayley-Menger coordinates, a coordinate system in terms of which each point of En is characterized by n + 1 distances to n + 1 points of a reference. We also show that this coordinate system provides a natural norm for the incomplete embedding problem. This paper provides the tools to treat the problem of filling out an incomplete distance matrix so that our previous procedure can then be used to embed the corresponding structure in a three-dimensional space.

Mathematics↗
PubMed1985

Solution of the embedding problem and decomposition of symmetric matrices.

A solution of the problem of calculating cartesian coordinates from a matrix of interpoint distances (the embedding problem) is reported. An efficient and numerically stable algorithm for the transformation of distances to coordinates is then obtained. It is shown that the embedding problem is intimately related to the theory of symmetric matrices, since every symmetric matrix is related to a general distance matrix by a one-to-one transformation. Embedding of a distance matrix yields a decomposition of the associated symmetric matrix in the form of a sum over outer products of a linear independent system of coordinate vectors. It is shown that such a decomposition exists for every symmetric matrix and that it is numerically stable. From this decomposition, the rank and the numbers of positive, negative, and zero eigenvalues of the symmetric matrix are obtained directly.

Chemical Phenomena↗