Jury returns on structure prediction.
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Amino Acid Sequence↗
Biomedical subjects
C Sander
Publications and source records attributed to C Sander.
TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes.
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Amino Acid Sequence↗
New triple-helical model for the shaft of the adenovirus fibre.
The adenovirus fibre is a trimeric protein with a globular head on a long thin shaft that projects from the twelve fivefold vertices of the virion. The shaft region of the fibre primary sequence has a unique pseudo-repeating motif of 15 residues. Using constraints derived from sequence analysis, the trimeric nature of the fibre, the experimental determination of the shaft length and general knowledge about protein structure, an atomic model of the fibre shaft has been constructed by computer modelling techniques. In the final model the three monomers form a left-handed triple-helical structure with threefold symmetry and with successive 15-residue repeats on the same chain related by an axial rise of 13.1 A and a left-handed azimuthal rotation of close to 300 degrees. Three threefold related beta-sheets with short strands are formed by inter-monomer main-chain hydrogen bonds giving rise to superhelical ribbons covering the surface of the shaft. The model satisfies criteria of extensive hydrogen bonding, reasonable backbone torsion angles, burial of most hydrophobic residues and good packing of the hydrophobic core. Furthermore, the model is consistent with the observed shaft length of about 290 A and its calculated X-ray fibre diffraction patterns shows the characteristic features found in the diffraction pattern of crystals of fibre, notably layer lines with a spacing of about 1/26 A-1 and strong meridional intensity at 1/4.4 A-1.
Adenoviruses, Human↗
An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.
The functionally diverse actin, hexokinase, and hsp70 protein families have in common an ATPase domain of known three-dimensional structure. Optimal superposition of the three structures and alignment of many sequences in each of the three families has revealed a set of common conserved residues, distributed in five sequence motifs, which are involved in ATP binding and in a putative interdomain hinge. From the multiple sequence alignment in these motifs a pattern of amino acid properties required at each position is defined. The discriminatory power of the pattern is in part due to the use of several known three-dimensional structures and many sequences and in part to the "property" method of generalizing from observed amino acid frequencies to amino acid fitness at each sequence position. A sequence data base search with the pattern significantly matches sugar kinases, such as fuco-, glucono-, xylulo-, ribulo-, and glycerokinase, as well as the prokaryotic cell cycle proteins MreB, FtsA, and StbA. These are predicted to have subdomains with the same tertiary structure as the ATPase subdomains Ia and IIa of hexokinase, actin, and Hsc70, a very similar ATP binding pocket, and the capacity for interdomain hinge motion accompanying functional state changes. A common evolutionary origin for all of the proteins in this class is proposed.
Actins↗
Evaluation of protein models by atomic solvation preference.
Important properties of globular proteins, such as the stability of the folded state, depend sensitively on interactions with solvent molecules. An excluded volume approximation to protein-solvent interaction, the solvent contact model, was used to derive atomic solvation preference parameters from a database of known protein structures. The ability of solvation preference to discriminate between correct and incorrect three-dimensional structures for a given sequence, or to identify the correct sequence placement in a given structure, was tested. Backbone co-ordinates were taken from experimentally known structures or hypothetical models and side-chain conformations (in rotamer space) were optimized by an efficient Monte Carlo algorithm using simulated annealing and simple potential functions. Discrimination by solvation preference was very clear between deliberately misfolded and correct globular models as well as between native-like and non-native-like topologies of combinatorially generated myoglobin models. Due to its statistical nature, the evaluation works best on entire protein models, while the identification of incorrect parts of models is more difficult. In one case locally incorrect chain tracing in a crystal structure was identified. The method is computationally fast compared to methods based on surface area calculations and is recommended for use as a diagnostic tool in model building based on sequence similarity, in folding simulations and in protein design.
Amino Acid Sequence↗
A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
A new family of mosaic proteins is defined by sequence analysis. The family is characterized by a 260 residue domain common to proteins of apparently diverse function and tissue specificity: sperm receptors Zp2 and Zp3, betaglycan (also called TGF-beta type III receptor), uromodulin, as well as the major zymogen granule membrane protein (GP-2). The location of the common domain is similar with respect to putative transmembrane regions. The results lead to the hypothesis that this type of domain has a common tertiary structure and that there is a functional similarity in the recognition mechanism of the sperm receptor system and the TGF-beta receptor complex.
Amino Acid Sequence↗
Molecular cloning and structural analysis of genes from Zea mays (L.) coding for members of the ras-related ypt gene family.
We have isolated, cloned, and characterized two cDNAs from Zea mays (L.), denoted yptm1 and yptm2, encoding proteins related to the ypt protein family. Amino acid similarity scores with YPT1 from yeast and ypt from mouse are in the range of 70% for yptm1 and 74% for yptm2, respectively, whereas similarities with p21 ras and other ras-related proteins are less than 40%. Most amino acid residues showing identity are clustered in the GTP/GDP binding domain. In addition, two cysteine residues close to the C-terminal ends, known to be palmitoylated and necessary for membrane binding in all eukaryotic ras-related proteins that have been characterized so far, are conserved in the maize genes as well. Northern blot hybridization analysis of poly(A)+ mRNA from etiolated maize coleoptiles revealed single mRNA species of approximately the same size as the isolated cDNAs. The gene for yptm1 is expressed at very low levels in maize coleoptiles and tissue culture cells. The gene for yptm2 is expressed at higher levels and is differentially represented in RNAs isolated from various organs of maize plants, with its highest level in leaves and flowers. The structural similarity of the genes identified suggests that they could be involved in the control of secretory processes.
Amino Acid Sequence↗
The internalization signal in the cytoplasmic tail of lysosomal acid phosphatase consists of the hexapeptide PGYRHV.
Lysosomal acid phosphatase (LAP) is rapidly internalized from the cell surface due to a tyrosine-containing internalization signal in its 19 amino acid cytoplasmic tail. Measuring the internalization of a series of LAP cytoplasmic tail truncation and substitution mutants revealed that the N-terminal 12 amino acids of the cytoplasmic tail are sufficient for rapid endocytosis and that the hexapeptide 411-PGYRHV-416 is the tyrosine-containing internalization signal. Truncation and substitution mutants of amino acid residues following Val416 can prevent internalization even though these residues do not belong to the internalization signal. It was shown recently that part of the LAP cytoplasmic tail peptide corresponding to 410-PPGY-413 forms a well-ordered beta turn structure in solution. Two-dimensional NMR spectroscopy of two modified LAP tail peptides, in which the single tyrosine was substituted either by phenylalanine or by alanine, revealed that the tendency to form a beta turn is reduced by 25% in the phenylalanine-containing peptide and by approximately 50% in the alanine-containing mutant peptide. Our results suggest, that in the short cytoplasmic tail of LAP tyrosine is required for stabilization of the right turn and that the aromatic ring system of the tyrosine residue is a contact point to the putative cytoplasmic receptor.
Acid Phosphatase↗
Selection of representative protein data sets.
The Protein Data Bank currently contains about 600 data sets of three-dimensional protein coordinates determined by X-ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence-structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server "netserv@embl-heidelberg.de." The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three-dimensional protein structures.
Algorithms↗
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
With the completion of the first phase of the European yeast genome sequencing project, the complete DNA sequence of chromosome III of Saccharomyces cerevisiae has become available (Oliver, S. G., et al., 1992, Nature 357, 38-46). We have tested the predictive power of computer sequence analysis of the 176 probable protein products of this chromosome, after exclusion of six problem cases. When the results of database similarity searches are pooled with prior knowledge, a likely function can be assigned to 42% of the proteins, and a predicted three-dimensional structure to a third of these (14% of the total). The function of the remaining 58% remains to be determined. Of these, about one-third have one or more probable transmembrane segments. Among the most interesting proteins with predicted functions are a new member of the type X polymerase family, a transcription factor with an N-terminal DNA-binding domain related to GAL4, a "fork head" DNA-binding domain previously known only in Drosophila and in mammals, and a putative methyltransferase. Our analysis increased the number of known significant sequence similarities on chromosome III by 13, to now 67. Although the near 40% success rate of identifying unknown protein function by sequence analysis is surprisingly high, the information gap between known protein sequences and unknown function is expected to widen and become a major bottleneck of genome projects in the near future. Based on the experience gained in this test study, we suggest that the development of an automated computer workbench for protein sequence analysis must be an important item in genome projects.
Acetolactate Synthase↗
A database of protein structure families with common folding motifs.
The availability of fast and robust algorithms for protein structure comparison provides an opportunity to produce a database of three-dimensional comparisons, called families of structurally similar proteins (FSSP). The database currently contains an extended structural family for each of 154 representative (below 30% sequence identity) protein chains. Each data set contains: the search structure; all its relatives with 70-30% sequence identity, aligned structurally; and all other proteins from the representative set that contain substructures significantly similar to the search structure. Very close relatives (above 70% sequence identity) rarely have significant structural differences and are excluded. The alignments of remote relatives are the result of pairwise all-against-all structural comparisons in the set of 154 representative protein chains. The comparisons were carried out with each of three novel automatic algorithms that cover different aspects of protein structure similarity. The user of the database has the choice between strict rigid-body comparisons and comparisons that take into account interdomain motion or geometrical distortions; and, between comparisons that require strictly sequential ordering of segments and comparisons, which allow altered topology of loop connections or chain reversals. The data sets report the structurally equivalent residues in the form of a multiple alignment and as a list of matching fragments to facilitate inspection by three-dimensional graphics. If substructures are ignored, the result is a database of structure alignments of full-length proteins, including those in the twilight zone of sequence similarity.(ABSTRACT TRUNCATED AT 250 WORDS)
Algorithms↗
Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.
What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.
Algorithms↗
Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology.
An unknown protein structure can be predicted with fair accuracy once an evolutionary connection at the sequence level has been made to a protein of known 3-D structure. In model building by homology, one typically starts with a backbone framework, rebuilds new loop regions, and replaces nonconserved side chains. Here, we use an extremely efficient Monte Carlo algorithm in rotamer space with simulated annealing and simple potential energy functions to optimize the packing of side chains on given backbone models. Optimized models are generated within minutes on a workstation, with reasonable accuracy (average of 81% side chain chi 1 dihedral angles correct in the cores of proteins determined at better than 2.5 A resolution). As expected, the quality of the models decreases with decreasing accuracy of backbone coordinates. If the back-bone was taken from a homologous rather than the same protein, about 70% side chain chi 1 angles were modeled correctly in the core in a case of strong homology and about 60% in a case of medium homology. The algorithm can be used in automated, fast, and reproducible model building by homology.
Algorithms↗
GCI: a network server for interactive 3D graphics.
The Graphics Command Interpreter (GCI) is an independent server module that can be interfaced to any program that needs interactive three-dimensional (3D) graphics capabilities. The principal advantage of GCI is its simplicity. Only a limited set of powerful features have been implemented, including object management, global and local transformations, rotation, translation, clipping, scaling, viewport operations, window management, menu handling and picking. GCI and the master (client) program it serves run concurrently, communicating over a local or remote TCP/IP network. GCI sets up socket communication and provides a 3D graphics window and a terminal emulator for the master program. Communication between the two programs is via ASCII strings over standard I/O channels. The implied language for messages is very simple. GCI interprets messages from the master program and implements them as changes of graphical objects or as text messages to the user. GCI provides the user with facilities to manipulate the view of the displayed 3D objects interactively, independently of the master program, and to communicate mouse-controlled selection of menu items or 3D points as well as keyboard strings to the master program. The program is written in C and initially implemented using the Silicon Graphics GL graphics library. As the need to link special libraries to the master program is completely avoided, GCI can very easily be interfaced to existing programs written in any language and running on any operating system capable of TCP/IP communication. The program is freely available.
Computer Communication Networks↗
A module of the DnaJ heat shock proteins found in malaria parasites.
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Amino Acid Sequence↗
The essential tyrosine of the internalization signal in lysosomal acid phosphatase is part of a beta turn.
For rapid endocytosis lysosomal acid phosphatase requires a Tyr-containing signal in its cytoplasmic domain, as do cell surface receptors mediating endocytosis and clustering in coated pits. To determine the structure of the internalization signal an 18 amino acid peptide representing the cytoplasmic tail of lysosomal acid phosphatase was analyzed by two-dimensional nuclear magnetic resonance spectroscopy. Part of the peptide, 5-PPGY-8, forms a well-ordered beta turn of type I in solution. Our result and data on the structure of the endocytosis signal of the low density lipoprotein receptor reported by Bansal and Gierasch in the accompanying paper represent experimental determinations of the three-dimensional structure of protein transport signals and suggest that the essential aromatic amino acid of internalization signals is recognized by a putative cytoplasmic receptor in the structural context of a tight turn.
Acid Phosphatase↗
(HX)n repeats: a pH-controlled protein-protein interaction motif of eukaryotic transcription factors?
A characteristic sequence repeat of type His-X, repeated several times in a row, is present in several eukaryotic transcription factors, e.g. HPHAHPHP in paired protein. Detailed molecular modelling and database searches lead to the suggestion that (HX)n repeats can mediate interaction between transcription factors in a pH-controlled fashion.
Amino Acid Sequence↗