Annotation of glycoproteins in the SWISS-PROT database.

SWISS-PROT is a protein sequence database, which aims to be nonredundant, fully annotated and highly cross-referenced. Most eukaryotic gene products undergo co- and/or post-translational modifications, and these need to be included in the database in order to describe the mature protein. SWISS-PROT includes information on many types of different protein modifications. As glycosylation is the most common type of post-translational protein modification, we are currently placing an emphasis on annotation of protein glycosylation in SWISS-PROT. Information on the position of the sugar within the polypeptide chain, the reducing terminal linkage as well as additional information on biological function of the sugar is included in the database. In this paper we describe how we account for the different types of protein glycosylation, namely N-linked glycosylation, O-linked glycosylation, proteoglycans, C-linked glycosylation and the attachment of glycosyl-phosphatidylinosital anchors to proteins.

GlycoMod--a software tool for determining glycosylation compositions from mass spectrometric data.

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS-PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease-produced peptides (including any post-translational modifications annotated in these databases) which have the potential to be glycosylated with either N- or O-linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.

SWISS-PROT: connecting biomolecular knowledge via a protein database.

With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database.

A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae.

Members of the RNA helicase protein family are defined by several motifs that have been widely conserved during evolution. They are found in all organisms-from bacteria to humans-and many viruses. The minimum number of RNA helicases present within a eukaryotic cell can be predicted from the complete sequence of the Saccharomyces cerevisiae genome. Recent progress in the functional analysis of various family members has confirmed the significance of RNA helicases for most cellular RNA metabolic processes. We have assembled a web resource that focuses on RNA helicases from the budding yeast Saccharomyces cerevisiae. It includes descriptions of RNA helicases and their functions, links to sequence- and yeast-specific databases, an extensive list of references, and links to non-yeast helicase web resources.

Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection.

We have developed a new algorithm to identify proteins by means of peptide mass fingerprinting. Starting from the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra and environmental data such as species, isoelectric point and molecular weight, as well as chemical modifications or number of missed cleavages of a protein, the program performs a fully automated identification of the protein. The first step is a peak detection algorithm, which allows precise and fast determination of peptide masses, even if the peaks are of low intensity or they overlap. In the second step the masses and environmental data are used by the identification algorithm to search in protein sequence databases (SWISS-PROT and/or TrEMBL) for protein entries that match the input data. Consequently, a list of candidate proteins is selected from the database, and a score calculation provides a ranking according to the quality of the match. To define the most discriminating scoring calculation we analyzed the respective role of each parameter in two directions. The first one is based on filtering and exploratory effects, while the second direction focuses on the levels where the parameters intervene in the identification process. Thus, according to our analysis, all input parameters contribute to the score, however with different weights. Since it is difficult to estimate the weights in advance, they have been computed with a generic algorithm, using a training set of 91 protein spectra with their environmental data. We tested the resulting scoring calculation on a test set of ten proteins and compared the identification results with those of other peptide mass fingerprinting programs.

A molecular scanner to automate proteomic research and to display proteome images.

Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today's commonly used high-throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, a number of limitations still adversely affect the rate of protein identification and annotation in 2-DE databases: the sequential excision process of pieces of gel containing protein; the enzymatic digestion step; the interpretation of mass spectra (reliability of identifications); and the manual updating of 2-DE databases. We present a highly automated method that generates a fully annoated 2-DE map. Using a parallel process, all proteins of a 2-DE are first simultaneously digested proteolytically and electro-transferred onto a poly(vinylidene difluoride) membrane. The membrane is then directly scanned by MALDI-TOF MS. After automated protein identification from the obtained peptide mass fingerprints using PeptIdent software (http://www.expasy.ch/tools/peptident.html + ++), a fully annotated 2-D map is created on-line. It is a multidimensional representation of a proteome that contains interpreted PMF data in addition to protein identification results. This "MS-imaging" method represents a major step toward the development of a clinical molecular scanner.

High-throughput mass spectrometric discovery of protein post-translational modifications.

The availability of genome sequences, affordable mass spectrometers and high-resolution two-dimensional gels has made possible the identification of hundreds of proteins from many organisms by peptide mass fingerprinting. However, little attention has been paid to how information generated by these means can be utilised for detailed protein characterisation. Here we present an approach for the systematic characterisation of proteins using mass spectrometry and a software tool FindMod. This tool, available on the internet at http://www.expasy.ch/sprot/findmod.html , examines peptide mass fingerprinting data for mass differences between empirical and theoretical peptides. Where mass differences correspond to a post-translational modification, intelligent rules are applied to predict the amino acids in the peptide, if any, that might carry the modification. FindMod rules were constructed by examining 5153 incidences of post-translational modifications documented in the SWISS-PROT database, and for the 22 post-translational modifications currently considered (acetylation, amidation, biotinylation, C-mannosylation, deamidation, flavinylation, farnesylation, formylation, geranyl-geranylation, gamma-carboxyglutamic acids, hydroxylation, lipoylation, methylation, myristoylation, N -acyl diglyceride (tripalmitate), O-GlcNAc, palmitoylation, phosphorylation, pyridoxal phosphate, phospho-pantetheine, pyrrolidone carboxylic acid, sulphation) a total of 29 different rules were made. These consider which amino acids can carry a modification, whether the modification occurs on N-terminal, C-terminal or internal amino acids, and the type of organisms on which the modification can be found. We illustrate the utility of the approach with proteins from 2-D gels of Escherichia coli and sheep wool, where post-translational modifications predicted by FindMod were confirmed by MALDI post-source decay peptide fragmentation. As the approach is amenable to automation, it presents a potentially large-scale means of protein characterisation in proteome projects.

Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number.

Two-dimensional (2-D) gel electrophoresis is often used in proteome projects to provide a global view of the proteins expressed in any cell or tissue type. Here we have investigated the effects of protein hydrophobicity and cellular protein copy number on a protein's presence or absence on a two-dimensional gel. The average hydropathy values of all known proteins from Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae were calculated, thus defining the range of protein hydrophobicity and hydrophilicity in these organisms. The average hydropathy values were then calculated for a total of 427 proteins from these species, which had been identified elsewhere on 2-D gels. Strikingly, it was seen that no highly hydrophobic proteins, as defined by average hydrophobicity values, have been found to date on 2-D gel separations of whole cell lysates. A clear hydrophobicity cutoff point was seen, above which current 2-D electrophoresis methods appear not to be useful for protein separation. The effect of cellular protein copy number on a protein's presence on a 2-D gel was investigated by means of a graphical model. This model showed how variations in protein loading and copy number per cell interact to determine the quantity of a protein that will be present on a 2-D gel. Considering the current maximum in 2-D gel loading capacity, it was found that 2-D probably can not visualize or produce analytical quantities of proteins present at less than 1000 copies per cell. We conclude that further developments of 2-D electrophoresis techniques are desirable to enable the visualization and analysis of all proteins expressed by a cell or tissue.

Protein identification with N and C-terminal sequence tags in proteome projects.

Genome sequences are available for increasing numbers of organisms. The proteomes (protein complement expressed by the genome) of many such organisms are being studied with two-dimensional (2D) gel electrophoresis. Here we have investigated the application of short N-terminal and C-terminal sequence tags to the identification of proteins separated on 2D gels. The theoretical N and C termini of 15, 519 proteins, representing all SWISS-PROT entries for the organisms Mycoplasma genitalium, Bacillus subtilis, Escherichia coli, Saccharomyces cerevisiae and human, were analysed. Sequence tags were found to be surprisingly specific, with N-terminal tags of four amino acid residues found to be unique for between 43% and 83% of proteins, and C-terminal tags of four amino acid residues unique for between 74% and 97% of proteins, depending on the species studied. Sequence tags of five amino acid residues were found to be even more specific. To utilise this specificity of sequence tags for protein identification, we created a world-wide web-accessible protein identification program, TagIdent (http://www.expasy.ch/www/tools.html), which matches sequence tags of up to six amino acid residues as well as estimated protein pI and mass against proteins in the SWISS-PROT database. We demonstrate the utility of this identification approach with sequence tags generated from 91 different E. coli proteins purified by 2D gel electrophoresis. Fifty-one proteins were unambiguously identified by virtue of their sequence tags and estimated pI and mass, and a further 11 proteins identified when sequence tags were combined with protein amino acid composition data. We conlcude that the TagIdent identification approach is best suited to the identification of proteins from prokaryotes whose complete genome sequences are available. The approach is less well suited to proteins from eukaryotes, as many eukaryotic proteins are not amenable to sequencing via Edman degradation, and tag protein identification cannot be unambiguous unless an organism's complete sequence is available.

Multiple parameter cross-species protein identification using MultiIdent--a world-wide web accessible tool.

Recent increases in the number of genome sequencing projects means that the amount of protein sequence in databases is increasing at an astonishing pace. In proteome studies, this is facilitating the identification of proteins from molecularly well-defined organisms. However, in studies of proteins from the majority of organisms, proteins must be identified by comparing analytical data to sequences in databases from other species. This process is known as cross-species protein identification. Here we present a new program, MultiIdent, which uses multiple protein parameters such as amino acid composition, peptide masses, sequence tags, estimated protein pI and mass, to achieve cross-species protein identification. The program is structured so that protein amino acid composition, which is highly conserved across species boundaries, first generates a set of candidate proteins. These proteins are then queried with other protein parameters such as sequence tags and peptide masses. A final list of database entries which considers all analytical parameters is presented, ranked by an integrated score. We illustrate the power of the approach with the identification of a set of standard proteins, and the identification of proteins from dog heart separated by two-dimensional gel electrophoresis. The MultiIdent program is available on the world-wide web at: http://www.expasy.ch/sprot/multiident.h tml.

Construction of the gyrB Database for the Identification and Classification of Bacteria.

Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities. However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level. We have therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences. We chose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species. We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences. The resultant data have been assembled into the gyrB database accessible via WWW.

Detailed peptide characterization using PEPTIDEMASS--a World-Wide-Web-accessible tool.

In peptide mass fingerprinting, there are frequently peptides whose masses cannot be explained. These are usually attributed to either a missed cleavage site during the chemical or enzymatic cutting process, the lack of reduction and alkylation of a protein, protein modifications like the oxidation of methionine, or the presence of protein post-translational modifications. However, they could equally be due to database errors, unusual splicing events, variants of a protein in a population, or artifactual protein modifications. Unfortunately the verification of each of these possibilities can be tedious and time-consuming. To better utilize annotated protein databases for the understanding of peptide mass fingerprinting data, we have written the program "PEPTIDEMASS". This program generates the theoretical peptide masses of any protein in the SWISS-PROT database, or of any sequence specified by the user. If the sequence is derived from the SWISS-PROT database, the program takes into account any annotations for that protein in order to generate the peptide masses. In this manner, the user can obtain the predicted masses of peptides from proteins which are known to have signal sequences, propeptides, transit peptides, simple post-translational modifications, and disulfide bonds. Users are also warned if any peptide masses are subject to change from protein isoforms, database conflicts, or an mRNA splicing variation. The program is freely accessible to the scientific community via the ExPASy World Wide Web server, at the URL address: http://www.expasy.ch/www/tools.html.

LALNVIEW: a graphical viewer for pairwise sequence alignments.

LALNVIEW is a graphical program for visualising local alignments between two sequences (protein or nucleic acids). Sequences are represented by coloured rectangles to give an overall picture of their similarities. LALNVIEW can display sequence features (exon, intron, active site, domain, propeptide, etc.) along with the alignment. When using LALNVIEW through our Web servers, sequence features are automatically extracted from database annotations (SWISS-PROT, GenBank, EMBL or HOVERGEN) and displayed with the alignment. LALNVIEW is a useful tool for analysing pairwise sequence alignments and for making the link between sequence homology and what is known about the structure or function of sequences. LALNVIEW executables for UNIX, Macintosh and PC computers are freely available from our server (http:// expasy.hcuge.ch/sprot/lalnview.html).

Multisystemic chromatolytic neuronal degeneration in Cairn terriers. A case with generalized cataplectic episodes.

Multisystemic chromatolytic neuronal degeneration, a newly recognized disease of Cairn Terriers, is described in a second affected North American puppy. In this puppy, the early onset of hind limb weakness at 11 weeks and rapid development of signs of diffuse CNS involvement were distinctive. Signs of cerebellar dysfunction were prominent, but bouts of cataplectic collapse in this puppy constituted the most distinguishing clinical feature. Although electroencephalograph (EEG) recordings lacked a true rapid eye movement (REM) pattern during cataplectic episodes, cervical electromyograph (EMG) potentials ceased or diminished, and imipramine injection was associated with arousal. Postmortem studies revealed that chromatolytic degeneration was very widespread, affecting many neuronal populations in the brain and spinal cord as well as neurons in sensory ganglia. Although the pattern of chromatolysis varied among affected perikarya, chromatolysis was consistently related to dispersion and loss of ribosomes. In this puppy, as opposed to six studied previously, thoracolumbar myelomalacia also occurred symmetrically in the dorsal horns and adjoining funicular white matter. The metabolic derangement underlying this chromatolytic neuronal degeneration and myelomalacia remains unknown.

Interictal afterdischarge in focal penicillin epilepsy: block by thalamic cooling.

Interictal spikes recorded from a penicillin focus in the precruciate cortex of urethane-anesthetized cats were followed by brief afterdischarge oscillations that occurred at a delay of 170 to 220 ms from the interictal spike and consisted of as many as five cycles at 16 to 22/s. The origin of this afterdischarge was investigated by cooling different subcortical sites and thus blocking them reversibly. At none of the sites did cooling result in a block of the interictal spike whereas cooling of the ventrolateral nucleus of the thalamus resulted in block of the afterdischarge. Other subcortical sites had either no or less reliable effects on it. We conclude that afterdischarge but not the interictal spike depends on thalamic input, either as a generator of the rhythm or as a trigger for a cortically maintained oscillation.

Interictal afterdischarge in focal penicillin epilepsy: thalamocortical unit activity.

The involvement of thalamic versus cortical structures for the initiation and maintenance of brief interictal afterdischarge was evaluated by recording extracellularly units and field potentials from different subcortical and cortical sites. Afterdischarge oscillations at 16 to 22/s that followed interictal spikes with a delay of 170 to 220 ms usually appeared 10 to 30 min after the topical application of penicillin to the cat's precruciate cortex. Units in the ventrolateral nucleus of the thalamus fired in burst discharges during cortical afterdischarge and less reliably during the cortical interictal spike. In contrast, units recorded at the cortical penicillin focus and homologous contralateral site remained silent during afterdischarge but had a typical burst discharge during the interictal spike. Although these data support a thalamic basis for the rhythm, the lack of an afterdischarge-like oscillation in the thalamic field potential and the independent appearance of afterdischarge and cortical recruiting waves elicited by stimulation of the nucleus reticularis would favor its cortical origin. In accordance with its frequency characteristics and data gained from earlier cooling studies we suggest a cortical mechanism requiring thalamic triggering for the generation of afterdischarge.

Caudate unit activity and somal diameters in intact and nigral lesioned cats.

In a search for morphofunctional relationships in the head of the caudate nucleus (CN), we recorded extracellular unit activity in intact cats and in cats that had received bilateral injections of 6-OHDA into the substantia nigra (SN) 30 days previously. Only units firing spontaneously and continuously for 2 min were studied. In dorsal regions, potentials were small and iterative at almost constant intervals; the somal diameters were relatively small. In the ventrolateral region, potentials were bigger and appeared in bursts; somal diameters were significantly larger (p less than 0.05). For the centromedial region a histogram of numbers of neurons as a function of diameters revealed a Gaussian distribution extending from small to large neurons. Most dorsal neurons increased their firing rate to radial nerve, visual, SN, and/or nucleus centralis medialis (NCM) stimulation. Ventral neurons usually responded with excitation followed by long lasting inhibition, particularly to SN and NCM stimulation. A few neurons responded to all four inputs and some showed long-lasting potentiation in response to low frequency stimulation, suggesting a more general function. Greatest convergence (65%) was found for NCM and SN inputs. In lesioned cats, there was no SN driving, NCM's inhibitory actions almost disappeared, and the excitatory action of the other stimuli was reduced.