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M Linial

Publications and source records attributed to M Linial.

At least 19 recordsLinked to original sources
PubMed2001

SUVi and BACH1: a new subfamily of mammalian helicases?

The RecQ family of DNA helicases have been shown to be important for the maintenance of genomic integrity in prokaryotes and eukaryotes. Members of this family are genes responsible for cancer predisposition disorders like Bloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome. Here, we show the sequence homologies between two recently identified mammalian helicases, namely SUVi and BACH1. These two genes also share strong homologies with other members of the RecQ family. On the basis of published data and sequence analysis we suggest that SUVi/BACH1 may represent a novel subfamily of mammalian helicases, functioning in the processing of lesions induced by different genotoxic agents.

Amino Acid Sequence↗
PubMed2001

Direct interaction of a brain voltage-gated K+ channel with syntaxin 1A: functional impact on channel gating.

Presynaptic voltage-gated K(+) (Kv) channels play a physiological role in the regulation of transmitter release by virtue of their ability to shape presynaptic action potentials. However, the possibility of a direct interaction of these channels with the exocytotic apparatus has never been examined. We report the existence of a physical interaction in brain synaptosomes between Kvalpha1.1 and Kvbeta subunits with syntaxin 1A, occurring, at least partially, within the context of a macromolecular complex containing syntaxin, synaptotagmin, and SNAP-25. The interaction was altered after stimulation of neurotransmitter release. The interaction with syntaxin was further characterized in Xenopus oocytes by both overexpression and antisense knock-down of syntaxin. Direct physical interaction of syntaxin with the channel protein resulted in an increase in the extent of fast inactivation of the Kv1.1/Kvbeta1.1 channel. Syntaxin also affected the channel amplitude in a biphasic manner, depending on its concentration. At low syntaxin concentrations there was a significant increase in amplitudes, with no detectable change in cell-surface channel expression. At higher concentrations, however, the amplitudes decreased, probably because of a concomitant decrease in cell-surface channel expression, consistent with the role of syntaxin in regulation of vesicle trafficking. The observed physical and functional interactions between syntaxin 1A and a Kv channel may play a role in synaptic efficacy and neuronal excitability.

Animals↗
PubMed2001

Involvement of extracellular signal-regulated kinase (ERK) in pardaxin-induced dopamine release from PC12 cells.

Pardaxin (PX), an ionophore-peptide neurotoxin isolated from the fish Pardachirus marmoratus, induces neurotransmitter release from neuronal preparations by both calcium-dependent and calcium-independent mechanisms. The aim of the present study was to investigate the role of extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) in pardaxin-induced dopamine (DA) release. The experiments were performed on variants of the PC12 cell line, an established cellular model for investigating DA release. Time course experiments indicated that PX, at nontoxic concentrations, stimulated ERK1 and ERK2 within 5 to 15 min, measured with a dual phospho-ERK antibody. PX stimulation of ERK activity was calcium (Ca(2+))-dependent and followed by ERK translocation to the nucleus. This effect was temporally related to PX-induced exocytosis, and measured by [(3)H]dopamine release as well as by a vesicle fusion-based enzyme-linked immunosorbent assay. Blocking ERK activity with the specific mitogen-activated protein kinase kinase inhibitors PD98059 (50 microM for 45 min) and UO126 (30 microM for 30 min) inhibited PX-induced exocytosis in the presence but not in the absence of extracellular Ca(2+). These results suggest the essential role of ERKs in PX-induced DA release under physiological conditions and support the hypothesis that ERKs are involved in regulating exocytosis.

Animals↗
PubMed2000

Estimating the probability for a protein to have a new fold: A statistical computational model.

Structural genomics aims to solve a large number of protein structures that represent the protein space. Currently an exhaustive solution for all structures seems prohibitively expensive, so the challenge is to define a relatively small set of proteins with new, currently unknown folds. This paper presents a method that assigns each protein with a probability of having an unsolved fold. The method makes extensive use of protomap, a sequence-based classification, and scop, a structure-based classification. According to protomap, the protein space encodes the relationship among proteins as a graph whose vertices correspond to 13,354 clusters of proteins. A representative fold for a cluster with at least one solved protein is determined after superposition of all scop (release 1.37) folds onto protomap clusters. Distances within the protomap graph are computed from each representative fold to the neighboring folds. The distribution of these distances is used to create a statistical model for distances among those folds that are already known and those that have yet to be discovered. The distribution of distances for solved/unsolved proteins is significantly different. This difference makes it possible to use Bayes' rule to derive a statistical estimate that any protein has a yet undetermined fold. Proteins that score the highest probability to represent a new fold constitute the target list for structural determination. Our predicted probabilities for unsolved proteins correlate very well with the proportion of new folds among recently solved structures (new scop 1.39 records) that are disjoint from our original training set.

Amino Acid Sequence↗
PubMed2000

ProtoMap: automatic classification of protein sequences and hierarchy of protein families.

The ProtoMap site offers an exhaustive classification of all proteins in the SWISS-PROT database, into groups of related proteins. The classification is based on analysis of all pairwise similarities among protein sequences. The analysis makes essential use of transitivity to identify homologies among proteins. Within each group of the classification, every two members are either directly or transitively related. However, transitivity is applied restrictively in order to prevent unrelated proteins from clustering together. The classification is done at different levels of confidence, and yields a hierarchical organization of all proteins. The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies. Many clusters contain protein sequences that are not classified by other databases. The hierarchical organization suggested by our analysis may help in detecting finer subfamilies in families of known proteins. In addition it brings forth interesting relationships between protein families, upon which local maps for the neighborhood of protein families can be sketched. The ProtoMap web server can be accessed at http://www.protomap.cs.huji.ac.il

Computer Graphics↗
PubMed2000

Methodologies for target selection in structural genomics.

As the number of complete genomes that have been sequenced keeps growing, unknown areas of the protein space are revealed and new horizons open up. Most of this information will be fully appreciated only when the structural information about the encoded proteins becomes available. The goal of structural genomics is to direct large-scale efforts of protein structure determination, so as to increase the impact of these efforts. This review focuses on current approaches in structural genomics aimed at selecting representative proteins as targets for structure determination. We will discuss the concept of representative structures/folds, the current methodologies for identifying those proteins, and computational techniques for identifying proteins which are expected to adopt new structural folds.

Databases, Factual↗
PubMed2000

Why aren't foamy viruses pathogenic?

Foamy viruses are complex retroviruses that lead to either highly cytopathic or persistent infections in vitro, but to non-pathogenic lifelong infections in naturally or accidentally infected hosts. Factors that could contribute to these benign persistent infections include regulated transcription from the two viral promoters, the functions of the Bet accessory protein and the host immune response.

Animals↗
PubMed2000

Culturing neuronal cells on surfaces coated by a novel polyethyleneimine-based polymer.

Maintaining cells in culture is essential for studying many aspects of cell biology and physiology. Cell culturing is dependent on proper anchorage of cells to the growth surfaces. For most cell lines, and especially for post-mitotic neurons, coated tissue culture plates are prerequisite for seeding. The most commonly used coating reagents are positively charged polymers such as poly-L-lysine or biologically purified adhesive molecules such as collagen. In this report, we present a simple procedure for synthesizing and for coating cell culture surfaces. The reagent is a biologically inert hydrophobized polyethyleneimine (PEI), which provides adequate adhesive properties for cultured cell lines including those of neuronal lineage. The hydrophobized PEI is branched PEI modified by octadecanyl groups bound to 2 mol% of the amino groups of the PEI. Unlike the native PEI that is water soluble, the modified PEI is soluble in ethanol, and thus resistant to solubilization in biological media. The protocol of coating was optimized for tissue culture plates as well as glass surfaces and in many respects this polymer outperformed other routinely used coating reagents. Neuronal cell lines, plated on the polymer-treated surfaces are resistant to manipulations including repeated media changes and extensive washing. The advantage of coating surfaces with the developed PEI-based polymer compared to other commonly used coating reagents is discussed.

Animals↗
PubMed2000

Using Bayesian networks to analyze expression data.

DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a "snapshot" of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998).

Algorithms↗
PubMed1999

ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space.

We investigate the space of all protein sequences in search of clusters of related proteins. Our aim is to automatically detect these sets, and thus obtain a classification of all protein sequences. Our analysis, which uses standard measures of sequence similarity as applied to an all-vs.-all comparison of SWISSPROT, gives a very conservative initial classification based on the highest scoring pairs. The many classes in this classification correspond to protein subfamilies. Subsequently we merge the subclasses using the weaker pairs in a two-phase clustering algorithm. The algorithm makes use of transitivity to identify homologous proteins; however, transitivity is applied restrictively in an attempt to prevent unrelated proteins from clustering together. This process is repeated at varying levels of statistical significance. Consequently, a hierarchical organization of all proteins is obtained. The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies. Different indices of validity were applied to assess the quality of our classification and compare it with the protein families in the PROSITE and Pfam databases. Our classification agrees with these domain-based classifications for between 64.8% and 88.5% of the proteins. It also finds many new clusters of protein sequences which were not classified by these databases. The hierarchical organization suggested by our analysis reveals finer subfamilies in families of known proteins as well as many novel relations between protein families.

Algorithms↗
PubMed1999

Depolarization affects the binding properties of muscarinic acetylcholine receptors and their interaction with proteins of the exocytic apparatus.

Membrane depolarization is the signal that triggers release of neurotransmitter from nerve terminals. As a result of depolarization, voltage-dependent Ca(2+) channels open, level of intracellular Ca(2+) increases. and release of neurotransmitter commences. Previous study had shown that in rat brain synaptosomes, muscarinic acetylcholine (ACh) receptors (mAChRs) interact with soluble NSF attachment protein receptor proteins of the exocytic machinery in a voltage-dependent manner. It was suggested that this interaction might control the rapid, synchronous release of acetylcholine. The present study investigates the mechanism for such a voltage-dependent interaction. Here we show that depolarization shifts mAChRs, specifically the m2 receptor subtype, to a low affinity state toward its agonists. At resting potential, mAChRs are in a high affinity state (K(d) of approximately 20 nM) and they shift to a low affinity state (K(d) of tens of microM) upon membrane depolarization. In addition, interaction between m2 receptor subtype and the exocytic machinery increases with receptor occupancy. Both phenomena are independent of Ca(2+) influx. We propose that these results may explain control of ACh release from nerve terminals. At resting potential the exocytic machinery is clamped due to its interaction with the occupied mAChR and depolarization relieves this interaction. This, together with Ca(2+) influx, enables release of ACh to commence.

Acetylcholine↗
PubMed1999

Nonlinear optical measurement of membrane potential around single molecules at selected cellular sites.

Membrane potential around single molecules has been measured by using the nonlinear optical phenomenon of second harmonic generation. This advance results from the interaction between a highly dipolar molecule with a selectively directed highly polarizable 1-nm gold particle. With this approach, a second harmonic signal, which is enhanced by the nanoparticle, is detected from a volume of nanometric dimensions. This present work clearly shows that functional cellular imaging around single molecules is possible by selectively directing an antibody with a 1-nm gold label to a specific membrane protein. The results of this work open the way for three-dimensional, high resolution functional imaging of membrane electrophysiology in cells and cellular networks.

Animals↗
PubMed1998

Ca2+-dependent exocytosis in mast cells is stimulated by the Ca2+ sensor, synaptotagmin I.

Mast cells secrete a variety of biologically active substances that mediate inflammatory responses. Synaptotagmin(s) (Syts) are a gene family of proteins that are implicated in the control of Ca2+-dependent exocytosis. In the present study, we investigated the possible occurrence and functional involvement of Syt in the control of mast cell exocytosis. Here, we demonstrate that both connective tissue type and mucosal-like mast cells express Syt-immunoreactive proteins, and that these proteins are localized almost exclusively to their secretory granules. Furthermore, expression of Syt I, the neuronal Ca2+ sensor, in rat basophilic leukemia cells (RBL-2H3), a tumor analogue of mucosal mast cells, resulted in prominent potentiation and acceleration of Ca2+-dependent exocytosis. Therefore, these findings implicate Syt as a Ca2+ sensor that mediates regulated secretion in mast cells to calcium ionophore.

Animals↗
PubMed1998

Expression and localization of muscarinic receptors in P19-derived neurons.

The muscarinic acetylcholine receptors are important in a variety of physiological processes such as induction of secretion from various glands and regulation of pacemaker activity, muscle tone, and neurotransmission. To date, the muscarinic receptor family includes five members (designated m1-m5), of which m1-m4 are abundant in brain and in peripheral tissues, and m5 is found exclusively in brain, and even there at very low levels. The expression of m1-m5 receptor subtypes was studied in neurons derived from the murine embryonal carcinoma cell line P19. These cells serve as a model system for differentiation and maturation of neurons resembling CNS neurons. Our results show that P19 neurons express mainly the m2, m3, and m5 subtypes. Low levels of m1 receptors are also detected and m4 subtype is practically absent. Furthermore, muscarinic receptors in P19 neurons are functional in activating second messenger signaling pathways. The localization of m2 receptors is predominantly presynaptic, whereas the m5 subtype is mainly postsynaptic. Consequently, P19 cells provide a model system for the study of pre- and postsynaptic muscarinic acetylcholine-receptor subtypes in a proper neuronal context. This is particularly valid for the rare m5 receptors.

Adenylyl Cyclase Inhibitors↗
PubMed1998

Highly sensitive ELISA-based assay for quantifying protein levels in neuronal cultures.

A simple assay for quantifying the expression level of proteins in situ is presented. The assay is performed directly in culture plates and simply requires incubating the cells (either fixed or in live cultures) with the appropriate antibody against the desired protein. Cells are then incubated with a peroxidase-conjugated secondary antibody followed by incubation with the soluble peroxidase substrate-tetramethylbenzidine. Antibody binding levels are quantified in an ELISA-based protocol by reading optical density at 450 nm. The assay is applicable for any surface-attached cell culture. The assay is highly sensitive, allowing detection of expressed proteins in a monolayer of cell cultured in a 96 well plate. The assay was optimized for a neuronal cell-line-P19. These are embryonal carcinoma cells which differentiate into neurons after treatment with retinoic acid. The neurons do not survive well in 96 well plates and are thus plated in 24 or 48 well plates. We demonstrate the use of the method for an in vivo labeling of neurons by quantifying epitopes which are exposed upon nerve stimulation. Advantages of a routine ELISA protocol in quantification over wide range of sensitivity and in performing simultaneous large number of repetitions and different controls are thus fully extended to live cell cultures.

Animals↗
PubMed1998

A map of the protein space--an automatic hierarchical classification of all protein sequences.

We investigate the space of all protein sequences. We combine the standard measures of similarity (SW, FASTA, BLAST), to associate with each sequence an exhaustive list of neighboring sequences. These lists induce a (weighted directed) graph whose vertices are the sequences. The weight of an edge connecting two sequences represents their degree of similarity. This graph encodes much of the fundamental properties of the sequence space. We look for clusters of related proteins in this graph. These clusters correspond to strongly connected sets of vertices. Two main ideas underlie our work: i) Interesting homologies among proteins can be deduced by transitivity. ii) Transitivity should be applied restrictively in order to prevent unrelated proteins from clustering together. Our analysis starts from a very conservative classification, based on very significant similarities, that has many classes. Subsequently, classes are merged to include less significant similarities. Merging is performed via a novel two phase algorithm. First, the algorithm identifies groups of possibly related clusters (based on transitivity and strong connectivity) using local considerations, and merges them. Then, a global test is applied to identify nuclei of strong relationships within these groups of clusters, and the classification is refined accordingly. This process takes place at varying thresholds of statistical significance, where at each step the algorithm is applied on the classes of the previous classification, to obtain the next one, at the more permissive threshold. Consequently, a hierarchical organization of all proteins is obtained. The resulting classification splits the space of all protein sequences into well defined groups of proteins. The results show that the automatically induced sets of proteins are closely correlated with natural biological families and super families. The hierarchical organization reveals finer sub-families that make up known families of proteins as well as many interesting relations between protein families. The hierarchical organization proposed may be considered as the first map of the space of all protein sequences. An interactive web site including the results of our analysis has been constructed, and is now accessible through http:/(/)www.protomap.cs.huji.ac.il

Algorithms↗
PubMed1997

Voltage-dependent interaction between the muscarinic ACh receptor and proteins of the exocytic machinery.

1. Release of neurotransmitter into the synaptic cleft is the last step in the chain of molecular events following the arrival of an action potential at the nerve terminal. The neurotransmitter exerts negative feedback on its own release. This inhibition would be most effective if exerted on the first step in this chain of events, i.e. a step that is mediated by membrane depolarization. Indeed, in numerous studies feedback inhibition was found to be voltage dependent. 2. The purpose of this study is to investigate whether the mechanism underlying feedback inhibition of transmitter release resides in interaction between the presynaptic autoreceptors and the exocytic apparatus, specifically the soluble NSF-attachment protein receptor (SNARE) complex. 3. Using rat synaptosomes we show that the muscarinic ACh autoreceptor (mAChR) is an integral component of the exocytic machinery. It interacts with syntaxin, synaptosomal-associated protein of 25 kDa (SNAP-25), vesicle-associated membrane protein (VAMP) and synaptotagmin as shown using both cross-linking and immunoprecipitation. 4. The interaction between mAChRs and both syntaxin and SNAP-25 is modulated by depolarization levels; binding is maximal at resting potential and disassembly occurs at higher depolarization. 5. This voltage-dependent interaction of mAChRs with the secretory core complex appears suitable for controlling the rapid, synchronous neurotransmitter release at nerve terminals.

Animals↗