Research Interests:
CueR (Cu export regulator) is a metalloregulator protein that "senses" Cu(I) ions with very high affinity, thereby stimulating DNA binding and the transcription activation of two other metalloregulator proteins. The crystal... more
CueR (Cu export regulator) is a metalloregulator protein that "senses" Cu(I) ions with very high affinity, thereby stimulating DNA binding and the transcription activation of two other metalloregulator proteins. The crystal structures of CueR when unbound or bound to DNA and a metal ion are very similar to each other, and the role of CueR and Cu(I) in initiating the transcription has not been fully understood yet. Using double electron-electron resonance (DEER) measurements and structure modeling, we investigate the conformational changes that CueR undergoes upon binding Cu(I) and DNA in solution. We observe three distinct conformations, corresponding to apo-CueR, DNA-bound CueR in the absence of Cu(I) (the "repression" state), and CueR-Cu(I)-DNA (the "activation" state). We propose a detailed structural mechanism underlying CueR's regulation of the transcription process. The mechanism explicitly shows the dependence of CueR activity on copper, ther...
Research Interests:
ATP-binding cassette (ABC) transporters use the energy of ATP hydrolysis to move molecules through cellular membranes. They are directly linked to human diseases, cancer multidrug resistance, and bacterial virulence. Very little is known... more
ATP-binding cassette (ABC) transporters use the energy of ATP hydrolysis to move molecules through cellular membranes. They are directly linked to human diseases, cancer multidrug resistance, and bacterial virulence. Very little is known of the conformational dynamics of ABC transporters, especially at the single-molecule level. Here, we combine single-molecule spectroscopy and a novel molecular simulation approach to investigate the conformational dynamics of the ABC transporter BtuCD. We observe a single dominant population of molecules in each step of the transport cycle and tight coupling between conformational transitions and ligand binding. We uncover transient conformational changes that allow substrate to enter the transporter. This is followed by a 'squeezing' motion propagating from the extracellular to the intracellular side of the translocation cavity. This coordinated sequence of events provides a mechanism for the unidirectional transport of vitamin B by BtuCD.
Research Interests:
There is ongoing debate regarding the mechanism through which cation/proton antiporters (CPAs), like Thermus thermophilus NapA (TtNapA) and Escherichia coli NapA (EcNhaA), alternate between their outward- and inward-facing conformations... more
There is ongoing debate regarding the mechanism through which cation/proton antiporters (CPAs), like Thermus thermophilus NapA (TtNapA) and Escherichia coli NapA (EcNhaA), alternate between their outward- and inward-facing conformations in the membrane. CPAs comprise two domains, and it is unclear whether the transition is driven by their rocking-bundle or elevator motion with respect to each other. Here we address this question using metadynamics simulations of TtNapA, where we bias conformational sampling along two axes characterizing the two proposed mechanisms: angular and translational motions, respectively. By applying the bias potential for the two axes simultaneously, as well as to the angular, but not the translational, axis alone, we manage to reproduce each of the two known states of TtNapA when starting from the opposite state, in support of the rocking-bundle mechanism as the driver of conformational change. Next, starting from the inward-facing conformation of EcNhaA, ...
Research Interests:
Research Interests:
Bioinformatics, Algorithms, Biological Sciences, Protein-Protein Interaction, Software, and 14 moreSequence alignment, Mathematical Sciences, Ligand Binding, Proteins, Computer User Interface Design, Amino Acids, Protein Sequence Analysis, Evolutionary rate, Oxford university, Amino Acid Profile, Amino Acid Sequence, Amino Acid Substitution Rates, Structure activity Relationship, and Molecular Sequence Data
The emergence of the unique H1N1 influenza A virus in 2009 resulted in a pandemic that has spread to over 200 countries. The constellation of molecular factors leading to the emergence of this strain is still unclear. Using a... more
The emergence of the unique H1N1 influenza A virus in 2009 resulted in a pandemic that has spread to over 200 countries. The constellation of molecular factors leading to the emergence of this strain is still unclear. Using a computational approach, we identified molecular determinants that may discriminate the hemagglutinin protein of the 2009 human pandemic H1N1 (pH1N1) strain from that of other H1N1 strains. As expected, positions discriminating the pH1N1 from seasonal human strains were located in or near known H1N1 antigenic sites, thus camouflaging the pH1N1 strain from immune recognition. For example, the alteration S145K (an antigenic position) was found as a characteristic of the pH1N1 strain. We also detected positions in the hemagglutinin protein differentiating classical swine viruses from pH1N1. These positions were mostly located in and around the receptor-binding pocket, possibly influencing binding affinity to the human cell. Such alterations may be liable in part fo...
Research Interests:
Multidisciplinary, Virulence, Humans, Mice, Animals, and 4 moreAmino Acids, Swine, Species Specificity, and Erythrocytes
In search of Botrytis cinerea cell death-inducing proteins, we found a xyloglucanase (BcXYG1), which induced strong necrosis and a resistance response in dicot plants. Expression of the BcXYG1 gene was strongly induced during the first 12... more
In search of Botrytis cinerea cell death-inducing proteins, we found a xyloglucanase (BcXYG1), which induced strong necrosis and a resistance response in dicot plants. Expression of the BcXYG1 gene was strongly induced during the first 12 hours post inoculation, and analysis of disease dynamics using PathTrack{copyright, serif} showed that a B. cinerea strain over expressing BcXYG1 produced early local necrosis supporting a role of BcXYG1 as an early cell death-inducing factor. The xyloglucanase activity of BcXYG1 was not necessary for induction of necrosis and plant resistance, as a mutant of BcXYG1 lacking the xyloglucanase enzymatic activity retained both functions. Residues in two exposed loops on the surface of BcXYG1 were found necessary for induction of cell death, but not for inducing plant resistance. Further analyses showed that BcXYG1 is apoplastic and possibly interacts with the proteins of plant cell membrane, and that the BcXYG1-cell death-promoting signal is mediated ...
Research Interests:
Outer membrane beta barrels (OMBBs) are found in the outer membrane of Gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently... more
Outer membrane beta barrels (OMBBs) are found in the outer membrane of Gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8-36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers and some function only in this state. Using a combination of sensitive sequence-comparison methods and co-evolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include 8-stranded barrels prevail. These multi-barrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multi-barrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis suggests that their functions are not essential, but rather beneficial in specific environments. A...
Research Interests:
Research Interests:
Molecular Evolution, Biological Sciences, Software, Environmental Sciences, Sequence alignment, and 13 moreAnimals, Nucleic Acids, Cattle, Protein Sequence Analysis, Amino Acid Profile, Pattern Search, Multiple Sequence Alignment, Amino Acid Sequence, Internet, Logistic Models, Furin, False Positive, and conserved sequence
The binding of Src to phospholipid membranes requires both hydrophobic insertion of its myristate into the hydrocarbon interior of the membrane and nonspecific electrostatic interaction of its N-terminal cluster of basic residues with... more
The binding of Src to phospholipid membranes requires both hydrophobic insertion of its myristate into the hydrocarbon interior of the membrane and nonspecific electrostatic interaction of its N-terminal cluster of basic residues with acidic phospholipids. We provide a theoretical description of the electrostatic partitioning of Src onto phospholipid membranes. Specifically, we use molecular models to represent a nonmyristoylated peptide corresponding to residues 2-19 of Src [nonmyr-Src(2-19); GSSKSKPKDPSQRRRSLE-NH2] and a phospholipid bilayer, calculate the electrostatic interaction by solving the nonlinear Poisson-Boltzmann equation, and predict the molar partition coefficient using statistical thermodynamics. The theoretical predictions agree with experimental data obtained by measuring the partitioning of nonmyr-Src(2-19) onto phospholipid vesicles: membrane binding increases as the mole percent of acidic lipid in the vesicles is increased, the ionic strength of the solution is decreased, or the net positive charge of the peptide is increased. The theoretical model also correctly predicts the measured partitioning of the myristoylated peptide, myr-Src(2-19); for example, adding 33% acidic lipid to electrically neutral vesicles increases the partitioning of myr-Src(2-19) 100-fold. Phosphorylating either serine 12 (by protein kinase C) or serine 17 (by cAMP-dependent protein kinase) decreases the partitioning of myr-Src(2-19) onto vesicles containing acidic lipid 10-fold. We investigated the effect of phosphorylation on the localization of Src to biological membranes by expressing fusion constructs of Src's N terminus with a soluble carrier protein in COS-1 cells; phosphorylation produces a small shift in the distribution of the Src chimeras from the plasma membrane to the cytosol.
Research Interests:
Biochemistry, Chemistry, Phospholipids, Medicine, Molecular modeling, and 15 moreCircular Dichroism, Animals, Membrane Lipids, Phosphorylation, Partition Coefficient, Protein Conformation, Amino Acid Sequence, Base Sequence, Ionic Strength, Experimental Data, Plasma Membrane, Biochemistry and cell biology, Molecular Sequence Data, Electrostatic interaction, and Medical biochemistry and metabolomics
Research Interests:
Chemical Engineering, Chemistry, Hydrogen, Medicine, Energy Metabolism, and 15 moreBiological Sciences, Physical sciences, Mathematical Computing, Potassium, Free Energy, Sodium, Finite Difference, Protein Conformation, Lipid bilayers, Poisson Boltzmann, Lipid Bilayer, Diffusion Rate, Biochemistry and cell biology, Molecular Structure, and Cell Membrane
Research Interests:
Research Interests:
Engineering, Physics, Chemistry, Biology, Cyanobacteria, and 14 moreMedicine, Multidisciplinary, Macromolecular X-Ray Crystallography, Sequence alignment, Escherichia coli, Motion, PLoS one, Protein Conformation, Amino Acid Sequence, PLANT PROTEINS, Protons, Chloroplasts, Molecular Sequence Data, and Peas
Research Interests:
Molecular Biology, Molecular Evolution, Molecular, Crystal structure, Humans, and 15 moreMutagenesis, Hypertension, Mechanism, Molecular Phylogenetics and Evolution, Protein Secondary Structure Prediction, Three Dimensional, Protein Conformation, Amino Acid Sequence, Recombinant Proteins, Site-directed Mutagenesis, Static Electricity, Biochemistry and cell biology, Molecular Sequence Data, Essential Hypertension, and conserved sequence
Research Interests:
Research Interests:
Computer Science, Algorithms, Computer Graphics, Biology, Medicine, and 15 moreBiological Sciences, DNA, Phylogeny, Environmental Sciences, Humans, Escherichia coli, Animals, Plants, Nucleic Acids, Biological evolution, Protein Domains, Amino Acid Sequence, Base Sequence, Internet, and Nucleic Acid Conformation
Research Interests:
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random... more
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as ‘themes’. At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-to-80 residues, that are unexpectedly shared between domains considered to have emerged independently. Among these ‘bridging themes’ are ones shared between the most an...
Research Interests:
Research Interests:
Thermodynamics, Chemistry, Biophysical Chemistry, Medicine, Biological Sciences, and 14 moreX Rays, Glutamate, Circular Dichroism, Physical sciences, Free Energy, Hydrogen Bond, CHEMICAL SCIENCES, Amino Acid Profile, Amino Acid Sequence, Experimental Data, Lipid Bilayer, Electron Paramagnetic Resonance, Biochemistry and cell biology, and Medical biochemistry and metabolomics
Proteins perform many of their biological roles through protein–protein, protein–DNA or protein–ligand interfaces. The identification of the amino acids comprising these interfaces often enhances our understanding of the biological... more
Proteins perform many of their biological roles through protein–protein, protein–DNA or protein–ligand interfaces. The identification of the amino acids comprising these interfaces often enhances our understanding of the biological function of the proteins. Many methods for the detection of functional interfaces have been developed, and large-scale analyses have provided assessments of their accuracy. Among them are those that consider the size of the protein interface, its amino acid composition and its physicochemical and geometrical properties. Other methods to this effect use statistical potential functions of pairwise interactions, and evolutionary information. The rationale of the evolutionary approach is that functional and structural constraints impose selective pressure; hence, biologically important interfaces often evolve at a slower pace than do other external regions of the protein. Recently, an algorithm, Rate4Site, and a web-server, ConSurf (http://consurf.tau.ac.il/)...
Research Interests:
We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence... more
We recently developed algorithmic tools for the identification of functionally important regions in proteins of known three dimensional structure by estimating the degree of conservation of the amino-acid sites among their close sequence homologues. Projecting the conservation grades onto the molecular surface of these proteins reveals patches of highly conserved (or occasionally highly variable) residues that are often of important biological function. We present a new web server, ConSurf, which automates these algorithmic tools. ConSurf may be used for high-throughput characterization of functional regions in proteins. Availability: The ConSurf web server is available at:http://consurf.tau.ac.il. Supplementary information: A set of examples is available at http://consurf.tau.ac.il under 'GALLERY'.
Research Interests:
Bioinformatics, Computer Science, Molecular Evolution, Biology, Structural Genomics, and 13 moreMedicine, Biological Sciences, Phylogeny, Sequence alignment, Mathematical Sciences, Molecular Phylogenetics and Evolution, Proteins, Computer User Interface Design, Amino Acids, Protein Sequence Analysis, Protein Conformation, Internet, and conserved sequence
Research Interests:
Research Interests:
Biophysics, Chemistry, Biophysical Chemistry, Magnetic Resonance Spectroscopy, Medicine, and 15 moreBiological Sciences, Computer Simulation, Micelles, Lipid Membranes, Free Energy, CHEMICAL SCIENCES, Amino Acids, Amino Acid Profile, Lipid bilayers, Amino Acid Sequence, Experimental Data, Lipid Bilayer, Molecular Sequence Data, Cell Membrane, and Databases as topic
Research Interests:
Microbiology, Electron Microscopy, Molecular Evolution, Biology, Medicine, and 15 moreHIV, Biological Sciences, Crystal structure, Cell line, Humans, Mutation, Drug Design, Capsid, Human immunodeficiency virus, HeLa cells, Amino Acid Profile, Amino Acid Sequence, Base Sequence, Cell Membrane, and Medical and Health Sciences
Research Interests:
Bioinformatics, Algorithms, Programming Languages, Computational Biology, Molecular Evolution, and 15 moreProteomics, Biological Sciences, DNA, Software, Humans, Mathematical Sciences, Maximum Likelihood, Molecular Phylogenetics and Evolution, Enzyme, Amino Acid Profile, Protein Conformation, In Silico, Likelihood Functions, binding sites, and conserved sequence
Research Interests:
Today many algorithms and programs produce biological networks as their primary output (explicit or implicit) . However, it is not always trivial to import this data to network viewer (e.g., Cytoscape). It is even harder to introduce 3D... more
Today many algorithms and programs produce biological networks as their primary output (explicit or implicit) . However, it is not always trivial to import this data to network viewer (e.g., Cytoscape). It is even harder to introduce 3D structure perspective via external molecular viewers (e.g., PyMol, Chimera, Jmol). We propose a framework that allows as-a-service exposure of such programs. Example 1: PPI server
Research Interests:
... Modeling Arnaud Chauvière, Luigi Preziosi, and Claude Verdier Clustering in Bioinformatics and Drug Discovery John D. MacCuish and Norah E. MacCuish Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R... more
... Modeling Arnaud Chauvière, Luigi Preziosi, and Claude Verdier Clustering in Bioinformatics and Drug Discovery John D. MacCuish and Norah E. MacCuish Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R Gabriel Valiente Computational ...
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Bioinformatics, Computer Science, Molecular Evolution, Biology, Membrane Proteins, and 15 moreMedicine, Biological Sciences, Sequence alignment, Mathematical Sciences, Case Study, Amino Acids, Protein Sequence Analysis, Amino Acid Profile, Amino Acid Substitution Rates, Membrane Protein, D structure, False Positive, DNA mutational analysis, Prediction Method, and Direct sequence
Research Interests:
Transmembrane (TM) helical proteins are of fundamental importance in many diverse biological processes. To understand these proteins functionally, it is necessary to characterize the forces that stabilize them. What are these forces (both... more
Transmembrane (TM) helical proteins are of fundamental importance in many diverse biological processes. To understand these proteins functionally, it is necessary to characterize the forces that stabilize them. What are these forces (both within the protein itself and between the protein and membrane) and how do they give rise to the multiple conformational states and complex activity of TM helical
Research Interests:
Research Interests:
Evolutionary Biology, Genetics, Molecular Evolution, Software, Computer Simulation, and 9 moreAnimals, Molecular biology and evolution, Molecular Phylogenetics and Evolution, Proteins, Protein Sequence Analysis, Protein Conformation, Bayes Theorem, Likelihood Functions, and Biochemistry and cell biology
Erythrokeratodermia variabilis (EKV) is a skin disorder characterized by variable (transient) erythemas and fixed keratosis. The disorder maps to chromosome 1p34–35, a location that contains the GJB3 gene encoding the ...
Research Interests:
Gap Junctions, Biology, Medicine, Biological Sciences, Protein Structure and Function, and 15 moreHumans, Keratinocytes, Mutation, Human Molecular Genetics, Lead, Pedigree, Keratosis, HeLa cells, Amino Acid Sequence, Amino Acid Substitution Rates, Molecular Sequence Data, DNA mutational analysis, Connexins, Erythema, and Medical and Health Sciences
Research Interests:
Human NHA2 is a poorly characterized Na+/H+ antiporter recently implicated in essential hypertension. We used a range of computational tools and evolutionary conservation analysis to build and validate a three-dimensional model of NHA2... more
Human NHA2 is a poorly characterized Na+/H+ antiporter recently implicated in essential hypertension. We used a range of computational tools and evolutionary conservation analysis to build and validate a three-dimensional model of NHA2 based on the crystal structure of a distantly related bacterial transporter, NhaA. The model guided mutagenic evaluation of transport function, ion selectivity and pH dependence of NHA2 by phenotype screening in yeast. We describe a cluster of essential, highly conserved titratable residues located in an assembly region made of two discontinuous helices of inverted topology, each interrupted by extended chain. Whereas in NhaA, oppositely charged residues compensate for partial dipoles generated within this assembly, in NHA2, polar but uncharged residues suffice. Our findings led to a model for transport mechanism that was compared to the well known electroneutral NHE1 and electrogenic NhaA subtypes. This study establishes NHA2 as a prototype for the poorly understood, yet ubiquitous, CPA2 antiporter family recently recognized in plants and metazoans and illustrates a structure-driven approach to derive functional information on a newly discovered transporter.
Research Interests:
Molecular Biology, Molecular Evolution, Molecular, Crystal structure, Humans, and 15 moreMutagenesis, Hypertension, Mechanism, Molecular Phylogenetics and Evolution, Protein Secondary Structure Prediction, Three Dimensional, Protein Conformation, Amino Acid Sequence, Recombinant Proteins, Site-directed Mutagenesis, Static Electricity, Biochemistry and cell biology, Molecular Sequence Data, Essential Hypertension, and conserved sequence
Research Interests:
Algorithms, Molecular Biology, Protein Folding, Molecular Evolution, Quality Control, and 15 moreMolecular Recognition, Phylogeny, Humans, Animals, Proteins, Phylogenetic Trees, Protein Domains, Hot Spot, Phylogenetic Tree, Protein Conformation, Multiple Sequence Alignment, Protein Modeling, Binding Site, Biochemistry and cell biology, and binding sites
Proteins share similar segments with one another. Such "reused parts"-which have been successfully incorporated into other proteins-are likely to offer an evolutionary advantage over de novo evolved segments, as most of the... more
Proteins share similar segments with one another. Such "reused parts"-which have been successfully incorporated into other proteins-are likely to offer an evolutionary advantage over de novo evolved segments, as most of the latter will not even have the capacity to fold. To systematically explore the evolutionary traces of segment "reuse" across proteins, we developed an automated methodology that identifies reused segments from protein alignments. We search for "themes"-segments of at least 35 residues of similar sequence and structure-reused within representative sets of 15,016 domains [Evolutionary Classification of Protein Domains (ECOD) database] or 20,398 chains [Protein Data Bank (PDB)]. We observe that theme reuse is highly prevalent and that reuse is more extensive when the length threshold for identifying a theme is lower. Structural domains, the best characterized form of reuse in proteins, are just one of many complex and intertwined evoluti...
Research Interests:
The receptor binding protein of parainfluenza virus, hemagglutinin-neuraminidase (HN), is responsible for actively triggering the viral fusion protein (F) to undergo a conformational change leading to insertion into the target cell and... more
The receptor binding protein of parainfluenza virus, hemagglutinin-neuraminidase (HN), is responsible for actively triggering the viral fusion protein (F) to undergo a conformational change leading to insertion into the target cell and fusion of the virus with the target cell membrane. For proper viral entry to occur, this process must occur when HN is engaged with host cell receptors at the cell surface. It is possible to interfere with this process through premature activation of the F protein, distant from the target cell receptor. Conformational changes in the F protein and adoption of the postfusion form of the protein prior to receptor engagement of HN at the host cell membrane inactivate the virus. We previously identified small molecules that interact with HN and induce it to activate F in an untimely fashion, validating a new antiviral strategy. To obtain highly active pretriggering candidate molecules we carried out a virtual modeling screen for molecules that interact wit...
Research Interests:
Microbiology and Mbio
Research Interests:
ABSTRACT
Research Interests:
Research Interests:
Tyrosine kinase receptors of the EGFR family play a significant role in vital cellular processes and in various cancers. EGFR members are unique among kinases, as the regulatory elements of their kinase domains are constitutively ready... more
Tyrosine kinase receptors of the EGFR family play a significant role in vital cellular processes and in various cancers. EGFR members are unique among kinases, as the regulatory elements of their kinase domains are constitutively ready for catalysis. Nevertheless, the receptors are not constantly active. This apparent paradox has prompted us to seek mechanisms of regulation in EGFR's cytoplasmic domain that do not involve conformational changes of the kinase domain. Our computational analyses, based on the three-dimensional structure of EGFR's kinase domain suggest that direct contact between the kinase and a segment from the C-terminal regulatory domains inhibits enzymatic activity. EGFR activation would then involve temporal dissociation of this stable complex, for example, via ligand-induced contact formation between the extracellular domains, leading to the reorientation of the transmembrane and intracellular domains. The model provides an explanation at the molecular le...
Research Interests:
Overexpression of the receptor tyrosine kinase (RTK) erbB2 (also designated neu or HER2) was implicated in causing a variety of human cancers, including mammary and ovarian carcinomas. Ligand-induced receptor dimerization is critical for... more
Overexpression of the receptor tyrosine kinase (RTK) erbB2 (also designated neu or HER2) was implicated in causing a variety of human cancers, including mammary and ovarian carcinomas. Ligand-induced receptor dimerization is critical for stimulation of the intrinsic protein tyrosine kinase (PTK) of RTKs. It was therefore proposed that PTK activity is stimulated as a result of the reorientation of the cytoplasmic domains within receptor dimers, leading to transautophosphorylation and stimulation of enzymatic activity. Here, we propose a molecular mechanism for rotation-coupled activation of the erbB2 receptor. Using a computational exploration of conformation space of the transmembrane (TM) segments of an erbB2 homodimer, we found two stable conformations of the TM domain. We suggest that these conformations correspond to the active and inactive states of erbB2, and that the receptor molecules may switch from one conformation to the other without crossing exceedingly unfavorable stat...