Binding in Biological News

Flexible neck in cell-receptor DC-SIGN targets more pathogens

... show that flexibility in the region near the binding sites of DC-SIGN plays a significant role in ... to block this interaction." To study the binding behavior of DC-SIGN (Dendritic Cell-Specific ... When the protein binds to a pathogen, binding sites on the cell receptor rearrange slightly, to ...

Computers aid in cracking deception in plants

... protein candidates by identifying protein binding sites in the soybean that match with those in the ... our case, we're trying to find a specific protein binding site among a group of proteins from the nematode that match a particular binding site in the soybean using a set of chemical ...

International team tracks clues to HIV

... virus, HIV-1 PR, by attaching themselves to its binding pocket. "There are a lot of people doing this ... strong, but there's potentially a very strong binding effect. The problem is, it's not the perfect ... about a very simple experiment to calculate the binding efficiency of a molecule in the HIV pocket, then ...

Princeton team's analysis of flu virus could lead to better vaccines

... suggest that if a way can be found to weaken the binding of the less effective antibodies, then this might ... ones that are well matched to and good at binding to the infecting virus, and ineffective ones that are poorly matched to and bad at binding to the infecting virus, and consequently stay out ...

6 young ASU faculty earn NSF Career awards

... is for $600,000 and will be used to study the binding mechanism of sequence specific DNA-binding ... initiation and DNA replication. Their binding is characterized by large conformational changes, ... It is not understood how the folding, bending and binding are coupled, and it is not understood what ...

Genetic switch potential key to new class of antibiotics

... change their spatial organization, which entails binding to a small signaling partner, promises to inform ... tRNA for protein building. The mRNA's ribosome binding site is instead locked up by the preQ1 ... it stacks on the RNA bases in the riboswitch binding pocket with high affinity, adding stability to ...

CSHL researchers explain process by which cells 'hide' potentially dangerous DNA segments

... methyl-decorated chromatin. The importance of binding strength The CSHL team in collaboration with ... into the Chp1 protein decreased the strength of binding to different levels. Even a five-fold decrease in binding strength prevented the mutation-bearing cells ...

Scripps scientists find structure of a protein that makes cancer cells resistant to chemotherapy

... another similarity between MsbA and P-gpboth binding cavities are lined with hydrophobic amino acidsit ... are additional amino acids for fine-tuning the binding to specific drugs." Knowing what the P-gp binding cavity looks like and precisely where substances ...

Scripps research scientists 'watch' as individual alpha-synuclein proteins change shape

... and an extended helix as the surface that it is binding to changes. Such shape shifting has rarely ... says. "It is interesting that with just a single binding partner, the protein can undergo so many dramatic ... protein reacts to what is in effect a different binding partner, even though it is the same small ...

Boehringer Ingelheim uses Genomatix' Next Generation Sequencing data analysis systems

... and peak finding, and performs automated binding pattern identification. For RNAseq experiments, ... groups of identified genes, transcription factor binding site (TFBS) analysis ( identification, over-representation, binding partner analysis, framework identification, ...

A pocketful of uranium

... to develop a protein that offers the uranyl ion a binding cavity in which it is surrounded by the protein's ... bind to the DNA. The nickel ion is located in a binding cavity in which it is surrounded by a square-planar arrangement of binding groups. By using several mutation steps, the ...

A new gene silencing platform -- silence is golden

... independent, functions. First is a target-gene binding domain that can be tailored to any gene. The second domain inhibits mRNA maturation by binding U1 snRNP, a component of the cellular splicing ... the oligonucleotide are independent so transcript binding and U1 ...

Genomatix joins Illumina-Connect program

... and peak finding, and performs automated binding pattern identification. For RNAseq experiments, ... groups of identified genes, transcription factor binding site (TFBS) analysis ( identification, over-representation, binding partner analysis, framework identification, ...

How chromosomes meet in the dark -- Switch that turns on X chromosome matchmaking

... This is an important mechanism as the binding togetgher of too many of too few of a particular ... researchers looked at a particular "DNA specific binding molecule" including a protein known as CTCF that ... beads that had almost the same number of chemical binding sites on their beads as the number of known ...

Scientists study how asbestos fibers trigger cancer in human cells

... events when the fiber touches the cell. Does the binding occur over minutes, or hours? And what processes ... study. "The hypothesis we're testing is that binding of cell surface receptors to asbestos fibers ... human cell. Understanding the intricacies of the binding process between the mineral and one or more ...

Gaps in adhesion

... the number of the links in the chain carrying the binding dopa adjuncts has no overall relevance for the ... that consisted completely of links with the binding dopa adjunct and some where it was only present ... to a certain extent, independent on the number of binding sites could be used to give the other links in ...

New data resource to advance computer-aided drug design

... been established to make important structural and binding data available so researchers can tackle this ... published literature as well as from Carlson's binding MOAD (for "Mother of All Databases"), which ... Wang, Ph.D., and provides experimentally measured binding data. The team will conduct experiments to ...

Atomic-resolution views suggest function of enzyme that regulates light-detecting signals in eye

... enzyme undergoes major structural changes upon binding of the cGMP molecule. Before binding occurs, the GAF domain is like an outstretched ... PDE enzyme," Heikaus said. Researchers think the binding to the domain may act as a switch that turns on ...

UC Davis researchers discover new drug target for inflammatory disease

... in screening potential drugs that can block the binding process and hopefully the immune response it ... and team evaluated the possibility of integrin binding by sPLA2-IIA using a computer program that ... be working to screen for molecules that block the binding of sPLA2-IIA to integrins and show that this ...

Structural biology spin-out tackles major diseases

... see the interaction between the hormone and the binding protein in exquisite detail. Our understanding ... drugs that consist of this pairing of hormone and binding protein that still allows them to activate the ... hormones and protective receptor domains (the binding proteins) that could be used to tackle major ...

N.Y. research team discovers how antidepressants and cocaine interact with brain cell targets

... The main surprise was the realization that two binding sites on the transporter molecule need to be ... Like a key engaging a lock mechanism, this second binding causes changes in the transporter throughout the ... binds in the deep site, unlike the antidepressant binding in the bacterial transporter. Therefore, the ...

Scientists reveal the key mechanisms for affinity between transient binding proteins

... between proteins, which recognise their binding partner by affinity features localized on the ... . "Knowing what determines protein-protein binding may have implications, for example, in the design ... that two proteins recognise each other as binding partners falls outside the lineal contact motif, ...

Researchers coat titanium with polymer to improve integration of joint replacements

... fibronectin, a protein in the body that acts as a binding site for cell surface receptors called integrins. ... It is important to control the integrins binding to the titanium implant because integrins provide ... bone formation. Therefore, controlling integrin binding to the titanium will result in targeted signals ...

New clues to how proteins dissolve and crystallize

... indicated that the large difference between the binding efficiency of the two cations (which are ... microjet technology to measure the selective binding of sodium and potassium to formate and acetate, ... absorption spectra tell you about the relative binding energies of sodium, potassium, and lithium." ...

A new idea for how anti-aging products delay ripening of fruit and wilting of flowers

... Plant cells possess copper-containing ethylene binding sites called ethylene receptors. (An ethylene ... that sits in the cell membrane and has a site for binding ethylene on the outside of the cell.) When ... works by beating ethylene to the receptors. By binding with a sufficient number of receptors chemically ...

The myth of runner's high revisited with brain imaging

... And further: 'Respectively the opioid receptor binding of the [18F]FDPN decreases, since there is a ... study could demonstrate a significantly decreased binding of the [18F]FDPN-ligand. This is a strong ... the high is experienced, the lower the binding of [18F]FDPN was in the PET scan. And this means ...

Bright lights: Mystery of glowing antibody solved by Scripps research scientists

... which relay biological reactions such as ligand binding and antibody-antigen actions into detectable ... from other antibody-stilbene complexes, where binding merely enhances stilbene fluorescence by ... of stilbene in solution. In fact, the unusual binding mode of stilbene in EP2-19GE2 is enabled by a ...

Uncharged organic molecule can bind negatively charged ions

... that gives us access to a whole new family of binding agents," said Amar Flood, who reports the ... processes. Attempts at manufacturing organic binding agents with positively charged parts is not hard, ... organic molecule whose center would serve as the binding spot. A halide ion might fit snugly inside the ...

Astronomy technology brings nanoparticle probes into sharper focus

... a single molecule, such as how the molecule is binding in a gene sequence, taking scientists a few steps ... reveal important information about the size and binding geometry of targeted molecules. We had no way ... nanoparticles are designed to recognize two binding sites on a single target. Then the particles are ...

Biophysical Society announces winners of 2008 Student Travel Awards

... Planar Model Membranes: Recruitment by Native binding Ligands versus GPI-anchored Proteins. Joel ... of Michigan, Quantitative Inference of Protein binding Affinities from FRET Imaging Data. Brannon ... c Induced By Changes of Ionic Strength and Anion binding to Protein Surface Charges. Leila Shokri, ...

CWRU School of Medicine has evidence vaccine against malaria will reduce disease

... malaria parasite. The research suggests a Duffy binding protein-based vaccine could provide protection ... antigen on human red blood cells and the Duffy binding protein expressed by the parasite to establish ... By interrupting the interaction of parasite binding to the red cell, the researchers and their ...

Researchers expand efforts to explore functional landscape of the human genome

... has two goals: to identify transcription factor binding sites by using chromatin immunoprecipitation ... researchers will identify transcription factor binding sites in the human genome using chromatin ... to computationally predict transcription factor binding sites that determine the activities of promoters. ...

MIT model could improve some drugs' effectiveness

... for improved efficacy. This can lead to improved binding affinities but the process is time-consuming, and ... and conformations, and predict the molecules' binding affinity for their targets based on the ... able to achieve a 140-fold improvement in its binding affinity. The authors expect the model will be ...

Chemists get grip on slippery lipids

... in this process by protein molecules called lipid binding domains. Understanding how these domains work ... various inflammatory diseases. Studying lipid binding domains is a specialty of Wonhwa Cho, ... describe mechanisms by which a particular binding domain -- the PX or "Phox" -- recognize specific ...

How cancer spreads by aggregating platelets

... rhodocytin stimulates platelet aggregation by binding to a protein called C-type lectin-like receptor 2 ... platelets in a way similar to a key (rhodocytin) binding to a lock (CLEC-2). By studying the details ... says. Preventing CLEC-2 and podoplanin from binding to each other may be a good therapeutic way of ...

Gene regulation in humans is closer than expected to simple organisms

... (transcription factors) to 6 - 10 nucleotide long binding sequences located on the DNA, activating or ... the regulated gene. Our ability to identify these binding sites is essential to understand the way ... study of functional human transcription factor binding sites that encompasses nearly ten thousand genes ...

Carnegie Mellon scientists investigate initial molecular mechanism that triggers neuronal firing

... until now. The docking site (or ligand binding domain) closes when glutamate binds to it. ... change is critical to understanding how binding regulates the protein channel, Kurnikova added. ... the molecular mechanism that switches the binding domains conformation from open to closed, ...

The tiny difference in the genes of bacteria

... certain dyes. Each dyed DNA fragment recognizes a single tandem repeat, binding at it. As a result, the researchers receive, for example, six red fragments binding a tandem of six repetitions. Then, the researchers analyzed the tandem ...

The tiny difference in the genes of bacteria

... certain dyes. Each dyed DNA fragment recognizes a single tandem repeat, binding at it. As a result, the researchers receive, for example, six red fragments binding a tandem of six repetitions. Then, the researchers analyzed the tandem ...

Researchers observe single protein dimers wavering between two symmetrically opposed structures

... shapes back and forth between different structures, depending on its binding to molecular partners. Now, a collaboration among the Deniz laboratory, ... thus alter their function. Theoretically, it would only take different binding partners or changes in the cell's pH, ions, or the presence of other small ...