Tag Archives: protein

The Best of Both Catalytic Worlds

By Guest PostOctober 13, 2012ScienceBerkeley, berkeley lab, biochemistry, biomolecule, california, cancer, catalysis program, catalyst, catalytic reactivity, chemical reaction, cholesterol medicine, complex reaction, cyclopropanation reaction, cyclopropane, dean toste, dendrimers, elad gross, enzyme, gabor somorjai, gold nanocluster, heterogeneous, homogeneous, industrial catalyst, metal catalysts, metal nanocluster, molecule, palladium, pamam, platinum, product selectivity, property, protein, recyclability, rhodium, substance, university

Berkeley Lab Researchers Develop New Technique for Heterogenizing Homogenous Nano Catalysts

Catalysts are substances that speed up the rates of chemical reactions without themselves being chemically changed. Industrial catalysts come in two main types – heterogeneous, in which the catalyst is in a different phase from the reactants; and homogeneous, in which catalyst and the reactants are in the same phase. Heterogeneous catalysts are valued for their sustainability because they can be recycled. Homogeneous catalysts are valued for their product selectivity as their properties can be easily tuned through relatively simple chemistry.

Researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have combined the best properties of both types of industrial catalysts by encapsulating nanoclusters of a metallic heterogeneous catalyst within the branched arms of the molecules known as dendrimers. (more…)

Sticky Paper Offers Cheap, Easy Solution for Paper-Based Diagnostics

By Guest PostOctober 4, 2012Scienceacidity, antibodies, arthur yu, biological molecule, chemical trick, daniel ratner, diabetes, diagnostic, disease, divinyl sulfone, DNA, fluorescent ricin, galactose, george whitesides, global, harvard university, health research, immune system, industrial solvent, jing shang, malaria, medical test, nitrocellulose, oldest technology, paper, paper stick, paul yager, plain paper, poison, pregnancy test, protein, rodrigo andrade, sticky membrane, university, Washington, ziploc bag

A current focus in global health research is to make medical tests that are not just cheap, but virtually free. One such strategy is to start with paper – one of humanity’s oldest technologies – and build a device like a home-based pregnancy test that might work for malaria, diabetes or other diseases.

A University of Washington bioengineer recently developed a way to make regular paper stick to medically interesting molecules. The work produced a chemical trick to make paper-based diagnostics using plain paper, the kind found at office supply stores around the world. (more…)

Berkeley Lab Scientists Create First 3-D Model of a Protein Critical to Embryo Development

By Guest PostSeptember 21, 2012Science3d model, aebp2, alessio maiolica, angstroms, arm1, arm2, berkeley lab, birth defect, cancer, chromatin environment, claudio ciferri, complex, complex 2, crystal structure, DNA, electron microscopy, eva nogales, franz herzog, function, gabriel lander, human, mass spectrometry, mechanism, model, molecular architecture, nucleosome, polycomb, prc2, progression, protein, protein biochemistry, repressive, ruedi aebersold, therapeutic drug

The first detailed and complete picture of a protein complex that is tied to human birth defects as well as the progression of many forms of cancer has been obtained by an international team of researchers led by scientists with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). Knowing the architecture of this protein, PRC2, for Polycomb Repressive Complex 2, should be a boon to its future use in the development of new and improved therapeutic drugs.

“We present a complete molecular organization of human PRC2 that offers an invaluable structural context for understanding all of the previous biochemical and functional data that has been collected on this complex,” says Berkeley Lab biophysicist Eva Nogales, an electron microscopy expert who led this research. “Our model should also be an invaluable tool for the design of new experiments aimed at asking detailed questions about the mechanisms that enable PRC2 to function and how those mechanisms might be exploited.” (more…)

Relieving Plant Stress Could Eventually Help Humans Relax

By Guest PostSeptember 14, 2012Scienceanimal model, arabidopsis mutant, biologist, biotechnology, cell, cell material, coal mine, disease, Environment, federica brandizzi, human growth, humans, ire1, michigan, multifunctional protein, plant, protein, state university, stress

EAST LANSING, Mich. — Humans could learn from how plants handle stress.

Federica Brandizzi, Michigan State University plant biologist, is using a grant from the National Institutes of Health to study how plants overcome stress as they grow. These pathways used to overcome stress are a key to growth. Without them plants, and animals, would die.

“When cells grow, they undergo trauma as growth is quite stressful,” Brandizzi said. “Since it’s very likely that these pathways have much in common between humans and plants, we should be able to gain insights into how plants and animals overcome stress and continue to grow as well.” (more…)

Yale Team Finds Order Amidst the Chaos Within the Human Genome; Mom and Dad’s Contributions Counted and Fossil DNA Not Dead After All

By Guest PostSeptember 6, 2012Sciencebiochemically, bottleneck, chao cheng, data mining, DNA, ekta khurana, elements, encode, encyclopedia, evolutionary remnant, fossil dna, gender specific, gene expression, genome, genome dynamic, human genome, joel rozowsky, junk, key function, koon kiu yan, mark gerstein, marker, middle manager, military, model organism, molecular interaction, non coding, protein, pseudogenes, regulation, rnas, social network, statistical model, worm, yale, yale researcher

The Encyclopedia of DNA Elements (ENCODE) project is the effort of hundreds of scientists to describe the workings of the human genome. Their research, outlined in 30 papers published in multiple journals Sept. 5, has confirmed our genome is far more complex than originally thought. Regions that contain instructions for making proteins, which carry out life’s functions, account for only about 1 percent of our genome. ENCODE has shed light on the other 99%. Almost 80 percent of the genome is biochemically active, much of it involved in some sort of regulation of genes. Vast regions of our DNA once considered “junk” contain some 400,000 regulators called enhancers, which play a key role activating or silencing genes despite residing far away from the gene itself. Yale University researchers played a key role ENCODE, helping to author 9 of the 30 papers published in four journals on Sept. 5. Some of their work is described below.

The massive Encyclopedia of DNA Elements (ENCODE) unveiled Sept. 5 reveals a human genome vastly more rich and complex than envisioned even a decade ago. In a key supporting paper published in the journal Nature, the lab of Yale’s Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics, has found order amidst the seeming chaos of trillions of potential molecular interactions. (more…)

To Cap or Not to Cap: Scientists Find New RNA Phenomenon That Challenges Dogma

By Guest PostSeptember 2, 2012Sciencebaskar bakthavachalu, brian kennedy, cancer, cell, cell life, chandrama mukherjee, cytoplasm, daniel schoenberg, deepak patil, embryonic development, gene, hibernation, messenger rna, mitotic cell cycle, molecule, mrna, neurological activity, ohio state university, protein, rna

COLUMBUS, Ohio – Some RNA molecules spend time in a restful state akin to hibernation rather than automatically carrying out their established job of delivering protein-building instructions in cells, new research suggests.

And instead of being a fluke or a mistake, the research suggests that this restful period appears to be a programmed step for RNA produced by certain types of genes, including some that control cell division and decide where proteins will work in a cell to sustain the cell’s life.

This could mean that protein production in cells is not as clear-cut as biology textbooks suggest, scientists say. (more…)

Form, Function and Folding: In Collaboration with Berkeley Lab, a Team of Scientists Move Toward Rational Design of Artificial Proteins

By Guest PostAugust 26, 2012Scienceamino acid, barney yoo, berkeley lab, bioinspired nanomaterial, blind structure, function, glenn butterfoss, ilya chorny, jonathan jaworski, ken dill, kent kirshenbaum, modeling, molecular foundry, n alkyl, natural selection, new york university, peptoid molecule, peptoid trimers, prediction, protein, protein sequence, qm, qm calculation, remd, richard bonneau, ronald zuckermann, stony brook university, structure, synthetic cousin, temple university, vincent voelz, xray crystallography

In the world of proteins, form defines function. Based on interactions between their constituent amino acids, proteins form specific conformations, folding and twisting into distinct, chemically directed shapes. The resulting structure dictates the proteins’ actions; thus accurate modeling of structure is vital to understanding functionality.

Peptoids, the synthetic cousins of proteins, follow similar design rules. Less vulnerable to chemical or metabolic breakdown than proteins, peptoids are promising for diagnostics, pharmaceuticals, and as a platform to build bioinspired nanomaterials, as scientists can build and manipulate peptoids with great precision. But to design peptoids for a specific function, scientists need to first untangle the complex relationship between a peptoid’s composition and its function-defining folded structure. (more…)

Some Harmful Effects of Light at Night Can Be Reversed, Study Finds

By Guest PostJuly 27, 2012Sciencebrain, chronic exposure, depression, depressive disorder, depressive symptom, drug, hamster, harmful effects, hippocampus, light, light cycle, light dark cycle, night, protein, randy nelson, rodent, siberian hamsters, tnf, tnf inhibitor, tracy bedrosian, tumor necrosis factor, xpro1595, zachary weil

COLUMBUS, Ohio – Chronic exposure to dim light at night can lead to depressive symptoms in rodents – but these negative effects can be reversed simply by returning to a standard light-dark cycle, a new study suggests.

While hamsters exposed to light at night for four weeks showed evidence of depressive symptoms, those symptoms essentially disappeared after about two weeks if they returned to normal lighting conditions.

Even changes in the brain that occurred after hamsters lived with chronic light at night reversed themselves after returning to a more normal light cycle. (more…)