Tag Archives: function

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…)

Neurons that Control Overeating also Drive Appetite for Cocaine

By Guest PostJune 25, 2012Scienceappetite, behavior, body, brain, brain function, cocaine, cognitive behavior, diabetes, diphtheria toxin, drug addiction, Environment, function, hypothalamus, jeremy bober, jozelia g ferreira, marcelo o dietrich, metabolic disorder, neurons, obesity, overeating, tamas l horvath, transgenic mice

Researchers at Yale School of Medicine have zeroed in on a set of neurons in the part of the brain that controls hunger, and found that these neurons are not only associated with overeating, but also linked to non-food associated behaviors, like novelty-seeking and drug addiction.

Published in the June 24 online issue of Nature Neuroscience, the study was led by Marcelo O. Dietrich, postdoctoral associate, and Tamas L. Horvath, the Jean and David W. Wallace Professor of Biomedical Research and chair of comparative medicine at Yale School of Medicine.

In attempts to develop treatments for metabolic disorders such as obesity and diabetes, researchers have paid increasing attention to the brain’s reward circuits located in the midbrain, with the notion that in these patients, food may become a type of “drug of abuse” similar to cocaine. Dietrich notes, however, that this study flips the common wisdom on its head. (more…)

Homing in on Higgs: Michigan Researchers Predict Summer Discovery

By Guest PostJune 4, 2012Scienceaaron armbruster, algorithms, atlas, atoms, bing zhou, CERN, Chicago, electromagnetic radiation, electrons, fermilab, forces, function, geneva, gordon kane, higgs, higgs boson, higgs field particles, homer neal, jianming qian, junjie zhu, Large Hadron Collider, laws, laws of nature, lhc, missing piece, Nature, neutrons, newton, particle physics, physics theory, protons, quarks, rudolf thun, standard model, stephen hawking, summer, switzerland, tevatron particle accelerator, university of michigan, vacuum like state

ANN ARBOR, Mich.— Whether the Higgs boson exists could be settled by the end of summer, say University of Michigan physicists involved in the search for the missing piece of particle physics’ Standard Model.

“We’re zooming in,” said Jianming Qian, physics professor in the College of Literature, Science & the Arts. “We are increasing the data set and improving our search algorithms. With certain luck, we may be able to discover it this summer, but it depends on nature.”

Qian is one of the 28 U-M researchers involved in experiments at CERN’s Large Hadron Collider (LHC) in Switzerland. He’ll spend most of his time through August in Geneva, where more than 1,000 scientists from around the world have been looking for Higgs since the collider turned on about four years ago. (more…)

Brighter, Smaller Probes to Uncover the Secret Lives of Proteins

By Guest PostMay 10, 20121 commentSciencealexis ostrowski, andrew mueller, berkeley lab, bruce cohen, cellular mechanism, daniel gargas, delia milliron, disease, elan katz, emory chan, erbium, function, gang han, imagine tracking, james schuck, lanthanide, live cell, los angeles, molecule, nanocrystal, nanoparticle, nayf4, photobleach, protein, radio transmitter, sodium yttrium fluoride, vistamar school, wanda robot, ytterbium

Berkeley Lab scientists create nanoparticle probes that may lead to a better understanding of diseases

Imagine tracking a deer through a forest by clipping a radio transmitter to its ear and monitoring the deer’s location remotely. Now imagine that transmitter is the size of a house, and you understand the problem researchers may encounter when they try to use nanoparticles to track proteins in live cells.

Understanding how a protein moves around a cell helps researchers understand the protein’s function and the cellular mechanisms for making and processing proteins. This information also helps researchers study disease, which at a cellular level may mean that a protein is malfunctioning, stops being made, or is sent to the wrong part of the cell. But nanoparticle probes that are too big can disrupt a protein’s normal activities. (more…)

Molecular Spectroscopy Tracks Living Mammalian Cells in Real Time as They Differentiate

By Guest PostMay 2, 2012Scienceals, alzheimer's disease, amino acid residues, apoptosis, bacteria, berkeley lab, carbohydrates, cell change, cell death, children, diabetes, fibroblasts, fluorescent dyes, fourier transform infrared, ftir, function, hans bechtel, hoi ying, hyperspectromicroscopy, ir, kevin loutherback, liang chen, lipids, macular degeneration, michael martin, mitochondrial diseases, pc12, phosphorylation, phosphorylation process, power plant, protein, rafael gomez sjoberg, retina, san diego, serine, spectromicroscopy, threonine, tyrosine, ultraviolet, university of california, zhao hao

Berkeley Lab scientists demonstrate the promise of synchrotron infrared spectroscopy of living cells for medical applications

Knowing how a living cell works means knowing how the chemistry inside the cell changes as the functions of the cell change. Protein phosphorylation, for example, controls everything from cell proliferation to differentiation to metabolism to signaling, and even programmed cell death (apoptosis), in cells from bacteria to humans. It’s a chemical process that has long been intensively studied, not least in hopes of treating or eliminating a wide range of diseases. But until now the close-up view – watching phosphorylation work at the molecular level as individual cells change over time – has been impossible without damaging the cells or interfering with the very processes that are being examined.

“To look into phosphorylation, researchers have labeled specific phosphorylated proteins with antibodies that carry fluorescent dyes,” says Hoi-Ying Holman of the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). “That gives you a great image, but you have to know exactly what to label before you can even begin.” (more…)

Locked RNA Editing Yields Odd Fly Behavior

By Guest PostApril 26, 2012Scienceabiotic factor, als, arthur sugden, asli sahin, brown university, cell, charles lawrence, dadar, enzyme adar, epilepsy, factor, fruit fly, function, genetic, jacquelyn dorsky, james jepson, lauren alpert, locking down, lou gehrigs disease, nucleus, organism, phenomenon, protein, rna, robert reenan, suicidal depression, temperature, wallflowers, yiannis savva

At the level of proteins, organisms can adapt by editing their RNA — and an editor can even edit itself. Brown University scientists working with fruit flies found that “locking down” the self-editing process at two extremes created some strange behaviors. They also found that the process is significantly affected by temperature.

PROVIDENCE, R.I. [Brown University] — Because a function of RNA is to be translated as the genetic instructions for the protein-making machinery of cells, RNA editing is the body’s way of fine-tuning the proteins it produces, allowing us to adapt. The enzyme ADAR, which does this editing job in the nervous system of creatures ranging from mice to men, even edits itself. In a new study that examined the self-editing process and locked it down at two extremes in fruit flies, Brown University scientists found some surprising insights into how this “fine-tuning of the fine-tuner” happens, including bizarre behavioral effects that come about when the self-editor can’t edit. (more…)

Rebuilding a Heart, Saving a Life

By Guest PostApril 19, 2012Healthamerican patient, angela irizarry, birthday, blood vessel, blue babies, bone marrow, bridgeport, cardiac surgeon, christopher breuer, circulatory system, claudia irizarry, congenital heart defect, connecticut, fda, function, gary kopf, hypoplastic, infection, inflammatory response, left heart syndrome, mark saltzman, natural cell, operation, organ, oxygenated blood, polymer, synthetic grafts, synthetic nature, tissue engineered, toshi shinoka, united states, yale doctor, young girl

A young girl in Bridgeport, Connecticut, born with one of the most serious, life-threatening congenital heart defects known, is on her way to living a normal life thanks to Yale doctors who developed and performed the first operation of its kind in the United States.

Angela Irizarry was the first American patient to receive a tissue-engineered blood vessel made of her own natural cells. (more…)

Scientists Find Possible Cause of Movement Defects in Spinal Muscular Atrophy

By Guest PostApril 15, 2012Healthamino acid, childhood disorder, christine beattie, emily caldwell, function, gene, genetic link, genetic manipulation, le hao, levels of protein, marc wolman, michael granato, motor neuron, muscle weakness, nerve cell, plastin 3, protein, sma, smn, spinal cord, spinal muscular atrophy, zebrafish

COLUMBUS, Ohio – An abnormally low level of a protein in certain nerve cells is linked to movement problems that characterize the deadly childhood disorder spinal muscular atrophy, new research in animals suggests.

Spinal muscular atrophy, or SMA, is caused when a child’s motor neurons – nerve cells that send signals from the spinal cord to muscles – produce insufficient amounts of what is called survival motor neuron protein, or SMN. This causes motor neurons to die, leading to muscle weakness and the inability to move. (more…)