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Schmidt-Rohr to join Chemistry faculty

March 19, 2014 By

Klaus Schmidt-RohrThe Department of Chemistry is looking forward to welcoming Klaus Schmidt-Rohr to the faculty this July.

Prof. Schmidt-Rohr is a highly regarded spectroscopist, with a background in both physics and chemistry.  His research is focused on materials and his recent studies have revised our understanding of the structure of Nafion membranes (the proton selective membranes on which most hydrogen fuel cells now depend), the surfaces of nanodiamonds, the molecular bases of bone strength, and the molecular composition of biochar.  Schmidt-Rohr approaches materials primarily through solid state NMR, with a distinctive emphasis on skillful spectral editing.  He has also complimented these experiments with innovative analyses of small angle x-ray scattering data.

Prof. Schmidt-Rohr received his Ph.D. from the University of Mainz in Germany and continued at the Max-Planck Institute in Mainz as a staff scientist. Following postdoctoral work at UC Berkeley, as a fellow of the BASF AG and the German National Science Foundation, he took a faculty position in the Department of Polymer Science & Engineering at the University of Massachusetts at Amherst.  More recently, he has been a Professor of Chemistry at Iowa State University.

Prof. Schmidt-Rohr’s pioneering work has been recognized with prestigious awards, including the Rudolph-Kaiser Prize from the German Physical Society, a Beckman Young Investigator Award from the Arnold and Mabel Beckman Foundation, an Alfred P. Sloan Research Fellowship, the John H. Dillon Medal of the Polymer Division of the American Physical Society, and fellowship in the American Association for the Advancement of Science and in the American Physical Society.

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Courses for Spring 2013 (I): Advanced NMR spectroscopy

November 2, 2012 By

Course registration for Spring 2013 has opened. I asked faculty to share details about new (and old) exciting and different courses being offered this spring.

Tom Pochapsky (Chemistry) writes:
Product Details

We are offering our CHEM 146 “Advanced NMR spectroscopy” course again in the spring, appropriate for grads and advanced undergrads in physics, chem, biochem, biophysics.   Pre-reqs are Physics 10 or equivalent, Math 10 or equivalent.   There is a laboratory component this year (using the 800), intro to theory of NMR and practical applications.  The text for the course is our book [ed.: NMR for Physical and Biological Scientists (Thomas Pochapsky and Susan Sondej Pochapsky, authors)], now available as an e-book.

 

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Otten named Damon Runyon Fellow

January 10, 2012 By

Renee Otten, a postdoctoral fellow in the Kern lab at Brandeis, has been awarded a November 2011 Damon Runyon Fellowship to support his postdoctoral research. Otten received his Ph.D. in 2011 from the University of Groningen, working on applying NMR spectroscopic methods to studying the relationship between protein structure and dynamics. The fellowship will support his continued efforts to use NMR to study dynamics and enzyme catalysis in protein kinases.

Filed Under: Biochemistry, labs, postdocs Tagged With: , , , , , ,

An Amyloid Organelle

December 23, 2011 By

There is a common notion that “If Nature can find a use for something, She will.” and this story has been gradually playing out for the cross-beta protein fold. Known generally as “amyloid”, the cross-beta fold was first identified in pathologies including neurodegenerative disorders such as Alzheimer’s and systemic amyloidoses such as amyotrophic lateral sclerosis (often referred to as “Lou Gehrig’s Disease”). This happenstance initially pegged the fold as a feature unique to abnormal proteins. However, it subsequently became clear that normal proteins subjected to abnormal conditions would also assume the cross-beta fold. Still, it seemed that the fold was a sign of proteins gone awry. Then came discoveries of cross-beta folds in native, functional proteins. Some are primarily extracellular bacterial proteins involved in negotiating air-water interfaces at sporulation. But some involve the intracellular packaging of proteins in humans. Now Brandeis investigators Eugenio Daviso, Marina Belenky and Judith Herzfeld, with MIT collaborators Marvin Bayro and Robert Griffin, have found that an entire organelle is assembled with the cross-beta fold.1 Gas vesicles, the pressure-resistant floatation organelles of aquatic micro-organisms, comprise a protein-encased gas bubble. Assembly and disassembly of these bodies allows the cells to navigate up and down the water column and the cross-beta fold of the protein shell lends the vesicles the strength and interfacial stability that is critical for their function.

(Left) Schematic of the architecture of a gas vesicle. The gas vesicle is a bipolar cylinder with conical end caps. The ribs of the vesicle comprise GvpA monomers assembled in a low pitch helix. The horizontal lines shown within one of these ribs illustrate the orientation of the β-strands of GvpA as determined previously by x-ray diffraction.2 The expanded view of this rib shows the contacts between β-strands that have now been detected with solid-state NMR, thus establishing the presence of a continuous cross-beta sheet.1

1.      Bayro M, Daviso E, Belenky M, Griffin RG and Herzfeld J*. An Amyloid Organelle: Solid State NMR Evidence for Cross-Beta Assembly of Gas Vesicles.  J. Biol. Chem., DOI 10.1074/jbc.M111.313049.

2.      Blaurock AE and Walsby AE (1976) Crystalline structure of the gas vesicle wall from Anabaena flos-aquae, J. Mol. Biol. 105, 183-199.

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No Dice

December 16, 2011 By

Magnetic resonance is a powerful tool for interrogating materials at the atomic level, whether in determining protein structures or imaging the body. The procedure entails measuring the dynamics of the magnetism after it has been perturbed by radio waves. Usually the evolution is sampled at equal intervals, which is straightforward over one evolution period. However, experiments increasingly involve transfers of magnetization between different groups of atoms and require measurements after each transfer. In such experiments, it can become overwhelming to sample all the points in each evolution period, from the early ones needed because they have the strongest signal, to the late points needed because they provide the resolution of different contributions. Therefore, much recent attention has been given to finding ways to sample non-uniformly. This work led to a consensus that if one drops points it is necessary to do so randomly to minimize artifacts. The problem is that one can randomly get a very bad sampling schedule and waste a whole experiment (worse yet without necessarily knowing that the sampling schedule is the problem). Now, a MIT-Brandeis team1 has shown that non-uniform sampling need not be random and that adhering closely to a suitable distribution function produces high quality results.

1.      Eddy MT, Ruben D, Griffin RG and Herzfeld J*.  Deterministic schedules for robust and reproducible non-uniform sampling in multidimensional NMR, J. Magn. Reson. (2011), doi:10.1016/j.jmr.2011.12.002

An example of cumulative distribution functions (top) and results (bottom) for non-random sampling (right) compared with random sampling (left).

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What is α-synuclein when it’s not aggregated?

October 24, 2011 By

In a recent paper in PNAS, co-lead authors Wei Wang (Indiana U. School of Medicine) and Iva Perovic (Chemistry Ph. D. program, Brandeis), together with researchers from Brandeis, Indiana, Scripps, NIH, Washington State, and Harvard, investigated the structure of the abundant small neuronal protein α-synuclein. α-Synuclein has been strongly associated with the disease process in Parkinson disease, both from histology (found in aggregates in Lewy bodies associated with disease) and from genetics (mutations in the gene associated with a rare familial form of Parkinson disease). The structure and function of α-synuclein is not well understood. It is an abundant neuronal protein, and appears to bind to lipids, vesicles, and plasma membrane. Heterologously expressed α-synuclein is often observed to be unfolded, and the biochemical role of the protein is still unidentified.

In this new study, α-synuclein was expressed as a GST fusion protein in E. coli and proteolytically cleaved to form α-synuclein with a 10 amino acid N-terminal extension. This protein was shown to form a stable tetrameter with alpha-helical content in the absence of lipids, using a combination of many techniques, including NMR spectroscopy, electron microscopy, circular dichroism and mass spectroscopy of cross-linked products. The authors combined this information to propose a model for the structure of native α-synuclein when it is not aggregated that is a tetramer based on amphipathic central helices.

Researchers in the Pochapsky, Petsko-Ringe and Agar labs at Brandeis participated in the study. Future work is aimed at understanding the function of this tetrameric form of the protein, with the hope of developing techniques to stabilize it and determine its function. For more information and interview with the authors, see the story at BrandeisNOW.

 

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