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

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.

 

Mapping hydrogens in chymotrypsin structures with neutron diffraction

In a new paper “Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station” published in this month’s edition of the journal Acta Cryst F, Biochemistry grad student Louis Lazar and co-workers from the Petsko-Ringe lab report progress on their project to determine exact hydrogen positions in proteins using neutron diffraction.

Neutron diffraction was chosen, as opposed to X-ray diffraction, because one can visualize hydrogen species directly using neutrons, while it is extremely difficult and in most cases impossible to do so using X-ray diffraction. They chose the protein γ-chymotrypsin in order to determine hydrogen positions, as it fills the necessary requirements to be suitable for a neutron diffraction experiment. These requirements include a very large crystal size (> 1 mm3), moderately sized unit cell axes (no dimension greater than 100 Å), and it must be very stable as well as well-characterized. γ-chymotrypsin is the stereotypical serine protease, cleaving C-terminal to aliphatic and aromatic residues and containing a catalytic triad of serine, histidine, and aspartate. This information on hydrogen placement can then be applied to improve computational methods in which said placement is paramount, such as molecular modeling and rational drug design.

The paper details the collection of neutron data at pD (pH*) 7.1, with the help of the scientists at the Los Alamos National Laboratory. In particular, from the initial maps, they note that the catalytic histidine is doubly protonated, while the serine and aspartate making up the catalytic triad do not show density for the presence of deuterium. In order to complete the study of γ-chymotrypsin, data at a variety of pH values must be collected; data at pD (pH*) 5.6 has already been collected (Acta Cryst F65, 317-320), and data at pD (pH*) 9.0 will be collected in the future.

see also: full text of article (Brandeis users)

Strage Award Goes to Douglas Theobald

Prof. Gregory Petsko writes:

It is with great pleasure that I announce the recipient of the 12th Annual Alberta Gotthardt and Henry Strage Award for Aspiring Young Science Faculty, Dr. Douglas Theobald of the Biochemistry Department.

Doug is one of Brandeis’ most accomplished young faculty members. Since his arrival at Brandeis, he has consistently demonstrated the ability to think deeply about some of the most fundamental problems in biology. His work on the resurrection of ancient proteins is among the most exciting research in the field of molecular evolution. Using what he terms “paleocrystallography” — in reality, a sort of Jurassic Park from ancestral molecules — he is aiming to visualize the structural changes that occur during the evolution of enzymes and protein complexes. With the high-resolution structures of reconstructed ancestral molecules, correlated with functional data from biochemical analyses, Doug will be able to test experimentally specific evolutionary hypotheses about protein evolution and gain an understanding of what functions can be rationally engineered. […] A theoretician who also has both feet firmly grounded in experiments, Doug is also a gited teacher.

The award ceremony and lecture will take place on Monday, April 11 at 1:00 pm in Gerstenzang 121. The title of Prof. Theobald’s lecture will be “Evolution of structure and function in biological macromolecules”

High resolution virus structures from electron cryo-microscopy

Professor of Biochemistry Nikolaus Grigorieff discusses recent progress in obtaining virus structures at 4 Å or better resolution from electron microscopy in a new review “Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy” in Current Opinon in Structural Biology.

Spring-loading the active site of cytochrome P450

Enzymes differ from other catalysts in the exceptional substrate selectivity they exhibit.  However, the active sites of related enzymes are often very similar, even though different substrates are acted upon (for example in the superfamily of cytochrome P450s).  How does a given enzyme preferentially bind a particular substrate?  In a new paper appearing in the jounal Metallomics, Chemistry grad student Marina Dang and Profs. Susan Sondej Pochapsky and Thomas Pochapsky use nuclear magnetic resonance (NMR) to identify a helical structure remote from the active site of the enzyme cytochrome P450cam that is responsive to changes in substrate.  They propose that this helix can adjust the position of residues that contact substrate in the enzyme active site, much like the spring that holds batteries in place against electrical contacts in a flashlight.

Seeing key hinges in the lever arm of myosin at the atomic level

In this week’s on-line issue of the Proceedings of the National Academy of Sciences (PNAS), Brandeis researchers Jerry H. Brown, V. S. Senthil Kumar, Elizabeth O’Neall-Hennessey, Ludmila Reshetnikova, and Michelle Nguyen-McCarty ’10, together with Professors Andrew Szent-Györgyi and Carolyn Cohen, and Brookhaven National Laboratory researcher Howard Robinson, reveal the existence of a pair of major new hinges in the muscle protein myosin.

Muscle consists of myosin-containing thick filaments with projections, i.e. myosin heads, that exert force on actin-containing thin filaments during contraction. Previous crystal structures of the myosin head from bay scallop striated muscles and vertebrate muscles have already shown how this motion is produced by the amplification of small conformational changes about hinges in the motor domain (MD) by the so-called lever arm, which consists of the converter and elongated light chain binding domain (LCD).  Just like a baseball bat or other lever arms we are all familiar with in the “real world”, this LCD of myosin has appeared to be relatively rigid in these crystal structures, as it needs to be to transmit force effectively. But it has also long been expected that in muscle the myosin head, including its lever arm, is likely to contain elastic elements so that force can be produced under various strains.

(Left) Schematic of a myosin molecule and (right) the two conformations of the heavy chain portion of the LCD.

The Brandeis researchers originally set out to crystallize a myosin LCD corresponding to that from the catch muscle of sea scallop because it contains a specialized sequence whose structure was predicted to give insight into how muscle contraction of smooth muscles is turned on and off. Remarkably, however, as described in the PNAS article, this LCD forms two different conformations in the crystal, about mechanically linked hinges in the part of the lever arm distal from the motor. For the first time — and quite unexpectedly— a potential major elastic element in the lever arm has been visualized at atomic resolution, one that allows the length of the lever arm to change by about 10%. Sequence comparisons strongly suggest that these specific hinges are likely to be found in the lever arms of all muscle myosins. These comparisons also indicate differences in the degree of flexibility about these hinges in the different myosins, perhaps helping to account for the different properties (e.g., speed of contraction) of different types of muscle.

This result may also be important for mechanical engineers. In 2009, one of the authors (JHB) wrote an article in American Scientist that expands the concept of biomimicry by describing potentially novel joints, switches, and other mechanical designs that can be derived from the structures of various proteins. The current results in the PNAS seem to add one more. As described by Olena Pylypenko and former Brandeis researcher Anne Houdusse in a commentary scheduled to accompany the print version of the PNAS article, the motion about the hinge of the myosin LCD resembles the motion of a foot relative to a leg about an ankle. A lever “arm” that can extend or compress about an “ankle” may thus be one more novel mechanical design that nature can teach us about.

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