COLLEGE 8 Seminar

Friday, June 14th, at 11:00

EMBL seminar room

Dr Stuart FISHER

Diamond Light Source - Didcot, UK

Abstract

Protonation state information can provide crucial details in the determination of enzyme mechanisms. This information is typically difficult to obtain from X-ray crystallographic structures due to the very low scattering power of hydrogen. For the past few years we have been developing methods to determine protonation states in proteins by analysing the bond lengths of ionisable amino acids in X-ray structures. By carefully considering the difference in bond length between, for example the two C-O bonds in aspartate, and the associated standard deviations, it is possible to determine (to within a statistical significance level) whether these amino acid residues are protonated. Our approach makes use of the SHELX package, and has consequently been very resource intensive, requiring extensive analysis of the generated output files. However, we have recently developed an automated approach, ‘Proton8’. Proton8 is a fully integrated software package which can convert pdb/mtz files to shelx ins/hkl files, automatically generate ligand restraints using phenix.elbow, set up multiple conformer occupancies, and generate ins files for partially restrained and full-matrix refinements. Furthermore Proton8 can be integrated with COOT, allowing the user to do interactive modeling and further refinement. Proton8 will therefore make this analysis technique available to a significantly larger user group.

Matthew Blakeley

College 8 Secretary

External visitors may ask for a site access to Karine Sultan (sultan@ill.fr)

General ILL Seminar organized by College 3

Tuesday, 18th June 2013, 11:00

Seminar room ILL1

Herma Büttner

ANSTO (Australian Nuclear Science and Technology Organisation)

ANSTO manufactures and supplies radiopharmaceuticals - more than 500,000 patient doses per year. Nuclear medicine production is one of the core businesses of ANSTO, which provides 85 per cent of the nuclear medicines that Australian hospitals use to diagnose and treat diseases such as cancer, heart disease, neurological disorders and other conditions. ANSTO's main nuclear medicine product is technetium-99m which is used in the majority of nuclear medicine imaging procedures, such as Single Photon Emission Computed Tomography (SPECT). It also supplies other reactor-produced isotopes (e.g., samarium-153, yttrium-90, chromium-51 and iodine-131) as well as a variety of cyclotron-produced nuclear medicines (e.g., fluorine-18, iodine-123, gallium-67 and thallium-201). This talk will not only provide information on ANSTO’s supply chain of radiopharmaceuticals, but also how it is used in ANSTO’s research. For example, molecular imaging is used in various aspects of medical research targeting cancer, cardiovascular, and immune diseases, as well as brain and mind diseases.

General ILL Seminar organized by College 3

Thursday, 20th June 2012, 11:00

ILL 4, room 158

Gunther Cronenberg

ATI, TU Wien

We present observations of transitions between quantum states of gravitationally bound neutrons using a three-part Rabi resonance spectroscopy setup. In our previous experiment ultra-cold neutrons were trapped in the gravitational field. Quantum interferences between different states have been observed by inducing transitions by mechanical vibration. The latest improvement, omitting the upper confining mirror, allows the shift from a frequency reference to a frequency standard, where the transition frequency depends solely on the neutrons mass, Plancks constant and Earth’s gravity. This tests Newton’s Inverse Square Low of Gravity at the micrometer regime which is sensitive to hypothetical Fifth Forces, particles beyond the Standard Model, and potential large extra dimensions of submillimetre size of space-time.

General ILL Seminar organised by College VII

Monday, June 24, 2013, 11h00
Conf. Room 1st Floor, ILL4

Henry Glyde

Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA

We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from finite time simulations. Typical data from simulations are limited to times of 1 to 10 ns and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to simulated values of the incoherent intermediate scattering function, Iinc(Q; t), for finite times. The Iinc(Q; t) and its Fourier transform, S(Q;ω), are observed in neutron scattering measurements. The infinite time MSD, ⟨r2⟩, appears as a parameter in the model and is determined by fits of the model to the finite time Iinc(Q; t). Specifically, the ⟨r2⟩ is defined in the usual way in terms of the Debye-Waller factor as I(Q; t = ∞) = exp(−Q2⟨ r2⟩ /3). The method is illustrated by obtaining the intrinsic MSD ⟨r2⟩ of hydrated lysozyme powder (h = 0.4 g water/g protein) over a wide temperature range. The intrinsic ⟨r2⟩ obtained from data out to 1 ns and to 10 ns is found to be the same. The intrinsic ⟨r2⟩ is approximately twice the value of the MSD that is reached in simulations after times of 1 ns which correspond to those observed using neutron instruments that have an energy resolution width of 1 µeV.

 M. Zbiri
(College VII Secretary)

Participants who have no badges allowing entrance to the ILL-ESRF site are kindly requested to give their names to Laurence Tellier (tellier@ill.fr).