Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed

Sub-nanometer-scale measurements of the interaction of ultrafast soft x-ray free-electron-laser pulses with matter

Femtosecond pulses from soft-x-ray free-electron lasers (FELs) [1] are ideal for directly probing matter at atomic length scales and timescales of atomic motion. An important component of understanding ultrafast phenomena of light-matter interactions is concerned with the onset of atomic motion which is impeded by the atoms inertia. This delay of structural changes will enable atomic-resolution flash-imaging [2-3] to be performed at upcoming x-ray FELs [4-5] with pulses intense enough to record the x-ray scattering from single molecules [6]. We explored this ultrafast high-intensity regime with the FLASH soft-x-ray FEL [7-8] by measuring the reflectance of nanostructured multilayer mirrors using pulses with fluences far in excess of the mirrors damage threshold. Even though the nanostructures were ultimately completely destroyed, we found that they maintained their integrity and reflectance characteristics during the 25-fs-long pulse, with no evidence for any structural changes during that time over lengths greater than 3 {angstrom}. In the recently built FLASH FEL [7], x-rays are produced from short electron pulses oscillating in a periodic magnet array, called an undulator, by the principle of self-amplification of spontaneous emission [9-10]. The laser quality of the x-ray pulses can be quantified by the peak spectral brilliance of the source, which is 10{sup 28} photons/(s mm2 mrad2 0.1% bandwidth) [8]; this is up to seven orders of magnitude higher than modern third-generation synchrotron sources. For our studies, the machine operated with pulses of 25 fs duration at a wavelength of 32.5 nm and energies up to 21 {micro}J. We focused these pulses to 3 x 10{sup 14} W/cm{sup 2} onto our nanostructured samples, resulting in an the unprecedented heating rate of 5 x 10{sup 18} K/s, while probing the irradiated structures at the nanometer length scale. The x-ray reflectivity of periodic nanometer-scale multilayers [11] is very sensitive to changes in the atomic positions and the refractive indices of the constituent materials, making them an ideal choice to study structural changes induced by ultrashort FEL pulses. The large multilayer reflectivity results from the cooperative interaction of the x-ray field with many layers of precisely fabricated thicknesses, each less than the x-ray wavelength. This Bragg or resonant reflection from the periodic structure is easily disrupted by any imperfection of the layers. The characteristics of the structure, such as periodicity or layer intermixing, can be precisely determined from the measurement of the Bragg reflectivity as a function of incidence angle. These parameters can be easily measured to a small fraction of the probe wavelength, as is well known in x-ray crystallography where average atomic positions of minerals or proteins are found to less than 0.01{angstrom}. Thus, we can explore ultrafast phenomena at length scales less than the wavelength, and investigate the conditions to overcome the effects of radiation damage by using ultrafast pulses

Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 angstrom resolution and determine its serial femtosecond crystallography structure to 3.5 angstrom resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution