Enhancement in resolution and lack of radiation damage in a rapidly frozen lysozyme crystal subjected to high-intensity synchrotron radiation

Development of an X-ray fluorescence holographic measurement system for protein crystals

Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2β2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm(3)) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures

Radiation damage is the major impediment for obtaining structural information from biological samples by using ionizing radiation such as x-rays or electrons. The knowledge of underlying processes especially at cryogenic temperatures is still fragmentary, and a consistent mechanism has not been found yet. By using a combination of single-crystal x-ray diffraction, small-angle scattering, and qualitative and quantitative radiolysis experiments, we show that hydrogen gas, formed inside the sample during irradiation, rather than intramolecular bond cleavage between non-hydrogen atoms, is mainly responsible for the loss of high-resolution information and contrast in diffraction experiments and microscopy. The experiments that are presented in this paper cover a temperature range between 5 and 160 K and reveal that the commonly used temperature in x-ray crystallography of 100 K is not optimal in terms of minimizing radiation damage and thereby increasing the structural information obtainable in a single experiment. At 50 K, specific radiation damage to disulfide bridges is reduced by a factor of 4 compared to 100 K, and samples can tolerate a factor of 2.6 and 3.9 higher dose, as judged by the increase of R(free) values of elastase and cubic insulin crystals, respectively.

Thermal expansion of hen egg-white lysozyme. Comparison of the 1.9 A resolution structures of the tetragonal form of the enzyme at 100 K and 298 K

The average structural and dynamic properties of tetragonal hen egg-white lysozyme have been compared, in structures refined at 1.9 A resolution, using data collected at 100 K and 298 K. The molecule expands by 1.8% over this temperature range with the expansion occurring primarily in its small sub-atomic-sized spaces in an anisotropic manner. Hen egg-white lysozyme consists of two domains: domain 1 (residues 40 to 88) is composed primarily of beta-sheet and is observed to expand by only 0.3%; domain 2 (residues 1 to 39 and 89 to 129) is chiefly alpha-helix and is observed to expand by 2.2%. This is consistent with previous observations that proteins composed primarily of alpha-helix expand more with temperature than do those composed primarily of beta-sheet. The largest movement in the molecule is undergone by the two domains of the structure that move further apart as the temperature is raised. This motion is not a cleft opening but rather consists of a tilt by 2.3 degrees of domain 1 away from domain 2. Within the individual domains the largest movement is undergone by loop T1 of domain 2, consisting of residues 17 to 23. This loop moves in the opposite direction to the rest of the molecule as the temperature is raised. Average temperature factors for the room-temperature and low-temperature structures are 15.2 A2 and 8.1 A2, respectively, when all protein atoms are considered, while these values are 14.0 A2 and 7.8 A2, when only main-chain atoms (N, C alpha, C) are taken into account. An examination of the main-chain averaged B-factor per residue shows that residues involved in intermolecular protein-protein contacts, with symmetry-related molecules, have somewhat lower B-factors than the average and undergo smaller than average changes in B-factor as the temperature is lowered.