High-Resolution Structure (1.33 Å) of a HEW Lysozyme Tetragonal Crystal Grown in the APCF Apparatus. Data and Structural Comparison with a Crystal Grown under Microgravity from SpaceHab-01 Mission

Abstract

Crystals of tetragonal hen egg-white lysozyme were grown using Advanced Protein Crystallization Facility (APCF) apparatus under a microgravity environment (SpaceHab-01 mission) and ground control conditions. Crystals were grown from NaCI as a crystallizing agent at pH 4.3. The X-ray diffraction patterns of the best diffracting ground-and space-grown crystals were recorded using synchrotron radiation and an image plate on the W32 beamline at LURE. Both ground-and space-grown crystals showed nearly equivalent maximum resolution of 1.3-1.4,~. Refinements were carried out with the program X-PLOR with final R values of 18.45 and 18.27% for structures from ground-and spacegrown crystals, respectively. The two structures are nearly identical with the root-mean-square difference on all protein atoms being 0.13/~. Some residues of the two refined structures show multiple alternative conformations. Two ions were localized into the electron-density maps of the two structures: one chloride ion at the interface between two symmetry-related molecules and one sodium ion stabilizing the loop Ser60-Leu75. The sodium ion is surrounded by six ligands which form a bipyramid around it at distances of 2.2-2.6 A,.

Structures of orthorhombic lysozyme grown at basic pH and its low-humidity variant

“…The other three well known forms, tetragonal (Vaney et al, 1996), triclinic (Walsh et al, 1998) and monoclinic (Nagendra et al, 1996) are obtained at around pH 4.6. Therefore, a major reason for analysing the orthorhombic form has been to delineate the effect of change in pH on the structure, if any.…”

nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions

“…Analogously one may define the partial incoherent intermediate scattering functions 29) and the weights w I ,inc = n I w ,inc , for ∈ M I , (3.30) such that the total incoherent scattering takes the form…”

“…[51]. The simulated system consists of one hen egg white lysozyme molecule [29] and 6775 water molecules. The simulations have been performed in the NpT ensemble using the the AMBER99SB [52] and SPC/E [26] force fields for the protein and the water molecules, respectively.…”

“…The simulation has been performed for a single lysozyme molecule [29] in the presence of 3403 water molecules. The molecular dynamics simulation over a time of 1ns was performed with the MMTK simulation package [42], using the Amber94 force field [27], periodic boundary conditions and a velocity-Verlet integrator with a time step of 1 f s. A thermodynamic NpT -ensemble [30,31], with T = 300K and p = 1atm was used.…”

“…[27] The system was enclosed in a rectangular box of an average size of 6.15 × 4.10 × 4.61 nm 3 , applying periodic boundary conditions. The lysozyme structure was taken from the Brookhaven protein data bank [28] (code 193L [29]) and hydrogen atoms were added to the structure according to standard criteria concerning the chemical bond structure of amino acids. To mimic realistic thermodynamic conditions the system was simulated in the thermodynamics NpT -ensemble, employing the extended system method [30,31] with an integration time step of 0.001 ps.…”