Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology and intermolecular contacts

Abstract

The structure of orthorhombic hen egg-white lysozyme (HEWL) crystallized at 310 K has been refined at 1.7 A resolution. Large displacements of the side-chain atoms with respect to the tetragonal structure were observed in many places, in contrast to small displacements of the main-chain atoms. A chloride-ion binding site was observed at an interface of two molecules, but at a different position to the binding site in the tetragonal form. The analysis of intermolecular contacts in the crystal has shown the presence of three independent intermolecular contacts which are called macrobonds A, B and C. Arginine side chains are frequently involved in these macrobonds, suggesting that the high frequency of this residue in HEWL may be a possible reason for the multiple polymorphs of this protein. The crystal forms were determined using a light-reflecting device on a four-circle diffractometer. Correlations between crystal forms and the three-dimensional macrobond networks were interpreted in terms of their components in various crystallographic planes, making use of approximate strengths of hydrogen-bond and van der Waals interatomic forces.

Dependence of the CaOx and MgOx growth rate on solution stoichiometry. Non-Kossel crystal growth

“…Table 1 shows the lðr; sÞ dependence quantitatively. Namely, the standard BCF relation between the step riser free energy a and l, a ¼ kTl lnðs þ 1Þ=19o (18) allows to estimate aðrÞ. Substituting to this equation kT ¼ 4 Â 10 À14 erg, the specific molecular volume o ¼ 1:4 Â 10 À22 cm 3 , and using the l data from the Table 1, we estimate the step riser free energies to be aðr ¼ 2Þ ¼ 170 erg=cm 2 and the higher figure aðr ¼ 5Þ ¼ 220 erg=cm 2 .…”

“…(9) describes the simplified system of either two components or two symmetrically not equivalent positions of the same molecule in the lattice unit cell. However, for instance, in orthorhombic lysozyme, identical molecules occupy four not equivalent positions [2,18] [19]. If the sequence in which the not equivalent positions in a 3D unit cell are being filled is strictly determined, then the kink propagation problem is reduced to the growth of a chain in which the number of components equals the number of these positions in the 3D lattice.…”

Characterization of dislocations in monoclinic hen egg-white lysozyme crystals by synchrotron monochromatic-beam X-ray topography

“…In the macrobond approach, the macrobond contact site is defined if at least one atom pair whose distance is less than 4Å exists between neighboring molecules [10]. The slicing energy is associated with the total energy of macrobond components that cross each crystallographic plane [11].…”

“…For main crystallographic planes in the monoclinic HEWL crystal, the slicing energies are estimated by macrobond approach [10]. In the macrobond approach, the macrobond contact site is defined if at least one atom pair whose distance is less than 4Å exists between neighboring molecules [10].…”

Crystal habits of cubic insulin from porcine pancreas and evaluation of intermolecular interactions by macrobond and EET analyses

“…It seems to be difficult to estimate the surface energy in protein crystals where the molecular interface is highly complex. Matsuura proposed a simple method based on this scheme, the macrobond analysis, and reported its validity for four crystal forms of lysozyme [15][16][17]. However, the applicability of the macrobond analysis to other proteins has not been established.…”