Molecular envelopes derived from protein powder diffraction data

Abstract

Author(s) of this paper may load this reprint on their own web site or institutional repository provided that this cover page is retained. Republication of this article or its storage in electronic databases other than as specified above is not permitted without prior permission in writing from the IUCr.For further information see http://journals.iucr.org/services/authorrights.html Many research topics in condensed matter research, materials science and the life sciences make use of crystallographic methods to study crystalline and non-crystalline matter with neutrons, X-rays and electrons. Articles published in the Journal of Applied Crystallography focus on these methods and their use in identifying structural and diffusioncontrolled phase transformations, structure-property relationships, structural changes of defects, interfaces and surfaces, etc. Developments of instrumentation and crystallographic apparatus, theory and interpretation, numerical analysis and other related subjects are also covered. The journal is the primary place where crystallographic computer program information is published.Crystallography Journals Online is available from journals.iucr.org J. Appl. Cryst. (2008 The preparation of single crystals suitable for X-ray analysis is frequently the most difficult step in structural studies of proteins. With the aid of two examples, it is shown that de novo solution of the crystallographic phase problem can be achieved at low resolution using microcrystalline powder samples via the single isomorphous replacement method. With synchrotron radiation and optimized instrumentation, high-quality powder patterns have been recorded, from which it was possible to generate phase information for structure factors up to 6 Å resolution. pH-and radiation-induced anisotropic lattice changes were exploited to reduce the problem of overlapping reflections, which is a major challenge in protein powder diffraction. The resulting data were of sufficient quality to compute molecular envelopes of the protein molecule and to map out the solvent channels in the crystals. The results show that protein powder diffraction can yield low-resolution data that are potentially useful for the characterization of microcrystalline proteins as novel micro-and mesoporous materials as well as for structural studies of biologically important macromolecules.

High-resolution powder X-ray data reveal the T6hexameric form of bovine insulin

“…The use of a systematic variation of sample-preparation conditions has been particularly useful for the detection of protein-ligand complex formation by variations of ligand concentration (Von Dreele, 2001, 2005, the identification of subsequent phase transitions with increasing pH in the case of human insulin (Karavassili et al, 2012) and the structure solution of the previously unknown SH3 domain of ponsin (Margiolaki, Wright, Wilmanns et al, 2007). The optimization of cryoprotection conditions and the preparation of heavy-atom derivatives could also exploit systematic powder experiments, as demonstrated in previous studies on hen egg-white lysozyme and porcine pancreatic elastase Wright et al, 2008;Basso et al, 2010).…”

“…One common phenomenon is an irreversible radiation-induced lattice expansion, although the mechanism by which this occurs is not fully understood (Ravelli et al, 2002). In many cases, lattice changes are anisotropic and can thus be exploited to improve the resolution of overlapping reflections in a powder pattern (Basso et al, 2005;Von Dreele, 2007;Besnard et al, 2007;Margiolaki, Wright, Wilmanns et al, 2007;Wright et al, 2008;Basso et al, 2010;Helliwell et al, 2010). In the case of powder diffraction data, significant changes in the lattice parameters accompanied by a gradual increase of peak broadening and a significant loss of intensity are common characteristics of radiation-damage effects (Margiolaki, Wright, Wilmanns et al, 2007).…”

Time-dependent analysis of K2PtBr6binding to lysozyme studied by protein powder and single crystal X-ray analysis

“…Protein powder diffraction continues to excite strong international interest; there are a variety of applications, including industrial protein characterization, such as polymorphs of insulin, as well as extending structure determination to yet smaller crystal samples, which would otherwise be outside the range of synchrotron X-ray data collection from a protein microcrystal [1][2][3][4][5]. Furthermore there are the upcoming X-ray Laser Facilities, with possibilities for protein nanocluster-crystallites' diffraction and de novo structure determination.…”

A new approach for structure analysis of two‐dimensional membrane protein crystals using X‐ray powder diffraction data

“…According to more recent studies, the synchrotron X‐ray powder diffraction technique has been successfully adapted to various proteins, using state of the art instrumentation and algorithms. Recent progress in powder diffraction data collection11 and interpretation9 has facilitated the study of several biologically interesting proteins 12–18. The successful solution of different protein structures has been achieved via traditional methods in single‐crystal crystallography, such as molecular replacement (MR),11, 13, 17 single isomorphous replacement revealing the molecular envelope,14 and multiple isomorphous replacement showing secondary structure elements of a model protein 15…”