Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-beta spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of beta-sheets, with the facing side chains of the two sheets interdigitated in a dry 'steric zipper'. Here we report some 30 other segments from fibril-forming proteins that form amyloid-like fibrils, microcrystals, or usually both. These include segments from the Alzheimer's amyloid-beta and tau proteins, the PrP prion protein, insulin, islet amyloid polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein and beta(2)-microglobulin, suggesting that common structural features are shared by amyloid diseases at the molecular level. Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.

Numerous soluble proteins convert to insoluble amyloid-like fibrils having common properties. Amyloid fibrils are associated with fatal diseases such as Alzheimer's, and amyloid-like fibrils can be formed in vitro. For the yeast protein Sup35, conversion to amyloid-like fibrils is associated with a transmissible infection akin to that caused by mammalian prions. A seven-residue peptide segment from Sup35 forms amyloid-like fibrils and closely related microcrystals, which here reveal the atomic structure of the cross-β spine. It is a double β-sheet, with each sheet formed from parallel segments stacked in-register. Sidechains protruding from the two sheets form a dry, tightly self-complementing steric zipper, bonding the sheets. Within each sheet, every segment is bound to its two neighbouring segments via stacks of both backbone and sidechain hydrogen bonds. The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic, and their tendency to form polymorphic structures.Four decades of research have established that amyloid-like fibrils of different proteins have a common structural 'cross-β' spine 1 . In 1959 Cohen and Calkins 2 observed elongated, unbranched fibrils in electron micrographs of diseased tissues, and in 1968 Glenner and Eanes 3 discovered that the fibrils exhibit an X-ray diffraction signature known as the cross-β pattern. This pattern shows 4 that the strongest repeating feature of the fibril is a set of β-sheets that are parallel to the fibril axis with their strands perpendicular to this axis. The hypothesis of a common molecular organization was supported by the finding 5 that amyloid fibrils from 6 different proteins, each associated with its own clinical syndrome, showed similar cross-β diffraction patterns. The degree of similarity pointed to 'a common core molecular structure.'Revealing the atomic details of this cross-β spine has been impeded by the limited order of fibrils isolated from diseased tissues, infected cells, and in vitro conversions of proteins to fibrils. There is also evidence for a diversity of crystalline and fibril structures 6-8 . Nevertheless, an arsenal of biophysical tools has defined important features. These tools include solid-state NMR 9-11 , model-building constrained by X-ray fiber and powder diffraction 6,7,12,13 , site-directed spin labeling 14,15 , cryo-electron microscopy 16,17 , and proline-scanning mutagenesis 18 . Despite numerous models suggested by these studies, until now no refined, fully objective atomic model has been available for the common spine structure.Correspondence and requests for materials should be addressed to D.E. (david@mbi.ucla.edu). The structures of GNNQQNY and NNQQNY have been deposited in the Protein Data Bank with accession codes 1yjp and 1yjo, respectively.. Competing Interests StatementThe authors declare that they have no competing financial interests.Supplementary Information accompanies the paper on www.nature.com/nature. We selected the yeast protein Sup35 for X-ray diffraction analy...

The SHADE web server estimates anisotropic displacement parameters for hydrogen atoms by combining a rigid-body analysis of the non-hydrogen-atom anisotropic displacement parameters (ADPs) with a contribution from internal atomic motion. The contributions from internal mean square displacements are based on a previously compiled database derived from analysis of neutron diffraction experiments. The estimated hydrogen-atom ADPs can be used as fixed parameters in advanced applications of high-resolution X-ray diffraction, such as electron density studies using multipole modelling. The resulting electron density models have been shown to be in excellent agreement with reference models based on atomic motion derived from neutron diffraction experiments.

Amyloid fibrils are found in association with at least two dozen fatal diseases. The tendency of numerous proteins to convert into amyloid-like fibrils poses fundamental questions for structural biology and for protein science in general. Among these are the following: What is the structure of the cross-beta spine, common to amyloid-like fibrils? Is there a sequence signature for proteins that form amyloid-like fibrils? What is the nature of the structural conversion from native to amyloid states, and do fibril-forming proteins have two distinct stable states, the native state and the amyloid state? What is the basis of protein complementarity, in which a protein chain can bind to itself? We offer tentative answers here, based on our own recent structural studies.

Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.

The discovery of receptors using templated synthesis enables the selection of strong receptors from complex mixtures.

Anisotropic displacement parameters (ADPs) are compared for H atoms estimated using three recently described procedures, both among themselves and with neutron diffraction results. The results convincingly demonstrate that all methods are capable of giving excellent results for several benchmark systems and identify systematic discrepancies for several atom types. A revised and extended library of internal H-atom mean-square displacements is presented for use with Madsen's SHADE web server [J. Appl. Cryst. (2006), 39, 757-758; http://shade.ki.ku.dk], and the improvement over the original SHADE results is substantial, suggesting that this is now the most readily and widely applicable of the three approximate procedures. Using this new library--SHADE2--it is shown that, in line with expectations, a segmented rigid-body description of the heavy atoms yields only a small improvement in the agreement with neutron results. The SHADE2 library, now incorporated in the SHADE web server, is recommended as a routine procedure for deriving estimates of H-atom ADPs suitable for use in charge-density studies on molecular crystals, and its widespread use should reveal remaining deficiencies and perhaps overcome the inherent bias in the majority of such studies.

Extensive and precise X-ray diffraction data for xylitol have been used to test different approaches to estimate nuclear parameters for H atoms in charge-density studies. The parameters from a neutron diffraction study of the same compound were taken as a reference. The resulting static charge densities obtained for the different approaches based on a multipole model were subjected to a topological analysis. The comparative analysis led to the following results. The procedure of extending the X-H bond to match bond lengths from neutron diffraction studies provides the best agreement with the neutron positional parameters. An isotropic model for the atomic displacements of H atoms is highly unsatisfactory and leads to significant deviations for the properties of the bond critical points including those that only involve non-H atoms. Anisotropic displacement parameters for H atoms can be derived from the X-ray data that are in agreement with the values from the neutron study, and the resulting charge-density models are in good agreement with the reference model. The anisotropic displacement parameters for H atoms are derived from the X-ray data as a sum of the external (rigid-body) and internal vibrations. The external vibrations are obtained from a TLS analysis of the ADPs of the non-H atoms and the internal vibrations from analysis of neutron diffraction studies of related compounds. The results from the analysis of positional and thermal parameters were combined to devise a 'best anisotropic' model, which was employed for three other systems where X-ray and neutron data were available. The results from the topological analysis of these systems confirm the success of the 'best anisotropic' model in providing parameters for the H atoms that give charge densities in agreement with the reference models based on H-atom parameters derived from neutron diffraction.