A re¯ection intensity integration method is presented based upon ab initio calculation of three-dimensional (x, y, 3) re¯ection boundaries from a few physical crystal and instrument parameters. It is especially useful in challenging circumstances, such as the case of a crystal that is far from spherical, anisotropic mosaicity, 1 2 peak splitting, interference from close neighbours, twin lattices or satellite re¯ections, and the case of streaks from modulated structures, all of which may frustrate the customary pro®le-learning and -®tting procedures. The method, called EVAL-14, has been implemented and extensively tested on a Bruker Nonius KappaCCD diffractometer.

A novel diffraction data integration method is presented, EVAL15, based upon ab initio calculation of three‐dimensional (x, y, ω) reflection profiles from a few physical crystal and instrument parameters. Net intensities are obtained by least‐squares fitting the observed profile with the calculated standard using singular value decomposition. This paper shows that profiles can be predicted satisfactorily and that accurate intensities are obtained. The detailed profile analysis has the additional advantage that specific physical properties of the crystal are revealed. The EVAL15 method is particularly useful in circumstances where other programs fail, such as regions of reciprocal space with weak scattering, crystals with anisotropic shape or anisotropic mosaicity, Kα1/Kα2 peak splitting, interference from close neighbours, twin lattices, or satellite reflections of modulated structures, all of which may frustrate the customary profile learning and fitting procedures. EVAL15 allows the deconvolution of overlapping reflections.

Amyloid fibrils are components of proteinaceous plaques that are associated with conformational diseases such as Alzheimer's disease, transmissible spongiform encephalopathies, and familial amyloidosis. Amyloid polypeptides share a specific quarternary structure element known as cross-␤ structure. Commonly, fibrillar aggregates are modified by advanced glycation end products (AGE). In addition, AGE formation itself induces protein aggregation. Both amyloid proteins and protein-AGE adducts bind multiligand receptors, such as receptor for AGE, CD36, and scavenger receptors A and B type I, and the serine protease tissue-type plasminogen activator (tPA). Based on these observations, we hypothesized that glycation induces refolding of globular proteins, accompanied by formation of cross-␤ structure. Using transmission electron microscopy, we demonstrate here that glycated albumin condensates into fibrous or amorphous aggregates. These aggregates bind to amyloid-specific dyes Congo red and thioflavin T and to tPA. In contrast to globular albumin, glycated albumin contains amino acid residues in ␤-sheet conformation, as measured with circular dichroism spectropolarimetry. Moreover, it displays cross-␤ structure, as determined with x-ray fiber diffraction. We conclude that glycation induces refolding of initially globular albumin into amyloid fibrils comprising cross-␤ structure. This would explain how glycated ligands and amyloid ligands can bind to the same multiligand "cross-␤ structure" receptors and to tPA.

The paper describes molecular dynamics (MD) simulations on the crystal structures of the Ibeta and II phases of cellulose. Structural proposals for each of these were made in the 1970s on the basis of X-ray diffraction data. However, due to the limited resolution of these data some controversies remained and details on hydrogen bonding could not be directly obtained. In contrast to structure factor amplitudes in X-ray diffraction, energies, as obtained from MD simulations, are very sensitive to the positions of the hydroxyl hydrogen atoms. Therefore the latter technique is very suitable for obtaining such structural details. MD simulations of the Ibeta phase clearly shows preference for one of the two possible models in which the chains are packed in a parallel orientation. Only the parallel-down mode (in the definition of Gardner and Blackwell (1974) J Biopolym 13: 1975-2001) presents a stable structure. The hydrogen bonding consists of two intramolecular hydrogen bonds parallel to the glycosidic linkage for both chains, and two intralayer hydrogen bonds. The layers are packed hydrophobically. All hydroxymethyl group are positioned in the tg conformation. For the cellulose II form it was found that, in contrast to what seemed to emerge from the X-ray fibre diffraction data, both independent chains had the gt conformation. This idea already existed because of elastic moduli calculations and 13C-solid state NMR data. Recently, the structure of cellotetraose was determined. There appear to be a striking similarity between the structure obtained from the MD simulations and this cellotetraose structure in terms of packing of the two independent molecules, the hydrogen bonding network and the conformations of the hydroxymethyl group, which were also gt for both molecules. The structure forms a 3D hydrogen bonded network, and the contribution from electrostatics to the packing is more pronounced than in case of the Ibeta structure. In contrast to what is expected, in view of the irreversible transition of the cellulose I to II form, the energies of the Ibeta form is found to be lower than that of II by 1 kcal mol(-1) per cellobiose.

Proteins can readily assemble into rigid, crystalline and functional structures such as viral capsids and bacterial compartments. Despite ongoing advances, it is still a fundamental challenge to design and synthesize protein-mimetic molecules to form crystalline structures. Here we report the lattice self-assembly of cyclodextrin complexes into a variety of capsid-like structures such as lamellae, helical tubes and hollow rhombic dodecahedra. The dodecahedral morphology has not hitherto been observed in self-assembly systems. The tubes can spontaneously encapsulate colloidal particles and liposomes. The dodecahedra and tubes are respectively comparable to and much larger than the largest known virus. In particular, the resemblance to protein assemblies is not limited to morphology but extends to structural rigidity and crystallinity—a well-defined, 2D rhombic lattice of molecular arrangement is strikingly universal for all the observed structures. We propose a simple design rule for the current lattice self-assembly, potentially opening doors for new protein-mimetic materials.

Tissue-type plasminogen activator (tPA) regulates fibrin clot lysis by stimulating the conversion of plasminogen into the active protease plasmin. Fibrin is required for efficient tPA-mediated plasmin generation and thereby stimulates its own proteolysis. Several fibrin regions can bind to tPA, but the structural basis for this interaction is unknown. Amyloid beta (Abeta) is a peptide aggregate that is associated with neurotoxicity in brains afflicted with Alzheimer's disease. Like fibrin, it stimulates tPA-mediated plasmin formation. Intermolecular stacking of peptide backbones in beta sheet conformation underlies cross-beta structure in amyloid peptides. We show here that fibrin-derived peptides adopt cross-beta structure and form amyloid fibers. This correlates with tPA binding and stimulation of tPA-mediated plasminogen activation. Prototype amyloid peptides, including Abeta and islet amyloid polypeptide (IAPP) (associated with pancreatic beta cell toxicity in type II diabetes), have no sequence similarity to the fibrin peptides but also bind to tPA and can substitute for fibrin in plasminogen activation by tPA. Moreover, the induction of cross-beta structure in an otherwise globular protein (endostatin) endows it with tPA-activating potential. Our results classify tPA as a multiligand receptor and show that cross-beta structure is the common denominator in tPA binding ligands.

A procedure is described to estimate the persistence length and related properties of a persistent polymer by MD simulations of a small fragment, including solvent effects. The procedure is applied to cellulose in aqueous solution, which leads to an upper limit of the persistence length of 145 ± 10 Å. The occurrence of small amounts of folded conformations seems to be indicated by comparison of the theoretical with experimental data. The behavior of the cellulose chain is consistent with the Kratky−Porod wormlike model.

The conformation and internal flexibility of a glycopeptide Manalpha1-6 (Xylbeta1-2)Manbeta1-4GlcNAcbeta1-4(Fucalpha1-3) GlcNAcbeta1-N(Asn-Glu-Ser-Ser), prepared from pineapple stem bromelain, have been analyzed using a combination of molecular dynamics (MD) simulations in water with NOESY 1H NMR spectroscopy. Theoretical NOESY cross-peak intensities were calculated by the CROSREL program on the basis of models, obtained from MD simulations, using a full relaxation matrix approach. Special attention was paid to the description of internal flexibility of the hexasaccharide moiety by the use of generalized order parameters, in combination with the application of an individual rotation correlation tme for each monosaccharide residue. The tetrapeptide moiety appeared to be very mobile during the MD simulations, which was confirmed by the absence of NOE cross peaks. For the oligosaccharide part a model was developed to estimate characteristic times for large reorientational motions around the glycosidic linkages, associated with conformational transitions. For the Manalpha1-6Man and the Fucalpha1-3GlcNAc linkages such a flexibility was found with a characteristic time of 2 ns. In contrast, the Xylbeta1-2Manbeta1-4GlcNAcbeta1-4GlcNAc part of the glycan appears to be relatively rigid.