Carl Henrik Görbitz

The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's β-amyloid polypeptide

Alzheimers beta-amyloid diphenylalanine motif has previously been shown to self-assemble into discrete and extraordinary stiff nanotubes; these nanotubes were initially thought to be distinct from the single crystal structure of diphenylalanine, but it is now shown that the X-ray powder diffraction pattern of the nanotubes is identical to the simulated pattern for the single crystal structure, affording a new foundation for understanding and rationalizing the properties of this remarkable organic material.

An exceptionally stable peptide nanotube system with flexible pores

The hydrophobic channels in the structure of the dipeptide L-alanyl-L-valine act as supramolecular hosts for organic solvent molecules. In a series of data collections, it is demonstrated that small molecules like acetonitrile, methanol and acetone can be removed from the channels by drying without impairing the structure of the hydrogen-bonded peptide host structure. The title compound is one of the very first organic molecules to be found to have this property. Alcohol guests larger than methanol are also absorbed, but they induce a doubling of two axes and a change in the shape and size of the pores. The observed structural modifications explain why these solvent molecules are more or less irreversibly trapped inside the channels.

What is the best crystal size for collection of X-ray data? Refinement of the structure of glycyl-L- serine based on data from a very large crystal

The dipeptide Gly-L-Ser was crystallized as part of a study on hydrogen-bonding patterns in the structures of dipeptides. Hydrogen-bond donors and acceptors have been assigned ranks (1 is best, 2 is next best etc.), and the observed hydrogen-bond connectivity is compared with the hypothetical pattern in which the rank n donor associates with the rank n acceptor (n = 1, 2,.), and with the pattern observed in the retroanalogue L-Ser-Gly, which contains the same functional groups. Crystallization of the title compound produced very bulky crystals. Rather than reducing the size of one of these before data collection, three data sets with different exposure times were collected with a Siemens SMART CCD diffractometer on a very large specimen (2.2 x 2.0 x 0.8 mm). The crystal was subsequently shaped into a 0.30 mm-diameter sphere for collection of two additional data sets. The discussion of the refinement results focus on the effect of absorption correction for the various data sets, and a comparison of geometrical and thermal parameters. One advantage of using a large crystal, the great speed with which data can be obtained, has been exemplified by collection of a complete data set of good quality in less than 25 min.

Crystallographic and Spectroscopic Studies of Peroxide-derived Myoglobin Compound II and Occurrence of Protonated FeIV–O

High resolution crystal structures of myoglobin in the pH range 5.2–8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe–O bond length (1.86–1.90 Å) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (<1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe–O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an FeIV–O species with a single bond. The presence of FeIV is indicated by a small isomer shift of δ = 0.07 mm/s from Mössbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.

Stapling of a 310-Helix with Click Chemistry

Short peptides are important as lead compounds and molecular probes in drug discovery and chemical biology, but their well-known drawbacks, such as high conformational flexibility, protease lability, poor bioavailability and short half-lives in vivo, have prevented their potential from being fully realized. Side chain-to-side chain cyclization, e.g., by ring-closing olefin metathesis, known as stapling, is one approach to increase the biological activity of short peptides that has shown promise when applied to 3(10)- and α-helical peptides. However, atomic resolution structural information on the effect of side chain-to-side chain cyclization in 3(10)-helical peptides is scarce, and reported data suggest that there is significant potential for improvement of existing methodologies. Here, we report a novel stapling methodology for 3(10)-helical peptides using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction in a model aminoisobutyric acid (Aib) rich peptide and examine the structural effect of side chain-to-side chain cyclization by NMR, X-ray diffraction, linear IR and femtosecond 2D IR spectroscopy. Our data show that the resulting cyclic peptide represents a more ideal 3(10)-helix than its acyclic precursor and other stapled 3(10)-helical peptides reported to date. Side chain-to-side chain stapling by CuAAC should prove useful when applied to 3(10)-helical peptides and protein segments of interest in biomedicine.

Structures of dipeptides: the head-to-tail story.

The hydrogen-bonding patterns in crystal structures of unprotected, zwitterionic dipeptides are dominated by head-to-tail chains involving the N-terminal amino groups and the C-terminal carboxylate groups. Patterns that include two concomitant chains, thus generating a hydrogen-bonded layer, are of special interest. A comprehensive survey shows that dipeptide structures can conveniently be divided into only four distinct patterns, differing by definition in the symmetry of the head-to-tail chains and amide hydrogen-bonding type, but also in other properties such as peptide conformation and the propensity to include solvent water or various organic guest molecules. Upon crystallization, the choice of pattern for a specific dipeptide is not random, but follows from the amino acid sequence.

The Crystal Structure of Peroxymyoglobin Generated Through Cryoradiolytic Reduction of Myoglobin Compound III During Data Collection.

Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallographic data collection. We have generated and solved the 1.30 A (1 A=0.1 nm) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe-O distance of 1.8 A and O-O bond of 1.3 A in accordance with a Fe(II)-O-O- (or Fe(III)-O-O2-) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metalloproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O-O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.

Non‐centrosymmetric racemates: space‐group frequencies and conformational similarities between crystallographically independent molecules

DL-Allylglycine (DL-2-amino-4-pentenoic acid, C5H9NO2) yields crystals with Pca2(1) symmetry and two crystallographically independent yet pseudo-inversion-related enantiomers. The distribution among the common space groups of other crystalline racemates with more than one molecule in the asymmetric unit has been established. The conformational similarities between crystallographically independent enantiomers in 114 non-centrosymmetric racemates were quantified using the r.m.s. deviation for a molecular superposition. The analysis shows that in the majority of crystals the conformations of the crystallographically independent molecules are very similar with mean r.m.s. deviation = 0.190 A. In almost 80% of the structures the mean r.m.s. deviations is in the interval 0-0.2 A. It is estimated that racemates constitute 23% of the centrosymmetric organic structures in the Cambridge Structural Database.

Solid-State Phase Transitions in dl-Norvaline Studied by Single-Crystal X-ray Diffraction

The amino acid DL-norvaline undergoes two solid-solid phase transitions between room temperature and -180 °C. Single-crystal X-ray diffraction studies show that the first of these transitions, taking place around -80 °C, is completely reversible with respect to crystal quality, whereas the second, taking place below -100 °C, is not due to crystal delamination. High-quality crystal structures were obtained for the higher temperature phase β (at -70 °C) and the intermediate temperature phase α (at -90 °C). They show that although side-chain disorder is present for both forms, the β-to-α phase transition induces significant side-chain rearrangements, which are accompanied by a substantial reduction in molecular volume. The observed polymorphs are compared with those found for DL-aminobutyric acid, DL-norleucine, and DL-methionine.

Single-crystal investigation of L-tryptophan with Z' = 16.

A complex, disorder-free structure in the space group P1 has been established for L-tryptophan, for which no crystal structure has previously been available. The 16 molecules in the asymmetric unit can be divided into two groups of eight; one where the side chains have gauche orientations and one with trans orientations. Molecules within each group have almost identical molecular geometries. The unit-cell parameters mimic a hexagonal cell, but deviations from 90° for the cell angles α = 84.421 (4) and β = 87.694 (4)° give a small tilt that rules out hexagonal symmetry. The hydrogen-bonding pattern resembles that found in the crystal structure of the racemic structure of DL-tryptophan, but a lower density combined with longer hydrogen bonds and inter-aromatic interactions show that the enantiomeric structure is less efficiently packed.