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Biomedical subjects

Carl Henrik Görbitz

Publications and source records attributed to Carl Henrik Görbitz.

At least 19 recordsLinked to original sources
PubMed2007

Microporous organic materials from hydrophobic dipeptides.

In the last few years dipeptides with two hydrophobic residues (hydrophobic dipeptides) have emerged as an unexpected source of stable microporous organic materials. Supramolecular self-assembly of the rather small building blocks is dictated by stringent demands on the hydrogen-bond formation by the peptide main chains and the aggregation of hydrophobic entities in the side chains. A systematic survey of structures derived from single-crystal X-ray diffraction studies has revealed the existence of two large classes of structures, differing in the dimensionality of the hydrogen-bonding patterns in the crystals and the nature of the channels. The present review summarizes the structural properties of the microporous dipeptides and discusses their potential applications.

Dipeptides↗
PubMed2006

Pearls on a string: a Z' = 7 structure for glycyl-L-valine.

The title peptide, C7H14N2O3, crystallizes with seven independent molecules in the asymmetric unit. All have essentially the same overall conformation, but some flexibility is exhibited by the glycine residue. It appears that the high Z' value, observed only three times before for an organic compound, permits formation of shorter hydrogen bonds in one of the two head-to-tail chains involving the N-terminal amino groups and the C-terminal carboxylate groups than found in a hypothetical model structure of glycyl-L-valine with Z' = 1, and that it furthermore alleviates strain associated with an eclipsed orientation of the amino group.

Crystallography, X-Ray↗
PubMed2006

L-Phenylalanyl-L-tryptophan 0.75-hydrate.

The title compound, C20H21N3O3.0.75H2O, crystallizes as exceedingly thin fibers. The crystal packing arrangement is related to those of other hydrophobic dipeptides with phenylalanine residues, but the structure has pseudo-tetragonal symmetry in an orthorhombic space group with four peptide molecules and three water molecules in the asymmetric unit.

Crystallography, X-Ray↗
PubMed2006

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

Alzheimer's 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.

Amyloid beta-Peptides↗
PubMed2006

Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.

Peroxidases, oxygenases and catalases have similar high-valent metal-ion intermediates in their respective reaction cycles. In this review, haem-based examples will be discussed. The intermediates of the haem-containing enzymes have been extensively studied for many years by different spectroscopic methods like UV-Vis, EPR (electron paramagnetic resonance), resonance Raman, Mössbauer and MCD (magnetic circular dichroism). The first crystal structure of one of these high-valent intermediates was on cytochrome c peroxidase in 1987. Since then, structures have appeared for catalases in 1996, 2002, 2003, putatively for cytochrome P450 in 2000, for myoglobin in 2002, for horseradish peroxidase in 2002 and for cytochrome c peroxidase again in 1994 and 2003. This review will focus on the most recent structural investigations for the different intermediates of these proteins. The structures of these intermediates will also be viewed in light of quantum mechanical (QM) calculations on haem models. In particular quantum refinement, which is a combination of QM calculations and crystallography, will be discussed. Only small structural changes accompany the generation of these intermediates. The crystal structures show that the compound I state, with a so called pi-cation radical on the haem group, has a relatively short iron-oxygen bond (1.67-1.76A) in agreement with a double-bond character, while the compound II state or the compound I state with a radical on an amino acid residue have a relatively long iron-oxygen bond (1.86-1.92A) in agreement with a single-bond character where the oxygen-atom is protonated.

Catalase↗
PubMed2005

L-Isoleucyl-L-serine 0.33-hydrate, L-phenylalanyl-L-serine and L-methionyl-L-serine 0.34-hydrate.

The structures of the title dipeptides, C9H18N2O4.0.33H2O, C12H16N2O4 and C8H16N2O4S.0.34H2O, complete a series of investigations focused on L-Xaa-L-serine peptides, where Xaa is a hydrophobic residue. All three structures are divided into hydrophilic and hydrophobic layers. The hydrophilic layers are thin for L-phenylalanyl-L-serine, rendered possible by an unusual peptide conformation, and thick for L-isoleucyl-L-serine and L-methionyl-L-serine, which include cocrystallized water molecules on the twofold axes.

Crystallography, X-Ray↗
PubMed2005

L-valyl-L-serine trihydrate.

The valine side chains in the crystal structure of the title compound [systematic name: 2-(2-ammonio-3-methylbutanamido)-3-hydroxypropanoate trihydrate], C8H16N2O4.3H2O, stack along an a axis of 4.77 A to form hydrophobic columns surrounded by remarkable water/hydroxyl shells. The peptide main chains are connected by hydrogen bonds in two-dimensional layers. The peptide molecules in each layer are related only by translation, and generate a very rare pattern. This is rendered possible through the formation of the shortest C(alpha)-H...O(carboxylate) interaction ever recorded.

Crystallography, X-Ray↗
PubMed2004

L-Phenylalanyl-L-isoleucine 0.88-hydrate.

The asymmetric unit in the crystal structure of the title compound, C(15)H(22)N(2)O(3).0.88H(2)O, contains two peptide molecules with completely different conformations. The structure is divided into hydrophobic and hydrophilic layers, with channels of water molecules at the layer interface.

Coumarins↗
PubMed2004

A crystallographic titration of the dipeptide L-isoleucyl-L-isoleucine.

The dipeptide L-Ile-L-Ile has been crystallized in four different protonation states, including as a cation, a zwitterion and an anion, as well as a dimeric cation in which two peptide molecules, linked by a strong -COO...H...OOC- hydrogen bond, share an overall positive charge of +1. This unprecedented series of crystal structures exhibits differences in hydrogen-bonding capabilities, conformational properties and molecular packing arrangements. The crystallization of L-Ile-L-Ile as an anion was achieved by slow evaporation from an NH(3)(l) solution to give the first ever ammonium salt of a peptide (or amino acid).

Anions↗
PubMed2004

Crystal structural studies of changes in the native dinuclear iron center of ribonucleotide reductase protein R2 from mouse.

Class I ribonucleotide reductase (RNR) catalyzes the de novo synthesis of deoxyribonucleotides in mammals and many other organisms. The RNR subunit R2 contains a dinuclear iron center, which in its diferrous form spontaneously reacts with O2, forming a mu-oxo-bridged diferric cluster and a stable tyrosyl radical. Here, we present the first crystal structures of R2 from mouse with its native dinuclear iron center, both under reducing and oxidizing conditions. In one structure obtained under reducing conditions, the iron-bridging ligand Glu-267 adopts the mu-(eta1,eta2) coordination mode, which has previously been related to O2 activation, and an acetate ion from the soaking solution is observed where O2 has been proposed to bind the iron. The structure of mouse R2 under oxidizing conditions resembles the nonradical diferric R2 from Escherichia coli, with the exception of the coordination of water and Asp-139 to Fe1. There are also additional water molecules near the tyrosyl radical site, as suggested by previous spectroscopic studies. Since no crystal structure of the active radical form has been reported, we propose models for the movement of waters and/or tyrosyl radical site when diferric R2 is oxidized to the radical form, in agreement with our previous ENDOR study. Compared with E. coli R2, two conserved phenylalanine residues in the hydrophobic environment around the diiron center have opposing rotameric conformations, and the carboxylate ligands of the diiron center in mouse R2 appear more flexible. Together, this might contribute to the lower affinity and cooperative binding of iron in mouse R2.

Animals↗
PubMed2004

L-Isoleucyl-L-phenylalanine dihydrate.

The structure of the title compound, C(15)H(22)N(2)O(3).2H(2)O, was derived from data collected on a very thin twinned needle. The peptide molecule is in a rare conformation normally associated with hydrophobic dipeptides that form nanotubes. Nevertheless, the present structure is divided into hydrophobic and hydrophilic layers.

Dipeptides↗
PubMed2004

Synthesis, structure, and ethene polymerisation catalysis of 1- or 2-silyl substituted bis[indenyl]zirconium(IV) dichlorides.

The systematic syntheses of 1- and 2-substituted silylindenes, with a wide variety of substitution patterns on the silyl moiety, and their corresponding zirconocene dichlorides are presented. The rac- and meso-diastereomers of the 1-substituted zirconocene dichlorides can in most cases be separated. Instable zirconocenes were observed for certain substitution patterns. Two of the obtained zirconocene dichlorides, bis[2-(dimethylsilyl)indenyl]zirconium dichloride (4a) and bis[2-(trimethylsilyl)indenyl]zirconium dichloride (4b), were characterised by single crystal X-ray diffraction. On the basis of DFT results, the two compounds are geometrically similar, i.e. the additional methyl group on the silyl moiety only affects the conformational energy profile. Differences in their catalyst performance in the homopolymerisation studies with ethane are thus attributed to conformational control. For the remaining complexes, sterically less demanding silyl groups seem to be favoured with respect to the catalyst performance. All the 2-isomers have lower polymerisation activities than the unsubstituted bis[indenyl]zirconium dichloride/MAO system. Curiously, the rac-bis[1-(dimethylphenylsilyl)indenyl]zirconium dichloride/MAO system is found to be the most active catalyst in ethene homopolymerisations.

Journal Article↗
PubMed2003

Water polymers in L-alanyl-L-methionine hemihydrate.

The side chains of L-alanyl-L-methionine hemihydrate, C(8)H(16)N(2)O(3)S.0.5H(2)O, form hydrophobic columns within a three-dimensional hydrogen-bond network that includes extended polymers of cocrystallized water molecules and C(alpha)-H.S interactions.

Alanine↗
PubMed2003

L-methionyl-L-alanine: a dipeptide with hexagonal symmetry and Z' = 7.

The crystal structure of L-methionyl-L-alanine, C(8)H(16)N(2)O(3)S, is very similar to that of L-valyl-L-alanine [Görbitz & Gundersen (1996). Acta Cryst. C52, 1764-1767] and other related dipeptides in space group P6(1), but there are seven molecules in the asymmetric unit. The Z value of 42 is the highest ever observed for a chiral molecule.

Alanine↗
PubMed2002

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.

Journal Article↗