Biomedical subjects

J P Lommerse

Publications and source records attributed to J P Lommerse.

6 recordsLinked to original sources

PubMed2000

A test of crystal structure prediction of small organic molecules.

A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing, the principal computer programs currently available were used. There were 11 participants who were allowed to propose at most three structures for each compound. No program gave consistently reliable results. However, seven proposed structures were close to an experimental one and were classified as "correct". One compound occurred in two polymorphs, but only one form was predicted correctly among the calculated structures. The basic problem with lattice energy based methods of crystal structure prediction is that many structures are found within a few kJ mol(-1) of the global minimum. The fine detail of the force-field methodology and parametrization influences the energy ranking within each method. Nevertheless, present methods may be useful in providing a set of structures as possible polymorphs for a given molecular structure.

Journal Article↗

PubMed1997

Primary structure of 21 novel monoantennary and diantennary N-linked carbohydrate chains from alphaD-hemocyanin of Helix pomatia.

The primary structures of 21 novel monoantennary and diantennary N-glycans of the glycoprotein alphaD-hemocyanin (alphaD-Hc) of Helix pomatia have been determined. Outer oligosaccharide fragments (antennae) were released from the glycoprotein by Smith degradation of an alphaD-Hc pronase digest. The major antenna, obtained following HPLC fractionation on Lichrosorb-NH2, was characterized using 1H-NMR spectroscopy, fast-atom-bombardment mass spectrometry, and linkage analysis, and corresponds to a pentasaccharide fragment. The intact carbohydrate chains of alphaD-Hc were released with peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase-F digestion, separated from the protein on Bio-Gel P-100, and subfractionated on Bio-Gel P-4. A portion of subfractions was reduced with sodium borodeuteride, and the non-reduced and reduced samples were further fractionated on CarboPac PA-1, Lichrosorb-NH2/Lichrosphere-NH2, and/or Lichrosphere-C18. Purified oligosaccharides and oligosaccharide-alditols were analyzed using 500/600-MHz 1H-NMR spectroscopy. In total, four novel types of antenna were identified, namely, [structures: see text] which are all attached to O-2 of alphaMan residues of the trimannosyl-N,N'-diacetylchitobiose core element, which is generally beta-1,2-xylosylated and alpha-1,6-fucosylated, Man(alpha1-6)[Man(alpha1-3)][+/-Xyl(beta1-2)]Man(beta1-4)GlcNAc(beta1-4) [+/-Fuc(alpha1-6)]GlcNAc.

Amidohydrolases↗

PubMed1997

IsoStar: a library of information about nonbonded interactions.

Crystallographic and theoretical (ab initio) data on intermolecular nonbonded interactions have been gathered together in a computerised library ('IsoStar'). The library contains information about the nonbonded contacts formed by some 250 chemical groupings. The data can be displayed visually and used to aid protein-ligand docking or the identification of bioisosteric replacements. Data from the library show that there is great variability in the geometrical preferences of different types of hydrogen bonds, although in general there is a tendency for H-bonds to form along lone-pair directions. The H-bond acceptor abilities of oxygen and sulphur atoms are highly dependent on intramolecular environments. The nonbonded contacts formed by many hydrophobic groups show surprisingly strong directional preferences. Many unusual nonbonded interactions are to be found in the library and are of potential value for designing novel biologically active molecules.

Biochemical Phenomena↗

PubMed1997

Characterising non-covalent interactions with the Cambridge Structural Database.

This review describes how the CSD can be used to study non-covalent interactions. Several different types of information may be obtained. First, the relative frequencies of various interactions can be studied; for example, we have shown that the terminal oxygen atoms of phosphate groups accept hydrogen bonds far more often than the linkage oxygens. Secondly, information can be obtained about the geometries of nonbonded contacts; for example, hydrogen bonds to P-O groups rarely form along the extension of the P-O bond, whereas short contacts between oxygen and carbon-bound iodine show a strong preference for linear C-I ... O angles. Thirdly, the CSD can be searched for novel interactions which may be exploited in inhibitor design; for example, the I ... O contacts just mentioned, and N-H ... pi hydrogen bonds. Finally, the CSD can suggest synthetic targets for medicinal chemistry; for example, molecules containing delocalised electron deficient groups such as trimethylammonium, pyridinium, thaizolium and dinitrophenyl have a good chance of binding to an active-site tryptophan. Although the CSD contains small-molecule crystal structures, not protein-ligand complexes, there is considerable evidence that the contacts seen in the two types of structures are similar. We have illustrated this a number of times in the present review and additional evidence has been given previously by Klebe. The major advantages of the CSD are its size, diversity and experimental accuracy. For these reasons, it is a useful tool for modellers engaged in rational inhibitor design.

Crystallography, X-Ray↗

PubMed1995

Conformational analysis of the xylose-containing N-glycan of pineapple stem bromelain as part of the intact glycoprotein.

The conformational behavior of the N-glycan Man alpha 1-6(Xyl beta 1-2)Man beta 1-4GlcNAc beta 1-4(Fuc alpha 1-3)GlcNAc beta of stem bromelain as part of the intact glycoprotein was investigated and compared with that of the same N-glycan as part of a bromelain-derived glycopeptide. Proton chemical shifts of the glycoprotein N-glycan were determined by 2D HOHAHA and 2D NOESY measurements, making use of the glycopeptide 1H NMR data. During each 2D NMR experiment about 4% of the glycoprotein denatured. Experimental data concerning interproton distances of the intact glycoprotein N-glycan were obtained by NOESY 1H NMR spectroscopy. Several theoretical models for the N-glycan, obtained by molecular dynamics simulations of the glycopeptide, were investigated. Comparison of experimental and theoretical NOESY cross peak intensities was performed with the program CROSREL. In comparison with the glycopeptide, the distribution of populations between two main conformations of the Fuc alpha 1-3GlcNAc linkage was altered. In addition, the omega = 60 degrees (gt) rotamer of the Man alpha 1-6Man linkage seems to be present for a significant period of time, whereas in the glycopeptide the omega = -60 degrees (gg) conformation exists exclusively. Except for the Xyl beta 1-2Man linkage, the mobilities around the glycosidic linkages in the glycoprotein were reduced compared with those in the glycopeptide, especially concerning the Fuc alpha 1-3GlcNAc and Man alpha 1-6Man linkages. These findings might be the result of an interaction of the polypeptide chain with the Fuc alpha/Man alpha side of the N-glycan. A qualitative analysis of the NMR spectra showed a larger degree of mobility in the denatured glycoprotein N-glycan than in the intact glycoprotein.

Amino Acid Sequence↗

PubMed1995

Conformations and internal mobility of a glycopeptide derived from bromelain using molecular dynamics simulations and NOESY analysis.

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.

Amino Acid Sequence↗