Identification of Protein-Mediated Indirect Noe Effects in a Disaccharide-Fab′ Complex by Transferred ROESY

Arepalli, Sivaram; Glaudemans, Cornelis P.J.; Daves, G. Doyle; Kovac, P.; Bax, Ad

doi:10.1006/jmrb.1995.1033

Cited by 80 publications

(75 citation statements)

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“…spin-diffusion effects, because ROES and transfer-ROES change their sign in this case (Arepalli et al, 1995;Asensio et al, 1995;Lian et al, 1994;Weimar et al, 1995). This becomes particularly important if relay protons in the binding pocket of a protein transfer magnetization among two otherwise distant protons of the ligand (Arepalli et al, 1995). Following this protocol, the following NOES and transfer-NOES could be ascribed to spin diffusion (very minor effects are not mentioned): Hle-HSd, H1c-H3b+H5b, Hld-H5', Hld-H6d, H5C-H3d.…”

Section: Resultsmentioning

confidence: 99%

“…For protein peptide-ligand complexes, intermolecular transfer-NOES have been observed and under more fortunate circumstances these effects could be used to dock the ligand in the binding site . For protein saccharide-ligand complexes, only m e case has been reported so far where very weak intermolecular transfer-NOES could be detected for a disaccharide in the binding site of a monoclonal antibody (Arepalli et al, 1995). In the case of the D. bitlorus-FPS complex, notable intermolecular transfer-NOES were detected.…”

Section: Observation Of Ligand-protein Transfer-noes Intermolecularmentioning

confidence: 96%

“…bound conformations of flexible saccharide ligands (Weimar et al, 1995;Asensio et al, 1995;Scheffler et al, 1995;Bundle et al, 1994;Bevilacqua et al, 1992), and, under certain circumstances, intermolecular transferNOEs between ligand and protein protons may be observed. So far, only one study has reported the observation of carbohydrateprotein transfer-NOES but the effects were rather weak and difficult to interpret (Arepalli et al, 1995).…”

mentioning

confidence: 99%

“…Our study describes transfer-NOE experiments for a saccharide ligand the size of a pentasaccharide. This is notable because most of the studies performed so far have concentrated on disaccharide ligands (Asensio et al, 1995;Arepalli et al, 1995;Bevilacqua et al, 1992) and some have used tri-or tetrasaccharides (Weimar et al, 1995;Scheffler et al, 1995;Bundle et al, 1994) as ligands. For peptide and nucleotide ligands, considerably more transfer-NOE experiments have been performed during recent years (Clore andGronenborn, 1982, 1983;Ni et al, 1989a, b;Perlman et al, 1994), and for comprehensive reviews the reader is referred to Moseley et al (1995), Ni (1994) and Lian et al (1994).…”

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confidence: 99%

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Transferred Nuclear Overhauser Enhancement (NOE) and Rotating‐Frame NOE Experiments Reflect the Size of the Bound Segment of the Forssman Pentasaccharide in the Binding Site of Dolichos Biflorus Lectin

Casset

Pérez²,

Etzler

et al. 1997

European Journal of Biochemistry

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A complex between the Forssman pentasaccharide a-D-GalNAc-( 1+3)-P-~-GalNAc-( 1+3)-a-~-Gal-(1+4)-P-~-Gal-( 1-4)-~-Glc and the seed lectin from Dolichos bz$hrus was studied using transfer-NOESY and transfer rotating frame NOE spectroscopy (ROESY) experiments. The evolution of transferred NOEs and ROES as a function of the pentasaccharide/lectin ratio was different for the non-reducing disaccharide moiety a-~-GalNAc-(l+3)-P-~-GalNAc compared to the rest of the molecule, which reflects distinct relaxation properties and effects of exchange broadening of the corresponding ligand resonances. Significantly, several intermolecular transferred NOEs were observed between protons of the nonreducing disaccharide moiety a-D-GalNAc-( 1 -3)-p-~-GalNAc and aliphatic as well as aromatic amino acid side chain protons in the binding pocket of the lectin. It is concluded that the non-reducing disaccharide fragment is buried in the lectin-binding pocket, whereas the reducing trisaccharide portion a-D-Gal-(1+4)-p-~-Gal-( 1-+4)-D-Glc has no immediate contacts with the protein. The experimental transfer NOE data were qualitatively compared to theoretical proton-proton distances from a model that was based on a previous homology modeling study of a complex between the disaccharide fragment a-D-GalNAc-(1+3)-p-~-GalNAc and D. bij7oru.s lectin. It was found that all intermolecular transferred NOEs matched short interatomic distances between ligand protons and aliphatic or aromatic amino acid side chain protons predicted by the theoretical model.

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Section: Resultsmentioning

confidence: 99%

Section: Observation Of Ligand-protein Transfer-noes Intermolecularmentioning

confidence: 96%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Transferred Nuclear Overhauser Enhancement (NOE) and Rotating‐Frame NOE Experiments Reflect the Size of the Bound Segment of the Forssman Pentasaccharide in the Binding Site of Dolichos Biflorus Lectin

Casset

Pérez²,

Etzler

et al. 1997

European Journal of Biochemistry

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“…In the special case of weakly bound ligands, with a high rate of exchange between the bound and the free states, transferred nuclear Overhauser effects (TRNOEs) 1 can be observed, giving information about the conformation of the carbohydrate in the binding site (Clore and Gronenborn, 1982;Ni, 1994). This method allowed the determination of the conformational changes undergone by oligosaccharides upon binding to ricin (Bevilacqua et al, 1990(Bevilacqua et al, , 1992, to antibodies (Glaudemans et al, 1990, Bundle et al, 1994, Arepalli et al, 1995, and to a human lectin (Cooke et al, 1994). Molecular modeling is a complementary tool for both x-ray and NMR methods.…”

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confidence: 99%

NMR, Molecular Modeling, and Crystallographic Studies of Lentil Lectin-Sucrose Interaction

Casset¹,

Hamelryck

Loris

et al. 1995

Journal of Biological Chemistry

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The conformational features of sucrose in the combining site of lentil lectin have been characterized through elucidation of a crystalline complex at 1.9-Å resolution, transferred nuclear Overhauser effect experiments performed at 600 Mhz, and molecular modeling. In the crystal, the lentil lectin dimer binds one sucrose molecule per monomer. The locations of 229 water molecules have been identified. NMR experiments have provided 11 transferred NOEs. In parallel, the docking study and conformational analysis of sucrose in the combining site of lentil lectin indicate that three different conformations can be accommodated. Of these, the orientation with lowest energy is identical with the one observed in the crystalline complex and provides good agreement with the observed transferred NOEs. These structural investigations indicate that the bound sucrose has a unique conformation for the glycosidic linkage, close to the one observed in crystalline sucrose, whereas the fructofuranose ring remains relatively flexible and does not exhibit any strong interaction with the protein. Major differences in the hydrogen bonding network of sucrose are found. None of the two inter-residue hydrogen bonds in crystalline sucrose are conserved in the complex with the lectin. Instead, a water molecule bridges hydroxyl groups O2-g and O3-f of sucrose.

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Mapping the active site of factor Xa by selective inhibitors: An NMR and MD study

Fraternali¹,

Do²,

Doan³

et al. 1998

Proteins

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The structure of two selective inhibitors, Ac-Tyr-Ile-Arg-Ile-Pro-NH2 and Ac-(4-Amino-Phe)-(Cyclohexyl-Gly)-Arg-NH2, in the active site of the blood clotting enzyme factor Xa was determined by using transferred nuclear Overhauser effect nuclear magnetic resonance (NMR) spectroscopy. They represent a family of peptidic inhibitors obtained by the screening of a vast combinatorial library. Each structure was first calculated by using standard computational procedures (distance geometry, simulated annealing, energy minimization) and then further refined by systematic search of the conformation of the inhibitor docked in the active site and repeating the simulated annealing and energy minimization. The final structure was optimized by molecular dynamics simulations of the inhibitor-complex in water. The NMR restraints were kept throughout the refinement. The inhibitors assume a compact, very well defined conformation, embedded into the substrate binding site not in the same way as a substrate, blocking thus the catalysis. The model allows to explain the mode of action, affinity, and specificity of the peptides and to map the active site.

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Identification of Protein-Mediated Indirect Noe Effects in a Disaccharide-Fab′ Complex by Transferred ROESY

Cited by 80 publications

References 0 publications

Transferred Nuclear Overhauser Enhancement (NOE) and Rotating‐Frame NOE Experiments Reflect the Size of the Bound Segment of the Forssman Pentasaccharide in the Binding Site of Dolichos Biflorus Lectin

Transferred Nuclear Overhauser Enhancement (NOE) and Rotating‐Frame NOE Experiments Reflect the Size of the Bound Segment of the Forssman Pentasaccharide in the Binding Site of Dolichos Biflorus Lectin

NMR, Molecular Modeling, and Crystallographic Studies of Lentil Lectin-Sucrose Interaction

Mapping the active site of factor Xa by selective inhibitors: An NMR and MD study

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