Related ArticlesA combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II.
Biochemistry. 2005 May 10;44(18):6729-37
Authors: Wen X, Yuan Y, Kuntz DA, Rose DR, Pinto BM
A combined STD-NMR/molecular modeling protocol to probe the binding modes of the glycosidase inhibitors kifunensine and salacinol to Drosophila melanogaster Golgi alpha-mannosidase II (dGMII) was tested. Saturation-transfer difference (STD) NMR experiments were carried out for the complexes of dGMII with these two inhibitors. The program AutoDock 3.0 was then used to optimize the interactions of the inhibitors with the residues in the active site of dGMII. Theoretical STD effects of the ligand protons in the complexes were calculated for the different binding modes with the recently developed CORCEMA-ST protocol. Comparison of experimental and theoretical effects then permitted selection of the likely binding modes of the ligands. The more rigid kifunensine was used initially to test the protocol. Excellent correlation between experimental and theoretical data was obtained for one of the binding modes that also corresponded to that observed in the crystal structure of the complex. The protocol was then extended to the more flexible salacinol. For the selected binding mode, good correlation of experimental and theoretical data for the five-membered ring was obtained; however, poor correlation for protons on the acyclic chain was obtained, suggesting flexibility in this portion of the molecule. Comparison of the selected binding mode with that from a crystal structure of salacinol with dGMII showed excellent superimposition of the five-membered ring but another orientation of the acyclic chain. The results suggest that reliable structural binding modes of a ligand to protein in aqueous solution can be provided with the combined use of STD-NMR spectroscopy, molecular modeling, and CORCEMA-ST calculations, although highly flexible portions of the ligand may be poorly defined.
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands*
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands*
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands*
Chemistry. 2011 Feb 1;17(5):1547-1560
Authors: Enríquez-Navas PM, Marradi M, Padro D, Angulo J, Penadés S
The structural and affinity details of the interactions of synthetic oligomannosides, linear (di-, tri-, and tetra-) and branched (penta- and hepta-),...
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A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands*
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands*
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands*
Chemistry. 2011 Jan 5;
Authors: Enríquez-Navas PM, Marradi M, Padro D, Angulo J, Penadés S
The structural and affinity details of the interactions of synthetic oligomannosides, linear (di-, tri-, and tetra-) and branched (penta- and hepta-), with the broadly...
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01-06-2011 11:21 AM
[NMR paper] The application of x-ray, NMR, and molecular modeling in the design of MMP inhibitors
The application of x-ray, NMR, and molecular modeling in the design of MMP inhibitors.
Related Articles The application of x-ray, NMR, and molecular modeling in the design of MMP inhibitors.
Curr Top Med Chem. 2004;4(12):1311-27
Authors: Rush TS, Powers R
The following review discusses the successful application of X-ray, NMR, and molecular modeling in the design of potent and selective inhibitors of matrix metalloproteinases (MMPs) and TNFalpha-converting enzyme (TACE) from Wyeth. The importance of protein and ligand mobility as it impacts...
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11-24-2010 09:25 PM
[NMR paper] Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular d
Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study.
Related Articles Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study.
Biopolymers. 2002 Nov 15;65(4):284-98
Authors: Dixon AM, Venable RM, Pastor RW, Bull TE
A peptide fragment from a protein hairpin turn region was modified by addition of isoleucine residues to both ends to enhance binding to lipid micelles; the resulting peptide (I(1)-I(2)-C(3)-N(4)-N(5)-P(6)-H(7)-I(8)-I(9)) contains the core...
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11-24-2010 08:58 PM
[NMR paper] CLOUDS, a protocol for deriving a molecular proton density via NMR.
CLOUDS, a protocol for deriving a molecular proton density via NMR.
CLOUDS, a protocol for deriving a molecular proton density via NMR.
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6707-12
Authors: Grishaev A, Llinás M
We demonstrate the feasibility of computing realistic spatial proton distributions for proteins in solution from experimental NMR nuclear Overhauser effect data only and with minimal assignments. The method, CLOUDS, relies on precise and abundant interproton distance restraints calculated via a relaxation matrix analysis of...
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[NMR paper] NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein
NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein linkage region of connective tissue proteoglycans.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif Related Articles NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein linkage region of connective tissue proteoglycans.
Glycobiology. 1999 Jul;9(7):669-77
Authors: Agrawal PK, Jacquinet JC, Krishna NR
Complete 1H and 13C NMR...
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A combined STD-NMR/molecular modeling protocol for predicting the binding modes of th
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