Related ArticlesFluorine-Protein Interactions and (19)F NMR Isotropic Chemical Shifts: An Empirical Correlation with Implications for Drug Design.
ChemMedChem. 2010 Nov 29;
Authors: Dalvit C, Vulpetti A
An empirical correlation between the fluorine isotropic chemical shifts, measured by (19)F NMR spectroscopy, and the type of fluorine-protein interactions observed in crystal structures is presented. The CF, CF(2), and CF(3) groups present in fluorinated ligands found in the Protein Data Bank were classified according to their (19)F NMR chemical shifts and their close intermolecular contacts with the protein atoms. Shielded fluorine atoms, i.e., those with increased electron density, are observed primarily in close contact to hydrogen bond donors within the protein structure, suggesting the possibility of intermolecular hydrogen bond formation. Deshielded fluorines are predominantly found in close contact with hydrophobic side chains and with the carbon of carbonyl groups of the protein backbone. Correlation between the (19)F NMR chemical shift and hydrogen bond distance, both derived experimentally and computed through quantum chemical methods, is also presented. The proposed "rule of shielding" provides some insight into and guidelines for the judicious selection of appropriate fluorinated moieties to be inserted into a molecule for making the most favorable interactions with the receptor.
PMID: 21117131 [PubMed - as supplied by publisher]
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
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Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.
BMC Struct Biol. 2011 May 12;11(1):24
Authors: Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA
ABSTRACT: BACKGROUND: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural...
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05-17-2011 06:21 PM
NMR and protein structure in drug design: application to cyclotides and conotoxins.
NMR and protein structure in drug design: application to cyclotides and conotoxins.
NMR and protein structure in drug design: application to cyclotides and conotoxins.
Eur Biophys J. 2011 Feb 3;
Authors: Daly NL, Rosengren KJ, Troeira Henriques S, Craik DJ
Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for determining the structures, dynamics and interactions of molecules, and the derived information can be useful in drug design applications. This article gives a brief overview of the role of NMR in drug design and...
[NMR paper] Lactic acid and protein interactions: implications for the NMR visibility of lactate
Lactic acid and protein interactions: implications for the NMR visibility of lactate in biological systems.
Related Articles Lactic acid and protein interactions: implications for the NMR visibility of lactate in biological systems.
Biochim Biophys Acta. 1999 Jan 4;1426(1):177-84
Authors: Chatham JC, Forder JR
The addition of bovine serum albumin (BSA) to a solution of lactate and alanine resulted in the disappearance of the 1H-NMR resonances from lactate but not alanine. As temperature is increased lactate becomes increasingly NMR visible and...
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11-18-2010 07:05 PM
[NMR paper] NMR for the design of functional mimetics of protein-protein interactions: one key is
NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges.
Related Articles NMR for the design of functional mimetics of protein-protein interactions: one key is in the building of bridges.
Biochem Cell Biol. 1998;76(2-3):177-88
Authors: Song J, Ni F
Using the design of bivalent and bridge-binding inhibitors of thrombin as an example, we review an NMR-based experimental approach for the design of functional mimetics of protein-protein interactions. The strategy includes: (i) identification...
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11-17-2010 11:06 PM
[NMR paper] NMR spectroscopy in structure-based drug design.
NMR spectroscopy in structure-based drug design.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR spectroscopy in structure-based drug design.
Curr Opin Biotechnol. 1999 Feb;10(1):42-7
Authors: Roberts GC
NMR methods for the study of motion in proteins continue to improve, and a number of studies of protein-ligand complexes relevant to drug design have been reported over the past year, for example, studies of fatty-acid-binding protein and SH2 and SH3 domains. These...
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08-21-2010 04:03 PM
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of
Abstract NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures,...
Fluorine-Protein Interactions and (19)F NMR Isotropic Chemical Shifts: An Empirical Correlation with Implications for Drug Design.
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