Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:2.7.10.2 (focal adhesion kinase)
 44,029 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The molecular recognition of streptomycin by Bacillus subtilis aminoglycoside-6-adenyl transferase has been analysed by a combination of NMR techniques and molecular dynamic simulations. This protein inactivates streptomycin by transferring an adenyl group to position six of the streptidine moiety. Our combined approach provides valuable information about the bioactive conformation for both the antibiotic and ATP and shows that the molecular recognition process for streptomycin involves a conformational selection phenomenon. The binding epitope for both ligands has also been analysed by 1D-STD experiments. Finally, the specificity of the recognition process with respect to the aminoglycoside and to the nucleotide has been studied.
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PMID:Molecular recognition of aminoglycoside antibiotics by bacterial defence proteins: NMR study of the structural and conformational features of streptomycin inactivation by Bacillus subtilis aminoglycoside-6-adenyl transferase. 1598 36

The catalytic subunit of cAMP-dependent protein kinase (PKA) can easily be expressed in Escherichia coli and is catalytically active. Four phosphorylation sites are known in PKA (S10, S139, T197 and S338), and the isolated recombinant protein is a mixture of different phosphorylated forms. Obtaining uniformly phosphorylated protein requires separation of the protein preparation leading to significant loss in protein yield. It is found that the mutant S10A/S139D/S338D has similar properties as the wild-type protein, whereas additional replacement of T197 with either E or D reduces protein expression yield as well as folding propensity of the protein. Due to its high sequence homology to Akt/PKB, which cannot easily be expressed in E. coli, PKA has been used as a surrogate kinase for drug design. Several mutations within the ATP binding site have been described to make PKA even more similar to Akt/PKB. Two proteins with Akt/PKB-like mutations in the ATP binding site were made (PKAB6 and PKAB8), and in addition S10, S139 and S338 phosphorylation sites have been removed. These proteins can be expressed in high yields but have reduced activity compared to the wild-type. Proper folding of all proteins was analyzed by 2D 1H, 15N-TROSY NMR experiments.
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PMID:Folding and activity of cAMP-dependent protein kinase mutants. 1602 85

We studied the interaction of mono- and polyunsaturated phosphatidylcholines with rhodopsin by 1H NMR saturation transfer difference spectroscopy with magic angle spinning (STD-MAS NMR). The results indicate a strong preference for interaction of rhodopsin with the polyunsaturated docosahexaenoic acid.
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PMID:Probing specific lipid-protein interaction by saturation transfer difference NMR spectroscopy. 1617 15

Dihydrofolate reductase (DHFR) is a pharmacologically important intracellular target enzyme for folate antagonists, including the antibacterial agent trimethoprim (TMP). The structures of DHFR from various sources with and without the bound ligands have been determined by X-ray crystallography and solution NMR spectroscopy. However, there is no crystal or solution NMR structure for the bovine DHFR/TMP complex. Here we report the solution structure of TMP within the binding pocket of bovine DHFR using a novel method developed in our laboratory, viz., STD-NMR intensity-restrained CORCEMA-ST optimization (SICO) utilizing experimental STD data on this complex, and demonstrate that its solution structure is essentially identical to the one in the crystal structure of the homologous chicken liver DHFR/TMP complex. The excellent agreement we obtain between the experimental and predicted STDs also serves as a validation of the CORCEMA-ST methodology.
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PMID:Determination of the conformation of trimethoprim in the binding pocket of bovine dihydrofolate reductase from a STD-NMR intensity-restrained CORCEMA-ST optimization. 1620 30

UDP-galactopyranose mutase (UGM) is the key enzyme involved in the biosynthesis of Galf. In this study, reliable structural binding modes of the natural substrate, UDP-Galp, and inhibitor, UDP, in the UGM active site were provided with the combined use of STD-NMR spectroscopy, molecular modeling, and CORCEMA-ST calculations. UDP-Galp and UDP exhibited similar binding epitopes recognized by UGM. However, the relative binding affinities of the ligands changed dramatically upon reduction of UGM, as explored by competitive STD-NMR experiments. UDP-Galp competes with UDP for binding to UGM, especially when UGM is in its reduced state. Docking studies for predicting the binding mode within the active site of the two monomers in UGM explored the possibility that the mobile loop might act as a gateway for substrate binding, and the structure of the binding cleft in monomer A might be a closer approximation of the substrate-bound active site than monomer B. Important information regarding the critical interactions of UGM with UDP-Galp has been obtained.
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PMID:Exploring the mechanism of binding of UDP-galactopyranose to UDP-galactopyranose mutase by STD-NMR spectroscopy and molecular modeling. 1624 24

A water-soluble polysaccharide named as FPS-1 was isolated from fuzi, the root of Aconitum carmichaeli Debx. by hot-water extraction, anion-exchange and gel-permeation chromatography and tested for its pharmacological activities. Its structural characteristics were investigated by FTIR, HPLC, NMR spectroscopy, methylation analysis and GLC-MS. Based on the data obtained, FPS-1 was determined to be an alpha-(1-->6)-d-glucan, with a weight-average molecular weight of about 14,000Da. The glucan is highly branched with a single glucose at the C-3 position every four residues, on average, along the main chain. In immunopharmacological studies, FPS-1 showed potent stimulating effects on murine lymphocyte proliferation induced by concanavalin A or lipopolysaccharide both in vitro and in vivo as well as on splenocyte antibody production.
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PMID:Isolation and structural characterization of an immunostimulating polysaccharide from fuzi, Aconitum carmichaeli. 1640 77

Protein domain swapping has been repeatedly observed in a variety of proteins and is believed to result from destabilization due to mutations or changes in environment. Based on results from our studies and others, we propose that structures of the domain-swapped proteins are mainly determined by their native topologies. We performed molecular dynamics simulations of seven different proteins, known to undergo domain swapping experimentally, under mildly denaturing conditions and found in all cases that the domain-swapped structures can be recapitulated by using protein topology in a simple protein model. Our studies further indicated that, in many cases, domain swapping occurs at positions around which the protein tends to unfold prior to complete unfolding. This, in turn, enabled prediction of protein structural elements that are responsible for domain swapping. In particular, two distinct domain-swapped dimer conformations of the focal adhesion targeting domain of focal adhesion kinase were predicted computationally and were supported experimentally by data obtained from NMR analyses.
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PMID:Topological determinants of protein domain swapping. 1640 60

Affinity index (AT value), adsorption heat, X-ray diffraction (XRD), and 13C and 29Si magic-angle spinning (MAS) NMR, FTIR, and Raman spectroscopies were used to study the interaction of highly siliceous MFI-, FAU-, and FER-type zeolites with adsorbed methylamine (MA). Compared with the data for methanol, the much higher AT values and adsorption heats, and significant changes in XRD patterns, 29Si MAS NMR spectra, and FTIR spectra for the zeolites after adsorption of MA, revealed a strong hydrogen-bonding interaction between the perfect framework of the zeolites and the adsorbed MAs. This interaction results from the fact that the H atom of the amine group attacks the [Si-O] framework to form a Si-OHN bond, which leads to the appearance of Si-N bonds in the zeolites at 323 K. Therefore, the zeolite framework can be modified with MA under mild conditions. The highly siliceous MFI zeolite and the H-ZSM-5 zeolite with SiO2/Al2O3=31:1 were modified with MA and investigated by temperature-programmed desorption of CO2. The modified zeolites exhibited greatly enhanced basic properties in comparison with those of the raw materials. The influence of defects in the zeolite on the adsorption and the interaction with MA is discussed.
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PMID:The leading role of association in framework modification of highly siliceous zeolites with adsorbed methylamine. 1645 2

Silica gels modified with n-alkyl chains (n = 18, 30) are prepared by two different synthetic routes and are examined by variable temperature FTIR and solid-state NMR spectroscopy. HPLC measurements of SRM 869, cis/trans ss-carotene isomers and xanthophylls isomers confirm the dependence of the separation mechanism on the alkyl chain length and the synthetic routes. The determination of the silane functionality and degree of cross-linking of silane ligands on the silica surface is achieved by 29Si CP/MAS NMR measurements. The structural order and mobility of the alkyl chains are investigated by means of variable temperature 13C CP/MAS NMR measurements. Variable temperature FTIR studies are performed where conformational order and flexibility of the alkyl chains in C18 and C30 phases are monitored through conformational sensitive CH2 symmetric, anti-symmetric stretching and wagging modes. In addition, the chromatographic properties of the C18 and C30 phases are determined. The results derived from the FTIR, NMR and HPLC measurements are discussed in the context of the applied synthetic routes and alkyl chain lengths.
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PMID:Influence of synthetic routes on the conformational order and mobility of C18 and C30 stationary phases. 1647 20

Using the hemiasterlin analogs taltobulin (I, HTI-286), II, and III as model compounds, we demonstrate that relaxation-compensated STD-NMR can be used as an effective tool to efficiently provide a qualitative epitope map for microtubule destabilizing peptides. Due to the disparate relaxation behavior of the protons in these model compounds, it was essential to collect STD with very short saturation times to render an accurate picture of the binding interaction. The conformation of HTI-286 (I) in complex with the protein was determined from TRNOESY/ROESY experiments and is similar to the X-ray crystal structure conformation observed for hemiasterlin methyl ester in the absence of protein.
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PMID:Mapping the bound conformation and protein interactions of microtubule destabilizing peptides by STD-NMR spectroscopy. 1676 96


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