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- Enzyme I (2)
- NMR spectroscopy (2)
- Signal transduction (2)
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- Bacterial phosphotransferase system (1)
- Biophysics (1)
- Chemical shift assignments (1)
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- Encounter complexes (1)
- Gd(III) complexes (1)
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- Isotopic labeling (1)
- MD simulations (1)
- Methyl TROSY (1)
- Methyl group labeling (1)
- Methyl labeling (1)
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- Paramagnetic spin-labeling (1)
- Phosphoenolypruvate: sugar phosphotransferase system (1)
- Phosphorylation enzymes (1)
- Protein hydration (1)
- Protein structure (1)
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Articles 1 - 9 of 9
Full-Text Articles in Bacterial Infections and Mycoses
Large Interdomain Rearrangement Triggered By Suppression Of Micro- To Millisecond Dynamics In Bacterial Enzyme I, Vincenzo Venditti, Vitali Tugarinov, Charles D. Schwieters, Alexander Grishaev, G. Marius Clore
Large Interdomain Rearrangement Triggered By Suppression Of Micro- To Millisecond Dynamics In Bacterial Enzyme I, Vincenzo Venditti, Vitali Tugarinov, Charles D. Schwieters, Alexander Grishaev, G. Marius Clore
Vincenzo Venditti
Enzyme I (EI), the first component of the bacterial phosphotransfer signal transduction system, undergoes one of the largest substrate-induced interdomain rearrangements documented to date. Here we characterize the perturbations generated by two small molecules, the natural substrate phosphoenolpyruvate and the inhibitor a-ketoglutarate, on the structure and dynamics of EI using NMR, small-angle X-ray scattering and biochemical techniques. The results indicate unambiguously that the open-to-closed conformational switch of EI is triggered by complete suppression of micro- to millisecond dynamics within the C-terminal domain of EI. Indeed, we show that a ligand-induced transition from a dynamic to a more rigid conformational state …
A Nmr Experiment For Simultaneous Correlations Of Valine And Leucine/Isoleucine Methyls With Carbonyl Chemical Shifts In Proteins, Vitali Tugarinov, Vincenzo Venditti, G. Marius Clore
A Nmr Experiment For Simultaneous Correlations Of Valine And Leucine/Isoleucine Methyls With Carbonyl Chemical Shifts In Proteins, Vitali Tugarinov, Vincenzo Venditti, G. Marius Clore
Vincenzo Venditti
A methyl-detected ‘out-and-back’ NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ileδ1, Leuδ and Valγ (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of 13Cα, 13Cβ and 13CO are known from prior NMR studies and where some losses in …
Structural Basis For Enzyme I Inhibition By Α-Ketoglutarate, Vincenzo Venditti, Rodolfo Ghirlando, G. Marius Clore
Structural Basis For Enzyme I Inhibition By Α-Ketoglutarate, Vincenzo Venditti, Rodolfo Ghirlando, G. Marius Clore
Vincenzo Venditti
Creating new bacterial strains in which carbon and nitrogen metabolism are uncoupled is potentially very useful for optimizing yields of microbial produced chemicals from renewable carbon sources. However, the mechanisms that balance carbon and nitrogen consumption in bacteria are poorly understood. Recently, α-ketoglutarate (αKG), the carbon substrate for ammonia assimilation, has been observed to inhibit Escherichia coli enzyme I (EI), the first component of the bacterial phosphotransferase system (PTS), thereby providing a direct biochemical link between central carbon and nitrogen metabolism. Here we investigate the EI-αKG interaction by NMR and enzymatic assays. We show that αKG binds with a KD …
Structure, Dynamics And Biophysics Of The Cytoplasmic Protein–Protein Complexes Of The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System, Vincenzo Venditti
Structure, Dynamics And Biophysics Of The Cytoplasmic Protein–Protein Complexes Of The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System, Vincenzo Venditti
Vincenzo Venditti
The bacterial phosphotransferase system (PTS) couples phosphoryl transfer, via a series of bimolecular protein–protein interactions, to sugar transport across the membrane. The multitude of complexes in the PTS provides a paradigm for studying protein interactions, and for understanding how the same binding surface can specifically recognize a diverse array of targets. Fifteen years of work aimed at solving the solution structures of all soluble protein–protein complexes of the PTS has served as a test bed for developing NMR and integrated hybrid approaches to study larger complexes in solution and to probe transient, spectroscopically invisible states, including encounter complexes. We review …
The Use Of A Ditopic Gd(Iii) Paramagnetic Probe For Investigating Α-Bungarotoxin Surface Accessibility, Andrea Bernini, Ottavia Spiga, Vincenzo Venditti, Filippo Prischi, Mauro Botta, Gianluca Croce, Angela Pui-Ling Tong, Wing-Talk Wong, Neri Niccolai
The Use Of A Ditopic Gd(Iii) Paramagnetic Probe For Investigating Α-Bungarotoxin Surface Accessibility, Andrea Bernini, Ottavia Spiga, Vincenzo Venditti, Filippo Prischi, Mauro Botta, Gianluca Croce, Angela Pui-Ling Tong, Wing-Talk Wong, Neri Niccolai
Vincenzo Venditti
Protein surface accessibility is a critical parameter which drives all intermolecular interaction processes. In this respect a big deal of information has been derived by analyzing paramagnetic perturbation profiles obtained from NMR protein spectra, particularly in the case that the effects due to different soluble paramagnets can be compared. Here Gd2L7, a neutral ditopic paramagnetic NMR probe, has been characterized in terms of structure and relaxivity and its paramagnetic perturbations on α-bungarotoxin CαH signals in 1H–13C HSQC (heteronuclear single quantum coherence) spectra have been analyzed. Then, these signal attenuations have been compared with the ones previously obtained in the presence …
An Efficient Protocol For Incorporation Of An Unnatural Amino Acid In Perdeuterated Recombinant Proteins Using Glucose-Based Media, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore
An Efficient Protocol For Incorporation Of An Unnatural Amino Acid In Perdeuterated Recombinant Proteins Using Glucose-Based Media, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore
Vincenzo Venditti
The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR field. Here, we describe a novel protocol for incorporating unnatural amino acids into fully deuterated proteins using glucose-based media (which are relevant to the production, for example, of amino acid-specific methyl-labeled proteins used in the study …
Conformational Selection And Substrate Binding Regulate The Monomer/Dimer Equilibrium Of The C-Terminal Domain Of Escherichia Coli Enzyme I, Vincenzo Venditti, G. Marius Clore
Conformational Selection And Substrate Binding Regulate The Monomer/Dimer Equilibrium Of The C-Terminal Domain Of Escherichia Coli Enzyme I, Vincenzo Venditti, G. Marius Clore
Vincenzo Venditti
The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by the binding of phosphoenolpyruvate (PEP) to the C-terminal domain (EIC) of enzyme I (EI), a highly conserved protein that is common to all sugar branches of the PTS. EIC exists in a dynamic monomer/dimer equilibrium that is modulated by ligand binding and is thought to regulate the overall PTS. Isolation of EIC has proven challenging, and conformational dynamics within the EIC domain during the catalytic cycle are still largely unknown. Here, we present …
Automated Sequence- And Stereo-Specific Assignment Of Methyl-Labeled Proteins By Paramagnetic Relaxation And Methyl–Methyl Nuclear Overhauser Enhancement Spectroscopy, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore
Automated Sequence- And Stereo-Specific Assignment Of Methyl-Labeled Proteins By Paramagnetic Relaxation And Methyl–Methyl Nuclear Overhauser Enhancement Spectroscopy, Vincenzo Venditti, Nicolas L. Fawzi, G. Marius Clore
Vincenzo Venditti
Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the …
A Structurally Driven Analysis Of Thiol Reactivity In Mammalian Albumins, Ottavia Spiga, Domenico Summa, Simone Cirri, Andrea Bernini, Vincenzo Venditti, Matteo De Chiara, Raffaella Priora, Simona Frosail, Antonios Margaritis, Danila Di Giuseppe, Paolo Di Simplicio, Neri Niccolai
A Structurally Driven Analysis Of Thiol Reactivity In Mammalian Albumins, Ottavia Spiga, Domenico Summa, Simone Cirri, Andrea Bernini, Vincenzo Venditti, Matteo De Chiara, Raffaella Priora, Simona Frosail, Antonios Margaritis, Danila Di Giuseppe, Paolo Di Simplicio, Neri Niccolai
Vincenzo Venditti
Understanding the structural basis of protein redox activity is still an open question. Hence, by using a structural genomics approach, different albumins have been chosen to correlate protein structural features with the corresponding reaction rates of thiol exchange between albumin and disulfide DTNB. Predicted structures of rat, porcine, and bovine albumins have been compared with the experimentally derived human albumin. High structural similarity among these four albumins can be observed, in spite of their markedly different reactivity with DTNB. Sequence alignments offered preliminary hints on the contributions of sequence-specific local environments modulating albumin reactivity. Molecular dynamics simulations performed on experimental …