Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications

Renault, Marie; Saurel, Olivier; Czaplicki, Jerzy; Demange, Pascal; Gervais, Virginie; Löhr, Frank; Réat, Valérie; Piotto, Martial; Milon, Alain

doi:10.1016/j.jmb.2008.10.021

Cited by 48 publications

(37 citation statements)

References 74 publications

(93 reference statements)

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“…1). The predicted structure has significant structural homology with an N-terminal transmembrane domain of KpOmpA from Klebsiella pneumoniae whose structure has been solved by X-ray crystallography (Renault et al, 2009). The template modeling (TM)-score is an efficient way to measure the similarity between the structure of KpOmpA solved by X-ray crystallography and the predicted structure of Omp1X.…”

Section: Resultsmentioning

confidence: 99%

Proteomic and functional analyses of a novel porin-like protein in Xanthomonas oryzae pv. oryzae

2014

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Proteomic analysis is a useful technique for postulating and elucidating protein functions. In the present work, a shotgun proteomic analysis was used to identify functions of the PXO_03968 gene (previously known as the ax21) from Xanthomonas oryzae pv. oryzae (Xoo), a causal agent for bacterial blight disease in rice. Structural prediction performed on the protein sequence encoded by PXO_03968 reveals that it encodes a putative porin-like protein, possessing a β-barrel domain with 10 β-strands and a signal peptide at the N-terminus. We renamed the gene as an omp1X (outer membrane protein 1 in Xoo), generated its knock out mutant (XooΔomp1X), and compared the protein expression level in the mutant to that in the wild type. A total of 106 proteins displayed more than 1.5-fold difference in expression between the mutant and the wild type strains. COG analysis revealed that these proteins are involved in cell motility as well as signal transduction. In addition, phenotypic analysis demonstrated that motility and biofilm formation in XooΔomp1X are lower than the wild type. These results provide new insights into the functions of outer membrane proteins in Gram-negative bacteria.

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Section: Resultsmentioning

confidence: 99%

Proteomic and functional analyses of a novel porin-like protein in Xanthomonas oryzae pv. oryzae

2014

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“…A pioneering solution NMR study revealed μs-ms interconversion of the catalytic loop of PagP between an excited and a nonexcited state, enabling both ligand binding and enzymatic catalysis (8). Nonenzymatic β-barrel channels exhibit more general dynamic features, such as loop flexibility and slow conformational exchange towards the extracellular barrel edges, altogether indicating relevance for substrate conductance and gating (9)(10)(11).…”

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confidence: 99%

Functional dynamics in the voltage-dependent anion channel

Villinger

Briones

Giller

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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127

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The voltage-dependent anion channel (VDAC), located in the outer mitochondrial membrane, acts as a gatekeeper for the entry and exit of mitochondrial metabolites. Here we reveal functional dynamics of isoform one of VDAC (VDAC1) by a combination of solution NMR spectroscopy, Gaussian network model analysis, and molecular dynamics simulation. Micro-to millisecond dynamics are significantly increased for the N-terminal six β-strands of VDAC1 in micellar solution, in agreement with increased B-factors observed in the same region in the bicellar crystal structure of VDAC1. Molecular dynamics simulations reveal that a charge on the membrane-facing glutamic acid 73 (E73) accounts for the elevation of N-terminal protein dynamics as well as a thinning of the nearby membrane. Mutation or chemical modification of E73 strongly reduces the micro-to millisecond dynamics in solution. Because E73 is necessary for hexokinase-I-induced VDAC channel closure and inhibition of apoptosis, our results imply that microto millisecond dynamics in the N-terminal part of the barrel are essential for VDAC interaction and gating.membrane protein | molecular dynamics | NMR spectroscopy | protein-lipid interactions | structure D ynamics of proteins provide the essential link between structure and function. Membrane protein dynamics are gaining more attention due to an increasing number of high-resolution structures. A versatile experimental method for the study of membrane protein dynamics is NMR spectroscopy, providing atomic resolution information from nanoseconds to seconds (for an overview see ref. 1). In addition, when a three-dimensional structure is available, insight into fast dynamics of proteins, which occur on the nanosecond time scale, might be gained from molecular dynamics (MD) simulation and elastic network models (2, 3).NMR studies have revealed large conformational changes essential for the physiological function of α-helical membrane proteins, such as the interaction of phospholamban with effectors modulating heart muscle contractility (4, 5) and antimicrobial peptides adopting different conformations in membranes or solution (6, 7). Less well characterized are motions of outer membrane β-barrels. A pioneering solution NMR study revealed μs-ms interconversion of the catalytic loop of PagP between an excited and a nonexcited state, enabling both ligand binding and enzymatic catalysis (8). Nonenzymatic β-barrel channels exhibit more general dynamic features, such as loop flexibility and slow conformational exchange towards the extracellular barrel edges, altogether indicating relevance for substrate conductance and gating (9-11).The voltage-dependent anion channel (VDAC) is one of the few β-barrel membrane proteins, the structure of which has been determined to date (12-14). Serving as the major pass-through for metabolites between mitochondria and the cytosol (15), the highly abundant channel is regarded as a key regulator of cellular energy metabolism (16). Metabolite flow is regulated by a voltage-dependent conformational c...

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“…To overcome this problem, a powerful method to reintroduce a perdeuterated sample is to biosynthetically incorporate protonated methyl groups of leucine, valine, and isoleucine by growing samples in minimal media with selectively labeled α-ketoisovalerate and α-ketobutyrate (Goto et al 1999). This method was successfully applied for the structural determination of numerous IMPs from the β-barrel family at first with OMP-X in DHPC (Hilty et al 2002), Kp OMP-A (Renault et al 2009), and VDAC (Hiller et al 2008). Other methyl protons can be targeted, such as those of alanine or methionine, by adding protonated amino acid into the culture media.…”

Section: Recent Developments In Nmrmentioning

confidence: 99%