ArticleBiophysical journal2004
OmpT: molecular dynamics simulations of an outer membrane enzyme.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 54 citations in OpenAlex.
- A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins.Biophysical journal · 2015Article
- Atomistic molecular-dynamics simulations enable prediction of the arginine permeation pathway through OccD1/OprD from Pseudomonas aeruginosa.Biophysical journal · 2014Article
- A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Reduced lateral mobility of lipids and proteins in crowded membranes.PLoS computational biology · 2013Article
- Structural basis for activation of an integral membrane protease by lipopolysaccharide.The Journal of biological chemistry · 2012Article
- Yersinia infection tools-characterization of structure and function of adhesins.Frontiers in cellular and infection microbiology · 2012Review
- Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane.Biochimica et biophysica acta · 2008Review
- Orientation of the Escherichia coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-State NMR.Biochemistry · 2008Article
- Article
- Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.European biophysics journal : EBJ · 2008Article
- Microseconds dynamics simulations of the outer-membrane protease T.Biophysical journal · 2008Article
- NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes.Biochimica et biophysica acta · 2007Article
- Positioning of proteins in membranes: a computational approach.Protein science : a publication of the Protein Society · 2006Article
- Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.Biophysical journal · 2006Article
- Molecular dynamics simulations of proteins in lipid bilayers.Current opinion in structural biology · 2005Review
- Lipid-protein interactions of integral membrane proteins: a comparative simulation study.Biophysical journal · 2004Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Five molecular dynamics simulations (total duration >25 ns) have been performed on the Escherichia coli outer membrane protease OmpT embedded in a dimyristoylphosphatidylcholine lipid bilayer. Globally the protein is conformationally stable. Some degree of tilt of the beta-barrel is observed relative to the bilayer plane. The greatest degree of conformational flexibility is seen in the extracellular loops. A complex network of fluctuating H-bonds is formed between the active site residues, such that the Asp210-His212 interaction is maintained throughout, whereas His212 and Asp83 are often bridged by a water molecule. This supports a catalytic mechanism whereby Asp83 and His212 bind a water molecule that attacks the peptide carbonyl. A configuration yielded by docking calculations of OmpT simulation snapshots and a model substrate peptide Ala-Arg-Arg-Ala was used as the starting point for an extended Huckel calculation on the docked peptide. These placed the lowest unoccupied molecular orbital mainly on the carbon atom of the central C=O in the scissile peptide bond, thus favoring attack on the central peptide by the water held by residues Asp83 and His212. The trajectories of water molecules reveal exchange of waters between the intracellular face of the membrane and the interior of the barrel but no exchange at the extracellular mouth. This suggests that the pore-like region in the center of OmpT may enable access of water to the active site from below. The simulations appear to reveal the presence of specific lipid interaction sites on the surface of the OmpT barrel. This reveals the ability of extended MD simulations to provide meaningful information on protein-lipid interactions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.