ArticleProceedings of the National Academy of Sciences of the United States of America2009
Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Targeting Outer Membrane Vesicles ofJournal of microbiology and biotechnology · 2026Review
- Diffusion of Carbamazepine in Hydrophobic Zeolites: A Comparative Study Using Classical and Machine-Learned Potentials.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Understanding Drug Permeability inLife (Basel, Switzerland) · 2025Review
- Improved Free-Energy Estimates for the Permeation of Bulky Antibiotic Molecules through Porin Channels Using Temperature-Accelerated Sliced Sampling.Journal of chemical theory and computation · 2025Article
- What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?Microbiology (Reading, England) · 2022Review
- Dawn of a New Era for Membrane Protein Design.Biodesign research · 2022Review
- The penetration of human defensin 5 (HD5) through bacterial outer membrane: simulation studies.Journal of molecular modeling · 2021Article
- Physicochemical Evidence thatInternational journal of molecular sciences · 2020Article
- Accumulation of ambient phosphate into the periplasm of marine bacteria is proton motive force dependent.Nature communications · 2020Article
- KScientific reports · 2018Article
- In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways.Scientific reports · 2018Article
- Understanding antibiotic resistance via outer membrane permeability.Infection and drug resistance · 2018Review
- Comparative Transcriptome Analysis ofFrontiers in microbiology · 2018Article
- Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction.Biophysical journal · 2017Article
- Exploring bacterial outer membrane barrier to combat bad bugs.Infection and drug resistance · 2017Review
- In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality.International journal of molecular sciences · 2016Article
- Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa.Biophysical journal · 2015Article
- Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.Biophysical journal · 2015Review
- The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.Nanomaterials (Basel, Switzerland) · 2015Article
- Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites.PloS one · 2015Article
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4 authors.
Funding
Abstract
The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of approximately 8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 microM is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a "charged brush" to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl(-) PMF. The difference in affinity and hence selectivity is due to the "Lys-cluster" motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl(-) by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.
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