Influence of the B-band O-antigen chain in the structure and electrostatics of the lipopolysaccharide membrane of Pseudomonas aeruginosa

Soares, Thereza A.; Straatsma, T. P.; Lins, Roberto D.

doi:10.1590/s0103-50532008000200018

Cited by 18 publications

(29 citation statements)

References 29 publications

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“…However, the arrangement of Ca 2+ counter‐ions in the membrane matrix due to the presence of the protein induces local changes of the electrostatic potential on the surface of the membrane as shown in Figure 10(A). In the absence of proteins, shown in Figure 10(B), the surface potential of the LPS membrane is predominantly electronegative with very few electropositive potential patches 22, 48. The presence of OprF induces an increase of charge polarization on the membrane surface as well as an increase of the positive potential in the area of protein insertion.…”

Section: Resultsmentioning

confidence: 98%

Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation

Straatsma

Soares

2008

Proteins

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The N-terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight-stranded anti-parallel β-barrel domain that folds into a membrane channel with low conductance. The structure of this protein has been modeled after the crystal structure of the homologous protein OmpA of Escherichia coli. A number of molecular dynamics simulations have been carried out for the homology modeled structure of OprF in an explicit molecular model for the rough lipopolysaccharide (LPS) outer membrane of P. aeruginosa. The structural stability of the outer membrane model as a result of the strong electrostatic interactions compared to simple lipid bilayers is restricting both the conformational flexibility and the lateral diffusion of the porin in the membrane. Constricting side-chain interactions within the pore are similar to those found in reported simulations of the protein in a solvated lipid bilayer membrane. Because of the strong interactions between the loop regions of OprF and functional groups in the saccharide core of the LPS, the entrance to the channel from the extracellular space is widened compared to the lipid bilayer simulations in which the loops are extruding in the solvent. The specific electrostatic signature of the LPS membrane, which results in a net intrinsic dipole across the membrane, is found to be altered by the presence of OprF, resulting in a small electrically positive patch at the position of the channel.

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Section: Resultsmentioning

confidence: 98%

Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation

Straatsma

Soares

2008

Proteins

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“…This is consistent with the notion that cationic particles interact with the O -polysaccharide domain of smooth LPS, because the O -polysaccharide presents anionic sites available for interaction with cationic nanoparticles that extend away from the bilayer surface. 50,51 …”

Section: Resultsmentioning

confidence: 99%

Lipopolysaccharide Density and Structure Govern the Extent and Distance of Nanoparticle Interaction with Actual and Model Bacterial Outer Membranes

Jacobson

Gunsolus

Kuech

et al. 2015

Environ. Sci. Technol.

109

119

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Design of nanomedicines and nanoparticle-based antimicrobial and antifouling formulations and assessment of the potential implications of nanoparticle release into the environment requires understanding nanoparticle interaction with bacterial surfaces. Here we demonstrate the electrostatically driven association of functionalized nanoparticles with lipopolysaccharides of Gram-negative bacterial outer membranes and find that lipopolysaccharide structure influences the extent and location of binding relative to the outer leaflet-solution interface. By manipulating the lipopolysaccharide content in Shewanella oneidensis outer membranes, we observed the electrostatically driven interaction of cationic gold nanoparticles with the lipopolysaccharide-containing leaflet. We probed this interaction by quartz crystal microbalance with dissipation monitoring (QCM-D) and second harmonic generation (SHG) using solid-supported lipopolysaccharide-containing bilayers. The association of cationic nanoparticles increased with lipopolysaccharide content, while no association of anionic nanoparticles was observed. The harmonic-dependence of QCM-D measurements suggested that a population of the cationic nanoparticles was held at a distance from the outer leaflet-solution interface of bilayers containing smooth lipopolysaccharides (those bearing a long O-polysaccharide). Additionally, smooth lipopolysaccharides held the bulk of the associated cationic particles outside of the interfacial zone probed by SHG. Our results demonstrate that positively charged nanoparticles are more likely to interact with Gram-negative bacteria than are negatively charged particles, and this interaction occurs primarily through lipopolysaccharides.

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“…Additionally, the QM/MM capability in NWChem has resulted in the development and refinement of force-field parameters, which can, in turn, be used in classical molecular dynamics simulations. Over the last two decades, classical parameters obtained using NWChem have been employed to address the underlying mechanisms of a variety of novel complex biological systems and their interactions (e.g., lipopolysaccharide membranes, carbohydrate moieties, mineral surfaces, radionuclides, and organophosphorous compounds), 307,308,[311][312][313][340][341][342][343][344] which has led to a significant expansion of the database of AMBER-and Glycam-compatible force fields and the GROMOS force field for lipids, carbohydrates, and nucleic acids. [345][346][347][348][349][350][351] For cases where a classical description of the environment is deemed insufficient, NWChem offers an option to perform an ONIOM type calculation.…”

Section: Hybrid Methodsmentioning

confidence: 99%

“…Some of the more unique features include setting up a system for quantum mechanically derived proton hopping (QHOP) simulations 305,306 and the setup of biological membranes from a single lipid-like molecule. This last capability has been successfully used for the first extensive simulation studies of complex asymmetric lipopolysaccharide membranes of Gram-negative microbes [307][308][309][310][311] and their role in the capture of recalcitrant environmental heavy metal ions, 312 microbial adhesion to geochemical surfaces, [313][314][315][316] and the structure and dynamics of trans-membrane proteins including ion transporters (Fig. 4).…”

Section: System Preparationmentioning

confidence: 99%

NWChem: Past, present, and future

Aprà

Bylaska

Jong

et al. 2020

The Journal of Chemical Physics

Self Cite

513

289

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Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

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Influence of the B-band O-antigen chain in the structure and electrostatics of the lipopolysaccharide membrane of Pseudomonas aeruginosa

Cited by 18 publications

References 29 publications

Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation

Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation

Lipopolysaccharide Density and Structure Govern the Extent and Distance of Nanoparticle Interaction with Actual and Model Bacterial Outer Membranes

NWChem: Past, present, and future

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