The Detailed Scattering Density Profile Model of Pg Bilayers as Determined by Molecular Dynamics Simulations, and Small-Angle Neutron and X-ray Scattering Experiments

Kučerka, Norbert; Holland, Bryan W.; Pan, Jianjun; Heberle, Frederick A.; Gray, C.G.; Tomberli, Bruno

doi:10.1016/j.bpj.2011.11.2764

Cited by 5 publications

(6 citation statements)

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“…Parameters describing structural details of the cytoplasmic membrane (CM) and outer membrane (OM) were fixed according to values reported from experiments and simulations on membrane mimic systems of E. coli cell membranes (De Siervo, 1969;Oursel et al, 2007;Lohner et al, 2008;Pandit & Klauda, 2012;Kučerka et al, 2012Kučerka et al, , 2015Leber et al, 2018), as detailed in Table 2 (see also Fig. 1 and the SI).…”

Section: Parameterization and Optimization Strategymentioning

confidence: 99%

“…The here-applied scattering contribution estimates are based on the latest experimental and computational reports on E. coli, including isolated cell components. Specifically, we used compositional and structural information about E. coli and its cell wall (Neidhardt et al, 1990;Seltmann & Holst, 2002;Schwarz-Linek et al, 2016); the cytoplasmic space and its components (Zimmerman & Trach, 1991;Tweeddale et al, 1998;Prasad Maharjan & Ferenci, 2003;Bennett et al, 2009;Guo et al, 2012;Lebedev et al, 2015); the bacterial ultrastructure (Hobot et al, 1984;Beveridge, 1999;Matias et al, 2003); the lipid membrane composition and structure (De Siervo, 1969;Oursel et al, 2007;Lohner et al, 2008;Pandit & Klauda, 2012;Kučerka et al, 2012Kučerka et al, , 2015Leber et al, 2018); the LPS specifics (Heinrichs et al, 1998;Mü ller-Loennies et al, 2003;Kučerka et al, 2008;Kim et al, 2016;Rodriguez-Loureiro et al, 2018;Micciulla et al, 2019); the periplasmic space (Burge et al, 1977;Labischinski et al, 1991;Pink et al, 2000;Gan et al, 2008); and the external bacterial components (Yamashita et al, 1998;Whitfield & Roberts, 1999;Stukalov et al, 2008;Turner et al, 2012). All this information has been condensed into SLDs , which are summarized in Fig.…”

Section: Overall Scattering Contributions and Compositional Modelingmentioning

confidence: 99%

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Evolution of the analytical scattering model of live Escherichia coli

Semeraro¹,

Marx²,

Mandl³

et al. 2021

J Appl Crystallogr

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A previously reported multi-scale model for (ultra-)small-angle X-ray (USAXS/SAXS) and (very) small-angle neutron scattering (VSANS/SANS) of live Escherichia coli was revised on the basis of compositional/metabolomic and ultrastructural constraints. The cellular body is modeled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was replaced by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data of E. coli ATCC 25922 over four orders of magnitude in length scale. Specifically, this approach provides detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. The model was also successfully applied to E. coli K12, used for the authors' original modeling, as well as for two other E. coli strains. Significant differences were detected between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of the approach outlined here to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labeling agents.

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Section: Parameterization and Optimization Strategymentioning

confidence: 99%

Section: Overall Scattering Contributions and Compositional Modelingmentioning

confidence: 99%

Evolution of the analytical scattering model of live Escherichia coli

Semeraro¹,

Marx²,

Mandl³

et al. 2021

J Appl Crystallogr

View full text Add to dashboard Cite

show abstract

“…Assuming the same lipid asymmetry as in the outer membrane, the inner leaflet of OMVs can be mimicked by a 3:1 mole mixture of palmitoyl-oleoyl-phosphatidylethanolamine (POPE) and palmitoyl-oleoyl-phosphatidylglygerol (POPG), respectively ( De Siervo, 1969 ; Lohner et al, 2008 ; Leber et al, 2018 ). The SLD membrane profiles of these lipids have been thoroughly investigated ( Kučerka et al, 2012, 2015 ). The outer leaflet might instead be dominated by LPS, whose lipid A possesses about 6 short C14:0 chains ( Kim et al, 2016 ), and the polar region can be approximated as two PG units, in terms of molecular volume and SLD.…”

Section: Appendix 1 Figurementioning

confidence: 99%

Lactoferricins access the cytosol of Escherichia coli within few seconds

Semeraro

Marx

Mandl

et al. 2021

Preprint

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We report the real-time response of E. coli to lactoferricin-derived antimicrobial peptides (AMPs) on length-scales bridging microscopic cell-sizes to nanoscopic lipid packing using millisecond time-resolved synchrotron small-angle X-ray scattering. Coupling a multi-scale scattering data analysis to biophysical assays for peptide partitioning revealed that the AMPs rapidly saturate the bacterial envelope and reach the cytosol within less than three seconds—much faster than previously considered. Final cytosolic AMP concentrations of ~ 100 mM suggest an efficient shut-down of metabolism as primary cause for bacterial killing. On the other hand, the damage of the cell envelope is a collateral effect of AMP activity that does not kill the bacteria. This implies that the impairment of the membrane barrier is a necessary but not sufficient condition for microbial killing by lactoferricins. The most efficient AMP studied exceeds others in both speed of reaching cytoplasm and lowest cytosolic peptide concentration.

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“…The here applied scattering contribution estimates are based on the latest experimental and computational reports on E. coli, including isolated cell components. Specifically, we used compositional and structural information about E. coli and its cell-wall (Neidhardt et al, 1990;Seltmann & Holst, 2002;Schwarz-Linek et al, 2015); the cytoplasmic space and its components (Zimmerman & Trach, 1991;Tweeddale et al, 1998;Maharjan & Ferenci, 2003;Bennett et al, 2009;Guo et al, 2012;Lebedev et al, 2015); the bacterial ultrastructure (Hobot et al, 1984;Beveridge, 1999;Matias et al, 2003); the lipid membrane composition and structure (De Siervo, 1969;Oursel et al, 2007;Lohner et al, 2008;Pandit & Klauda, 2012;Kučerka et al, 2012;Kučerka et al, 2015;Leber et al, 2018); the LPS specifics (Heinrichs et al, 1998;Müller-Loennies et al, 2003;Kučerka et al, 2008;Kim et al, 2016;Rodriguez-Loureiro et al, 2018;Micciulla et al, 2019); the periplasmic space (Burge et al, 1977;Labischinski et al, 1991;Pink et al, 2000;Gan et al, 2008); and the external bacterial components (Yamashita et al, 1998;Whitfield & Roberts, 1999;Stukalov et al, 2008;Turner et al, 2012). All this information has been condensed into SLDs ρ, which are summarized in The benefit of this detailed description becomes clear considering the ability of SANS to nullify or enhance contrast for a given molecular entity, depending on the applied H 2 O/D 2 O ratio.…”

Section: Overall Scattering Contributions and Compositional Modellingmentioning

confidence: 99%

“…Experiment-specific parameters were termed "local", while others were designated as "global" parameters. Further, parameters describing structural details of the cytoplasmic and outer membranes were fixed according to values reported from experiments and simulations on membrane mimic systems of E. coli cell membranes (De Siervo, 1969;Oursel et al, 2007;Lohner et al, 2008;Pandit & Klauda, 2012;Kučerka et al, 2012;Kučerka et al, 2015;Leber et al, 2018), as detailed Tab. 2 (see also Fig.…”

Section: Parametrization and Optimization Strategymentioning

confidence: 99%

Evolution of the Analytical Scattering Model of LiveEscherichia Coli

Semeraro

Marx

Mandl

et al. 2020

Preprint

View full text Add to dashboard Cite

We have revised a previously reported multi-scale model for (ultra) small angle X-ray (USAXS/SAXS) and (very) small angle neutron scattering (VSANS/SANS) of live Escherichia coli based on compositional/metabolomic and ultrastructural constraints. The cellular body is modelled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was substituted by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data of E. coli ATCC 25922 over four orders of magnitude in length scale, providing specifically detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. Consecutively, the model was also successfully applied to E. coli K12, used for our original modelling, as well as for two other E. coli strains, detecting significant differences between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of our approach to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labelling agents.

show abstract

The Detailed Scattering Density Profile Model of Pg Bilayers as Determined by Molecular Dynamics Simulations, and Small-Angle Neutron and X-ray Scattering Experiments

Cited by 5 publications

References 0 publications

Evolution of the analytical scattering model of live Escherichia coli

Evolution of the analytical scattering model of live Escherichia coli

Lactoferricins access the cytosol of Escherichia coli within few seconds

Evolution of the Analytical Scattering Model of LiveEscherichia Coli

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