DNA and lipid bilayers: self-assembly and insertion

Khalid, Syma; Bond, Peter J.; Holyoake, John; Hawtin, R. W.; Sansom, Mark S. P.

doi:10.1098/rsif.2008.0239.focus

Cited by 65 publications

(79 citation statements)

References 37 publications

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“…In the present study, the ribosomal proteins, the trigger factor and the nascent peptide were modeled at a united-atom level. The ribosomal RNAs were described with a coarse-grained RNA model [54] developed recently on the basis of the MARTINI force field. The rest of the systems, including water and ions, were modeled by means of the MARTINI force field.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Dynamic Behavior of Trigger Factor on the Ribosome

Deeng

Chan

Sluis

et al. 2016

Journal of Molecular Biology

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Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ribosome-binding domain (RBD) mainly to ribosomal protein uL23 at the tunnel exit on the large ribosomal subunit. Whereas earlier structural data suggested that TF binds as a rigid molecule to the ribosome, recent comparisons of structural data on substrate-bound, ribosome-bound, and TF in solution from different species suggest that this chaperone is a rather flexible molecule. Here, we present two cryo-electron microscopy structures of TF bound to ribosomes translating an mRNA coding for a known TF substrate from Escherichia coli of a different length. The structures reveal distinct degrees of flexibility for the different TF domains, a conformational rearrangement of the RBD upon ribosome binding, and an increase in rigidity within TF when the NC is extended. Molecular dynamics simulations agree with these data and offer a molecular basis for these observations.

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Section: Accepted Manuscriptmentioning

confidence: 99%

Dynamic Behavior of Trigger Factor on the Ribosome

Deeng

Chan

Sluis

et al. 2016

Journal of Molecular Biology

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“…Models of DNA with approximately ten coarse-grained units per nucleotide have been successfully used to study the interaction of DNA with lipids, 39,40 but in order to explore assembly transitions simpler models are required. In particular, models whose coarse-grained scale is approximately that of the nucleotide may provide the ideal compromise between resolution and computational speed for assembly transitions.…”

Section: Introductionmentioning

confidence: 99%

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Ouldridge¹,

Louis²,

Doye³

2011

The Journal of Chemical Physics

450

697

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We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson-Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an "average base" description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.

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“…In general, biomolecular simulation is a well-established and constantly progressing research area [13][14][15][16][17][18]. A standard technique is atomistic molecular dynamics, which relies on models where every atom is represented explicitly by a corresponding interaction site; while potentially accurate, atomistic simulations are notoriously time-consuming.…”

Section: Introductionmentioning

confidence: 99%

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

Orsi

Noro

Essex

2010

J. R. Soc. Interface.

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Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel 'dual-resolution' molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup -glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a 'destabilizing' tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed.

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DNA and lipid bilayers: self-assembly and insertion

Cited by 65 publications

References 37 publications

Dynamic Behavior of Trigger Factor on the Ribosome

Dynamic Behavior of Trigger Factor on the Ribosome

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

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