Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data

Langham, Allison A.; Waring, Alan J.; Kaznessis, YN

doi:10.1186/1471-2091-8-11

Cited by 26 publications

(28 citation statements)

References 55 publications

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“…However, the interpretation of experimental results is often modeldependent, making theoretical studies of micelles a crucial stage to obtain relevant molecular pictures. Molecular dynamics (MD) simulations on SDS micelles have therefore been performed at the coarse-grained (CG) [16][17][18][19], united-atom (UA) [20][21][22][23][24], and all-atom (AA) [25][26][27] resolutions. However, the limitations of the method are related to the description of the molecule at each resolution (ideal bond lengths, angles, dihedrals, and partial charges distribution) [28] that usually remains based on general parameter sets covering wide areas of biochemistry [29] and therefore missing the specificity of the newly investigated systems.…”

Section: Introductionmentioning

confidence: 99%

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

2014

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Sodium dodecyl sulfate (SDS) is a well-known anionic detergent widely used in both experimental and theoretical investigations. Many molecular dynamics (MD) simulation have been performed on the SDS molecule at coarse-grained (CG), united-atom (UA), and all-atom (AA) resolutions. However, these simulations are usually based on general parameters determined from large sets of molecules, and as a result, peculiar molecular specificities are often poorly represented. In addition, the parameters (ideal bond lengths, angles, dihedrals and charge distribution) differ according to the resolution, highlighting a lack of coherence. We therefore propose a new set of parameters for CG, UA, and AA resolutions based on a high quantum mechanics (QM) level optimization of the detergent structure and the charge distribution. For the first time, QM-optimized parameters were directly applied to build the AA, UA, and CG model of the SDS molecule, leading to a more coherent description. As a test case, MD simulations were then performed on SDS preformed micelles as previous experimental and theoretical investigations allow direct comparison with our new sets of parameters. While all three models yield similar macromolecular properties (size, shape, and accessible surface) perfectly matching previous results, the attribution of more coherent parameters to SDS enables the description of the specific interactions inside and outside the micelle. These more consistent parameters can now be used to accurately describe new multi-scale systems involving the SDS molecule.

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Section: Introductionmentioning

confidence: 99%

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

2014

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“…The most commonly used micellar membrane-mimicking systems are aqueous solutions of surfactants such as dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) [10][11][12][13][14]. DPC provides a zwitterionic surface on the micelles that adequately mimic biological membranes of the vertebrates, whereas the SDS micelles, with negatively charged headgroups, adequately imitate the bacterial membrane [15]. However, to mimic electrostatic properties of the vertebrate plasma, a membrane model characterized by a slight prevalence of the negative charge, such as that in the DPC/SDS mixed micelles, can be used as well [16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Thermodynamics, size, and dynamics of zwitterionic dodecylphosphocholine and anionic sodium dodecyl sulfate mixed micelles

Sikorska

Wyrzykowski

Szutkowski

et al. 2015

J Therm Anal Calorim

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The thermodynamic properties of micellization for dodecylphosphocholine (DPC), sodium dodecyl sulfate (SDS), and their mixtures were studied using isothermal titration calorimetry. NMR relaxation measurements were used to explore molecular mobility of the DPC-containing micelles, whereas the diffusion measurements were taken to determine the micelle size. The DPC/SDS mixed systems reveal a tendency to form two kinds of micelles in buffered solution at lower temperatures. An increase in temperature as well as the transfer of the DPC/SDS mixed micelles from buffered to unbuffered solution results in only a single-step micellization process. The average size of the DPC-containing micelles is only slightly dependent on the SDS fraction. Examination of the data of spin-spin relaxation (T 2 ) shows that methylene protons on the polar headgroup of DPC and methylene protons (H1) on the hydrocarbon chain in the micellar systems studied reveal a heterogeneous dynamic behavior reflected in a twocomponent T 2 relaxation in the whole temperature range. The latter is the main constituent of the rigid interfacial layer core protecting the penetration of water into the hydrophobic interior.

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“…In earlier studies, we have shown that simulations converge to their final equilibrium state with respect to the distance between the centres of mass of the peptide and the micelle irrespective of the initial peptide position [14,15], and recently, we demonstrated that simulations are in excellent agreement with FTIR experiments [19]. Without loss of generality, here each peptide in the peptide–SDS simulations was placed in the simulation box with its centre of mass coinciding with that of the SDS micelle.…”

Section: Methodsmentioning

confidence: 77%

“…We use the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) protocol [28] to compute the relative binding free energies of IsCT and two of its analogues to SDS and DPC micelles. These are considered simple, computationally inexpensive models of bacterial and mammalian membranes, respectively [15,19]. …”

Section: Introductionmentioning

confidence: 99%

Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

Sayyed-Ahmad

Khandelia

Kaznessis

2009

Molecular Simulation

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We present relative binding free energy calculations for six antimicrobial peptide-micelle systems, three peptides interacting with two types of micelles. The peptides are the scorpion derived antimicrobial peptide (AMP), IsCT and two of its analogues. The micelles are dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles. The interfacial electrostatic properties of DPC and SDS micelles are assumed to be similar to those of zwitterionic mammalian and anionic bacterial membrane interfaces, respectively. We test the hypothesis that the binding strength between peptides and the anionic micelle SDS can provide information on peptide antimicrobial activity, since it is widely accepted that AMPs function by binding to and disrupting the predominantly anionic lipid bilayer of the bacterial cytoplasmic membrane. We also test the hypothesis that the binding strength between peptides and the zwitterionic micelle DPC can provide information on peptide haemolytic activities, since it is accepted that they also bind to and disrupt the zwitterionic membrane of mammalian cells. Equilibrium structures of the peptides, micelles and peptide-micelle complexes are obtained from more than 300 ns of molecular dynamics simulations. A thermodynamic cycle is introduced to compute the binding free energy from electrostatic, non-electrostatic and entropic contributions. We find relative binding free energy strengths between peptides and SDS to correlate with the experimentally measured rankings for peptide antimicrobial activities, and relative free energy binding strengths between peptides and DPC to correlate with the observed rankings for peptide haemolytic toxicities. These findings point to the importance of peptide-membrane binding strength for antimicrobial activity and haemolytic activity.

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Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data

Cited by 26 publications

References 55 publications

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

Thermodynamics, size, and dynamics of zwitterionic dodecylphosphocholine and anionic sodium dodecyl sulfate mixed micelles

Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

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