Voltage-dependent energetics of alamethicin monomers in the membrane

Mottamal, Madhusoodanan; Lazaridis, Themis

doi:10.1016/j.bpc.2006.02.005

Cited by 46 publications

(67 citation statements)

References 48 publications

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“…It is not, however, present in most in vitro experiments. If desired, the membrane potential can easily be included in the calculations of the type presented here [85]. A positive membrane potential on the same side as the peptides will provide a driving force for translocation and will also lower the barriers.…”

Section: Discussionmentioning

confidence: 99%

Implicit membrane treatment of buried charged groups: Application to peptide translocation across lipid bilayers

Lazaridis

Leveritt

PeBenito

2014

Biochimica et Biophysica Acta (BBA) - Biomembranes

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The energetic cost of burying charged groups in the hydrophobic core of lipid bilayers has been controversial, with simulations giving higher estimates than certain experiments. Implicit membrane approaches are usually deemed too simplistic for this problem. Here we challenge this view. The free energy of transfer of amino acid side chains from water to the membrane center predicted by IMM1 is reasonably close to all-atom free energy calculations. The shape of the free energy profile, however, for the charged side chains needs to be modified to reflect the all-atom simulation findings (IMM1-LF). Membrane thinning is treated by combining simulations at different membrane widths with an estimate of membrane deformation free energy from elasticity theory. This approach is first tested on the voltage sensor and the isolated S4 helix of potassium channels. The voltage sensor is stably inserted in a transmembrane orientation for both the original and the modified model. The transmembrane orientation of the isolated S4 helix is unstable in the original model, but a stable local minimum in IMM1-LF, slightly higher in energy than the interfacial orientation. Peptide translocation is addressed by mapping the effective energy of the peptide as a function of vertical position and tilt angle, which allows identification of minimum energy pathways and transition states. The barriers computed for the S4 helix and other experimentally studied peptides are low enough for an observable rate. Thus, computational results and experimental studies on the membrane burial of peptide charged groups appear to be consistent.

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Section: Discussionmentioning

confidence: 99%

Implicit membrane treatment of buried charged groups: Application to peptide translocation across lipid bilayers

Lazaridis

Leveritt

PeBenito

2014

Biochimica et Biophysica Acta (BBA) - Biomembranes

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“…3A) by spontaneous insertion and aggregation of 4-6 individual ALM helices into a helix bundle (22). Although some debate about the exact mechanism of the voltage-gated transport in ALM pores remains (25)(26)(27), research indicates that at positive applied transmembrane voltages on the insertion side (cis-side) ALM forms barrel-staved functional open pores big enough for small monovalent cations to diffuse through, whereas these pores do not form at zero bias or negative bias (25). Some evidence (28) indicates that at negative membrane potentials ALM helices do not span the entire transmembrane thickness, yet at the positive membrane potentials the helices tilt enough to penetrate the membrane completely and form a channel.…”

Section: Resultsmentioning

confidence: 99%

Bioelectronic silicon nanowire devices using functional membrane proteins

Misra

Martinez

Huang

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

151

147

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Modern means of communication rely on electric fields and currents to carry the flow of information. In contrast, biological systems follow a different paradigm that uses ion gradients and currents, flows of small molecules, and membrane electric potentials. Living organisms use a sophisticated arsenal of membrane receptors, channels, and pumps to control signal transduction to a degree that is unmatched by manmade devices. Electronic circuits that use such biological components could achieve drastically increased functionality; however, this approach requires nearly seamless integration of biological and manmade structures. We present a versatile hybrid platform for such integration that uses shielded nanowires (NWs) that are coated with a continuous lipid bilayer. We show that when shielded silicon NW transistors incorporate transmembrane peptide pores gramicidin A and alamethicin in the lipid bilayer they can achieve ionic to electronic signal transduction by using voltage-gated or chemically gated ion transport through the membrane pores.bionanoelectronics ͉ ion channels ͉ silicon nanowires ͉ lipid bilayers ͉ membrane transport

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“…Recently, the IMM1 model has been extended to model lipid bilayers with a transmembrane potential [126,127], with aqueous pores [128,129], with anionic lipids [130], and mixed lipid bilayers with lateral pressure effects [131]. The transmembrane potential can be considered by introducing the analytical solution of the PB equation [102] or by introducing an empirical monotonic function along the membrane normal [126,127].…”

Section: Molecular Models For Membranes and Membrane Proteinsmentioning

confidence: 99%

“…The transmembrane potential can be considered by introducing the analytical solution of the PB equation [102] or by introducing an empirical monotonic function along the membrane normal [126,127]. This method makes it possible to study mechanisms of voltage-dependent insertion of peptide and channel gating in the implicit solvent.…”

Section: Molecular Models For Membranes and Membrane Proteinsmentioning

confidence: 99%

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori

Miyashita²,

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

127

108

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This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov.

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Voltage-dependent energetics of alamethicin monomers in the membrane

Cited by 46 publications

References 48 publications

Implicit membrane treatment of buried charged groups: Application to peptide translocation across lipid bilayers

Implicit membrane treatment of buried charged groups: Application to peptide translocation across lipid bilayers

Bioelectronic silicon nanowire devices using functional membrane proteins

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

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