Naturally occurring and synthetic peptides may be a novel class of clinically useful antibiotics. A large body of experimental data on structure function relationships for such peptides is available, ...but the molecular mechanism of their action remains elusive in most cases. Computer simulations can give detailed insights into the interactions between peptides and lipid bilayers, at least one crucial step in the antimicrobial mechanism. Here we review recent simulations of antimicrobial peptides and discuss potential future contributions of computer simulations in understanding and ultimately designing antimicrobial peptides.
SLC4 transporters are involved in the transport of HCO3‾, CO32‾, Na+, Cl‾ and H+ required for regulation of pH and ion homeostasis in several important physiological processes. Dysfunction of these ...transporters can lead to acid‐base abnormalities, pH dysregulation, and various disease processes. Understanding of their transport mechanism is therefore critical for development of pharmacological strategies for SLC4‐related diseases. The studies of the SLC4 transport mechanisms have been hindered by lack of information on the specific substrate binding sites within the protein matrix. No binding sites have been resolved in the two previously published structures of SLC4 proteins, the chloride/bicarbonate anion exchanger 1 (AE1, SLC4A1) and the electrogenic sodium carbonate cotransporter 1 (NBCe1, SLC4A4), although putative binding sites have been identified on the basis of these structures from computational modelling and functional mutagenesis experiments. Here we present a new cryo‐EM structure at 3.4Å of the outward facing open (OF) conformation of the sodium dependent chloride/bicarbonate exchanger (NDCBE, SLC4A8) 1, which exchanges Na+‐CO32‾ for Cl‾, combining the feature functionalities of both AE1 and NBCe1. The structure resolves for the first time a Na+ and a CO32‾ ion bound at the center of the protein in the area of the previously identified putative binding site S1 in NBCe1 and AE1. Mutation of the residues involved in ion binding leads to significant impairment of NDCBE transport. Computational modelling with the new NDCBE structure outlines two separate ion pathways for cations and anions in the OF cavity and demonstrates that a Na+ ion bound at D800 is necessary for anion binding in site S1 and that a Na+‐CO32‾ ion pair in this site is the most likely ion load. A second anion binding site, S2, is also identified in the permeation cavity in proximity to site S1. We conclude that Na+‐dependent transport in the SLC4 family is influenced both by thermodynamic effects at the S1 binding site and by permeation effects governed by the residues lining the cation and anion permeation pathways in the OF cavity and site S2.
1 Wang W, Tsirulnikov K, Zhekova HR, et al. Cryo‐EM structure of the sodium‐driven chloride/bicarbonate exchanger NDCBE. Nat Commun. 2020;12: 5690
Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways ...than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.
We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and ...longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)4 are used to examine peptide aggregation in different environments, in water, and at the water–octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.
We describe computer simulations of pore formation and membrane rupture of phospholipid bilayers under mechanical and electrical stress. On the nanosecond simulation time scale, pores are induced by ...a lateral pressure exceeding −200 bar or by an applied electric field of 0.5 V/nm.
We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic ...properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu
18 side chains. If all of the Glu
18 side chains are ionised, the bundle is unstable; if none of the Glu
18 side chains are ionized, the bundle is stable. pK
A calculations suggest that either zero or one ionized Glu
18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996.
Biophys. J. 70:1643–1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle.
Voltage-gated sodium channels are important in initiating and propagating nerve impulses in various tissues, including cardiac muscle, skeletal muscle, the brain, and the peripheral nerves. ...Hyperexcitability of these channels leads to such disorders as cardiac arrhythmias (Na(v)1.5), myotonias (Na(v)1.4), epilepsies (Na(v)1.2), and pain (Na(v)1.7). Thus, there is strong motivation to identify isoform-specific blockers and the molecular determinants underlying their selectivity among these channels. μ-Conotoxin KIIIA blocks rNa(v)1.2 (IC(50), 5 nM), rNa(v)1.4 (37 nM), and hNa(v)1.7 (97 nM), expressed in mammalian cells, with high affinity and a maximal block at saturating concentrations of 90 to 95%. Mutations of charged residues on both the toxin and channel modulate the maximal block and/or affinity of KIIIA. Two toxin substitutions, K7A and R10A, modulate the maximal block (52-70%). KIIIA-H12A and R14A were the only derivatives tested that altered Na(v) isoform specificity. KIIIA-R14A showed the highest affinity for Na(v)1.7, a channel involved in pain signaling. Wild-type KIIIA has a 2-fold higher affinity for Na(v)1.4 than for Na(v)1.7, which can be attributed to a missing outer vestibule charge in domain III of Na(v)1.7. Reciprocal mutations Na(v)1.4 D1241I and Na(v)1.7 I1410D remove the affinity differences between these two channels for wild-type KIIIA without affecting their affinities for KIIIA-R14A. KIIIA is the first μ-conotoxin to show enhanced activity as pH is lowered, apparently resulting from titration of the free N terminus. Removal of this free amino group reduced the pH sensitivity by 10-fold. Recognition of these molecular determinants of KIIIA block may facilitate further development of subtype-specific, sodium channel blockers to treat hyperexcitability disorders.
The partitioning behavior of small molecules in lipid bilayers is important in a variety of areas including membrane protein folding and pharmacology. However, the inhomogeneous nature of lipid ...bilayers on a nanometer length scale complicates experimental studies of membrane partitioning. To gain more insight in the partitioning of a small molecule into the lipid bilayer, we have carried out atomistic computer simulations of hexane in a dioleoyl phosphatidylcholine model membrane. We have been able to obtain spatially resolved free energy, entropy, enthalpy, and heat capacity profiles based on umbrella sampling calculations at three different temperatures. In agreement with experiment, hexane partitions preferentially to the center of the bilayer. This process is driven almost entirely by a favorable entropy change, consistent with the hydrophobic effect. In contrast, partitioning to the densest region of the acyl chains is dominated by a favorable enthalpy change with a small entropy change, which is consistent with the “nonclassical” hydrophobic effect or “bilayer” effect. We explain the features of the entropy and enthalpy profiles in terms of density and free volume in the system.
Two 40
ns molecular dynamics simulations of a palmitoyl-oleoyl phosphatidylserine (POPS) lipid bilayer in the liquid crystalline phase with Na
+ counterions and NaCl were carried out to investigate ...the structure of the negatively charged lipid bilayer and the effect of salt (NaCl) on the lipid bilayer structure. Na
+ ions were found to penetrate deep into the ester region of the water/lipid interface of the bilayer. Interaction of the Na
+ ions with the lipid bilayer is accompanied by a loss of water molecules around the ion and a simultaneous increase in the number of ester carbonyl oxygen atoms binding the ion, which define an octahedral and square pyramidal geometry. The amine group of the lipid molecule is involved in the formation of inter- and intramolecular hydrogen bonds with the carboxylate and the phosphodiester groups of the lipid molecule. The area per lipid of the POPS bilayer is unaffected by the presence of 0.15M NaCl. There is a small increase in the order parameter of carbon atoms in the beginning of the alkyl chain in the presence of NaCl. This is due to a greater number of Na
+ ions being coordinated by the ester carbonyl oxygen atoms in the water/lipid interface region of the POPS bilayer.
1. Introduction 475 1.1 Ion channels 475 1.1.1 Gramicidin 476 1.1.2 Helix bundle channels 477 1.1.3 K channels 480 1.1.4 Porins 483 1.1.5 Nicotinic acetylcholine receptor 483 1.1.6 Physiological ...properties 483 1.2 Simulations 484 1.2.1 Atomistic versus mean-field simulations 484 2. Atomistic simulations 485 2.1 Modelling of ion-interaction parameters 485 2.1.1 Interatomic distances and the problem of ionic radii 486 2.1.2 Solvation energy 487 2.1.3 Hydration shells and coordination numbers 489 2.1.4 Parameters in common use and transferability 491 2.1.5 Summary 491 2.2 Water in pores versus bulk 491 2.2.1 Simple pore models 494 2.2.2 gA 495 2.2.3 Alm 496 2.2.4 LS36 (and LS24) 496 2.2.5 Nicotinic receptor M2δ5 497 2.2.6 Influenza A M2 497 2.2.7 K channels 497 2.2.8 nAChR 498 2.2.9 Porins 498 2.2.10 Relevance 499 2.2.11 Problems with simulations 501 2.3 Dynamics of ions in pores 503 2.3.1 Simple pore models 503 2.3.2 Helix bundles 504 2.3.3 gA and KcsA 505 2.4 Energetics of permeation and ion selectivity 509 2.4.1 Potential and free energy profiles 509 2.4.2 gA 510 2.4.3 α-Helix bundles 511 2.4.4 KcsA 512 2.4.5 Ion selectivity 514 2.4.6 Problems of estimating energetic profiles 515 2.5 Conformational changes 516 2.5.1 gA 516 2.5.2 Alm and LS3 516 2.5.3 KcsA 517 2.6 Protonation states 523 3. Coarse-grained simulations 524 3.1 Introduction 524 3.1.1 Predicting conductance magnitudes 525 3.2 Electro-diffusion: the Nernst–Planck approach 526 3.2.1 Calculating the potential profile from Poisson and PB theory 528 3.2.2 Calculating the potential profile from BD simulations 530 3.2.3 Combining Nernst–Planck and Poisson: PNP 530 3.3 Beyond PNP 532 3.4 BD simulations 532 3.4.1 Basic theory in ion channels 532 3.4.2 Incorporating the environment 533 3.5 Applications 535 3.5.1 Model systems 535 3.5.1.1 Solving the Poisson and PB equation for channel-like geometries 535 3.5.1.2 Comparing PB, PNP and BD 536 3.5.2 Applications to known structures 537 3.5.2.1 gA 537 3.5.2.2 Porin 539 3.5.2.3 LS3 540 3.5.2.4 Alm 542 3.5.2.5 nAChR 542 3.5.2.6 KcsA 543 3.6 pKa calculations 543 3.7 Selectivity 544 3.7.1 Anion/cation selectivity 545 3.7.2 Monovalent/divalent ion selectivity 545 4. Problems 546 4.1 Atomistic simulations 546 4.1.1 Problems 546 4.1.2 Parameters 548 4.2 BD 549 4.3 Mean-field simulations 549 5. Conclusions 550 5.1 Progress 550 5.2 The future 550 6. Acknowledgements 551 7. References 551 Ion channels are proteins that form ‘holes’ in membranes through which selected ions move
passively down their electrochemical gradients. The ions move quickly, at (nearly) diffusion
limited rates (ca. 107 ions s−1 per channel). Ion channels are central to many properties of cell
membranes. Traditionally they have been the concern of neuroscientists, as they control the
electrical properties of the membranes of excitable cells (neurones, muscle; Hille, 1992).
However, it is evident that ion channels are present in many types of cell, not all of which
are electrically excitable, from diverse organisms, including plants, bacteria and viruses
(where they are involved in functions such as cell homeostasis) in addition to animals. Thus
ion channels are of general cell biological importance. They are also of biomedical interest,
as several dizeases (‘channelopathies’) have been described which are caused by changes in
properties of a specific ion channel (Ashcroft, 2000). Moreover, passive diffusion channels for
substances other than ions are common (porins, aquaporins), as are active membrane
transport processes coupled to ion gradients or ATP hydrolysis. An understanding of ion
channels may also provide a gateway to understanding these processes.
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