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The average locations of backbone and side chain atoms of ACTH (1-24) in a) DPC micelle and b) DMPC bilayer from the center of the respective lipid systems. The distributions of the components of the lipid are plotted on the vertical axis. The two horizontal lines indicate the interfacial area.
Source publication
The structure and interactions of the 1-24 fragment of the adrenocorticotropin hormone, ACTH (1-24), with membrane have been studied by molecular dynamics (MD) simulation in an NPT ensembles in two explicit membrane mimics, a dodecylphosphocholine (DPC) micelle and a dimyristoylphosphatidylcholine (DMPC) bilayer. The starting configuration of the p...
Contexts in source publication
Context 1
... 2a shows the RDFs of the water oxygen atoms, peptide backbone, DPC hydrocarbon chain, and DPC head groups from the COM of the micelle. Also shown are the average locations of the backbone and side chain atoms of individ- ual residues with respect to the COM of the micelle (Figure 3a). The distribution of water did not extend much within 12 Å of the micelle COM, rendering a "dry interior" in the micellar system. ...
Context 2
... 1-10 segment of the peptide backbone is located on 17.5-21.0 Å from the micellar COM with a maximum distribution at ~19.2 Å, which falls entirely into the DPC head group area and partly into the interfacial area defined above ( Figure 3a). The 11-24 segment, on the other hand, falls mostly in the 23.0-37.0 ...
Context 3
... peptide backbone traverses from the hydrophobic interior through head group area and beyond into the bulk waters. The backbone of the 1-10 segment of the peptide was within the region of 12-16 Å from the center of the bilayer (Figure 3b). This region is inside the head group region and is much deeper than what neutron diffraction study of similar peptides in lipid bilayers indicated. ...
Context 4
... residues of the segment 12-16 resided entirely in the head group area while residues 17-24 fully in the bulk water. The residues in the 14-24 segment showed a substantially increased distance from the bilayer surface (at 23-38 Å), ranging from 21 Å for Gly 14 to 35 Å for the last three C-terminal residues (Figure 3b). The distance of the latter segment from the bilayer surface clearly indicates the lack of interaction between this segment with either the lipid head groups or the hydrophobic interior, similar to the DPC case. ...
Citations
... Among these techniques, one that can provide detailed information on the dynamics and structure of the peptides and proteins at an atomistic level is the molecular dynamic (MD) simulation using explicit lipids. Gao and Wong, using NMR as well as MD on peptides in micelles and bilayers,[11][12][13]showed that the gross features of the structure of the peptide and the location and orientation of the peptide with respect to the membrane–water interface are similar between micelles and bilayers. On the other hand, the use of micelles as membrane mimics is not without its detractors. ...
... Intermolecular NOE between the side chains of the polar 11–24 segment and the lipid protons are completely absent. This conclusion was corroborated by chemical shifts and linewidth measurements,[11]and MD simulation.[12]NOE cross-peaks in human apoprotein A-I (142–187) in 50% protonated SDS[76]suggest that both the helices and the interhelical region of the peptide bind to the SDS micelle. ...
... NMR and other techniques to elucidate the mode of binding of peptides to micelles has been fruitful. Recently, MD simulations of peptides and proteins in explicit micelles[12,13,15,[96][97][98]have been used in combination with NMR to determine the mode of interaction.[11,12,43,99]It is encouraging to find that in such studies consistent results have been obtained to date from NMR and MD simulations. ...
INTRODUCTION In this article, solution NMR techniques and studies of peptides and proteins solubilized in isotropic micellar systems are described. Studies of peptides and proteins in isotropic bicellar systems will also be included in this report. Studies of proteins and peptides in anisotropic lipid bilayers using solid-state NMR techniques will not be included except occasionally as comparisons to the micellar results. One exception is a brief descrip-tion of using dilute bicellar solutions to orient proteins for the purpose of measuring residual dipolar cou-plings (RDC) (section ''Bicelles as an Orienting Medium for Measuring Residual Dipolar Couplings in Protein Structure Determination''). This article is not intended to be an exhaustive review of all relevant studies in the literature. Rather, the important techni-ques in this field of study will be described and illustrated by a few pertinent examples from the litera-ture and readers are encouraged to use the citations to locate further information. A majority of the examples presented in this review are focused on peptides. The NMR methodology and the information that can be obtained from NMR studies of proteins and peptides in micelles will be overviewed in the section ''NMR Methodology.'' In the subsequent sections, the structure of the micelle-bound peptides/proteins, the affinity or partition of peptides in micelles, and the mode of binding of peptides/proteins to micelles will be discussed. In the final section, NMR studies of membrane proteins reconstituted in micelles will be presented.
... Like the lipid bilayers of real membranes, micelles possess a well-defined hydrophobic core and a flexible, hydrophilic interface and are commonly used in place of monolayers or bilayers in experimental methods such as NMR spectroscopy (24)(25)(26)(27). Simulations in micelles are much less time and resource consuming than simulations in lipid bilayers, due to their smaller size and faster relaxation times, which have been shown through both direct experiments and simulations to be on the order of 500-1,000 ps for micelles (28)(29)(30)(31)(32), in contrast with lipid bilayers, which require tens of nanoseconds (33,34). ...
... Molecular dynamics studies of micelles have been performed for many types of micelles, including anionic micelles such as those formed by sodium dodecyl sulfate (SDS) (29,(35)(36)(37)(38); zwitterionic micelles (e.g., dodecylphosphocholine, DPC) (30,31,(39)(40)(41); and a few mixed composition micelles (42,43). DPC micelles are considered to be acceptable models of eukaryotic cell membranes, which are generally rich in zwitterionic phospholipids. ...
Recent advances in molecular dynamics (MD) simulation methods and in available computational resources have allowed for more reliable simulations of biological phenomena. From all-atom MD simulations, we are now able to visualize in detail the interactions between antimicrobial peptides (AMPs) and a variety of membrane mimics. This helps us to understand the molecular mechanisms of antimicrobial activity and toxicity. This chapter describes how to set up and conduct molecular dynamics simulations of AMPs and membrane mimics. Details are given for the construction of systems of interest for studying AMPs, which can include simulations of peptides in water, micelles, or lipid bilayers. Explanations of the parameters needed for running a simulation are provided as well.
... This structure was obtained after extensive minimisation and dynamics of about 1 ns in a cubic simulation cell. The force field parameters for DPC molecules were obtained from the work of Wong and Kamath [30]. Similarly, the parameters for the force field and the initial coordinates of the SDS micelle-water complex were taken from molecular dynamic (MD) simulations carried out by MacKerell [31]. ...
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.
... Conversely, it is not clear what the correct value of the applied surface tension should be for simulations in the NP z γT ensemble [25,27], particularly for a small bilayer patch with an embedded peptide. Lipid bilayer simulations are further encumbered by the much slower relaxation time of lipid molecules in bilayers as compared to micelles [28][29][30][31][32], which would require much longer simulation times to sample relevant peptide conformations. For further discussion of the benefits and shortcomings of micelles as membrane mimics, the reader is referred to references [12,33]. ...
... The topology and parameters for DPC were obtained by combining the dodecyl chain of dodecylsulfate with the phosphocholine head group. The starting coordinates for the micelle were obtained from molecular dynamics simulations carried out by Kamath and Wong [30]. Previous simulations of peptide-micelle systems carried out by our group [12,33,[35][36][37] indicate that a single DPC molecule frequently separates from the main micelle relatively quickly in the presence of a peptide. ...
We have carried out molecular dynamics simulations of the naturally occurring protegrin PG-1 peptide and two of its mutants, PC-9 and PC-13 in the presence of a dodecyl-phosphocholine (DPC) micelle. The effects of mutations that disrupt the β-sheet structure in the case of PC-9 and reduce the charge at the C-terminus in the case of PC-13 are analyzed. It is found that the surface-bound conformations of the peptides are severely affected by both mutations. PG-1 exhibits a conformation in which the C-terminus and the β-hairpin turn interact strongly with the micelle lipid head groups, while its N-terminal strand bends away from the micelle and resides in the aqueous region; PC-13 exhibits strong interactions with the micelle at its N-terminus as well as the β-hairpin turn region, while retaining a much more compact conformation than PG-1; PC-9 achieves a highly distorted conformation relative to the homologous PG-1 structure, which allows both its termini and the β-hairpin region to interact with the micelle. These significant differences observed as a result of seemingly minor mutations to the sequences of the three peptides are explained in terms of the interplay between residue charges, structural rigidity and amphiphilic interactions. Conservative inferences are made bridging these biophysical interactions and the pharmacological profiles of the peptides.
... Micelles provide a minimalistic system for the study of activity and toxicity; like lipid bilayers , micelles possess a well-defined hydrophobic core and a flexible, hydrophilic interface and are commonly used in place of monolayers or bilayers in experimental methods such as NMR spectroscopy15161718. Recently, studies of a variety of AMPs including, piscidin, magainin, and aurein, have been conducted in micelles192021222324 . Importantly , they have faster time scales of motion252627282930 and smaller system size, which reduce the required simulation length to one that is computationally feasible. DPC micelles simulate eukaryotic cell membranes, which are generally rich in zwitterionic phospholipids. ...
We applied a combined experimental and computational approach to ascertain how peptides interact with host and microbial membrane surrogates, in order to validate simulation methodology we hope will enable the development of insights applicable to the design of novel antimicrobial peptides. We studied the interactions of two truncated versions of the potent, but cytotoxic, antimicrobial octadecapeptide protegrin-1, PC-72 [LCYCRRRFCVC] and PC-73 [CYCRRRFCVC].
We used a combination of FTIR, fluorescence spectroscopy and molecular dynamics simulations to examine the peptides' interactions with sodium dodecylsulfate (SDS) and dodecylphosphocholine (DPC) micelles. The relative amounts of secondary structure determined by FTIR agreed with those from the simulations. Fluorescence spectroscopy, deuterium exchange experiments and the simulations all indicate that neither peptide embeds itself deeply into the micelle core. Although molecular simulations placed both peptides at the micelle-water interface, further examination revealed differences in how certain residues interacted with the micelle core.
We demonstrate here the accuracy of molecular dynamics simulations methods through comparison with experiments, and have used the simulation results to enhance the understanding of how these two peptides interact with the two types of micelles. We find agreement between simulation and experimental results in the final structure of the peptides and in the peptides final conformation with respect to the micelle. Looking in depth at the peptide interactions, we find differences in the interactions between the two peptides from the simulation data; Leu-1 on PC-72 interacts strongly with the SDS micelle, though the interaction is not persistent--the residue withdraws and inserts into the micelle throughout the simulation.
... Similar observations were made about the scorpion-derived AMP IsCT and its analogs, although there is no direct evidence of a carpet-based mechanism [27]. The major families of helical peptides which operate by the carpet mechanism include the dermaseptins [37] and cecropins [17]. OVIS falls in this category, and is an analog of the human AMP LL-37 [30], which is thought to operate by the carpet mechanism as well. ...
Molecular dynamics simulations of three related helical antimicrobial peptides have been carried out in zwitterionic diphosphocholine (DPC) micelles and anionic sodiumdodecylsulfate (SDS) micelles. These systems can be considered as model mammalian and bacterial membrane interfaces, respectively. The goal of this study is to dissect the differences in peptide composition which make the mutant peptides (novispirin-G10 and novispirin-T7) less toxic than the parent peptide ovispirin (OVIS), although all three peptides have highly antibacterial properties. Compared to G10 and T7, OVIS inserts deepest into the DPC micelle. This correlates well with the lesser toxicity of G10 and T7. There is strong evidence which suggests that synergistic binding of hydrophobic residues drives binding of OVIS to the micelle. The helical content of G10 and T7 is reduced in the presence of DPC, and this leads to less amphipathic peptide structures, which bind weakly to the micelle. Simulations in SDS were carried out to compare the influence of membrane electrostatics on peptide structure. All three peptides bound strongly to SDS, and retained helical form. This corresponds well with their equally potent antibacterial properties. Based on the simulations, we argue that secondary structure stability often leads to toxic properties. We also propose that G10 and T7 operate by the carpet mechanism of cell lysis. Toxicity of peptides operating by the carpet mechanism can be attenuated by reducing the peptide helical content. The simulations successfully capture experimental binding states, and the different depths of binding of the three peptides to the two micelles correlate with their antibacterial and toxic properties.
... The time scales of motion are significantly faster for micelles than for lipid bilayers. Micelle relaxation times have been shown, through experiment [35] and simulation, to be on the order of 500-1000 ps [23,[36][37][38], in contrast with lipid bilayers, which require tens of nanoseconds [32]. For a study such as this one, involving simulations of three peptides in two different systems, it would not be feasible to simulate six systems for the hundreds of nanoseconds required by lipid bilayers. ...
... There have been many successful studies in which micelle membrane mimics have been used to provide a detailed picture of the interaction with a peptide [24,37,41,42]. Using NMR techniques, van den Hooven and coworkers studied nisin in both DPC and SDS micelles in order to determine its structure -function relationship [31]. ...
... Structures for PC101, PC104, and PC107 were created using homology modeling as described in [50], a reliable method given the level of sequence similarity and the highly constrained nature of the b-sheet structure of all four peptides. The starting coordinates of the SDS micelle-water complex were obtained from simulations carried out by MacKerell [21], and the DPC micelle-water complex coordinates were obtained from Wong and coworkers [37]. The system is composed of a 60-molecule micelle, 4375 water molecules (4377 for the DPC system), 0.15 mM NaCl electrolyte, a single peptide and appropriate counterions. ...
In this work the effects of the charge of the C-terminus of protegrin-like peptides on activity and toxicity are examined by molecular dynamics simulations. Simulations are done in sodium dodecylsulphate and dodecylphosphocholine micelles, bacterial and mammalian membrane mimics, respectively. Three protegrin mutants are examined and it is found that while the peptides interact in different ways, the peptides all insert into the SDS micelles equally as deep, in agreement with their equal activities as determined by previous experimental work. There are clear differences in the interactions with the DPC micelles and it is demonstrated that simulations with DPC micelles can predict levels of toxicity of such peptides. We also see that removing the positive charge from the sequence of protegrin-1 does not have positive effects on the resulting peptide's toxicity, but that replacing the positive charge with a negative charge reduces the toxicity.
... The primary advantage of using micelles as opposed to lipid bilayers are the faster time scales of motion of SDS lipids. It has been shown both experimentally [8] and by molecular dynamics simulations [26,35,37], that the slowest relaxation times of lipids in SDS and DPC micellar solutions are of the order of 500-1000 ps. The only exception to this is the slower relaxation times of counterions in simulations [19]. ...
... Simulations of micelles of various anionic and zwitterionic lipid micellar systems [2,16,19,26,29,32,[35][36][37][38] have been successfully used to interpret and supplement the information obtained from experimental methods like NMR, Xray diffraction, CD spectroscopy and FTIR spectroscopy. In the past few years, simulation force fields like CHARMM, AMBER and GROMACS have been fairly well parameterized to accurately simulate hydrated lipid assemblies. ...
We report long time scale simulations of the 18-residue helical antimicrobial peptide ovispirin-1 and its analogs novispirin-G10 and novispirin-T7 in SDS micelles. The SDS micelle serves as an economical and effective model for a cellular membrane. Ovispirin, which is initially placed along a micelle diameter, diffuses out to the water-SDS interface and stabilizes to an interface-bound steady state in 16.35 ns of simulation. The final conformation, orientation, and the structure of ovispirin are in good agreement with the experimentally observed properties of the peptide in presence of lipid bilayers. The simulation succeeds in capturing subtle differences of the membrane-bound peptide structure as predicted by solid state NMR. The novispirins also undergo identical diffusion patterns and similar final conformations. Although the final interface-bound states are similar, the simulations illuminate the structural and binding properties of the mutant peptides which make them less toxic compared to ovispirin. Based on previous data and the current simulations, we propose that introduction of a bend/hinge at the center of helical antimicrobial peptides (containing a specific C-terminal motif), without disrupting the helicity of the peptides might attenuate host-cell toxicity as well as improve membrane binding properties to bacterial cellular envelopes.
... The crystal structure of glucagon shows a helical region corresponding to about 16 residues of R-helix, extended at either end by four residues of less regular, right-handed helix (16). The helix is amphipathic with the hydrophobic face of the N-terminal portion (residues 5-14) on the side of the helix opposite to the hydrophobic face of the C-terminal portion (residues [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29]. In the crystal, glucagon exists as a trimer in which these hydrophobic portions can make intermolecular contact, thereby stabilizing the pattern of reversed amphipathic surfaces along the peptide chain. ...
... The solution structure of glucagon has been previously determined by nuclear magnetic resonance (NMR) 1 spectroscopy in the presence of perdeuterated dodecylphosphocholine micelles (19). The backbone conformation includes an unstructured region (residues 1-4), a predominantly extended segment (residues 5-9), one helixlike turn (residues [10][11][12][13][14], another stretch of extended chain (residues [14][15][16][17], and three turns of a distorted R-helix (residues [17][18][19][20][21][22][23][24][25][26][27][28][29]. The orientation of the C-terminal helix with respect to the structural elements of the N-terminal region was not established. ...
... This truncated form of glucagon-like peptide-1 (GLP-1) shows 50% sequence homology with glucagon ( Figure 1) and is extended at the C-terminus by one residue and an amide cap. The solution structure is similar to glucagon, with four regions: a random-coil section (residues 1-6); an N-terminal R-helix (residues 7-14); a "loose helix" (residues 15-17); a C-terminal R-helix (residues [18][19][20][21][22][23][24][25][26][27][28][29][30]. Again, no relationship was established between the two helices, although a helical distortion, leading to a helix phase shift, was suggested for residues 15-17 connecting the two helical segments (21). ...
Glucagon, a 29-residue peptide hormone, plays an important role in glucose homeostasis and in diabetes mellitus. Several glucagon antagonists and agonists have been developed, but limited structural information is available to clarify the basis of their biological activity. The solution structure of the potent glucagon antagonist, [desHis1, desPhe6, Glu9]glucagon amide, was determined by homonuclear 2D NMR spectroscopy at pH 6.0 and 37 degrees C in perdeuterated dodecylphosphocholine micelles. The overall backbone root-mean-square deviation (rmsd) for the structured portion (residues 7-29, glucagon numbering) of the micelle-bound 27-residue peptide is 1.36 A for the 15 lowest-energy structures, after restrained molecular dynamics simulation. The structure consists of four regions (segment backbone rmsd in A): an unstructured N-terminal segment between residues 2 and 5 (1.68), an irregular helix between residues 7 and 14 (0.79), a hinge region between residues 15 and 18 (0.54), and a well-defined alpha-helix between residues 19 and 29 (0.33). The two helices form an L-shaped structure with an angle of about 90 degrees between the helix axes. There is an extended hydrophobic cluster, which runs along the inner surface of the L-structure and incorporates the side chains of the hydrophobic residues of each of the amphipathic helices. The outer surface contains the hydrophilic side chains, with two salt bridges (D15-R18 and R17-D21) implied from close approach of the charged groups. This result is the first clear indication of an overall tertiary fold for a glucagon analogue in the micelle-bound state. The relationship of the two helical structural elements may have important implications for the biological activity of the glucagon antagonist.
Recently, we had reported a synthetic positively charged leucine-rich 14-residue-long antimicrobial peptide (AMP, LL-14: NH3+-LKWLKKLLKWLKKL-CONH2), which was highly active and cytotoxic relative to its valine analogue (VV-14). However, the thermodynamics underlying this differential toxicity and antimicrobial activity was unclear. Understanding the energetics of peptide binding to micelles (simplest membrane mimic, viz., SDS as a bacterial membrane and DPC as a eukaryotic membrane) and the effect of Leu → Val peptide mutations on the stability of the peptide:micelle complexes are of great academic interest and relevant for the rational design of potent and selective AMPs for therapeutic use. Here, we have reported the molecular dynamics free energy simulations that allowed us to quantitatively estimate the strength of peptide discrimination (based on single- or multiple-site Leu/Val mutations in LL-14) by membrane mimetic micelles (SDS and DPC) and decipher the energetics underlying peptide selectivity by micelles. The Leu-containing peptide (LL-14) was found to be preferred for micelle (SDS and DPC) binding relative to its Val analogues (single or multiple Val mutants). The strength of the preference depended on the position of the Leu/Val mutation in the peptide. Surprisingly, the N-terminal LL-14 single mutation (Leu → Val: L1V) was found to fine-tune the electrostatic interactions, resulting in the highest peptide selectivity (ΔΔG ∼ 8 kcal/mol for both SDS and DPC). However, the mechanism of L1V peptide selectivity was distinctly different for SDS and DPC micelles. SDS ensured high selectivity by disrupting the peptide:micelle salt bridge, whereas DPC desolvated the broken-peptide-backbone hydrogen bond in the V1 peptide:micelle complex. Mutations (Leu → Val) in the middle positions of the LL-14 (4th, 7th, 8th, and 11th) were disfavored by the micelles primarily due to the loss of peptide:micelle hydrophobic interactions. Peptides differing at the C-terminal (i.e., L14V) were recognized by SDS micelles (ΔΔG ∼ 4 kcal/mol) by altering peptide:micelle interactions. L14V mutation, on the other hand, did not play any role in the peptide:DPC binding, as no direct interactions between the C-terminal and DPC micelle were observed due to obvious electrostatic reasons. The strength of selectivity favoring LL-14 binding against VV-14 was found to be much higher for DPC micelles (ΔΔG ∼ 25 kcal/mol) relative to SDS micelles (ΔΔG ∼ 19 kcal/mol). The loss of the peptide:micelle hydrophobic contact in response to LL-14 → VV-14 mutation was found to be significantly larger for DPC relative to SDS micelles, resulting in higher discriminatory power for the former. Peptide:SDS salt bridges seemed to prevent the loss of peptide:micelle hydrophobic contact to some extent, leading to weaker selectivity for SDS micelles. High selectivity of DPC micelles provided an efficient mechanism for VV-14 dissociation from DPC micelles, whereas low-selectivity of SDS micelles ensured binding of both LL-14 and VV-14. To the best of our knowledge, this is the first study in which the experimental observations (antimicrobial activity and toxicity) between leucine-rich and valine-rich peptides have been explained by establishing a direct link between the energetics and structures.
