Free Energetics of Arginine Permeation into Model DMPC Lipid Bilayers: Coupling of Effective Counterion Concentration and Lateral Bilayer Dimensions

Mechanisms and underlying thermodynamic determinants of translocation of charged cationic peptides such as cell-penetrating peptides across the cellular membrane continue to receive much attention. Two widely held views include endocytotic and non-endocytotic (diffusive) processes of permeant transfer across the bilayer. Considering a purely diffusive process, we consider the free energetics of translocation of a monoarginine peptide mimic across a model DMPC bilayer. We compute potentials of mean force for the transfer of a charged monoarginine peptide unit from water to the center of a 1,2-dimyristoyl-<i>sn</i>-glycero-3-phosphocholine (DMPC) model lipid bilayer. We use fully atomistic molecular dynamics simulations coupled with the adaptive biasing force (ABF) method for free energy estimation. The estimated potential of mean force difference from bulk to bilayer center is 6.94 ± 0.28 kcal/mol. The order of magnitude of this prediction is consistent with past experimental estimates of arginine partitioning into physiological bilayers in the context of translocon-based experiments, though the correlation between the bench and computer experiments is not unambiguous. Moreover, the present value is roughly one-half of previous estimates based on all-atom molecular dynamics free energy calculations. We trace the differences between the present and earlier calculations to system sizes used in the simulations and the dependence of the contributions to the free energy from various system components (water, lipids, ions, peptide) on overall system size. By varying the bilayer lateral dimensions in simulations using only sufficient numbers of counterions to maintain overall system charge neutrality, we find the possibility of an inherent convergent transfer free energy value

Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics

Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure and surface tension effects, experiments invoke porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales of the translocation process, we use umbrella sampling molecular dynamics simulations with a lipid-density-based order parameter to investigate membrane-pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and membrane bending rigidities in three different lipid classes. The pore-formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. The pore-formation free energy is higher in peptide–lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment

Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics

Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure and surface tension effects, experiments invoke porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales of the translocation process, we use umbrella sampling molecular dynamics simulations with a lipid-density-based order parameter to investigate membrane-pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and membrane bending rigidities in three different lipid classes. The pore-formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. The pore-formation free energy is higher in peptide–lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations

Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics

Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure and surface tension effects, experiments invoke porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales of the translocation process, we use umbrella sampling molecular dynamics simulations with a lipid-density-based order parameter to investigate membrane-pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and membrane bending rigidities in three different lipid classes. The pore-formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. The pore-formation free energy is higher in peptide–lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment

Versatile Analytical Platform Based on Graphene-Enhanced Infrared Attenuated Total Reflection Spectroscopy

Graphene, with its unique properties including atomic thickness, atomic uniformity, and delocalized π bonds, has been reported as a promising alternative material versus noble metals for surface-enhanced spectroscopies. Here, a simple and effective graphene-enhanced infrared absorption (GEIRA) strategy was developed based on infrared attenuated total reflection spectroscopy (IR-ATR). The IR signals of a broad range of molecules were significantly enhanced using graphene-decorated diamond ATR crystal surfaces versus conventional ATR waveguides. Utilizing rhodamine 6G (R6G) as the main model molecule, the experimental conditions were optimized, and potential enhancement mechanisms are discussed. Aqueous sample solutions were directly analyzed utilizing graphene dispersions, which eliminates harsh experimental conditions, tedious sample pretreatment, and sophisticated fabrication/patterning routines at the ATR waveguide surface. The GEIRA approach presented here provides simple experimental procedures, convenient operation, and excellent reproducibility, promoting a more widespread usage of graphene in surface-enhanced infrared absorption spectroscopy

Versatile Analytical Platform Based on Graphene-Enhanced Infrared Attenuated Total Reflection Spectroscopy

Graphene, with its unique properties including atomic thickness, atomic uniformity, and delocalized π bonds, has been reported as a promising alternative material versus noble metals for surface-enhanced spectroscopies. Here, a simple and effective graphene-enhanced infrared absorption (GEIRA) strategy was developed based on infrared attenuated total reflection spectroscopy (IR-ATR). The IR signals of a broad range of molecules were significantly enhanced using graphene-decorated diamond ATR crystal surfaces versus conventional ATR waveguides. Utilizing rhodamine 6G (R6G) as the main model molecule, the experimental conditions were optimized, and potential enhancement mechanisms are discussed. Aqueous sample solutions were directly analyzed utilizing graphene dispersions, which eliminates harsh experimental conditions, tedious sample pretreatment, and sophisticated fabrication/patterning routines at the ATR waveguide surface. The GEIRA approach presented here provides simple experimental procedures, convenient operation, and excellent reproducibility, promoting a more widespread usage of graphene in surface-enhanced infrared absorption spectroscopy

Space-Confined Growth of Defect-Rich Molybdenum Disulfide Nanosheets Within Graphene: Application in The Removal of Smoke Particles and Toxic Volatiles

In this work, molybdenum disulfide/reduced graphene oxide (MoS₂/RGO) hybrids are synthesized by a spatially confined reaction to insert the growth of defect-rich MoS₂ nanosheets within graphene to enable incorporation into the polymer matrix for the application in the removal of smoke particles and toxic volatiles. The steady-state tube furnace result demonstrates that MoS₂/RGO hybrid could considerably reduce the yield of CO and smoke particles. The TG-IR coupling technique was utilized to identify species of toxic volatiles including aromatic compounds, CO, and hydrocarbons and to investigate the removal effect of MoS₂/RGO hybrids on reducing toxic volatiles. The removal of smoke particles and toxic volatiles was attributed to the adsorption capacity derived from edges sites of MoS₂ and the honeycomb lattice of graphene, as well as the inhibition of nanobarrier resulting from two-dimensional structure. The work will offer a strategy for fabricating graphene-based hybrids by the space-confined synthesis and exploiting the application of space-confined graphene-based hybrid

Vertically Aligned Nickel 2‑Methylimidazole Metal–Organic Framework Fabricated from Graphene Oxides for Enhancing Fire Safety of Polystyrene

In this work, flowerlike nickel 2-methylimidazole metal–organic framework (Ni-MOF) was prepared by a solvothermal method. Vertically aligned Ni-MOF was fabricated from graphene oxide (GO) solution in the same way. The combination of GO and Ni-MOF (GOF) obviously suppressed the agglomeration of Ni-MOF sheets. As-synthesized, GOF has bigger pore volume and specific surface area, which are beneficial for volatile degradation products adsorption. It is noteworthy that the addition of GOF obviously reduced the fire hazard of polystyrene (PS). More than 33% decrease in the peak heat release rate for the PS/GOF composite was obtained when the content of the additives is only 1.0 wt %. Meanwhile, the reductions of total smoke and CO production were also prominent during the combustion of PS/GOF, respectively 21% and 52.3% decreases compared with that of pure PS. The synergism effects between layered GO and porous Ni-MOF realized the improved performances of PS. Thus, this work paves a feasible pathway to design efficient flame retardants for enhancing fire safety of polymers

Translocation Thermodynamics of Linear and Cyclic Nonaarginine into Model DPPC Bilayer via Coarse-Grained Molecular Dynamics Simulation: Implications of Pore Formation and Nonadditivity

Structural mechanisms and underlying thermodynamic determinants of efficient internalization of charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, and their variants, into cells, cellular constructs, and model membrane/lipid bilayers (large and giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center on endocytotic and nonendocytotic (diffusive) processes. Espousing the view of a purely diffusive internalization process (supported by recent experimental evidence, [Säälik, P.; et al. <i>J. Controlled Release</i> <b>2011</b>, <i>153</i>, 117–125]), we consider the underlying free energetics of the translocation of a nonaarginine peptide (Arg₉) into a model DPPC bilayer. In the case of the Arg₉ cationic peptide, recent experiments indicate a higher internalization efficiency of the cyclic structure (cyclic Arg₉) relative to the linear conformer. Furthermore, recent all-atom resolution molecular dynamics simulations of cyclic Arg₉ [Huang, K.; et al. <i>Biophys. J.</i>, <b>2013</b>, <i>104</i>, 412–420] suggested a critical stabilizing role of water- and lipid-constituted pores that form within the bilayer as the charged Arg₉ translocates deep into the bilayer center. Herein, we use umbrella sampling molecular dynamics simulations with coarse-grained Martini lipids, polarizable coarse-grained water, and peptide to explore the dependence of translocation free energetics on peptide structure and conformation via calculation of potentials of mean force along preselected reaction paths allowing and preventing membrane deformations that lead to pore formation. Within the context of the coarse-grained force fields we employ, we observe significant barriers for Arg₉ translocation from bulk aqueous solution to bilayer center. Moreover, we do not find free-energy minima in the headgroup–water interfacial region, as observed in simulations using all-atom force fields. The pore-forming paths systematically predict lower free-energy barriers (ca. 90 kJ/mol lower) than the non pore-forming paths, again consistent with all-atom force field simulations. The current force field suggests no preference for the more compact or covalently cyclic structures upon entering the bilayer. Decomposition of the PMF into the system’s components indicates that the dominant stabilizing contribution along the pore-forming path originates from the membrane as both layers of it deformed due to the formation of pore. Furthermore, our analysis revealed that although there is significant entropic stabilization arising from the enhanced configurational entropy exposing more states as the peptide moves through the bilayer, the enthalpic loss (as predicted by the interactions of this coarse-grained model) far outweighs any former stabilization, thus leading to significant barrier to translocation. Finally, we observe reduction in the translocation free-energy barrier for a second Arg₉ entering the bilayer in the presence of an initial peptide restrained at the center, again, in qualitative agreement with all-atom force fields