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Shunsaku Kimura - One of the best experts on this subject based on the ideXlab platform.
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engineering ph responsive switching of donor π acceptor chromophore alignments along a Peptide Nanotube scaffold
RSC Advances, 2020Co-Authors: Yuki Tabata, Shunsaku Kimura, Yusuke Kamano, Hirotaka UjiAbstract:A cyclic tri-β-Peptide cyclo(β-Ala-β-Ala-β-Lys) having diethylaminonaphthalimide at the β-Lys side chain (CP3Npi) self-assembled into a Peptide Nanotube in a solution of HFIP and water. CD spectra of the CP3Npi Nanotubes show a negative Cotton effect at 441 nm and a positive Cotton effect at 393 nm, indicating that D–π–A naphthalimide chromophores are aligned in a left-handed chiral way along the Nanotube. The CP3Npi Nanotubes bear positive charges under acidic conditions retaining the Nanotube structure but pH-responsive switching of D–π–A naphthalimide alignments along the Nanotube between a left-handed chiral and random arrangement was observed. The Peptide Nanotube is a stable scaffold for attaining pH-responsive alignment switching of side-chain chromophores.
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Engineering pH-responsive switching of donor–π–acceptor chromophore alignments along a Peptide Nanotube scaffold
RSC Advances, 2020Co-Authors: Yuki Tabata, Shunsaku Kimura, Yusuke Kamano, Hirotaka UjiAbstract:A cyclic tri-β-Peptide cyclo(β-Ala-β-Ala-β-Lys) having diethylaminonaphthalimide at the β-Lys side chain (CP3Npi) self-assembled into a Peptide Nanotube in a solution of HFIP and water. CD spectra of the CP3Npi Nanotubes show a negative Cotton effect at 441 nm and a positive Cotton effect at 393 nm, indicating that D–π–A naphthalimide chromophores are aligned in a left-handed chiral way along the Nanotube. The CP3Npi Nanotubes bear positive charges under acidic conditions retaining the Nanotube structure but pH-responsive switching of D–π–A naphthalimide alignments along the Nanotube between a left-handed chiral and random arrangement was observed. The Peptide Nanotube is a stable scaffold for attaining pH-responsive alignment switching of side-chain chromophores.
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The effect of macrodipole orientation on the piezoelectric response of cyclic β-Peptide Nanotube bundles on gold substrates
Polymer Journal, 2019Co-Authors: Yuki Tabata, Shota Mitani, Tomoya Imai, Shunsaku KimuraAbstract:Two kind of cyclic tri-β-Peptides, cyclo(β-Ala(nap)-β-Ala-β-Ala (C3NAA)), and cyclo(β-Ala(nap)-ED-SA) (C3NES), are synthesized. The orientation of the Peptide Nanotube bundles changes from horizontal to perpendicular on the guanidium-terminated SAM due to the methanol-vapor annealing process. The C3NAA Nanotube bundles positioned horizontally along the gold substrate generate a relatively large surface potential, and the converse piezoelectric response is as high as approximately 9 pm/V. A cyclic tri-β-Peptide containing β-naphthylalanine (β-Ala(nap)), cyclo(β-Ala(nap)-β-Ala-β-Ala) (C3NAA), and its analog with an ethylenediamine-succinic acid sequence (ED-SA), cyclo(β-Ala(nap)-ED-SA) (C3NES) self-assemble into Peptide Nanotube bundles on gold, where the surfaces of the substrates are modified by the self-assembled monolayers (SAMs). The C3NAA Nanotube generates a threefold larger macrodipole along the long axis of the Nanotube than is present on the C3NES Nanotube. The orientation of the Peptide Nanotube bundles change from horizontal to perpendicular on the substrates due to the methanol-vapor annealing process. The surface potential of the C3NAA Nanotube bundle on the guanidium-terminated SAM is larger than that of the C3NES Nanotube bundle due to the larger macrodipole of the C3NAA Nanotube than the C3NES Nanotube, but the converse piezoelectric responses are insignificant. On the other hand, the C3NAA Nanotube bundles positioned horizontally along the gold substrate generate a relatively large surface potential, and the converse piezoelectric response is as high as approximately 9 pm/V. The piezoelectric response likely becomes larger when the macrodipole is perpendicular to the applied electric field and is sensitive to the extent to which the dipoles are arranged in a noncentrosymmetric structure.
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The effect of macrodipole orientation on the piezoelectric response of cyclic β-Peptide Nanotube bundles on gold substrates
Polymer Journal, 2019Co-Authors: Yuki Tabata, Shota Mitani, Tomoya Imai, Shunsaku KimuraAbstract:Two kind of cyclic tri-β-Peptides, cyclo(β-Ala(nap)-β-Ala-β-Ala (C3NAA)), and cyclo(β-Ala(nap)-ED-SA) (C3NES), are synthesized. The orientation of the Peptide Nanotube bundles changes from horizontal to perpendicular on the guanidium-terminated SAM due to the methanol-vapor annealing process. The C3NAA Nanotube bundles positioned horizontally along the gold substrate generate a relatively large surface potential, and the converse piezoelectric response is as high as approximately 9 pm/V. A cyclic tri-β-Peptide containing β-naphthylalanine (β-Ala(nap)), cyclo(β-Ala(nap)-β-Ala-β-Ala) (C3NAA), and its analog with an ethylenediamine-succinic acid sequence (ED-SA), cyclo(β-Ala(nap)-ED-SA) (C3NES) self-assemble into Peptide Nanotube bundles on gold, where the surfaces of the substrates are modified by the self-assembled monolayers (SAMs). The C3NAA Nanotube generates a threefold larger macrodipole along the long axis of the Nanotube than is present on the C3NES Nanotube. The orientation of the Peptide Nanotube bundles change from horizontal to perpendicular on the substrates due to the methanol-vapor annealing process. The surface potential of the C3NAA Nanotube bundle on the guanidium-terminated SAM is larger than that of the C3NES Nanotube bundle due to the larger macrodipole of the C3NAA Nanotube than the C3NES Nanotube, but the converse piezoelectric responses are insignificant. On the other hand, the C3NAA Nanotube bundles positioned horizontally along the gold substrate generate a relatively large surface potential, and the converse piezoelectric response is as high as approximately 9 pm/V. The piezoelectric response likely becomes larger when the macrodipole is perpendicular to the applied electric field and is sensitive to the extent to which the dipoles are arranged in a noncentrosymmetric structure.
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Electronic Properties of Cyclic β-Peptide Nanotube Bundles Reflecting Structural Arrangement
Chemistry Letters, 2019Co-Authors: Yuki Tabata, Tomoya Imai, Yusuke Kamano, Hirotaka Uji, Shunsaku KimuraAbstract:Three kinds of cyclic tri-β-Peptides having different numbers of benzyl ester groups are synthesized. The cyclic Peptides formed Peptide Nanotube bundles showing different surface potentials, piezo...
Mark A. Ratner - One of the best experts on this subject based on the ideXlab platform.
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Coarse-Grained Molecular Dynamics Study of Cyclic Peptide Nanotube Insertion into a Lipid Bilayer†
The journal of physical chemistry. A, 2009Co-Authors: Hyonseok Hwang, George C. Schatz, Mark A. RatnerAbstract:Coarse-grained (CG) molecular dynamics (MD) simulations are performed to study the insertion of cyclic Peptide Nanotubes into cell membranes and to examine whether cyclic Peptide Nanotubes can function as an ion channel and thereby as an antibacterial agent. To do so, the two coarse-grained (CG) models for lipid molecules and for proteins developed by Marrink et al. (J. Phys. Chem. B 2004, 108, 750) and by Shih et al. (J. Phys. Chem. B 2006, 110, 3674), respectively, were extended and modified. These CG models were verified by performing CG MD and all-atom (AA) MD simulations for a cyclic Peptide Nanotube, 8 × cyclo[(−d-Ala-l-Glu-d-Ala-l-Gln−)2], in water and by comparing the results from the two simulations. Comparison between static and dynamic (water transport) properties obtained from both simulations shows good agreement. To study Nanotube insertion, a CG cyclic Peptide Nanotube, 8 × cyclo[(−Trp-d-Leu−)4], was prepared above the surface of a CG DPPC lipid bilayer, restrained with constraints, and equ...
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steered molecular dynamics studies of the potential of mean force of a na or k ion in a cyclic Peptide Nanotube
Journal of Physical Chemistry B, 2006Co-Authors: Hyonseok Hwang, George C. Schatz, Mark A. RatnerAbstract:Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic Peptide Nanotube, cyclo[-(d-Ala-Glu-d-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the Nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the Nanotube and tha...
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Ion Current Calculations Based on Three Dimensional Poisson−Nernst−Planck Theory for a Cyclic Peptide Nanotube
The journal of physical chemistry. B, 2006Co-Authors: Hyonseok Hwang, George C. Schatz, Mark A. RatnerAbstract:Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic Peptide Nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the Nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the Peptide Nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the Nanotube. The dominant cation and the minimum anion concentrations inside the cyclic Peptide Nanotube suggest that these cyclic Peptide Nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the Peptide Nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.
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ion current calculations based on three dimensional poisson nernst planck theory for a cyclic Peptide Nanotube
Journal of Physical Chemistry B, 2006Co-Authors: Hyonseok Hwang, George C. Schatz, Mark A. RatnerAbstract:Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic Peptide Nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the Nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the Peptide Nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the Nanotube. The dominant cation and the minimum anion concentrations inside the cyclic Peptide Nanotube suggest that these cyclic Peptide Nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the Peptide Nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.
Hyonseok Hwang - One of the best experts on this subject based on the ideXlab platform.
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conformational effects in the transport of glucose through a cyclic Peptide Nanotube a molecular dynamics simulation study
Journal of Physical Chemistry B, 2018Co-Authors: Yongil Seo, George C. Schatz, Yeonho Song, Hyonseok HwangAbstract:The transport behavior of glucose through a cyclic Peptide Nanotube (CPN), composed of 8 × cyclo[-(Trp-d-Leu)4-Gln-d-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-d-glucose, equatorial (4C1) and axial (1C4) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of 1C4 are ma...
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Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study
2018Co-Authors: Yongil Seo, George C. Schatz, Yeonho Song, Hyonseok HwangAbstract:The transport behavior of glucose through a cyclic Peptide Nanotube (CPN), composed of 8 × cyclo[-(Trp-d-Leu)4-Gln-d-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-d-glucose, equatorial (4C1) and axial (1C4) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of 1C4 are maintained during permeation of 1C4 through the CPN. The retention of intramolecular hydrogen bonds and the spherical shape of 1C4 give rise to considerably weaker orientational preferences and higher diffusion coefficients for 1C4 than those of 4C1 inside and outside the CPN. Due to larger dipole moments induced by the alignment of hydroxyl and hydroxymethyl groups, 1C4 has more favorable interactions with the CPN backbone at the channel entrances and inside the channel than 4C1. In the middle of the CPN channel, entropic gains originating from higher orientational and translational degrees of freedom of 1C4 than those of 4C1 also contribute to lower free energy wells for 1C4 inside the CPN. This work reveals that the conformational variation and intramolecular hydrogen bond formation of β-d-glucose can have important effects on the energetics and dynamics of glucose transport through CPNs, providing insight into the translocation mechanism of d-glucose into the cell through glucose transporters (GLUTs) and the dynamics of glucose confined in silica nanochannels. It is also demonstrated that CPNs can indeed facilitate the permeation of small hydrophilic molecules such as glucose and can be utilized as a novel carrier system for hydrophilic drug compounds into the cell
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energetic and dynamic analysis of transport of na and k through a cyclic Peptide Nanotube in water and in lipid bilayers
Journal of Physical Chemistry B, 2016Co-Authors: Yeonho Song, George C. Schatz, Ji Hye Lee, Hoon Hwang, Hyonseok HwangAbstract:Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a cyclic Peptide Nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel a...
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Energetic and Dynamic Analysis of Transport of Na+ and K+ through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers
2016Co-Authors: Yeonho Song, George C. Schatz, Ji Hye Lee, Hoon Hwang, Hyonseok HwangAbstract:Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a cyclic Peptide Nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to a decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. The PMF and diffusivity profiles for Na+ and K+ reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system, while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na+ and K+ ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition, this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly
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Potential of Mean Force Calculations for Ion Selectivity in a Cyclic Peptide Nanotube
Bulletin of the Korean Chemical Society, 2012Co-Authors: Kyu-min Choi, Chan Ho Kwon, Hong Lae Kim, Hyonseok HwangAbstract:, the dehydration freeenergy barriers are not eliminated by an interaction between the anion and the Peptide Nanotube, leading to thehigh free energy barriers in the PMF profile. Calculations of the coordination numbers of the ions with oxygenatoms pertaining to either water molecules or carbonyl groups in the Peptide Nanotube reveal that thestabilization of the cations in the midplane regions of the Nanotube arises from the favorable interaction of thecations with the negatively charged carbonyl oxygens.Key Words : Cyclic Peptide Nanotube, Ion selectivity, Molecular dynamics simulation, Potential of meanforce, Umbrella samplingIntroductionIon channels, which is a class of transmembrane proteins,have drawn great attention because they play a significantrole in nerve and muscle excitation, sensory transduction,and hormone secretion.
George C. Schatz - One of the best experts on this subject based on the ideXlab platform.
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conformational effects in the transport of glucose through a cyclic Peptide Nanotube a molecular dynamics simulation study
Journal of Physical Chemistry B, 2018Co-Authors: Yongil Seo, George C. Schatz, Yeonho Song, Hyonseok HwangAbstract:The transport behavior of glucose through a cyclic Peptide Nanotube (CPN), composed of 8 × cyclo[-(Trp-d-Leu)4-Gln-d-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-d-glucose, equatorial (4C1) and axial (1C4) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of 1C4 are ma...
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Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study
2018Co-Authors: Yongil Seo, George C. Schatz, Yeonho Song, Hyonseok HwangAbstract:The transport behavior of glucose through a cyclic Peptide Nanotube (CPN), composed of 8 × cyclo[-(Trp-d-Leu)4-Gln-d-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-d-glucose, equatorial (4C1) and axial (1C4) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of 1C4 are maintained during permeation of 1C4 through the CPN. The retention of intramolecular hydrogen bonds and the spherical shape of 1C4 give rise to considerably weaker orientational preferences and higher diffusion coefficients for 1C4 than those of 4C1 inside and outside the CPN. Due to larger dipole moments induced by the alignment of hydroxyl and hydroxymethyl groups, 1C4 has more favorable interactions with the CPN backbone at the channel entrances and inside the channel than 4C1. In the middle of the CPN channel, entropic gains originating from higher orientational and translational degrees of freedom of 1C4 than those of 4C1 also contribute to lower free energy wells for 1C4 inside the CPN. This work reveals that the conformational variation and intramolecular hydrogen bond formation of β-d-glucose can have important effects on the energetics and dynamics of glucose transport through CPNs, providing insight into the translocation mechanism of d-glucose into the cell through glucose transporters (GLUTs) and the dynamics of glucose confined in silica nanochannels. It is also demonstrated that CPNs can indeed facilitate the permeation of small hydrophilic molecules such as glucose and can be utilized as a novel carrier system for hydrophilic drug compounds into the cell
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energetic and dynamic analysis of transport of na and k through a cyclic Peptide Nanotube in water and in lipid bilayers
Journal of Physical Chemistry B, 2016Co-Authors: Yeonho Song, George C. Schatz, Ji Hye Lee, Hoon Hwang, Hyonseok HwangAbstract:Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a cyclic Peptide Nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel a...
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Energetic and Dynamic Analysis of Transport of Na+ and K+ through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers
2016Co-Authors: Yeonho Song, George C. Schatz, Ji Hye Lee, Hoon Hwang, Hyonseok HwangAbstract:Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a cyclic Peptide Nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to a decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. The PMF and diffusivity profiles for Na+ and K+ reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system, while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na+ and K+ ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition, this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly
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Coarse-Grained Molecular Dynamics Study of Cyclic Peptide Nanotube Insertion into a Lipid Bilayer†
The journal of physical chemistry. A, 2009Co-Authors: Hyonseok Hwang, George C. Schatz, Mark A. RatnerAbstract:Coarse-grained (CG) molecular dynamics (MD) simulations are performed to study the insertion of cyclic Peptide Nanotubes into cell membranes and to examine whether cyclic Peptide Nanotubes can function as an ion channel and thereby as an antibacterial agent. To do so, the two coarse-grained (CG) models for lipid molecules and for proteins developed by Marrink et al. (J. Phys. Chem. B 2004, 108, 750) and by Shih et al. (J. Phys. Chem. B 2006, 110, 3674), respectively, were extended and modified. These CG models were verified by performing CG MD and all-atom (AA) MD simulations for a cyclic Peptide Nanotube, 8 × cyclo[(−d-Ala-l-Glu-d-Ala-l-Gln−)2], in water and by comparing the results from the two simulations. Comparison between static and dynamic (water transport) properties obtained from both simulations shows good agreement. To study Nanotube insertion, a CG cyclic Peptide Nanotube, 8 × cyclo[(−Trp-d-Leu−)4], was prepared above the surface of a CG DPPC lipid bilayer, restrained with constraints, and equ...
Jianfen Fan - One of the best experts on this subject based on the ideXlab platform.
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separation of chloroform from a dilute solution using a cyclic Peptide Nanotube a molecular dynamics study
Journal of Molecular Graphics & Modelling, 2018Co-Authors: Xin Zhao, Jianfen Fan, Lingling ZhangAbstract:Abstract This work firstly explored the potential application of a cyclic Peptide Nanotube (CPNT) in the separation of chloroform from a dilute solution. Four hydrophobic CPNTs of 8 × (W L )4,5 and 8 × (A L )4,5 all exhibit excellent adsorption characteristics to chloroform. The CPNT diameter, side chain structures and the concentration of chloroform in a solution all affect the adsorption characteristics of chloroform. CHCl3 molecules are overwhelmingly adsorbed on the surfaces of these CPNTs as a cluster, and sporadically reside inside the channels, consistent with the chloroform's potentials of mean force (PMFs) inside and outside the channels. The distribution characteristics, molecular orientations and interactions with the surroundings of chloroform inside and outside four CPNTs embedded in individual dilute CHCl3/water solutions were analyzed in detail, providing referable information of the adsorption characteristics of a hydrophobic CPNT to chloroform.
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Dynamic behavior and selective adsorption of a methanol/water mixture inside a cyclic Peptide Nanotube.
Journal of molecular modeling, 2018Co-Authors: Jianfen Fan, Xin Zhao, Lingling ZhangAbstract:Present molecular dynamics simulations indicate that the methanol component in a methanol/water mixture is more likely to be trapped in a cyclic Peptide Nanotube (CPNT), while water molecules tend to be present at the channel mouths as transient guests. Channel water resides mainly between methanol and the CPNT wall, resulting in a distinct decrease in the H-bond number per channel methanol. Six designed CPNTs with different channel diameters and outer surface characteristics all possess distinct selectivity to methanol over water. Of these, the amphipathic 8 × (AQ)4-CPNT exhibits the best performance. Results in this study provide basic information for the application of a CPNT to enrich methanol from a methanol/water mixture. Graphical Abstract Typical overview of water and methanol molecular distribution in cyclic Peptide Nanotubes.
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transport properties of simple organic molecules in a transmembrane cyclic Peptide Nanotube
Journal of Molecular Modeling, 2016Co-Authors: Jianfen Fan, Mingming Zhang, Pei Pei Weng, Hui Fang LinAbstract:Multiple molecular dynamics simulations have been performed to explore the transport properties of single methane, methanol, and ethanol molecules through the water-filled transmembrane cyclic Peptide Nanotube (CPNT) of \( 8\times {\left(\mathrm{W}\underline {\mathrm{L}}\right)}_4-\mathrm{POPE} \), as well as the potential application of this CPNT in the separation of an alcohol/water mixture. Molecular size and hydrophilicity/hydrophobicity were found to significantly influence molecular diffusion behavior in the channel. Methane and ethanol display more explicit distributions in midplane regions, while methanol mainly occurs in α-plane zones. Methane and ethanol drift faster near an α-plane zone, whereas methanol diffuses uniformly throughout the whole transmembrane region. The dipole orientation of channel methanol is significantly affected by the bare carbonyl groups at the tube mouths and flips mainly in gap 4, whereas the rotation of ethanol is blocked. Ball-shaped hydrophobic methane experiences more flips in gap 4. The PMF (potential of mean force) profiles of the three organic molecules disclose their different diffusion behaviors in the CPNT. Amphiphilic alcohols are able to form direct H-bonds with channel water and the tube. Both single and double water bridges with the tube were observed in the methanol and ethanol systems. The different adsorption behaviors of the alcohols and water in the dehydrated CPNT may lead to the potential application of the CPNT as a means of separating alcohols from water.
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transport behavior of a single ca2 k and na in a water filled transmembrane cyclic Peptide Nanotube
Journal of Chemical Information and Modeling, 2015Co-Authors: Xiliang Yan, Jianfen Fan, Mingming ZhangAbstract:Molecular dynamics simulations have been performed to investigate the transport properties of a single Ca2+, K+, and Na+ in a water-filled transmembrane cyclic Peptide Nanotube (CPNT). Two transmembrane CPNTs, i.e., 8×(WL)n=4,5/POPE (with uniform lengths but various radii), were applied to clarify the dependence of ionic transport properties on the channel radius. A huge energy barrier keeps Ca2+ out of the octa-CPNT, while Na+ and K+ can be trapped in two CPNTs. The dominant electrostatic interaction of a cation with water molecules leads to a high distribution of channel water around the cation and D-defects in the first and last gaps, and significantly reduces the axial diffusion of channel water. Water-bridged interactions were mostly found between the artificially introduced Ca2+ and the framework of the octa-CPNT, and direct coordinations with the tube wall mostly occur for K+ in the octa-CPNT. A cation may drift rapidly or behave lazily in a CPNT. K+ behaves most actively and can visit the whole de...
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Exploring the dynamic behaviors and transport properties of gas molecules in a transmembrane cyclic Peptide Nanotube.
The journal of physical chemistry. B, 2013Co-Authors: Jianfen Fan, Xiliang YanAbstract:The dynamic behaviors and transport properties of O2, CO2, and NH3 molecules through a transmembrane cyclic Peptide Nanotube (CPNT) of 8×cyclo-(WL)4/POPE have been investigated by steered molecular dynamics (SMD) simulations and adaptive biasing force (ABF) samplings. Different external forces are needed for three gas molecules to enter the channel. The periodic change of the pulling force curve for a gas traveling through the channel mainly arises from the regular and periodic arrangement of the composed CP subunits of the CPNT. Radial distribution functions (RDFs) between gas and water disclose the density decrease of channel water, which strongly aggravates the discontinuity of H-bond formation between a gas molecule and the neighboring water. Compared to hardly any H-bond formation between CO2 (or O2) and the framework of the CPNT, NH3 can form abundant H-bonds with the carbonyl/amide groups of the CPNT, leading to a fierce competition to NH3-water H-bonded interactions. In addition to direct H-bonded interactions, all three gases can form water bridges with the tube. The potential profile of mean force coincides with the occurring probability of a gas molecule along the tube axis. The energy barriers at two mouths of the CPNT elucidate the phenomenon that CO2 and O2 are thoroughly confined in the narrow lumen while NH3 can easily go outside the tube. Intermolecular interactions of each gas with channel water and the CPNT framework and the formation of H-bonds and water bridges illuminate the different gas translocation behaviors. The results uncover interesting and comprehensive mechanisms underlying the permeation characteristics of three gas molecules traveling through a transmembrane CPNT.