1
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Moral R, Paul S. Exploring Cyclic Peptide Nanotube Stability Across Diverse Lipid Bilayers and Unveiling Water Transport Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:882-895. [PMID: 38134046 DOI: 10.1021/acs.langmuir.3c03030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Cyclic Peptide Nanotubes (CPNTs) have emerged as compelling candidates for various applications, particularly as nanochannels within lipid bilayers. In this study, the stability of two CPNTs, namely 8 × [(Cys-Gly-Met-Gly)2] and 8 × [(Gly-Leu)4], are comprehensively investigated across different lipid bilayers, including 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a mixed model membrane (POPE/POPG), and a realistic yeast model membrane. The results demonstrate that both CPNTs maintain their tubular structures in all lipid bilayers, with [(Cys-Gly-Met-Gly)2] showing increased stability over an extended period in these lipid membranes. The insertion of CPNTs shows negligible impact on lipid bilayer properties, including area per lipid, volume per lipid, and bilayer thickness. The study demonstrates that the CPNT preserves its two-line water movement pattern within all the lipid membranes, reaffirming their potential as water channels. The MSD curves further reveal that the dynamics of water molecules inside the nanotube are similar for all the bilayer systems with minor differences that arise due to different lipid environments.
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Affiliation(s)
- Rimjhim Moral
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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2
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Kim N, Lee JH, Song Y, Lee JH, Schatz GC, Hwang H. Molecular Dynamics Simulation Study of the Protonation State Dependence of Glutamic Acid Transport through a Cyclic Peptide Nanotube. J Phys Chem B 2023. [PMID: 37369069 DOI: 10.1021/acs.jpcb.3c02285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The effect of the protonation state of glutamic acid on its translocation through cyclic peptide nanotubes (CPNs) was assessed by using molecular dynamics (MD) simulations. Anionic (GLU-), neutral zwitterionic (GLU0), and cationic (GLU+) forms of glutamic acid were selected as three different protonation states for an analysis of energetics and diffusivity for acid transport across a cyclic decapeptide nanotube. Based on the solubility-diffusion model, permeability coefficients for the three protonation states of the acid were calculated and compared with experimental results for CPN-mediated glutamate transport through CPNs. Potential of mean force (PMF) calculations reveal that, due to the cation-selective nature of the lumen of CPNs, GLU-, so-called glutamate, shows significantly high free energy barriers, while GLU+ displays deep energy wells and GLU0 has mild free energy barriers and wells inside the CPN. The considerable energy barriers for GLU- inside CPNs are mainly attributed to unfavorable interactions with DMPC bilayers and CPNs and are reduced by favorable interactions with channel water molecules through attractive electrostatic interactions and hydrogen bonding. Unlike the distinct PMF curves, position-dependent diffusion coefficient profiles exhibit comparable frictional behaviors regardless of the charge status of three protonation states due to similar confined environments imposed by the lumen of the CPN. The calculated permeability coefficients for the three protonation states clearly demonstrate that glutamic acid has a strong protonation state dependence for its transport through CPNs, as determined by the energetics rather than the diffusivity of the protonation state. In addition, the permeability coefficients also imply that GLU- is unlikely to pass through a CPN due to the high energy barriers inside the CPN, which is in disagreement with experimental measurements, where a considerable amount of glutamate permeating through the CPN was detected. To resolve the discrepancy between this work and the experimental observations, several possibilities are proposed, including a large concentration gradient of glutamate between the inside and outside of lipid vesicles and bilayers in the experiments, the glutamate activity difference between our MD simulations and experiments, an overestimation of energy barriers due to the artifacts imposed in MD simulations, and/or finally a transformation of the protonation state from GLU- to GLU0 to reduce the energy barriers. Overall, our study demonstrates that the protonation state of glutamic acid has a strong effect on the transport of the acid and suggests a possible protonation state change for glutamate permeating through CPNs.
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Affiliation(s)
- Namho Kim
- Department of Biochemistry, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Ji Hye Lee
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Yeonho Song
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Jeong-Hyung Lee
- Department of Biochemistry, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - George C Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Hyonseok Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
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3
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Lu Q, Regan DP, Barlow DE, Fears KP. Antimicrobial efficacy of cyclic α- and β-peptides incorporated in polyurethane coatings. Biointerphases 2023; 18:031008. [PMID: 37289032 DOI: 10.1116/6.0002515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023] Open
Abstract
Microbial growth on surfaces poses health concerns and can accelerate the biodegradation of engineered materials and coatings. Cyclic peptides are promising agents to combat biofouling because they are more resistant to enzymatic degradation than their linear counterparts. They can also be designed to interact with extracellular targets and intracellular targets and/or self-assemble into transmembrane pores. Here, we determine the antimicrobial efficacy of two pore-forming cyclic peptides, α-K3W3 and β-K3W3, against bacterial and fungal liquid cultures and their capacity to inhibit biofilm formation on coated surfaces. These peptides display identical sequences, but the additional methylene group in the peptide backbone of β-amino acids results in a larger diameter and an enhancement in the dipole moment. In liquid cultures, β-K3W3 exhibited lower minimum inhibitory concentration values and greater microbicidal power in reducing the number of colony forming units (CFUs) when exposed to a gram-positive bacterium, Staphylococcus aureus, and two fungal strains, Naganishia albida and Papiliotrema laurentii. To evaluate the efficacy against the formation of fungal biofilms on painted surfaces, cyclic peptides were incorporated into polyester-based thermoplastic polyurethane. The formation of N. albida and P. laurentii microcolonies (105 per inoculation) for cells extracted from coatings containing either peptide could not be detected after a 7-day exposure. Moreover, very few CFUs (∼5) formed after 35 days of repeated depositions of freshly cultured P. laurentii every 7 days. In contrast, the number of CFUs for cells extracted from the coating without cyclic peptides was >8 log CFU.
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Affiliation(s)
- Qin Lu
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
| | - Daniel P Regan
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
| | - Daniel E Barlow
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
| | - Kenan P Fears
- Chemistry Division, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC 20375
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4
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Agles AA, Bourg IC. Structure-Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca). J Phys Chem B 2023; 127:1828-1841. [PMID: 36791328 PMCID: PMC10159261 DOI: 10.1021/acs.jpcb.2c07129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/31/2023] [Indexed: 02/17/2023]
Abstract
Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities─and their impacts on environmental processes─requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca-Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ∼0.6 nm between alginate strands.
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Affiliation(s)
- Avery A. Agles
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Ian C. Bourg
- Department
of Civil and Environmental Engineering and High Meadows Environmental
Institute, Princeton University, Princeton, New Jersey 08544, United States
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5
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Bellotto O, D'Andrea P, Marchesan S. Nanotubes and water-channels from self-assembling dipeptides. J Mater Chem B 2023. [PMID: 36790014 DOI: 10.1039/d2tb02643k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging.
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Affiliation(s)
- Ottavia Bellotto
- Chem. Pharm. Sc. Dept., University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy.
| | - Paola D'Andrea
- Life Sc. Dept., University of Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Silvia Marchesan
- Chem. Pharm. Sc. Dept., University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy. .,INSTM, Unit of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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6
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Moral R, Paul S. Influence of salt and temperature on the self-assembly of cyclic peptides in water: a molecular dynamics study. Phys Chem Chem Phys 2023; 25:5406-5422. [PMID: 36723368 DOI: 10.1039/d2cp05160e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is found in the literature that cyclic peptides (CPs) are able to self-assemble in water to form cyclic peptide nanotubes (CPNTs) and are used extensively in the field of nanotechnology. Several factors influence the formation and stability of these nanotubes in water. However, an extensive study of the contribution of several important factors is still lacking. The purpose of this study is to explore the effect of temperature and salt (NaCl) on the association tendency of CPs. Furthermore, the self-association behavior of CPs in aqueous solutions at various temperatures is also thoroughly discussed. Cyclo-[(Asp-D-Leu-Lys-D-Leu)2] is considered for this study and a series of classical molecular dynamics (MD) simulations at three different temperatures, viz. 280 K, 300 K, and 320 K, both in pure water and in NaCl solutions of different concentrations are carried out. The calculations of radial distribution functions, preferential interaction parameters, cluster formation and hydrogen bonding properties suggest a strong influence of NaCl concentration on the association propensity of CPs. Low NaCl concentration hinders CP association while high NaCl concentration facilitates the association of CPs. Besides this, the association of CPs is found to be enhanced at low temperature. Furthermore, the thermodynamics of CP association is predominantly found to be enthalpy driven in both the presence and absence of salt. No crossover between enthalpy and entropy in CP association is observed. In addition, the MM-GBSA method is used to investigate the binding free energies of the CP rings that self-assembled to form nanotube like structures at all three temperatures.
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Affiliation(s)
- Rimjhim Moral
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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7
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Song Q, Cheng Z, Kariuki M, Hall SCL, Hill SK, Rho JY, Perrier S. Molecular Self-Assembly and Supramolecular Chemistry of Cyclic Peptides. Chem Rev 2021; 121:13936-13995. [PMID: 33938738 PMCID: PMC8824434 DOI: 10.1021/acs.chemrev.0c01291] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 01/19/2023]
Abstract
This Review focuses on the establishment and development of self-assemblies governed by the supramolecular interactions between cyclic peptides. The Review first describes the type of cyclic peptides able to assemble into tubular structures to form supramolecular cyclic peptide nanotubes. A range of cyclic peptides have been identified to have such properties, including α-peptides, β-peptides, α,γ-peptides, and peptides based on δ- and ε-amino acids. The Review covers the design and functionalization of these cyclic peptides and expands to a recent advance in the design and application of these materials through their conjugation to polymer chains to generate cyclic peptide-polymer conjugates nanostructures. The Review, then, concentrates on the challenges in characterizing these systems and presents an overview of the various analytical and characterization techniques used to date. This overview concludes with a critical survey of the various applications of the nanomaterials obtained from supramolecular cyclic peptide nanotubes, with a focus on biological and medical applications, ranging from ion channels and membrane insertion to antibacterial materials, anticancer drug delivery, gene delivery, and antiviral applications.
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Affiliation(s)
- Qiao Song
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Zihe Cheng
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Maria Kariuki
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Sophie K. Hill
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Julia Y. Rho
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Sébastien Perrier
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick Medical
School, University of Warwick, Coventry CV4 7AL, U.K.
- Faculty
of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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8
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Silk MR, Price JR, Mohanty B, Leiros HKS, Lund BA, Thompson PE, Chalmers DK. Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics. Chemistry 2021; 27:14489-14500. [PMID: 34415083 DOI: 10.1002/chem.202102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/07/2022]
Abstract
Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by 1 H-D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.
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Affiliation(s)
- Mitchell R Silk
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jason R Price
- Australian Synchrotron, The Australian Nuclear Science and Technology Organisation (ANSTO), 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Bjarte A Lund
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
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9
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Gong T, Fan J. Study on the Assembly Mechanisms and Transport Properties of Transmembrane End-Charged Cyclic Peptide Nanotubes. J Chem Inf Model 2021; 61:2754-2765. [PMID: 34128668 DOI: 10.1021/acs.jcim.1c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, two end-charged cyclic peptide nanotubes (CPNTs) embedded in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) were designed to simulate transmembrane ion channels. Density functional theory (DFT) computations at the level of M06-2X/6-31G give different assembling modes of the negatively charged ELWL-CPNT and positively charged RLWL-CPNT as (L-L)(D-L)(D-D)(L-L)(D-D)(L-L)(D-D) and (D-D)(L-L)(D-D)(L-L)(D-D)(L-L)(D-D), respectively. Molecular dynamics (MD) simulations indicate that a charge at a CPNT end obviously affects the structure of the channel water chain and the diffusion behavior of K+. The regions with the highest probability of H-bond defects in the channel water chains are gap5 and gap2 in ELWL/POPE-CPNT and RLWL/POPE-CPNT, respectively. K+ can easily enter either CPNT by desolvation, and behaves more actively in RLWL/POPE-CPNT, shuttling rapidly and frequently between an α-plane zone and an adjacent midplane region. Results of this work reveal that a charge at the end of an ionic channel may significantly alter the transport characteristics of the channel.
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Affiliation(s)
- Ting Gong
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
| | - Jianfen Fan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
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10
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Calvelo M, Lynch CI, Granja JR, Sansom MSP, Garcia-Fandiño R. Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes. ACS NANO 2021; 15:7053-7064. [PMID: 33739081 PMCID: PMC8485350 DOI: 10.1021/acsnano.1c00155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/23/2023]
Abstract
Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.
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Affiliation(s)
- Martin Calvelo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Charlotte I. Lynch
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Juan R. Granja
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Rebeca Garcia-Fandiño
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
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11
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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12
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Zelenovskiy PS, Domingues EM, Slabov V, Kopyl S, Ugolkov VL, Figueiredo FML, Kholkin AL. Efficient Water Self-Diffusion in Diphenylalanine Peptide Nanotubes. ACS APPLIED MATERIALS & INTERFACES 2020; 12:27485-27492. [PMID: 32463652 DOI: 10.1021/acsami.0c03658] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanotubes of self-assembled dipeptides exemplified by diphenylalanine (FF) demonstrate a wide range of useful functional properties, such as high Young's moduli, strong photoluminescence, remarkable piezoelectricity and pyroelectricity, optical waveguiding, etc., and became the object of intensive research due to their ability to combine electronic and biological functions in the same material. Two types of nanoconfined water molecules (bound water directly interacting with the peptide backbone and free water located inside nanochannels) are known to play a key role in the self-assembly of FF. Bound water provides its structural integrity, whereas movable free water influences its functional response. However, the intrinsic mechanism of water motion in FF nanotubes remained elusive. In this work, we study the sorption properties of FF nanotubes directly considering them as a microporous material and analyze the free water self-diffusion at different temperatures. We found a change in the regime of free water diffusion, which is attributed to water cluster size in the nanochannels. Small clusters of less than five molecules per unit cell exhibit ballistic diffusion, whereas, for larger clusters, Fickian diffusion occurs. External conditions of around 40% relative humidity at 30 °C enable the formation of such large clusters, for which the diffusion coefficient reaches 1.3 × 10-10 m2 s-1 with an activation energy of 20 kJ mol-1, which increases to attain 3 × 10-10 m2 s-1 at 65 °C. The observed peculiarities of water self-diffusion along the narrow FF nanochannels endow this class of materials with a new functionality. Possible applications of FF nanotubes in nanofluidic devices are discussed.
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Affiliation(s)
- Pavel S Zelenovskiy
- Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Eddy M Domingues
- Department of Materials Engineering and Ceramics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Vladislav Slabov
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Svitlana Kopyl
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Valery L Ugolkov
- Institute of Silicate Chemistry, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Filipe M L Figueiredo
- Department of Materials Engineering and Ceramics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Andrei L Kholkin
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
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13
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Maroli N, Kolandaivel P. Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach. J Biomol Struct Dyn 2019; 38:186-199. [DOI: 10.1080/07391102.2019.1570341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nikhil Maroli
- Computational Biology Division, DRDO BU CLS, Coimbatore, India
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14
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Zhang L, Fan J, Qu M. MD Simulations on the Transport Behaviors of Mixed Na+ and Li+ in a Transmembrane Cyclic Peptide Nanotube under an Electric Field. J Chem Inf Model 2018; 59:170-180. [DOI: 10.1021/acs.jcim.8b00593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lingling Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jianfen Fan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Mengnan Qu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
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15
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Liu J, Zhang H, Li Y, Liu Z. Disorder in Aqueous Solutions and Peak Broadening in X-ray Photoelectron Spectroscopy. J Phys Chem B 2018; 122:10600-10606. [PMID: 30359023 DOI: 10.1021/acs.jpcb.8b10325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The microscopic structure and photoelectron spectra of an aqueous solution are investigated with ab initio molecular dynamics simulations and ambient pressure X-ray photoelectron spectroscopy (AP-XPS). The simulation results show that the structural fluctuations in an aqueous solution can lead to remarkable peak broadening (∼1 eV) of ionic species, which is in good agreement with the results from AP-XPS experiments. We find that this broadening of the XPS peaks can be directly correlated with the local structural fluctuations in the aqueous solution, such as the evolution of solvation shells. This work demonstrates that the rich dynamics of solvation shells in aqueous solutions can be revealed by combining advanced simulations with in situ AP-XPS, and may stimulate new developments in the in situ XPS characterization of complex electrochemical reactions.
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Affiliation(s)
- Jian Liu
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China.,State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology , Chinese Academy of Sciences , Shanghai 200050 , China
| | - Hui Zhang
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology , Chinese Academy of Sciences , Shanghai 200050 , China
| | - Yimin Li
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China.,State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology , Chinese Academy of Sciences , Shanghai 200050 , China
| | - Zhi Liu
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 201210 , China.,State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology , Chinese Academy of Sciences , Shanghai 200050 , China
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16
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Hsieh WH, Liaw J. Applications of cyclic peptide nanotubes (cPNTs). J Food Drug Anal 2018; 27:32-47. [PMID: 30648586 PMCID: PMC9298616 DOI: 10.1016/j.jfda.2018.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022] Open
Abstract
Self-assembled cyclic peptide nanotubes (cPNTs) have recently drawn particular attention as one of the most intriguing nanostructures in the field of nanotechnology. Given their unique features including high surface area, increased drug loading, environmental stability, enhanced permeation, and modifiable drug release, these hollow tubular structures can be constructed with cyclic di-, tri-, tetra-, hexa-, octa-, and decapeptides with various amino acid sequences, enantiomers, and functionalized side chains and can be applied for antiviral and antibacterial drugs, drug delivery and gene delivery vectors, organic electronic devices, and ionic or molecular channels. Recent publications have presented promising results regarding the use of cPNTs as drugs or biomedical devices. However, there is an urgent need for the further in vivo nanotoxicity and safety testing of these nanotubes to evaluate their suitability in different fields.
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Affiliation(s)
- Wei-Hsien Hsieh
- Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Jiahorng Liaw
- Department of Pharmaceutics, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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17
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Seo Y, Song Y, Schatz GC, Hwang H. Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study. J Phys Chem B 2018; 122:8174-8184. [DOI: 10.1021/acs.jpcb.8b05591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yongil Seo
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Yeonho Song
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - George C. Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hyonseok Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
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18
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Dynamic behavior and selective adsorption of a methanol/water mixture inside a cyclic peptide nanotube. J Mol Model 2018; 24:184. [PMID: 29959542 DOI: 10.1007/s00894-018-3712-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/07/2018] [Indexed: 11/27/2022]
Abstract
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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19
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Zhao X, Fan JF, Si XL, Zhang LL, Qu MN. Separation of chloroform from a dilute solution using a cyclic peptide nanotube: A molecular dynamics study. J Mol Graph Model 2018; 83:74-83. [PMID: 29778743 DOI: 10.1016/j.jmgm.2018.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 12/07/2022]
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 × (WL)4,5 and 8 × (AL)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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Affiliation(s)
- Xin Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Jian Fen Fan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Xia Lan Si
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Ling Ling Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Meng Nan Qu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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20
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Li C, Meckler SM, Smith ZP, Bachman JE, Maserati L, Long JR, Helms BA. Engineered Transport in Microporous Materials and Membranes for Clean Energy Technologies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1704953. [PMID: 29315857 DOI: 10.1002/adma.201704953] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/12/2017] [Indexed: 05/25/2023]
Abstract
Many forward-looking clean-energy technologies hinge on the development of scalable and efficient membrane-based separations. Ongoing investment in the basic research of microporous materials is beginning to pay dividends in membrane technology maturation. Specifically, improvements in membrane selectivity, permeability, and durability are being leveraged for more efficient carbon capture, desalination, and energy storage, and the market adoption of membranes in those areas appears to be on the horizon. Herein, an overview of the microporous materials chemistry driving advanced membrane development, the clean-energy separations employing them, and the theoretical underpinnings tying membrane performance to membrane structure across multiple length scales is provided. The interplay of pore architecture and chemistry for a given set of analytes emerges as a critical design consideration dictating mass transport outcomes. Opportunities and outstanding challenges in the field are also discussed, including high-flux 2D molecular-sieving membranes, phase-change adsorbents as performance-enhancing components in composite membranes, and the need for quantitative metrologies for understanding mass transport in heterophasic materials and in micropores with unusual chemical interactions with analytes of interest.
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Affiliation(s)
- Changyi Li
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA, 94720, USA
| | - Stephen M Meckler
- Department of Chemistry, The University of California, Berkeley, CA, 94720, USA
| | - Zachary P Smith
- Department of Chemical Engineering, The Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jonathan E Bachman
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA, 94720, USA
| | - Lorenzo Maserati
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Jeffrey R Long
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA, 94720, USA
- Department of Chemistry, The University of California, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Brett A Helms
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
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21
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Lin H, Fan J, Weng P, Si X, Zhao X. Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface. J Phys Chem A 2017; 121:6863-6873. [PMID: 28836781 DOI: 10.1021/acs.jpca.7b02465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, nine kinds of amino acid residues, i.e., alanine (A), leucine (L), valine (V), isoleucine (I), tryptophan (W), glutamine (Q), threonine (T), serine (S), and cysteine (C), were selected to construct seven cyclic peptide nanotubes (CPNTs) with diverse hydrophilic/hydrophobic external surfaces, which were further separately inserted at the water/hexane interface to investigate their microstructures and interfacial properties. Molecular dynamics (MD) simulations reveal that all the CPNTs except the QT- and VL-CPNTs have different degrees of tilt, fracture, and shedding at the interface. The end-CPs are more susceptible to the effect of the surroundings than the mid-CPs. The interactions of individual CP subunits with the neighborings disclose the firmness of the mid-CPs and the dissociation of the end-CPs. The results indicate that a hydrophobic CPNT is prone to stay at the interface, while a hydrophilic CPNT easily enters the water phase, resulting in many H-bonds with water. Results in this work enrich the dynamic properties of a hydrophilic/hydrophobic CPNT at the biphase interface at the atomic level.
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Affiliation(s)
- Huifang Lin
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou 215123, People's Republic of China
| | - Jianfen Fan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou 215123, People's Republic of China
| | - Peipei Weng
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou 215123, People's Republic of China
| | - Xialan Si
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou 215123, People's Republic of China
| | - Xin Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University , Suzhou 215123, People's Republic of China
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22
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Maroli N, Kolandaivel P. Structure, stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)3]) cyclic peptide nanotube: a molecular dynamics study. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1366653] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nikhil Maroli
- Computational Biology Division, DRDO BU CLS, Tamil Nadu, India
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23
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Yang S, Ding H, Wang R, Dai X, Shi X, Qiao Y. Molecular dynamics simulation studies of transmembrane transport of chemical components in Chinese herbs and the function of platycodin D in a biological membrane. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2017. [DOI: 10.1016/j.jtcms.2017.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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24
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Song Y, Lee JH, Hwang H, Schatz GC, Hwang H. Energetic and Dynamic Analysis of Transport of Na+ and K+ through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers. J Phys Chem B 2016; 120:11912-11922. [DOI: 10.1021/acs.jpcb.6b09638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yeonho Song
- Department of Chemistry and Institute for Molecular Science and Fusion
Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Ji Hye Lee
- Department of Chemistry and Institute for Molecular Science and Fusion
Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Hoon Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion
Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - George C. Schatz
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hyonseok Hwang
- Department of Chemistry and Institute for Molecular Science and Fusion
Technology, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
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25
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Different transport behaviors of NH4 + and NH3 in transmembrane cyclic peptide nanotubes. J Mol Model 2016; 22:233. [DOI: 10.1007/s00894-016-3081-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
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26
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Xu J, Fan JF, Zhang MM, Weng PP, Lin HF. Transport properties of simple organic molecules in a transmembrane cyclic peptide nanotube. J Mol Model 2016; 22:107. [DOI: 10.1007/s00894-016-2965-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/15/2016] [Indexed: 01/21/2023]
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27
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Li R, Fan J, Li H, Yan X, Yu Y. Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes. J Chem Phys 2015; 143:015101. [DOI: 10.1063/1.4923010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rui Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jianfen Fan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Hui Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Xiliang Yan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Yi Yu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
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28
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Yu Y, Fan J, Yan X, Xu J, Zhang M. Tilt Behavior of an Octa-Peptide Nanotube in POPE and Affects on the Transport Characteristics of Channel Water. J Phys Chem A 2015; 119:4723-34. [DOI: 10.1021/acs.jpca.5b01380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yi Yu
- College
of Chemistry, Chemical
Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jianfen Fan
- College
of Chemistry, Chemical
Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Xiliang Yan
- College
of Chemistry, Chemical
Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jian Xu
- College
of Chemistry, Chemical
Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Mingming Zhang
- College
of Chemistry, Chemical
Engineering and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
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29
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Yan X, Fan J, Yu Y, Xu J, Zhang M. Transport behavior of a single Ca(2+), K(+), and Na(+) in a water-filled transmembrane cyclic peptide nanotube. J Chem Inf Model 2015; 55:998-1011. [PMID: 25894098 DOI: 10.1021/acs.jcim.5b00025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations have been performed to investigate the transport properties of a single Ca(2+), 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 Ca(2+) 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 Ca(2+) 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 deca-CPNT quickly. The first solvation shells of Ca(2+) and Na(+) are basically saturated in two CPNTs, while the hydration of K(+) is incomplete in the octa-CPNT. The solvation structure of Ca(2+) in the octa-CPNT is most stable, while that of K(+) in the deca-CPNT is most labile. Increasing the channel radius induces numerous interchange attempts between the first-shell water molecules of a cation and the ones in the outer region, especially for the K(+) system.
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Affiliation(s)
- Xiliang Yan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
| | - Jianfen Fan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
| | - Yi Yu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
| | - Jian Xu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
| | - Mingming Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, People's Republic of China
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30
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Ruiz L, Wu Y, Keten S. Tailoring the water structure and transport in nanotubes with tunable interiors. NANOSCALE 2015; 7:121-132. [PMID: 25407508 DOI: 10.1039/c4nr05407e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Self-assembly of cyclic peptide nanotubes (CPNs) in polymer thin films has opened up the possibility of creating separation membranes with tunable nanopores that can differentiate molecules at the sub-nanometer level. While it has been demonstrated that the interior chemistry of the CPNs can be tailored by inserting functional groups in the nanopore lumen (mCPNs), a design strategy for picking the chemical modifications that lead to particular transport properties has not been established. Drawing from the knowledgebase of functional groups in natural amino acids, here we use molecular dynamics simulations to elucidate how bioinspired mutations influence the transport of water through mCPNs. We show that, at the nanoscale, factors besides the pore size, such as electrostatic interactions and steric effects, can dramatically change the transport properties. We recognize a novel asymmetric structure of water under nanoconfinement inside the chemically functionalized nanotubes and identify that the small non-polar glycine-mimic groups that minimize the steric constraints and confer a hydrophobic character to the nanotube interior are the fastest transporters of water. Our computationally developed experiments on a realistic material system circumvent synthetic challenges, and lay the foundation for bioinspired principles to tailor artificial nanochannels for separation applications such as desalination, ion-exchange and carbon capture.
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Affiliation(s)
- Luis Ruiz
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3109, USA.
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31
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Li H, Fan JF, Li R, Yu Y, Yan XL. Molecular dynamics studies on the influences of a gradient electric field on the water chain in a peptide nanotube. J Mol Model 2014; 20:2370. [DOI: 10.1007/s00894-014-2370-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/29/2014] [Indexed: 11/28/2022]
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32
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Li R, Fan J, Li H, Yan X, Yu Y. Exploring the Dynamic Behaviors and Transport Properties of Gas Molecules in a Transmembrane Cyclic Peptide Nanotube. J Phys Chem B 2013; 117:14916-27. [DOI: 10.1021/jp408769u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rui Li
- College of Chemistry, Chemical Engineering
and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jianfen Fan
- College of Chemistry, Chemical Engineering
and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Hui Li
- College of Chemistry, Chemical Engineering
and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Xiliang Yan
- College of Chemistry, Chemical Engineering
and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
| | - Yi Yu
- College of Chemistry, Chemical Engineering
and Materials Science, Soochow University, Suzhou 215123, People’s Republic of China
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33
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Song X, Fan J, Liu D, Li H, Li R. Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube. J Mol Model 2013; 19:4271-82. [DOI: 10.1007/s00894-013-1899-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 05/26/2013] [Indexed: 11/24/2022]
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34
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Zhang QL, Jiang WZ, Liu J, Miao RD, Sheng N. Water transport through carbon nanotubes with the radial breathing mode. PHYSICAL REVIEW LETTERS 2013; 110:254501. [PMID: 23829739 DOI: 10.1103/physrevlett.110.254501] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Molecular dynamics simulations are performed to investigate the water permeation across the single-walled carbon nanotube with the radial breathing mode (RBM) vibration. It is found that the RBM can play a significant role in breaking the hydrogen bonds of the water chain, accordingly increasing the net flux dramatically, and reducing drastically the average number of water molecules inside the tube with the frequency ranging from 5000 to 11 000 GHz, while far away from this frequency region the transport properties of water molecules are almost unaffected by the RBM. This phenomenon can be understood as the resonant response of the water molecule chain to the RBM. Our findings are expected to be helpful for the design of high-flux nanochannels and the understanding of biological activities, especially the water channelling.
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Affiliation(s)
- Qi-Lin Zhang
- Department of Physics, Southeast University, Nanjing 211189, China
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35
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Molecular dynamics simulation of water conduction within carbon nanotube. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-012-5492-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Vijayaraj R, Van Damme S, Bultinck P, Subramanian V. Theoretical studies on the transport mechanism of 5-fluorouracil through cyclic peptide based nanotubes. Phys Chem Chem Phys 2013; 15:1260-70. [DOI: 10.1039/c2cp42038d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation. J Mol Model 2012; 19:601-11. [DOI: 10.1007/s00894-012-1588-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
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38
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Vijayaraj R, Van Damme S, Bultinck P, Subramanian V. Molecular Dynamics and Umbrella Sampling Study of Stabilizing Factors in Cyclic Peptide-Based Nanotubes. J Phys Chem B 2012; 116:9922-33. [DOI: 10.1021/jp303418a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Vijayaraj
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai
600 020, India
- Department
of Inorganic and
Physical Chemistry, Ghent University, Krijgslaan
281(S3), Gent 9000, Belgium
| | - S. Van Damme
- Department
of Inorganic and
Physical Chemistry, Ghent University, Krijgslaan
281(S3), Gent 9000, Belgium
| | - P. Bultinck
- Department
of Inorganic and
Physical Chemistry, Ghent University, Krijgslaan
281(S3), Gent 9000, Belgium
| | - V. Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai
600 020, India
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39
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Liu J, Fan J, Cen M, Song X, Liu D, Zhou W, Liu Z, Yan J. Dependences of Water Permeation through Cyclic Octa-peptide Nanotubes on Channel Length and Membrane Thickness. J Chem Inf Model 2012; 52:2132-8. [DOI: 10.1021/ci300185c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jian Liu
- Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, People’s Republic of China
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40
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Hu XB, Chen Z, Tang G, Hou JL, Li ZT. Single-Molecular Artificial Transmembrane Water Channels. J Am Chem Soc 2012; 134:8384-7. [DOI: 10.1021/ja302292c] [Citation(s) in RCA: 341] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiao-Bo Hu
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Zhenxia Chen
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Gangfeng Tang
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Jun-Li Hou
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Zhan-Ting Li
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
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41
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Vijayaraj R, Van Damme S, Bultinck P, Subramanian V. Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition. Phys Chem Chem Phys 2012; 14:15135-44. [DOI: 10.1039/c2cp42030a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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García-Fandiño R, Amorín M, Castedo L, Granja JR. Transmembrane ion transport by self-assembling α,γ-peptide nanotubes. Chem Sci 2012. [DOI: 10.1039/c2sc21068a] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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