1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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
| | | |
Collapse
|
6
|
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
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Farrokhpour H, Mansouri A, Rajabi AR, Najafi Chermahini A. The effect of the diameter of cyclic peptide nanotube on its chirality discrimination. J Biomol Struct Dyn 2018; 37:691-701. [DOI: 10.1080/07391102.2018.1436090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology , Isfahan, 84156-83111, Iran
| | - Alireza Mansouri
- Department of Chemistry, Isfahan University of Technology , Isfahan, 84156-83111, Iran
| | - Ahmad Reza Rajabi
- Department of Chemistry, Isfahan University of Technology , Isfahan, 84156-83111, Iran
| | | |
Collapse
|
9
|
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
| | | |
Collapse
|
10
|
|
11
|
Alsina MA, Gaillard JF, Keten S. Conformational changes during permeation of Na + through a modified cyclic peptide nanotube promote energy landscape roughness. Phys Chem Chem Phys 2016; 18:31698-31710. [PMID: 27841425 DOI: 10.1039/c6cp06585f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Using a metadynamics approach, we investigate the potential of mean force for Na+ permeation inside a cyclic peptide nanotube (CPN) with modified interior as a function of ion position, coordination number, and lumen chemistry. We show that functionalizing the lumen of a CPN with a methyl-benzoic acid group introduces non-periodic variations in the internal energy of the nanotube, which dictate the overall free energy roughness during the permeation of Na+. These non-periodic variations arise from the structural dynamics of the functional group, where changes in the dihedral angles induced by the proximity of the ion give rise to conformational changes that increase landscape roughness and thereby decrease transport rate. Our computational framework emphasizes the advantages of using the coordination number as a collective variable to investigate the available conformations during ion permeation through CPNs, and reveals new structure-function relations for chemically tunable CPNs, paving the way for rational design of nano-porous systems with tunable selectivity and flux.
Collapse
Affiliation(s)
- Marco A Alsina
- Department of Civil & Environmental Engineering, 2145 Sheridan Road, Evanston, IL 60208-3109, USA.
| | - Jean-François Gaillard
- Department of Civil & Environmental Engineering, 2145 Sheridan Road, Evanston, IL 60208-3109, USA.
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Tech A133, Evanston, IL 60208-3109, USA.
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
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]
|
14
|
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Li X, Yang K, Su J, Guo H. Water transport through a transmembrane channel formed by arylene ethynylene macrocycles. RSC Adv 2014. [DOI: 10.1039/c3ra43545h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
17
|
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
| |
Collapse
|
18
|
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]
|