1
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Bystrov VS. Molecular self-assembled helix peptide nanotubes based on some amino acid molecules and their dipeptides: molecular modeling studies. J Mol Model 2024; 30:257. [PMID: 38976043 DOI: 10.1007/s00894-024-05995-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
CONTEXT The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides-the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed. METHOD The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree-Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree-Fock (RHF) and in the unrestricted Hartree-Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak-Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO - EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package.
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Affiliation(s)
- Vladimir S Bystrov
- Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290, Pushchino, Moscow Region, Russia.
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2
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Zelenovskii P, Soares M, Bornes C, Marin-Montesinos I, Sardo M, Kopyl S, Kholkin A, Mafra L, Figueiredo F. Detection of helical water flows in sub-nanometer channels. Nat Commun 2024; 15:5516. [PMID: 38951494 PMCID: PMC11217464 DOI: 10.1038/s41467-024-49878-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/21/2024] [Indexed: 07/03/2024] Open
Abstract
Nanoscale flows of liquids can be revealed in various biological processes and underlie a wide range of nanofluidic applications. Though the integral characteristics of these systems, such as permeability and effective diffusion coefficient, can be measured in experiments, the behaviour of the flows within nanochannels is still a matter of speculation. Herein, we used a combination of quadrupolar solid-state NMR spectroscopy, computer simulation, and dynamic vapour sorption measurements to analyse water diffusion inside peptide nanochannels. We detected a helical water flow coexisting with a conventional axial flow that are independent of each other, immiscible, and associated with diffusion coefficients that may differ up to 3 orders of magnitude. The trajectory of the helical flow is dictated by the screw-like distribution of ionic groups within the channel walls, while its flux is governed by external water vapour pressure. Similar flows may occur in other types of nanochannels containing helicoidally distributed ionic groups and be exploited in various nanofluidic lab-on-a-chip devices.
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Affiliation(s)
- Pavel Zelenovskii
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, 3810-193, Portugal.
| | - Márcio Soares
- Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Carlos Bornes
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, 128 43, Prague, Czech Republic
| | - Ildefonso Marin-Montesinos
- Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Mariana Sardo
- Department of Chemistry & 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, Aveiro, 3810-193, Portugal
| | - Andrei Kholkin
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Luís Mafra
- Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Filipe Figueiredo
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, 3810-193, Portugal
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3
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Alikin D, Yuzhakov V, Semiletova L, Slabov V, Kuznetsov D, Gimadeeva L, Shur V, Kopyl S, Kholkin A. Piezoactive Bioorganic Diphenylalanine Films: Mechanism of Phase Formation. ACS Biomater Sci Eng 2023; 9:6715-6723. [PMID: 38032859 DOI: 10.1021/acsbiomaterials.3c01507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Self-organized peptides are unique materials with various applications in biology, medicine, and nanotechnology. Many of these applications require fabrication of homogeneous thin films having high piezoelectric effect and sufficiently low roughness. Recently, a facile method for the controlled deposition of flat solid films of the most studied peptide, diphenylalanine (FF), has been proposed, which is based on the crystallization of FF in the amorphous phase under the action of water vapor. This method is very advantageous compared with crystallization from a liquid phase reported previously. Here, we thoroughly investigate the mechanism of solid-state transformation from the amorphous to crystalline phase. The study revealed that the process proceeds in two distinct stages, maintaining clamped condition of self-assembling building blocks that preserve the films' morphology and high piezoelectric activity. We emphasize the critical role of water diffusion that governs two-dimensional growth of crystalline domains in FF films, merging in very dense, flat, and homogeneous films. These findings open a wide perspective for using this methodology for the direct fabrication of biofilms from the amorphous phase. We thus expect the application of these films to various nanotechnological applications of self-assembled structures.
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Affiliation(s)
- Denis Alikin
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Vladimir Yuzhakov
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Larisa Semiletova
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Vladislav Slabov
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro 3810-193, Portugal
| | - Dmitrii Kuznetsov
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Lubov Gimadeeva
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Vladimir Shur
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - Svitlana Kopyl
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro 3810-193, Portugal
| | - Andrei Kholkin
- School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro 3810-193, Portugal
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4
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Chen J, Qiu Z, Huang J. Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes. ACS OMEGA 2023; 8:42936-42950. [PMID: 38024738 PMCID: PMC10652825 DOI: 10.1021/acsomega.3c06071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/22/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.
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Affiliation(s)
- Jinfeng Chen
- College
of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Key
Laboratory of Structural Biology of Zhejiang Province, School of Life
Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
AI Therapeutics Lab, Westlake Laboratory
of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Zongyang Qiu
- Key
Laboratory of Structural Biology of Zhejiang Province, School of Life
Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
AI Therapeutics Lab, Westlake Laboratory
of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- Key
Laboratory of Structural Biology of Zhejiang Province, School of Life
Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake
AI Therapeutics Lab, Westlake Laboratory
of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
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5
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Alves WA, King GM, Guha S. Looking into a crystal ball: printing and patterning self-assembled peptide nanostructures. NANOSCALE 2022; 14:15607-15616. [PMID: 36268821 DOI: 10.1039/d2nr03750e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The solution processability of organic semiconductors and conjugated polymers along with the advent of nanomaterials as conducting inks have revolutionized next-generation flexible consumer electronics. Another equally important class of nanomaterials, self-assembled peptides, heralded as next-generation materials for bioelectronics, have a lot of potential in printed technology. In this minireview, we address the self-assembly process in dipeptides, their application in electronics, and recent progress in three-dimensional printing. The prospect of a generalizable path for nanopatterning self-assembled peptides using ice lithography and its challenges are further discussed.
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Affiliation(s)
- Wendel A Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09219-580 Santo Andre, Sao Paulo, Brazil
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.
- Joint with Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Suchismita Guha
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.
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6
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Kim Y, Park H, Kim Y, Lee C, Park H, Lee JH. Control of the Biodegradability of Piezoelectric Peptide Nanotubes Integrated with Hydrophobic Porphyrin. ACS APPLIED MATERIALS & INTERFACES 2022; 14:38778-38785. [PMID: 35983899 DOI: 10.1021/acsami.2c09751] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Diphenylalanine (FF) is a piezoelectric material that is widely known for its high piezoelectric constant, self-assembly characteristics, and ease of manufacture. Because of its biocompatible nature, it is useful for implantable applications. However, its use in real applications is challenging because it degrades too easily in the body due to its solubility in water (0.76 g/mL). Upon incorporation of hydrophobic and biocompatible porphyrins into the FF, the degradability of the piezoelectric FF and their piezoelectric nanogenerators (PENGs) is controlled. Porphyrin-incorporated FFs are also formed as piezoelectric nanostructures well aligned on the substrate through self-assembly, and their piezoelectric properties are comparable to those of FF. The FF-based PENG degrades in only 5 min, whereas the FF-porphyrin-based PENG produces a stable output for >15 min in phosphate-buffered saline. This strategy for realizing biodegradable functional materials and devices with tunable degradation rates in the body can be applied to many implantable electronics.
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Affiliation(s)
- Yerin Kim
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Hyojin Park
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Yuseok Kim
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Cheoljae Lee
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Hyosik Park
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Ju-Hyuck Lee
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- Energy Science and Engineering Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
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7
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Bystrov VS, Filippov SV. Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis. J Mol Model 2022; 28:81. [PMID: 35247081 DOI: 10.1007/s00894-022-05074-2] [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: 11/15/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes (PNT) based on diphenylalanine (FF) dipeptide with different initial isomers of the left (L-FF) and right (D-FF) chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both chiralities are investigated using quantum-chemical DFT and semi-empirical methods, which are in consistent with the known experimental data. To study the effect of nano-sized clusters of water molecules embedded in the inner hydrophilic cavity on the properties of nanotubes (including the changes in their dipole moments and polarizations), as well as the changes in the structure and properties of water clusters themselves (their own dipole moments and polarizations), the surfaces of internal cavities of nanotubes and outer surfaces of water cluster structures for both types of chirality are analyzed. A specially developed method of visual differential analysis of structural features of (bio)macromolecular structures is applied for these studies. The results obtained of a number of physical properties (interacting energies, dipole moments, polarization values) are given for various cases and analyzed in comparison with the known data. These data are necessary for analyzing the interactions of water molecules with hydrophilic parts of nanotube molecules based on FF, such as COO- and NH3 + , since they determine many properties of the structures under study. The data obtained are useful for further analysis of the possible adhesion and capture of medical molecular components by active layers of FF-based PNT, which can be designed for creating capsules for targeted delivery of pharmaceuticals and drugs on their basis.
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Affiliation(s)
- Vladimir S Bystrov
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences (IMPB RAS- Branch of KIAM RAS), 142290, Pushchino, Moscow region, Russia.
| | - Sergey V Filippov
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences (IMPB RAS- Branch of KIAM RAS), 142290, Pushchino, Moscow region, Russia
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8
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Almohammed S, K. Orhan O, Daly S, O’Regan DD, Rodriguez BJ, Casey E, Rice JH. Electric Field Tunability of Photoluminescence from a Hybrid Peptide-Plasmonic Metal Microfabricated Chip. JACS AU 2021; 1:1987-1995. [PMID: 35574042 PMCID: PMC8611722 DOI: 10.1021/jacsau.1c00323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Indexed: 06/14/2023]
Abstract
Enhancement of fluorescence through the application of plasmonic metal nanostructures has gained substantial research attention due to the widespread use of fluorescence-based measurements and devices. Using a microfabricated plasmonic silver nanoparticle-organic semiconductor platform, we show experimentally the enhancement of fluorescence intensity achieved through electro-optical synergy. Fluorophores located sufficiently near silver nanoparticles are combined with diphenylalanine nanotubes (FFNTs) and subjected to a DC electric field. It is proposed that the enhancement of the fluorescence signal arises from the application of the electric field along the length of the FFNTs, which stimulates the pairing of low-energy electrons in the FFNTs with the silver nanoparticles, enabling charge transport across the metal-semiconductor template that enhances the electromagnetic field of the plasmonic nanoparticles. Many-body perturbation theory calculations indicate that, furthermore, the charging of silver may enhance its plasmonic performance intrinsically at particular wavelengths, through band-structure effects. These studies demonstrate for the first time that field-activated plasmonic hybrid platforms can improve fluorescence-based detection beyond using plasmonic nanoparticles alone. In order to widen the use of this hybrid platform, we have applied it to enhance fluorescence from bovine serum albumin and Pseudomonas fluorescens. Significant enhancement in fluorescence intensity was observed from both. The results obtained can provide a reference to be used in the development of biochemical sensors based on surface-enhanced fluorescence.
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Affiliation(s)
- Sawsan Almohammed
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Okan K. Orhan
- School
of Physics, AMBER, and CRANN Institute, Trinity College Dublin, The University of Dublin, Dublin D02 PN40, Ireland
| | - Sorcha Daly
- School
of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - David D. O’Regan
- School
of Physics, AMBER, and CRANN Institute, Trinity College Dublin, The University of Dublin, Dublin D02 PN40, Ireland
| | - Brian J. Rodriguez
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Eoin Casey
- School
of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - James H. Rice
- School
of Physics, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
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9
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Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations. NANOMATERIALS 2021; 11:nano11092415. [PMID: 34578731 PMCID: PMC8471708 DOI: 10.3390/nano11092415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 02/05/2023]
Abstract
The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.
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10
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Sheehan F, Sementa D, Jain A, Kumar M, Tayarani-Najjaran M, Kroiss D, Ulijn RV. Peptide-Based Supramolecular Systems Chemistry. Chem Rev 2021; 121:13869-13914. [PMID: 34519481 DOI: 10.1021/acs.chemrev.1c00089] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.
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Affiliation(s)
- Fahmeed Sheehan
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Ankit Jain
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Mohit Kumar
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, Barcelona 08028, Spain
| | - Mona Tayarani-Najjaran
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
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11
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Salehli F, Aydin AO, Chovan D, Kopyl S, Bystrov V, Thompson D, Tofail SA, Kholkin A. Nanoconfined water governs polarization‐related properties of self‐assembled peptide nanotubes. NANO SELECT 2021. [DOI: 10.1002/nano.202000220] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ferid Salehli
- Department of Physical Engineering Istanbul Technical University Maslak Istanbul Turkey
| | - Abuzer O. Aydin
- Department of Physical Engineering Istanbul Technical University Maslak Istanbul Turkey
| | - Drahomir Chovan
- Department of Physics & Bernal Institute University of Limerick Limerick Ireland
| | - Svitlana Kopyl
- Department of Physics & CICECO – Aveiro Institute of Materials University of Aveiro Aveiro Portugal
| | - Vladimir Bystrov
- Institute of Mathematical Problems of Biology Keldysh Institute of Applied Mathematics, RAS Pushchino Moscow region Russia
| | - Damien Thompson
- Department of Physics & Bernal Institute University of Limerick Limerick Ireland
| | - Syed A.M. Tofail
- Department of Physics & Bernal Institute University of Limerick Limerick Ireland
| | - Andrei Kholkin
- Department of Physics & CICECO – Aveiro Institute of Materials University of Aveiro Aveiro Portugal
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12
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Pinheiro M, da Cunha AR, Marinho AMR, Silva SYS, Andrade-Filho T, Gester R. Solvent polarity effects on thermochemical and NMR parameters of spilanthol pharmacological agent: an experimental and DFT investigation. Struct Chem 2020. [DOI: 10.1007/s11224-020-01573-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Bystrov VS, Coutinho J, Zelenovskiy PS, Nuraeva AS, Kopyl S, Filippov SV, Zhulyabina OA, Tverdislov VA. Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules. J Mol Model 2020; 26:326. [PMID: 33140163 DOI: 10.1007/s00894-020-04564-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022]
Abstract
DFT (VASP) and semi-empirical (HyperChem) calculations for the L- and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside L-FF and D-FF PNT and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.
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Affiliation(s)
- Vladimir S Bystrov
- Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290, Pushchino, Moscow region, Russia.
| | - Jose Coutinho
- Department of Physics & I3N, University of Aveiro, Campus Santiago, 3810-193, Aveiro, Portugal
| | - Pavel S Zelenovskiy
- School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia.,Department of Chemistry & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Alla S Nuraeva
- School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia
| | - Svitlana Kopyl
- Department of Physics & CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Sergei V Filippov
- Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290, Pushchino, Moscow region, Russia
| | - Olga A Zhulyabina
- Faculty of Physics, Lomonosov Moscow State University, 119991, Moscow, Russia
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14
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Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis. NANOMATERIALS 2020; 10:nano10101999. [PMID: 33050446 PMCID: PMC7600064 DOI: 10.3390/nano10101999] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/31/2022]
Abstract
The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.
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15
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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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16
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Raman Spectra of Diphenylalanine Microtubes: Polarisation and Temperature Effects. CRYSTALS 2020. [DOI: 10.3390/cryst10030224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Diphenylalanine microtubes have remarkable physical properties that allow one to use them in electronics. In this work, we measured polarised temperature-dependent Raman spectra in self-assembled diphenylalanine microtubes grown from the solution. We observed the anomalous temperature behaviour of the Raman lines. Their temperature changes were minimal, which required a significant improvement in the resolution and stability of Raman measurements. The anomalies in the behaviour of the spectra at about 178 K, 235 K, 255 K, 278 K, 296 K, 398 K and 412 K were observed. The structural phase transition at 398 K is irreversible. This transition is associated with the release of water molecules from nanochannels. The irreversible phase transition has a temperature range of about 10 K.
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17
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Silva CB, da Silva Filho JG, Pinheiro GS, Teixeira AMR, de Sousa FF, Freire PTC. High-pressure studies on l,l-dileucine crystals by Raman spectroscopy and synchrotron X-ray diffraction combined with DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117899. [PMID: 31839580 DOI: 10.1016/j.saa.2019.117899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/24/2019] [Accepted: 12/02/2019] [Indexed: 06/10/2023]
Abstract
The vibrational properties of the dipeptide l-leucyl-l-leucine hydrate were investigated through Raman and infrared spectroscopy. With the aid of first principle calculations using the density functional theory, the assignment of the vibrational modes from the material was furnished. In addition, the behavior of the crystal under high pressure was investigated using Raman spectroscopy (~8 GPa) and synchrotron X-ray diffraction (~26 GPa). The results show significant changes in both the X-ray diffractogram and the Raman spectra, suggesting that l-leucyl-l-leucine hydrate undergoes a phase transition between 2.3 and 2.9 GPa. Finally, for pressures above 16 GPa the broadening of X-ray peaks suggests a disorder in the crystal lattice induced by high-pressure effects.
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Affiliation(s)
- C B Silva
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, Campus do Pici, 60.455-760 Fortaleza, CE, Brazil.
| | - J G da Silva Filho
- Instituto de Centro de Ciências Sociais, Saúde e Tecnologia, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | - G S Pinheiro
- Departamento de Física, Universidade Federal do Piaui, campus Ministro Petrônio Portella, 64.049-550, Teresina, PI, Brazil
| | - A M R Teixeira
- Departamento de Física, Universidade Regional do Cariri, 63.010-970 Juazeiro do Norte, CE, Brazil
| | - F F de Sousa
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66.075-110 Belém, PA, Brazil
| | - P T C Freire
- Departamento de Física, Universidade Federal do Ceará, C.P. 6030, Campus do Pici, 60.455-760 Fortaleza, CE, Brazil
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18
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Pérez-Mellor A, Le Barbu-Debus K, Zehnacker A. Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits. Chirality 2020; 32:693-703. [PMID: 32078197 DOI: 10.1002/chir.23195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/21/2022]
Abstract
The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.
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Affiliation(s)
- Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, University Paris-Sud, Université Paris-Saclay, Orsay, France
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19
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Bystrov VS, Zelenovskiy PS, Nuraeva AS, Kopyl S, Zhulyabina OA, Tverdislov VA. Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes. J Mol Model 2019; 25:199. [DOI: 10.1007/s00894-019-4080-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/28/2019] [Indexed: 12/26/2022]
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20
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Structural behavior of phenylalanine–tryptophan peptide nanotubes at anhydrous conditions: a theoretical investigation. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2457-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Pelin JNBD, Gatto E, Venanzi M, Cavalieri F, Oliveira CLP, Martinho H, Silva ER, Aguilar AM, Souza JS, Alves WA. Hybrid Conjugates Formed between Gold Nanoparticles and an Amyloidogenic Diphenylalanine-Cysteine Peptide. ChemistrySelect 2018. [DOI: 10.1002/slct.201801345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Juliane N. B. D. Pelin
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
| | - Emanuela Gatto
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Italy
| | - Mariano Venanzi
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Italy
| | - Francesca Cavalieri
- Department of Chemical and Biomolecular Engineering; The University of Melbourne; Australia
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Italy
| | | | - Herculano Martinho
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
| | - Emerson R. Silva
- Departamento de Biofísica; Universidade Federal de São Paulo; 04023-062 São Paulo Brazil
| | - Andrea M. Aguilar
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas; Universidade Federal de São Paulo; Diadema 09972-270 Brazil
| | - Juliana S. Souza
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
| | - Wendel A. Alves
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; 09210-580 Santo André Brazil
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22
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Zelenovskiy P, Kornev I, Vasilev S, Kholkin A. On the origin of the great rigidity of self-assembled diphenylalanine nanotubes. Phys Chem Chem Phys 2018; 18:29681-29685. [PMID: 27775117 DOI: 10.1039/c6cp04337b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The elastic properties of the nanotubes of self-assembled aromatic dipeptide diphenylalanine are investigated by means of Raman spectroscopy and a mass-in-mass 1D model. Analysis of nanotubes' lattice vibrations reveals the essential contribution of the water in the nanochannel core of the tubes to the Young's modulus and high water mobility along the channel. Direct measurements of the Young's modulus performed by nanoindentation confirm the obtained results.
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Affiliation(s)
- Pavel Zelenovskiy
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia.
| | - Igor Kornev
- SPMS Laboratory, Ecole Centrale Paris, Chatenay-Malabry, 92295, France
| | - Semen Vasilev
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia.
| | - Andrei Kholkin
- Institute of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg, 620000, Russia. and Physics Department & CICECO - Aveiro Institute of Materials, University of Aveiro, Aveiro, 3810-193, Portugal
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23
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Wang J, Yuan C, Han Y, Wang Y, Liu X, Zhang S, Yan X. Trace Water as Prominent Factor to Induce Peptide Self-Assembly: Dynamic Evolution and Governing Interactions in Ionic Liquids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1702175. [PMID: 28976074 DOI: 10.1002/smll.201702175] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/12/2017] [Indexed: 05/22/2023]
Abstract
The interaction between water and biomolecules including peptides is of critical importance for forming high-level architectures and triggering life's functions. However, the bulk aqueous environment has limitations in detecting the kinetics and mechanisms of peptide self-assembly, especially relating to interactions of trace water. With ionic liquids (ILs) as a nonconventional medium, herein, it is discovered that trace amounts of water play a decisive role in triggering self-assembly of a biologically derived dipeptide. ILs provide a suitable nonaqueous environment, enabling us to mediate water content and follow the dynamic evolution of peptide self-assembly. The trace water is found to be involved in the assembly process of dipeptide, especially leading to the formation of stable noncovalent dipeptide oligomers in the early stage of nucleation, as evident by both experimental studies and theoretical simulations. The thermodynamics of the growth process is mainly governed by a synergistic effect of hydrophobic interaction and hydrogen bonds. Each step of assembly presents a different trend in thermodynamic energy. The dynamic evolution of assembly process can be efficiently mediated by changing trace water content. The decisive role of trace water in triggering and mediating self-assembly of biomolecules provides a new perspective in understanding supramolecular chemistry and molecular self-organization in biology.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuchun Han
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yilin Wang
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiaomin Liu
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Suojiang Zhang
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
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24
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25
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Yuan C, Li S, Zou Q, Ren Y, Yan X. Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly. Phys Chem Chem Phys 2017; 19:23614-23631. [DOI: 10.1039/c7cp01923h] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.
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Affiliation(s)
- Chengqian Yuan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Ying Ren
- Center for Mesoscience
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
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26
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Ishikawa MS, Busch C, Motzkus M, Martinho H, Buckup T. Two-step kinetic model of the self-assembly mechanism for diphenylalanine micro/nanotube formation. Phys Chem Chem Phys 2017; 19:31647-31654. [DOI: 10.1039/c7cp06611b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Formation via nucleation of FF-MNTs is based on a 2-step kinetic model and is driven by electric dipole re-orientation.
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Affiliation(s)
- M. S. Ishikawa
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
| | - C. Busch
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
| | - M. Motzkus
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
| | - H. Martinho
- Centro de Ciências Naturais e Humanas
- Universidade Federal do ABC
- Santo André-SP
- Brazil
| | - T. Buckup
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
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27
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Khanra S, Ghosh K, Ferreira FF, Alves WA, Punzo F, Yu P, Guha S. Probing nonlinear optical coefficients in self-assembled peptide nanotubes. Phys Chem Chem Phys 2017; 19:3084-3093. [DOI: 10.1039/c6cp07879f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Second harmonic generation polarimetry from individual self-assembled peptide nanotubes is used to obtain the ratio of the nonlinear coefficients.
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Affiliation(s)
- Soma Khanra
- Department of Physics and Astronomy
- University of Missouri
- Columbia
- USA
| | - Kartik Ghosh
- Physics
- Astronomy
- and Materials Science
- Missouri State University
- Springfield
| | - Fabio F. Ferreira
- Centro de Ciências Naturais e Humanas
- Universidade Federal do ABC
- 09219-580 Santo Andre
- Brazil
| | - Wendel A. Alves
- Centro de Ciências Naturais e Humanas
- Universidade Federal do ABC
- 09219-580 Santo Andre
- Brazil
| | - Francesco Punzo
- Dipartimento di Scienze del Farmaco
- Sezione Chimica
- Università degli Studi di Catania
- Viale Andrea Doria 6
- 95125 Catania
| | - Ping Yu
- Department of Physics and Astronomy
- University of Missouri
- Columbia
- USA
| | - Suchismita Guha
- Department of Physics and Astronomy
- University of Missouri
- Columbia
- USA
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