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Nayak S, Das K, Sivagnanam S, Baskar S, Stewart A, Kumar D, Maity B, Das P. Cystine-cored diphenylalanine appended peptide-based self-assembled fluorescent nanostructures direct redox-responsive drug delivery. iScience 2024; 27:109523. [PMID: 38577103 PMCID: PMC10993133 DOI: 10.1016/j.isci.2024.109523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
Fabrication of stimuli-responsive superstructure capable of delivering chemotherapeutics directly to the cancer cell by sparing healthy cells is crucial. Herein, we developed redox-responsive hollow spherical assemblies through self-assembly of disulfide-linked cysteine-diphenylalanine (SN). These fluorescent hollow spheres display intrinsic green fluorescence, are proteolytically stable and biocompatible, and allow for real-time monitoring of their intracellular entry. The disulfide bond facilitates selective degradation in the presence of high glutathione (GSH) concentrations, prevalent in cancer cells. We achieved efficient encapsulation (68.72%) of the anticancer drug doxorubicin (Dox) and demonstrated GSH-dependent, redox-responsive drug release within cancerous cells. SN-Dox exhibited a 20-fold lower effective concentration (2.5 μM) for compromising breast cancer cell viability compared to non-malignant cells (50 μM). The ability of SN-Dox to initiate DNA damage signaling and trigger apoptosis was comparable to that of the unencapsulated drug. Our findings highlight the potential of SN for creating site-specific drug delivery vehicles for sustained therapeutic release.
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Affiliation(s)
- Suman Nayak
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
| | - Kiran Das
- Department of Systems Biology, Centre of Biomedical Research (CBMR), SGPGI campus, Raebareli Road, Lucknow, Uttar Pradesh 226014, India
| | - Subramaniyam Sivagnanam
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
| | - Shyamvarnan Baskar
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
| | - Adele Stewart
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Dinesh Kumar
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research (CBMR), SGPGI campus, Raebareli Road, Lucknow, Uttar Pradesh 226014, India
| | - Biswanath Maity
- Department of Systems Biology, Centre of Biomedical Research (CBMR), SGPGI campus, Raebareli Road, Lucknow, Uttar Pradesh 226014, India
| | - Priyadip Das
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
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2
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Reyes C, Patarroyo MA. Self-assembling peptides: Perspectives regarding biotechnological applications and vaccine development. Int J Biol Macromol 2024; 259:128944. [PMID: 38145690 DOI: 10.1016/j.ijbiomac.2023.128944] [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: 08/08/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
Self-assembly involves a set of molecules spontaneously interacting in a highly coordinated and dynamic manner to form a specific supramolecular structure having new and clearly defined properties. Many examples of this occur in nature and many more came from research laboratories, with their number increasing every day via ongoing research concerning complex biomolecules and the possibility of harnessing it when developing new applications. As a phenomenon, self-assembly has been described on very different types of molecules (biomolecules including), so this review focuses on what is known about peptide self-assembly, its origins, the forces behind it, how the properties of the resulting material can be tuned in relation to experimental considerations, some biotechnological applications (in which the main protagonists are peptide sequences capable of self-assembly) and what is yet to be tuned regarding their research and development.
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Affiliation(s)
- César Reyes
- PhD Biotechnology Programme, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá DC 111321, Colombia; Structure Analysis Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá DC 111321, Colombia; Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A.), Calle 222#55-37, Bogotá DC 111166, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá DC 111321, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá DC 111321, Colombia.
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3
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Thapa S, Clark F, Schneebeli ST, Li J. Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study. J Chem Theory Comput 2024; 20:375-384. [PMID: 38013425 PMCID: PMC11070933 DOI: 10.1021/acs.jctc.3c00699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Peptide self-assembly is critical for biomedical and material discovery and production. While it is costly to experimentally test every possible peptide design, computational assessment provides an affordable solution to evaluate many designs and prioritize synthesis and characterization. Following a theoretical investigation, we present a systematic analysis of all-atom and coarse-grained simulations to predict peptide self-assembly. Benchmarking studies of two model dipeptides allow us to assess the impacts of intrinsic properties (such as amino acids and terminal modifications) and external environment (such as salinity) on the simulated aggregation. Further examination of 20 oligopeptides containing two to five amino acids shows good agreement among our theory, simulations, and prior experimental observations. The success rate of our prediction is 90%. Therefore, our theory, simulation, and analysis can be useful to identify peptide designs that can self-assemble and predict the potential nanostructures. These findings lay the ground for future virtual screening of peptide-assembled nanostructures and computer-aided biologics design.
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Affiliation(s)
- Subhadra Thapa
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | - Finley Clark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
| | - Severin. T. Schneebeli
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
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4
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Avelar S Silva J, Militão Vasconcelos DL, Araújo de Lima R, Cordeiro AJP, Tarso C Freire P. Structural and vibrational analysis of glycyl-L-phenylalanine and phase transition under high-pressure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123383. [PMID: 37725884 DOI: 10.1016/j.saa.2023.123383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
The structural and vibrational properties of the glycyl-L-phenylalanine dipeptide were investigated using vibrational spectroscopy (Raman and infrared) and first-principle calculations. Raman spectroscopy measurements were performed between 100 and 3200 cm-1 and infrared spectroscopy from 100 and 3200 cm-1 under ambient conditions. The conformational analysis of the zwitterionic form of the dipeptide was performed using the B3LYP functional, the 6-311++ base set and the Polarizable Continuum Model of solvation, determining the lowest energy conformation and assigning the vibrational modes. The effect of pressure on the glycyl-1-phenylalanine crystal was investigated using the Raman spectroscopy between 0.0 and -7.1 GPa in the spectral region of 100 - 3200 cm-1. As a result, conformational changes around 1.0 GPa were observed in the lattice modes and in some internal modes, showing a reorganization of the molecule in the crystal. In the decompression process, it was observed that the conformational change is reversible and the original Raman spectrum is recoverd.
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Affiliation(s)
- José Avelar S Silva
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil.
| | - Daniel L Militão Vasconcelos
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil; Faculdade de Educação Ciências e Letras do Sertão Central, Universidade Estadual do Ceará, CEP 63.902-098 Quixadá, CE, Brazil
| | - Raphaela Araújo de Lima
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil
| | - Adrya J P Cordeiro
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil
| | - Paulo Tarso C Freire
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil.
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5
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Ge Y, Wang X, Zhu Q, Yang Y, Dong H, Ma J. Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids. J Chem Theory Comput 2023; 19:6718-6732. [PMID: 37725682 DOI: 10.1021/acs.jctc.3c00809] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing properties has attracted intense attention. However, predicting peptide assembly at atomic resolution is a challenge due to both the structural flexibility of peptides and the associated huge computational costs. A machine learning-guided adaptive parametrization method was proposed for developing a mixed atomic and coarse-grained (CG) model through a multiobjective optimization strategy. Our model incorporates the united-atom (UA) model for diphenylalanine (P) and the polarizable electrostatic-variable coarse-grained (VaCG) model for aqueous ionic liquid [BMIM]+[BF4]- solution. In this mixed model, the coupling van der Waals (vdW) interaction is addressed by introducing virtual sites (VS) in the UA model to interact with solvent CG beads. The coupling parameters, including the electrostatic parameter and vdW parameters, are automatically optimized through ML-guided adaptive parametrization. The performance of this model was tested by some microstructural properties, e.g., the average number of P-P intermolecular hydrogen bonds (HBs) and radius distribution functions (RDFs) between P and different fragments of IL, in comparison with all-atom (AA) simulations. The computational cost is significantly reduced using such a parametrization scheme, which could search tens of thousands of force-field parameter sets, while needing only a small fraction of them to be assessed with molecular dynamics (MD) simulations. We used such a mixed resolution model to investigate the self-assembly in IL-water mixtures with variants of IL concentration (X). The long-range-ordered fibril structure is formed in a pure water system (X = 0). With an increase of IL concentrations, the formation of an ordered self-assembly nanostructure is prohibited, instead forming branched fibril at X = 2 mol % or amorphous aggregates when X > 10 mol %, resulting from the interplay between π-stacking and HB interactions between P and IL. The qualitative agreement between the simulated structures and the observed morphologies in experiments indicates the applicability of ML-guided parametrization strategy in the study of complex systems, such as polymers, lipid bilayers, and polysaccharides.
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Affiliation(s)
- Yang Ge
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xueping Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuqin Yang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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6
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Monti M, Scarel E, Hassanali A, Stener M, Marchesan S. Diverging conformations guide dipeptide self-assembly into crystals or hydrogels. Chem Commun (Camb) 2023; 59:10948-10951. [PMID: 37605851 DOI: 10.1039/d3cc02682e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The prediction of dipeptide assembly into crystals or gels is challenging. This work reveals the diverging conformational landscape that guides self-organization towards different outcomes. In silico and experimental data enabled deciphering of the electronic circular dichroism (ECD) spectra of self-assembling dipeptides to reveal folded or extended conformers as key players.
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Affiliation(s)
- M Monti
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - E Scarel
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - A Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - M Stener
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
| | - S Marchesan
- Chem. Pharm. Sc. Dept., University of Trieste, Via L. Giorgieri 1, Trieste 34127, Italy.
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7
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Bystrov V, Likhachev I, Filippov S, Paramonova E. Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1905. [PMID: 37446422 DOI: 10.3390/nano13131905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules-namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF. In this work, helical nanotubes were assembled from linear sequences of FF molecules with these initially different chiralities. The chirality of the obtained nanotubes was calculated by various methods, including calculation by dipole moments. In addition, a statistical analysis of the results obtained was performed. A comparative analysis of the structures of nanotubes was also performed using the method of visual differential analysis. It was found that FF PNTs obtained by the MD self-assembly method form helical nanotubes of different chirality. The regimes that form nanotubes of right chirality D from initial L-FF dipeptides and nanotubes of left chirality L from D-FF dipeptides are revealed. This corresponds to the law of changing the sign of the chirality of molecular helical structures as the level of their hierarchical organization becomes more complicated.
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Affiliation(s)
- Vladimir Bystrov
- Institute of Mathematical Problems of Biology-Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia
| | - Ilya Likhachev
- Institute of Mathematical Problems of Biology-Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia
| | - Sergey Filippov
- Institute of Mathematical Problems of Biology-Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia
| | - Ekaterina Paramonova
- Institute of Mathematical Problems of Biology-Branch of Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Russia
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8
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Divanach P, Fanouraki E, Mitraki A, Harmandaris V, Rissanou AN. Self-Assembly of Phenylalanine-Leucine, Leucine-Phenylalanine, and Cyclo(-leucine-phenylalanine) Dipeptides through Simulations and Experiments. J Phys Chem B 2023; 127:4208-4219. [PMID: 37148280 DOI: 10.1021/acs.jpcb.2c08576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
For over two decades, peptide self-assembly has been the focus of attention and a great source of inspiration for biomedical and nanotechnological applications. The resulting peptide nanostructures and their properties are closely related to the information encoded within each peptide building block, their sequence, and their modes of self-organization. In this work. we assess the behavior and differences between the self-association of the aromatic-aliphatic Phe-Leu dipeptide compared to its retro-sequence Leu-Phe and cyclic Cyclo(-Leu-Phe) counterparts, using a combination of simulation and experimental methods. Detailed all-atom molecular dynamics (MD) simulations offer a quantitative prediction at the molecular level of the conformational, dynamical and structural properties of the peptides' self-assembly, while field emission scanning electron microscopy (FESEM) experiments allow microscopic observation of the self-assembled end-structures. The complementarity and qualitative agreement between the two methods not only highlights the differences between the self-assembly propensity of cyclic and linear retro-sequence peptides but also sheds light on underlying mechanisms of self-organization. The self-assembling propensity was found to follow the order: Cyclo(-Leu-Phe) > Leu-Phe > Phe-Leu.
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Affiliation(s)
- Peter Divanach
- Department of Materials Science and Technology, University of Crete, GR-70013 Voutes Campus, Greece
- Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas, (FORTH), Nikolaou Plastira 100, Vassilika Vouton, GR-71110 Heraklion, Crete, Greece
| | - Eirini Fanouraki
- Department of Materials Science and Technology, University of Crete, GR-70013 Voutes Campus, Greece
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, GR-70013 Voutes Campus, Greece
- Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas, (FORTH), Nikolaou Plastira 100, Vassilika Vouton, GR-71110 Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Anastassia N Rissanou
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
- National Hellenic Research Foundation, Theoretical & Physical Chemistry Institute, 48 Vassileos Constantinou Avenue, GR-11635 Athens, Greece
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9
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Sivagnanam S, Das K, Pan I, Barik A, Stewart A, Maity B, Das P. Functionalized Fluorescent Nanostructures Generated from Self-Assembly of a Cationic Tripeptide Direct Cell-Selective Chemotherapeutic Drug Delivery. ACS APPLIED BIO MATERIALS 2023; 6:836-847. [PMID: 36757106 DOI: 10.1021/acsabm.2c00996] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Nanodrug delivery systems (NDDs) capable of conveying chemotherapeutics directly into malignant cells without harming healthy ones are of significant interest in the field of cancer therapy. However, the development of nanostructures with the requisite biocompatibility, inherent optical properties, cellular penetration ability, encapsulation capability, and target selectivity has remained elusive. In an effort to develop cell-selective NDDs, we have synthesized a cationic tripeptide Boc-Arg-Trp-Phe-OMe (PA1), which self-assembles into well-ordered spheres in 100% aqueous medium. The inherent fluorescence properties of the peptide PA1 were shifted from the ultraviolet to the visible region by the self-assembly. These fluorescent nanostructures are proteolytically stable, photostable, and biocompatible, with characteristic blue fluorescence signals that permit us to monitor their intracellular entry in real time. We also demonstrate that these tripeptide spherical structures (TPSS) have the capacity to entrap the chemotherapeutic drug doxorubicin (Dox), shuttle the encapsulated drug within cancerous cells, and initiate the DNA damage signaling cascade, which culminates in apoptosis. Next, we functionalized the TPSS with an epithelial-cell-specific epithelial cell adhesion molecule aptamer. Aptamer-conjugated PA1 (PA1-Apt) facilitated efficient Dox delivery into the breast cancer epithelial cell line MCF7, resulting in cell death. However, cells of the human cardiomyocyte cell line AC16 were resistant to the cell killing actions of PA1-Apt. Together, these data demonstrate that not only can the self-assembly of cationic tripeptides like PA1 be exploited for efficient drug encapsulation and delivery but their unique chemistry also allows for functional modifications, which can improve the selectivity of these versatile NDDs.
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Affiliation(s)
- Subramaniyam Sivagnanam
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur 603203, Tamil Nadu, India
| | - Kiran Das
- Department of Systems Biology, Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Ieshita Pan
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 602105, Tamil Nadu, India
| | - Atanu Barik
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, Maharashtra, India
| | - Adele Stewart
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Biswanath Maity
- Department of Systems Biology, Centre of Biomedical Research (CBMR), SGPGI Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Priyadip Das
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur 603203, Tamil Nadu, India
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10
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Bandeira CCS, Foiani LMC, Carlos GB, Ishikawa MS, Ferreira PMGL, da Silva Martinho H. Solvent-dependent formation kinetics of L,L-diphenylalanine micro/nanotubes. Phys Chem Chem Phys 2023; 25:5107-5113. [PMID: 36722992 DOI: 10.1039/d2cp03491c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Investigating the molecular mechanism underlying the aggregation process of amyloid fibers is of great importance both for its implications in several degenerative diseases and for the design of new materials based on self-assembly. In particular, micro/nanotubes of L,L-diphenylalanine have been investigated as a model of amyloid plaques in Alzheimer's disease and also for their broad range of physical properties, e.g., good thermo- and mechanical stability, semiconductivity, piezoelectricity and optical properties. It has been reported that the assembly/disassembly dynamics of L,L-diphenylalanine crystals is influenced by the solvent composition being triggered by evaporation of solvents. In fact the solvatomorphism of this peptide-based nanomaterial is complex and rich attracting great attention. Here we investigated the growing kinetics of the micro/nanotubes of L,L-diphenylalanine in samples prepared with toluene, ethanol, and acetic acid solvents by time-resolved Raman spectroscopy. Our results indicated that the self-assembly in this case competes with the water evaporation process contrary to what is reported by samples prepared with widely used solvent 1,1,1,3,3,3-hexafluoro-2-propanol. We note that exclusively tubular structures (being hollow for the toluene solvent case) were observed. Interestingly our results support the fact that for acetic acid, ethanol, and toluene the micro/nanotube formation process is autocatalytic instead of being nucleation-dominating as reported for samples prepared using solvent 1,1,1,3,3,3-hexafluoro-2-propanol.
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Affiliation(s)
| | | | - Giovana Bonano Carlos
- Universidade Federal do ABC (UFABC), Av. dos Estados 5001, Santo André-SP, 09210-580, Brazil.
| | - Mariana Sayuri Ishikawa
- Universidade Federal do ABC (UFABC), Av. dos Estados 5001, Santo André-SP, 09210-580, Brazil.
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11
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Dube T, Panda JJ. Anti-Glioma Activity Achieved by Dual Blood-Brain Barrier/Glioma Targeting Naive Chimeric Peptides-Based Co-Assembled Nanophototheranostics. Pharmaceutics 2023; 15:pharmaceutics15010265. [PMID: 36678895 PMCID: PMC9863651 DOI: 10.3390/pharmaceutics15010265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/02/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Peptide monomers can either self-assemble with themselves enacting a solo-component assembly or they can co-assemble by interacting with other suitable partners to mediate peptide co-assembly. Peptide co-assemblies represent an innovative class of naive, multifunctional, bio-inspired supramolecular constructs that result in the production of nanostructures with widespread functional, structural, and chemical multiplicity. Herein, the co-assembly of novel chimeric peptides (conjugates of T7 (HAIYPRH)/t-Lyp-1 (CGNKRTR) peptides and aurein 1.2 (GLFDIIKKIAESF)) has been explored as a means to produce glioma theranostics exhibiting combinatorial chemo-phototherapy. Briefly, we have reported here the design and solid phase synthesis of a naive generation of twin-functional peptide drugs incorporating the blood-brain barrier (BBB) and glioma dual-targeting functionalities along with anti-glioma activity (G-Anti G and B-Anti G). Additionally, we have addressed their multicomponent co-assembly and explored their potential application as glioma drug delivery vehicles. Our naive peptide drug-based nanoparticles (NPs) successfully demonstrated a heightened glioma-specific delivery and anti-glioma activity. Multicomponent indocyanine green (ICG)-loaded peptide co-assembled NPs (PINPs: with a hydrodynamic size of 348 nm and a zeta-potential of 5 mV) showed enhanced anti-glioma responses in several cellular assays involving C6 cells. These included a mass demolition with no wound closure (i.e., a 100% cell destruction) and around 63% collaborative chemo-phototoxicity (with both a photothermal and photodynamic effect) after near infrared (NIR) 808 laser irradiation. The dual targeting ability of peptide bioconjugates towards both the BBB and glioma cells, presents new opportunities for designing tailored and better peptide-based nanostructures or nanophototheranostics for glioma.
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12
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Adhikary R, Das A. Atomistic Pictures of Self-Assembled Helical Peptide Nanofibers. J Phys Chem B 2022; 126:9476-9492. [PMID: 36350248 DOI: 10.1021/acs.jpcb.2c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Spontaneous self-assembly of peptides has been at the forefront of supramolecular chemistry and materials science research over the last two decades. Despite the wealth of information on the morphology of the assembled objects, atomic resolution details of molecular arrangements inside them are largely unknown. In this paper, we investigated non-covalent assemblies of zwitterionic l-phenylalanine tripeptides in water using all-atom explicit-solvent molecular dynamics computer simulations. Our studies produced atomistic pictures of spontaneously assembled nanofibers composed of hundreds of peptide molecules. The dimensions of the nanofibers varied from 10 to 18 nm, with irregular helical twists along the long axes. Previously published experimental data, acquired under similar conditions, provided direct validation of the fibrous morphology and indirect support for the non-trivial helicity observed in our simulations. Quantitative analyses of peptide-water and peptide-peptide interactions revealed heterogeneous local environments of molecules across the nanometer length scales. The combination of electrostatic, hydrogen bonding, van der Waals, and hydrophobic interactions, adopted by a single molecule, was dependent on its relative position inside the fiber. Despite the presence of three hydrophobic phenyl groups, very few molecules were found to be completely shielded from the surrounding water, indicating a subtle role of the hydrophobic effect. Limited conformational flexibility of the tripeptide, along with bare electrostatic interactions, appeared to play a crucial role in the emergence of fibrous morphology of the nanostructures. Our analyses led us to formulate plausible qualitative explanations of the assembly behavior in terms of thermodynamic driving forces and kinetic considerations. We established a clear relationship between details of chemical interactions operating within few molecules and characteristics of the self-assembled states at much longer length scales.
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Affiliation(s)
- Rumela Adhikary
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Avisek Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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13
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Wei H, Min J, Wang Y, Shen Y, Du Y, Su R, Qi W. Bioinspired porphyrin-peptide supramolecular assemblies and their applications. J Mater Chem B 2022; 10:9334-9348. [PMID: 36373597 DOI: 10.1039/d2tb01660e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Inspired by the hierarchical chiral assembly of porphyrin-proteins in photosynthetic systems, the hierarchical self-assembly of porphyrin-amino acids/peptides provides a novel strategy for constructing functional materials. How to artificially simulate the assembly of porphyrins, proteins, and other cofactors in the photosynthesis system to obtain persistent strong light capture, charge separation and catalytic reactions has become an important concern in the construction of biomimetic photosynthesis systems. This paper summarizes the different assembly strategies adopted in recent years, the effects of driving forces on self-assembly, and the application of porphyrin-peptides in catalysis and biomedicine, and briefly discusses the challenges and prospects for future research.
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Affiliation(s)
- Hao Wei
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China. .,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Yaohui Du
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
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14
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NMR and vibrational spectroscopic studies on the structure and self-assembly of Two de novo dipeptides in methanol. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Pérez-Madrigal MM, Gil AM, Casanovas J, Jiménez AI, Macor LP, Alemán C. Self-assembly pathways in a triphenylalanine peptide capped with aromatic groups. Colloids Surf B Biointerfaces 2022; 216:112522. [PMID: 35561635 DOI: 10.1016/j.colsurfb.2022.112522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 11/25/2022]
Abstract
Peptide derivatives and, most specifically, their self-assembled supramolecular structures are being considered in the design of novel biofunctional materials. Although the self-assembly of triphenylalanine homopeptides has been found to be more versatile than that of homopeptides containing an even number of residues (i.e. diphenylalanine and tetraphenylalanine), only uncapped triphenylalanine (FFF) and a highly aromatic analog blocked at both the N- and C-termini with fluorenyl-containing groups (Fmoc-FFF-OFm), have been deeply studied before. In this work, we have examined the self-assembly of a triphenylalanine derivative bearing 9-fluorenylmethyloxycarbonyl and benzyl ester end-capping groups at the N- and C-termini, respectively (Fmoc-FFF-OBzl). The antiparallel arrangement clearly dominates in β-sheets formed by Fmoc-FFF-OBzl, whereas the parallel and antiparallel dispositions are almost isoenergetic in Fmoc-FFF-OFm β-sheets and the parallel one is slightly favored for FFF. The effects of both the peptide concentration and the medium on the self-assembly process have been examined considering Fmoc-FFF-OBzl solutions in a wide variety of solvent:co-solvent mixtures. In addition, Fmoc-FFF-OBzl supramolecular structures have been compared to those obtained for FFF and Fmoc-FFF-OFm under identical experimental conditions. The strength of π-π stacking interactions involving the end-capping groups plays a crucial role in the nucleation and growth of supramolecular structures, which determines the resulting morphology. Finally, the influence of a non-invasive external stimulus, ultrasounds, on the nucleation and growth of supramolecular structures has been examined. Overall, FFF-based peptides provide a wide range of supramolecular structures that can be of interest in the biotechnological field.
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Affiliation(s)
- Maria M Pérez-Madrigal
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), EEBE, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain.
| | - Ana M Gil
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jordi Casanovas
- Departament de Química, Universitat de Lleida, Escola Politècnica Superior, C/ Jaume II no. 69, 25001 Lleida, Spain
| | - Ana I Jiménez
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena P Macor
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), EEBE, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; IITEMA-CONICET, Departamento de Química, Facultad de Ciencias Exactas Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal Nro. 3, X5804BYA Río Cuarto, Córdoba, Argentina
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), EEBE, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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16
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Morozova AS, Ziganshina SA, Ziganshin MA, Bukharaev AA. Self-Organization of Di- and Triglycine Oligopeptides in Thin Films on the Hydrophilic and Hydrophobic Silicon Surface under Exposure to Organic Compounds Vapors. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222070155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Wang L, Xu R, Liu R, Ge P, Sun W, Tian M. Self-Assembly of NaOL-DDA Mixtures in Aqueous Solution: A Molecular Dynamics Simulation Study. Molecules 2021; 26:molecules26237117. [PMID: 34885699 PMCID: PMC8659107 DOI: 10.3390/molecules26237117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
The self-assembly behaviors of sodium oleate (NaOL), dodecylamine (DDA), and their mixtures in aqueous solution were systematically investigated by large-scale molecular dynamics simulations, respectively. The interaction mechanisms between the surfactants, as well as the surfactants and solvent, were revealed via the radial distribution function (RDF), cluster size, solvent-accessible surface area (SASA), hydrogen bond, and non-bond interaction energy. Results showed that the molecules more easily formed aggregates in mixed systems compared to pure systems, indicating higher surface activity. The SASA values of DDA and NaOL decreased significantly after mixing, indicating a tighter aggregation of the mixed surfactants. The RDF results indicated that DDA and NaOL strongly interacted with each other, especially in the mixed system with a 1:1 molar ratio. Compared to van der Waals interactions, electrostatic interactions between the surfactant molecules were the main contributors to the improved aggregation in the mixed systems. Besides, hydrogen bonds were found between NaOL and DDA in the mixed systems. Therefore, the aggregates in the mixed systems were much more compact in comparison with pure systems, which contributed to the reduction of the repulsive force between same molecules. These findings indicated that the mixed NaOL/DDA surfactants had a great potential in application of mineral flotation.
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Marshall LJ, Matsarskaia O, Schweins R, Adams DJ. Enhancement of the mechanical properties of lysine-containing peptide-based supramolecular hydrogels by chemical cross-linking. SOFT MATTER 2021; 17:8459-8464. [PMID: 34494056 DOI: 10.1039/d1sm01136g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Exposure of lysine-containing peptide-based gelators to the cross-linking agent glutaraldehyde allows tuning of gel mechanical properties. The effect of cross-linking depends on the position of the lysine residue in the peptide chain, the concentration of gelator and the conditions under which cross-linking takes place. Through control of these factors, cross-linking leads to increased gel strength.
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Affiliation(s)
- Libby J Marshall
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Ralf Schweins
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Dave J Adams
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
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19
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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20
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Tan T, Guo Z, Wang Y, Ji Y, Hu J, Zhang Y. Gelation of a Pentapeptide in Alcohols. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8961-8970. [PMID: 34297581 DOI: 10.1021/acs.langmuir.1c00841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Properties of solvents such as polarity and H-bond-forming ability are critical for the formation of an organogel and have a significant impact on the gel behavior, as solvents are the majority of organogel systems. However, so far, there is still a lack of systematic studies regarding the effects of molecular structures of solvents on the characteristics of organogels. Motivated by revealing such a relationship, in this paper, we studied the morphologies of assemblies, gelation behaviors, and secondary structures of a pentapeptide termed EAF-5 in a wide variety of alcohols. The side chains and lengths of carbon chains of the solvent molecules were found to play a critical role in the self-assembly and gelation of EAF-5. EAF-5 was capable of self-assembling into fibers and entangling into a network in alcohols including ethanol, propanol, butanol, n-pentanol, and n-hexanol, which further immobilized the corresponding alcohols to form gels. In these organogels, increasing β-sheet secondary structures of the peptides were formed by introducing side chains and extending the length of primary alcohol molecules. We hypothesized that alcohol molecules with extended lengths and side chains reduced the gelator-solvent interactions and promoted the gelator-gelator interactions, resulting in the self-assembly of EAF-5 into fibril structures and development of gels. These findings provide a new sight into the interactions between gelators and solvents and are helpful for designing peptide-based organogelators.
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Affiliation(s)
- Tingyuan Tan
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Guo
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuwen Ji
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Hu
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yi Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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21
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Synthesis, Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications. Molecules 2021; 26:molecules26154587. [PMID: 34361740 PMCID: PMC8348434 DOI: 10.3390/molecules26154587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/04/2021] [Accepted: 07/17/2021] [Indexed: 12/19/2022] Open
Abstract
There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures.
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22
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Arnittali M, Rissanou AN, Amprazi M, Kokkinidis M, Harmandaris V. Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments. Int J Mol Sci 2021; 22:ijms22115931. [PMID: 34073028 PMCID: PMC8199364 DOI: 10.3390/ijms22115931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023] Open
Abstract
In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.
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Affiliation(s)
- Maria Arnittali
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | - Anastassia N. Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Correspondence: ; Tel.: +30-2810-393746
| | - Maria Amprazi
- Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece; (M.A.); (M.K.)
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece; (M.A.); (M.K.)
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
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23
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Erdoğan H. Cation-based approach to morphological diversity of diphenylalanine dipeptide structures. SOFT MATTER 2021; 17:5221-5230. [PMID: 33949599 DOI: 10.1039/d1sm00083g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Different approaches are taken in order to examine the spontaneous arrangement processes of dipeptide structures. One of these approaches is to examine the effects of common cations on dipeptide structures' self-assembly processes. In this study, the effects of Al3+, Cu2+, Pb2+, Hg2+, Mg2+, Zn2+, Cd2+, Fe2+ and Ni2+ cations on the self-assembly processes of diphenylalanine (FF) dipeptide molecules were investigated. A detailed examination was made of the self-assembly of FF dipeptides in the presence of Hg2+, and a spherical architecture structure was shown. The morphological diversity resulting from the effects of Hg2+ cations at different concentrations on FF dipeptides was explained using Scanning Electron Microscopy (SEM), X-ray Diffraction, (XRD), and Fourier Transform Infrared Spectroscopy (FTIR) techniques. It is thought that this work will contribute to the indexing of the effects of toxic species such as Hg2+ on dipeptides, which are the smallest peptide units obtained. We think that the examination of FF dipeptides in the structures of amyloid plaques, which are thought to affect neurological disorders such as Alzheimer's and Parkinson's, will prompt further studies.
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Affiliation(s)
- Hakan Erdoğan
- University of Health Sciences Turkey, Gülhane Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 06018 Ankara, Turkey.
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Yang J, Chen M, Lee H, Xu Z, Zhou Z, Feng SP, Kim JT. Three-Dimensional Printing of Self-Assembled Dipeptides. ACS APPLIED MATERIALS & INTERFACES 2021; 13:20573-20580. [PMID: 33896166 DOI: 10.1021/acsami.1c03062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peptide-based materials are emerging as smart building blocks for nanobiodevices due to the programmability of their properties via the molecular constituents or arrangements. Many clever molecular self-assembly approaches have been devised to produce peptide crystalline structures. However, their freeform shaping remains a challenge due to the intrinsic self-assembly nature. Here, we report the fabrication of freeform, crystalline diphenylalanine (FF) peptide structures by combining meniscus-guided 3D printing with molecular self-assembly. Self-assembly in 3D-printed FF arises from mild thermal activation under precise temperature control of the build platform. After thorough characterizations, we demonstrate layer-by-layer, crystalline 3D printing with a high spatial resolution of 2 μm laterally and 200 nm vertically. The 3D-printed FF exhibits piezoelectricity originating from its crystalline character, showing the potential to become a key constituent for bioelectronic devices. We expect this technique to open up the possibility to create functional devices based on self-assembled organic materials without design restrictions.
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Affiliation(s)
- Jihyuk Yang
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Mojun Chen
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Heekwon Lee
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhaoyi Xu
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhiwen Zhou
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shien-Ping Feng
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ji Tae Kim
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Rissanou AN, Keliri A, Arnittali M, Harmandaris V. Self-assembly of diphenylalanine peptides on graphene via detailed atomistic simulations. Phys Chem Chem Phys 2021; 22:27645-27657. [PMID: 33283818 DOI: 10.1039/d0cp03671d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, which next is followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200 ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50 ns cylindrical structures, the microscopic signal of the macroscopic fibrillar ones, are formed. Strong π-π* interactions between FF and the graphene lead to a parallel orientation to the graphene layer of the phenyl rings within a characteristic time of 80 ns, similar to the one indicated by the time evolution of the number of adsorbed FF atoms at the surface. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. The self-assembly of dipeptides and their adsorption onto the graphene surface destruct the hydrogen bond network of water, in the vicinity of FF, however, the total number of hydrogen bonds in all systems increases, promoting the formed structures.
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Affiliation(s)
- Anastassia N Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
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To T, Sakamoto Y, Sadakane K, Matsugami M, Takamuku T. Aggregation of the Dipeptide Leu-Gly in Alcohol-Water Binary Solvents Elucidated from the Solvation Structure for Each Moiety. J Phys Chem B 2021; 125:240-252. [PMID: 33395527 DOI: 10.1021/acs.jpcb.0c08809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aggregation of a dipeptide, l-leucine-glycine (Leu-Gly), at 100 mmol dm-3 has been observed in 1,1,1,3,3,3-hexafluoroisopropanol (HFIP)-water and 2-propanol (2-PrOH)-water solvents at various alcohol mole fractions, xA, using the dynamic light scattering technique and molecular dynamics (MD) simulations. Leu-Gly was dissolved into the HFIP solvents at the concentration over the entire xA range, while the dipeptide was not dissolved in the 2-PrOH solvents above xA = 0.6. Interestingly, the MD snapshots showed different shapes of Leu-Gly aggregates in the HFIP and 2-PrOH solvents. A linear-shaped aggregate forms in the former; in contrast, a spherical-shaped aggregate is generated in the latter. The solvation structure of each moiety of Leu-Gly in the HFIP and 2-PrOH solvents was observed using experimental and theoretical techniques,1H and 13C NMR, IR, and 19F-1H HOESY measurements and MD simulations. These results gave us the reasons for the different shapes of Leu-Gly aggregates in both solvents. In the HFIP solvents, most of the moieties of the dipeptide are easily solvated by HFIP. This induces the elongated structure of Leu-Gly, leading to the electrostatic interaction between the N- (NH3+ group) and C- (COO- group) terminals of dipeptide molecules. On the other hand, in the 2-PrOH solvents, water molecules that initially solvate the moieties of Leu-Gly, such as the N- and C-terminals and the peptide linkage, are not easily eliminated even as the xA is close to 0.6. The water molecules can bridge such moieties of Leu-Gly to form spherical-shaped aggregates. The diffusion coefficients of Leu-Gly in both alcohol-water binary solvents were experimentally determined by NMR DOSY to estimate the geometries of the aggregates in the solvents. The sizes of Leu-Gly aggregates obtained by DOSY for both solvent systems were consistent with those estimated from the MD snapshots.
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Affiliation(s)
- Takahiro To
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Yusuke Sakamoto
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto 610-0394, Japan
| | - Masaru Matsugami
- Faculty of Liberal Arts, National Institute of Technology (KOSEN), Kumamoto College, 2659-2 Suya, Koshi, Kumamoto 861-1102, Japan
| | - Toshiyuki Takamuku
- Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
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Self-association process of tetracycline antibiotic in different aqueous solutions: a joint experimental study and molecular dynamics simulation. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-01977-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Das R, Gayakvad B, Shinde SD, Rani J, Jain A, Sahu B. Ultrashort Peptides—A Glimpse into the Structural Modifications and Their Applications as Biomaterials. ACS APPLIED BIO MATERIALS 2020; 3:5474-5499. [DOI: 10.1021/acsabm.0c00544] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bhavinkumar Gayakvad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Jyoti Rani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Alok Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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Rissanou AN, Simatos G, Siachouli P, Harmandaris V, Mitraki A. Self-assembly of Alanine-Isoleucine and Isoleucine-Isoleucine Dipeptides through Atomistic Simulations and Experiments. J Phys Chem B 2020; 124:7102-7114. [PMID: 32697595 DOI: 10.1021/acs.jpcb.0c03025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A detailed investigation of the structural and conformational properties of alanine-isoleucine (Ala-Ile) and isoleucine-isoleucine (Ile-Ile) dipeptides is presented in water and in methanol solvents. We propose a consistent combination of complementary simulation and experimental methods, covering a broad range of length and time scales, from the very short (i.e., atomic level), via all-atom molecular dynamics (MD) simulations, up to the macroscopic one, via scanning electron microscopy (SEM) experiments. The examined samples from both simulations and experiment cover a board range of concentrations since these are usually in different concentration windows (i.e., high values in simulations vs low values in experiments). In the present study, there is an overlapping concentration regime and a qualitative agreement between simulation and experimental results is observed. The effect of temperature on the formed structures is found to be small, from both simulation and experiments, when temperature varies from 278 to 300 K. Furthermore, the differences of Ala-Ile and Ile-Ile dipeptides from dialanine (Ala-Ala) and diphenylalanine (Phe-Phe) dipeptides in similar conditions are highlighted. Based on various measures, the strength of the self-assembly propensity of the four dipeptides in aqueous solutions attains the following order: Phe-Phe > Ala-Ile > Ala-Ala > Ile-Ile.
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Affiliation(s)
- Anastassia N Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-70013 Heraklion, Greece.,Department of Mathematics and Applied Mathematics, University of Crete, GR-70013 Heraklion, Crete, Greece
| | - Georgios Simatos
- Department of Materials Science and Technology, University of Crete, GR-70013 Heraklion, Greece
| | - Panagiota Siachouli
- Department of Mathematics and Applied Mathematics, University of Crete, GR-70013 Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-70013 Heraklion, Greece.,Department of Mathematics and Applied Mathematics, University of Crete, GR-70013 Heraklion, Crete, Greece.,Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, GR-70013 Heraklion, Greece.,Institute of Electronic Structure and Laser, (IESL)-FORTH, 70013 Heraklion, Crete, Greece
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Kadeeja A, Joseph S, Abraham JN. Self-assembly of novel Fmoc-cardanol compounds into hydrogels - analysis based on rheological, structural and thermal properties. SOFT MATTER 2020; 16:6294-6303. [PMID: 32462156 DOI: 10.1039/d0sm00670j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydrogels of low molecular weight molecules are particularly appealing for various biomedical applications such as drug delivery, tissue engineering, and antitumor therapy due to their excellent biocompatibility, biodegradability, and easy availability. Fmoc-peptide hydrogels form an essential category of these hydrogels. Herein we report a new class of Fmoc hydrogels in which cardanol (3-pentadecyl phenol (PDP)) is covalently linked with fluorenylmethyloxycarbonyl group. Cardanol is a plant-based renewable raw material, readily obtained from Cashew Nut Shell Liquid (CNSL). The long aliphatic chain of pentadecyl phenol helps in bringing a structural incompatibility and generates different nanostructures such as nanospheres, nanotapes, and nanofibers depending on Fmoc substitution and the solvents used. Stable hydrogels were formed from Fmoc-PDP in DMSO/H2O, and the critical aggregation concentration (CAC) and critical gelation concentration (CGC) were determined. The role of non-covalent forces such as hydrogen-bonding, hydrophobicity, and π-π stacking interactions in governing self-assembly to hydrogel formation was studied for Fmoc, DiFmoc and Boc groups attached to PDP. The thermal properties were analyzed, and smectic and nematic phases were identified for the molecules depending on the substitutions involved. Overall the study supports the mechanisms of aggregation and gelation in novel Fmoc-cardanol derivatives.
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Affiliation(s)
- Aliya Kadeeja
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr Homibhabha Road, Pune, 411008, India.
| | - Seena Joseph
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr Homibhabha Road, Pune, 411008, India.
| | - Jancy Nixon Abraham
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr Homibhabha Road, Pune, 411008, India.
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31
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Banerjee P, Mondal D, Ghosh M, Mukherjee D, Nandi PK, Maiti TK, Sarkar N. Selective Self-Assembly of 5-Fluorouracil through Nonlinear Solvent Response Modulates Membrane Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2707-2719. [PMID: 32097563 DOI: 10.1021/acs.langmuir.9b03544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Controllable self-assembly and understanding of the interaction between single metabolite fibrils and live-cell membranes have paramount importance in providing minimal treatment in several neurodegenerative disorders. Here, utilizing the nonlinear nature and peculiar hydrogen bonding behavior of the dimethyl sulfoxide (DMSO)-water mixture, the selective self-assembly of a single metabolite 5-fluorouracil (5-FU) is achieved. A direct correlation between water availability and selective self-assembly of 5-FU is ratified from the excited-state dynamics. The specific fibrillar structures of 5-FU exhibit a great potential to modulate live cell membrane fluidity and model membrane lipid distribution. After 5-FU fibril addition, a disorder of H-bonded water molecules arises several layers beyond the first hydration shell of the polar headgroups, which essentially modifies interfacial water structure and dynamics. Overall, our results shed light on the role of solvent to govern specific self-assembly and also lay the foundation accounting for the earlier stage of several diseases and multidrug resistance.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Meghna Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Devdeep Mukherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Pratyush Kiran Nandi
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Tapas Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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32
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Banerjee P, Pyne A, Sarkar N. Understanding the Self-Assembling Behavior of Biological Building Block Molecules: A Spectroscopic and Microscopic Approach. J Phys Chem B 2020; 124:2065-2080. [PMID: 32081003 DOI: 10.1021/acs.jpcb.9b09123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
"Mother nature" utilizes molecular self-assembly as an efficient tool to design several fascinating supramolecular architectures from simple building blocks like amino acids, peptides, and nucleobases. The self-assembling behavior of various biologically important molecules, morphological outcomes, molecular mechanism of association, and finally their applications in the real world draw broad interest from chemical and biological point of views. In this present Feature Article, the amyloid hypothesis is extended to include nonproteinaceous single metabolites that invoke a new paradigm for the pathology of inborn metabolic disorders. In this scenario, we dedicate this paper to understanding the morphological consequences and mechanistic insight of the self-assembly of some important amino acids (e.g., l-phenylalanine, l-tyrosine, glycine, etc.) and nucleobases (adenine and eight uracil moiety derivatives). Using proper spectroscopic and microscopic tools, distinct assembling mechanisms of different amino acids and nucleobases have been established. Again, lanthanides, polyphenolic compounds such as crown ethers, and a worldwide drink, beer, are elegantly employed as inhibitors of the resulting fibrillar aggregated structures. As a consequence, this study will cover literally a vast region in the self-assembling outcomes of single biologically important molecules, and therefore, we expect that a detailed understanding of such morphological outcomes using spectroscopic and microscopic approaches may open a new paradigm in this burgeoning field.
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Affiliation(s)
- Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Arghajit Pyne
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302 WB, India
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33
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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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34
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Abraham JN, Pawar P, Kootteri DK. Self‐Assembly of Di‐Guanine Peptide Nucleic Acid Amphiphiles into Fractal Patterns. ChemistrySelect 2019. [DOI: 10.1002/slct.201902677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jancy N. Abraham
- Polymer Science and Engineering DivisionCSIR-National Chemical Laboratory Dr. Homibhabha road Pune– 411008 India
| | - Prabhakar Pawar
- Indian Institute of Science Education and Research Dr. Homibhabha road Pune– 411008 India
| | - Dilna K. Kootteri
- Polymer Science and Engineering DivisionCSIR-National Chemical Laboratory Dr. Homibhabha road Pune– 411008 India
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35
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Dutta R, Sil S, Kundu S, Nandi S, Sarkar N. Multi-stimuli responsive fabrication of supramolecular assemblies using ionic self-assembly approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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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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37
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Xiong Q, Jiang Y, Cai X, Yang F, Li Z, Han W. Conformation Dependence of Diphenylalanine Self-Assembly Structures and Dynamics: Insights from Hybrid-Resolution Simulations. ACS NANO 2019; 13:4455-4468. [PMID: 30869864 DOI: 10.1021/acsnano.8b09741] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The molecular design of peptide-assembled nanostructures relies on extensive knowledge pertaining to the relationship between conformational features of peptide constituents and their behavior regarding self-assembly, and characterizing the conformational details of peptides during their self-assembly is experimentally challenging. Here, we demonstrate that a hybrid-resolution modeling method can be employed to investigate the role that conformation plays during the assembly of terminally capped diphenylalanines (FF) through microsecond simulations of hundreds or thousands of peptides. Our simulations discovered tubular or vesicular nanostructures that were consistent with experimental observation while reproducing critical self-assembly concentration and secondary structure contents in the assemblies that were measured in our experiments. The atomic details provided by our method allowed us to uncover diverse FF conformations and conformation dependence of assembled nanostructures. We found that the assembled morphologies and the molecular packing of FFs in the observed assemblies are linked closely with side-chain angle and peptide bond orientation, respectively. Of various conformations accessible to soluble FFs, only a select few are compatible with the assembled morphologies in water. A conformation resembling a FF crystal, in particular, became predominant due to its ability to permit highly ordered and energetically favorable FF packing in aqueous assemblies. Strikingly, several conformations incompatible with the assemblies arose transiently as intermediates, facilitating key steps of the assembly process. The molecular rationale behind the role of these intermediate conformations were further explained. Collectively, the structural details reported here advance the understanding of the FF self-assembly mechanism, and our method shows promise for studying peptide-assembled nanostructures and their rational design.
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Affiliation(s)
- Qinsi Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Xiang Cai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
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38
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Anderson J, Lake PT, McCullagh M. Initial Aggregation and Ordering Mechanism of Diphenylalanine from Microsecond All-Atom Molecular Dynamics Simulations. J Phys Chem B 2018; 122:12331-12341. [PMID: 30511861 DOI: 10.1021/acs.jpcb.8b10335] [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
Self-assembled diphenylalanine (FF) nanostructures have recently been demonstrated to be interesting materials for antibacterial and anticancer applications. These applications, among others, seek to take advantage of the high-order and resulting appealing physical properties of FF nanostructures by modifying the peptide in some way to achieve specific functionality. To rationally design modifications to the dipeptide that allow for this behavior, the driving forces of FF self-assembly must be understood. Molecular simulations have been utilized to assess these properties but have yielded conflicting conclusions due to inconsistencies in models chosen as well as the lack of quantitative analyses on the specific driving forces. Here, we present an all-atom explicit solvent molecular dynamics-based study on different length scales of FF aggregation. We utilize a free energy decomposition analysis as well as a dimer cluster analysis to identify the initial aggregation driving force to be FF intermolecular electrostatics, whereas solvent-mediated forces drive crystal growth. These data are consistent with the hypothesis that all hydrophobic dipeptides will have a similar initial aggregation mechanism until a critical aggregate size is reached, at which point crystallization occurs and subsequent crystal growth is dominated by solvent-mediated forces. We demonstrate that this proposed mechanism is testable by infrared spectroscopy focusing on the blueshift of the amide I peak as well as the ordering of the carboxylate peak.
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Affiliation(s)
- Jakob Anderson
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Peter T Lake
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
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40
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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41
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Brown N, Lei J, Zhan C, Shimon LJW, Adler-Abramovich L, Wei G, Gazit E. Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System. ACS NANO 2018; 12:3253-3262. [PMID: 29558116 PMCID: PMC6333291 DOI: 10.1021/acsnano.7b07723] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.
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Affiliation(s)
- Noam Brown
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Chemical Physics, School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiangtao Lei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People’s Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People’s Republic of China
| | - Linda J. W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, the Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People’s Republic of China
- Corresponding Authors: .
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding Authors: .
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Mushnoori S, Schmidt K, Nanda V, Dutt M. Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition. Org Biomol Chem 2018; 16:2499-2507. [PMID: 29565077 DOI: 10.1039/c8ob00130h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Harnessing the self-assembly of peptide sequences has demonstrated great promise in the domain of creating high precision shape-tunable biomaterials. The unique properties of peptides allow for a building block approach to material design. In this study, self-assembly of mixed systems encompassing two peptide sequences with identical hydrophobic regions and distinct polar segments is investigated. The two peptide sequences are diphenylalanine and phenylalanine-asparagine-phenylalanine. The study examines the impact of molecular composition (namely, the total peptide concentration and the relative tripeptide concentration) on the morphology of the self-assembled hybrid biological material. We report a rich polymorphism in the assemblies of these peptides and explain the relationship between the peptide sequence, concentration and the morphology of the supramolecular assembly.
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Affiliation(s)
- Srinivas Mushnoori
- Department of Chemical and Biochemical Engineering, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, New Jersey, USA.
| | - Kassandra Schmidt
- Department of Biomedical Engineering, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, New Jersey, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, New Jersey, USA and Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, New Jersey, USA
| | - Meenakshi Dutt
- Department of Chemical and Biochemical Engineering, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, New Jersey, USA.
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Lee H, In B, Mehta PK, Kishore MYLN, Lee KH. Dual Role of a Fluorescent Peptidyl Probe Based on Self-Assembly for the Detection of Heparin and for the Inhibition of the Heparin-Digestive Enzyme Reaction. ACS APPLIED MATERIALS & INTERFACES 2018; 10:2282-2290. [PMID: 29280619 DOI: 10.1021/acsami.7b15411] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The detection of fluorescent probes for biomolecules and control of the function of a complex through a recognition process have not been investigated intensively. A fluorescent peptidyl probe (1) based on the self-assembly stimulated by heparin was synthesized. The fluorescent probe with an aggregation-induced emission fluorophore formed a self-assembling complex with heparin, resulting in a sensitive and selective turn-on response to heparin compared to its biological competitors. The detection limits for heparin were measured to be 138.0 pM (R2 = 0.976) in aqueous solution and 2.6 nM (R2 = 0.996) in aqueous solution containing human serum. Nanosized aggregates formed through the self-assembly of the complex showed potent resistance against the heparin-digestive enzyme. The dual role of the probe for the detection of heparin and the inhibition of heparinase-mediated digestion through the recognition process was used for the real-time monitoring of the enzyme activity of heparinase for the digestion of heparin. Furthermore, the dual role of the probe was applied for the detection of the oversulfated chondroitin sulfate contaminant in heparin.
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Affiliation(s)
- Hyeri Lee
- Center for Design and Applications of Molecular Catalysts, Department of Chemistry and Chemical Engineering, Inha University , Incheon 402-751, South Korea
| | - Byunggyu In
- Center for Design and Applications of Molecular Catalysts, Department of Chemistry and Chemical Engineering, Inha University , Incheon 402-751, South Korea
| | - Pramod Kumar Mehta
- Center for Design and Applications of Molecular Catalysts, Department of Chemistry and Chemical Engineering, Inha University , Incheon 402-751, South Korea
| | - Mallela Y L N Kishore
- Center for Design and Applications of Molecular Catalysts, Department of Chemistry and Chemical Engineering, Inha University , Incheon 402-751, South Korea
| | - Keun-Hyeung Lee
- Center for Design and Applications of Molecular Catalysts, Department of Chemistry and Chemical Engineering, Inha University , Incheon 402-751, South Korea
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Xing R, Yuan C, Li S, Song J, Li J, Yan X. Charge-Induced Secondary Structure Transformation of Amyloid-Derived Dipeptide Assemblies from β-Sheet to α-Helix. Angew Chem Int Ed Engl 2018; 57:1537-1542. [DOI: 10.1002/anie.201710642] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/12/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Ruirui Xing
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
| | - Jingwen Song
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Junbai Li
- Key Laboratory of Colloid and Interface Science, Center for Molecular Sciences; Institute of Chemistry; Chinese Academy of Sciences; 100190 Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
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45
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Xing R, Yuan C, Li S, Song J, Li J, Yan X. Charge-Induced Secondary Structure Transformation of Amyloid-Derived Dipeptide Assemblies from β-Sheet to α-Helix. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710642] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ruirui Xing
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
| | - Jingwen Song
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Junbai Li
- Key Laboratory of Colloid and Interface Science, Center for Molecular Sciences; Institute of Chemistry; Chinese Academy of Sciences; 100190 Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
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46
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Parappurath A, Abraham JN. Novel Pentadecyl Phenol-Tagged L-Tryptophan Molecules: Synthesis, Self- Assembly and Liquid Crystalline Properties. ChemistrySelect 2018. [DOI: 10.1002/slct.201702171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Akhil Parappurath
- Polymer Science and Engineering Division CSIR-National Chemical Laboratory; Dr. Homibhabha road Pune India - 411008
| | - Jancy Nixon Abraham
- Polymer Science and Engineering Division CSIR-National Chemical Laboratory; Dr. Homibhabha road Pune India - 411008
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47
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Uyaver S, Hernandez HW, Habiboglu MG. Self-assembly of aromatic amino acids: a molecular dynamics study. Phys Chem Chem Phys 2018; 20:30525-30536. [DOI: 10.1039/c8cp06239k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Common structures identified in the assembly of aromatic amino acids and their mixtures include the four-fold tube (a and b) and the zig-zag structure (c and d).
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48
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Kumar V, Singh R, Joshi KB. Biotin–avidin interaction triggers conversion of triskelion peptide nanotori into nanochains. NEW J CHEM 2018. [DOI: 10.1039/c7nj04248e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Triskelion biotinylated peptide is self-assembled into nanotorus structures followed by dimerization and chain formation in the presence of avidin.
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Affiliation(s)
- Vikas Kumar
- Dr Harisingh Gour Central University Sagar
- India
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49
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Subbalakshmi C, Basak P, Nagaraj R. Self-assembly of t-butyloxycarbonyl protected dipeptide methyl esters composed of leucine, isoleucine, and valine into highly organized structures from alcohol and aqueous alcohol mixtures. Biopolymers 2017; 108. [DOI: 10.1002/bip.23033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/05/2017] [Accepted: 05/26/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Chivukula Subbalakshmi
- CSIR-Centre for Cellular and Molecular Biology; Uppal Road; Hyderabad Telangana 500007 India
| | - Pratyay Basak
- Nanomaterials Laboratory, Inorganic & Physical Chemistry Division; CSIR-Indian Institute of Chemical Technology, Uppal Road; Hyderabad Telangana 500007 India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology; Uppal Road; Hyderabad Telangana 500007 India
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50
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Seoudi RS, Mechler A. Design Principles of Peptide Based Self-Assembled Nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:51-94. [DOI: 10.1007/978-3-319-66095-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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