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Dykeman-Bermingham PA, Stingaciu LR, Do C, Knight AS. Dynamic Implications of Noncovalent Interactions in Amphiphilic Single-Chain Polymer Nanoparticles. ACS Macro Lett 2024; 13:889-895. [PMID: 38959296 DOI: 10.1021/acsmacrolett.4c00269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Single-chain polymer nanoparticles (SCNPs) combine the chemical diversity of synthetic polymers with the intricate structure of biopolymers, generating versatile biomimetic materials. The mobility of polymer chain segments at length scales similar to secondary structural elements in proteins is critical to SCNP structure and thus function. However, the influence of noncovalent interactions used to form SCNPs (e.g., hydrogen-bonding and biomimetic secondary-like structure) on these conformational dynamics is challenging to quantitatively assess. To isolate the effects of noncovalent interactions on SCNP structure and conformational dynamics, we synthesized a series of amphiphilic copolymers containing dimethylacrylamide and monomers capable of forming these different interactions: (1) di(phenylalanine) acrylamide that forms intramolecular β-sheet-like cross-links, (2) phenylalanine acrylamide that forms hydrogen-bonds but lacks a defined local structure, and (3) benzyl acrylamide that has the lowest propensity for hydrogen-bonding. Each SCNP formed folded structures comparable to those of intrinsically disordered proteins, as observed by size exclusion chromatography and small angle neutron scattering. The dynamics of these polymers, as characterized by a combination of dynamic light scattering and neutron spin echo spectroscopy, was well described using the Zimm with internal friction (ZIF) model, highlighting the role of each noncovalent interaction to additively restrict the internal relaxations of SCNPs. These results demonstrate the utility of local scale interactions to control SCNP polymer dynamics, guiding the design of functional biomimetic materials with refined binding sites and tunable kinetics.
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Affiliation(s)
- Peter A Dykeman-Bermingham
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Laura R Stingaciu
- NScD, SNS, Oak Ridge National Laboratory, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Changwoo Do
- NScD, SNS, Oak Ridge National Laboratory, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Abigail S Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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2
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Dykeman-Bermingham PA, Bogen MP, Chittari SS, Grizzard SF, Knight AS. Tailoring Hierarchical Structure and Rare Earth Affinity of Compositionally Identical Polymers via Sequence Control. J Am Chem Soc 2024; 146:8607-8617. [PMID: 38470430 DOI: 10.1021/jacs.4c00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Macromolecule sequence, structure, and function are inherently intertwined. While well-established relationships exist in proteins, they are more challenging to define for synthetic polymer nanoparticles due to their molecular weight, sequence, and conformational dispersities. To explore the impact of sequence on nanoparticle structure, we synthesized a set of 16 compositionally identical, sequence-controlled polymers with distinct monomer patterning of dimethyl acrylamide and a bioinspired, structure-driving di(phenylalanine) acrylamide (FF). Sequence control was achieved through multiblock polymerizations, yielding unique ensembles of polymer sequences which were simulated by kinetic Monte Carlo simulations. Systematic analysis of the global (tertiary- and quaternary-like) structure in this amphiphilic copolymer series revealed the effect of multiple sequence descriptors: the number of domains, the hydropathy of terminal domains, and the patchiness (density) of FF within a domain, each of which impacted both chain collapse and the distribution of single- and multichain assemblies. Furthermore, both the conformational freedom of chain segments and local-scale, β-sheet-like interactions were sensitive to the patchiness of FF. To connect sequence, structure, and target function, we evaluated an additional series of nine sequence-controlled copolymers as sequestrants for rare earth elements (REEs) by incorporating a functional acrylic acid monomer into select polymer scaffolds. We identified key sequence variables that influence the binding affinity, capacity, and selectivity of the polymers for REEs. Collectively, these results highlight the potential of and boundaries of sequence control via multiblock polymerizations to drive primary sequence ensembles hierarchical structures, and ultimately the functionality of compositionally identical polymeric materials.
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Affiliation(s)
- Peter A Dykeman-Bermingham
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew P Bogen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Supraja S Chittari
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Savannah F Grizzard
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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3
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Prajapati KP, Anand BG, Ansari M, Tiku AB, Kar K. Tryptophan self-assembly yields cytotoxic nanofibers containing amyloid-mimicking and cross-seeding competent conformers. NANOSCALE 2022; 14:16270-16285. [PMID: 36300424 DOI: 10.1039/d2nr03544h] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Dietary consumption of Trp via protein-based foods is essential for the maintenance of crucial metabolic processes including the synthesis of proteins and several vital metabolites such as serotonin, melatonin, acetyl CoA, and NADP. However, the abnormal build-up of Trp is known to cause familial hypertryptophanemia and several brain-related medical complications. The molecular mechanism of the onset of such Trp-driven health issues is largely unknown. Here, we show that Trp, under the physiologically mimicked conditions of temperature and buffer, undergoes a concentration driven self-assembly process, yielding amyloid-mimicking nanofibers. Viable H-bonds, π-π interactions and hydrophobic contacts between optimally coordinated Trp molecules become important factors for the formation of a Trp nanoassembly that displays a hydrophobic exterior and a hydrophilic interior. Importantly, Trp nanofibers were found to possess high affinity for native proteins, and they act as cross-seeding competent conformers capable of nucleating amyloid formation in globular proteins including whey protein β-lactoglobulin and type II diabetes linked insulin hormone. Moreover, these amyloid mimicking Trp nanostructures showed toxic effects on neuroblastoma cells. Since the key symptoms in hypertryptophanemia such as behavioural defects and brain-damaging oxidative stress are also observed in amyloid related disorders, our findings on amyloid-like Trp-nanofibers may help in the mechanistic understanding of Trp-related complications and these findings are equally important for innovation in applied nanomaterials design and strategies.
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Affiliation(s)
- Kailash Prasad Prajapati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| | - Bibin Gnanadhason Anand
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| | - Masihuzzaman Ansari
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| | - Ashu Bhan Tiku
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| | - Karunakar Kar
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
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4
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Warren JL, Dykeman-Bermingham PA, Knight AS. Controlling Amphiphilic Polymer Folding beyond the Primary Structure with Protein-Mimetic Di(Phenylalanine). J Am Chem Soc 2021; 143:13228-13234. [PMID: 34375094 PMCID: PMC9362848 DOI: 10.1021/jacs.1c05659] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While methods for polymer synthesis have proliferated, their functionality pales in comparison to natural biopolymers-strategies are limited for building the intricate network of noncovalent interactions necessary to elicit complex, protein-like functions. Using a bioinspired di(phenylalanine) acrylamide (FF) monomer, we explored the impact of various noncovalent interactions in generating ordered assembled structures. Amphiphilic copolymers were synthesized that exhibit β-sheet-like local structure upon collapsing into single-chain assemblies in aqueous environments. Systematic analysis of a series of amphiphilic copolymers illustrated that the global collapse is primarily driven by hydrophobic forces. Hydrogen-bonding and aromatic interactions stabilize local structure, as β-sheet-like interactions were identified via circular dichroism and thioflavin T fluorescence. Similar analysis of phenylalanine (F) and alanine-phenylalanine acrylamide (AF) copolymers found that distancing the aromatic residue from the polymer backbone is sufficient to induce β-sheet-like local structure akin to the FF copolymers; however, the interactions between AF subunits are less stable than those formed by FF. Further, hydrogen-bond donating hydrophilic monomers disrupt internal structure formed by FF within collapsed assemblies. Collectively, these results illuminate design principles for the facile incorporation of multiple facets of protein-mimetic, higher-order structure within folded synthetic polymers.
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Affiliation(s)
- Jacqueline L Warren
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter A Dykeman-Bermingham
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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5
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Rohani Shirvan A, Hemmatinejad N, Bahrami SH, Bashari A. Synthesis and Characterization of Phenylalanine Nanotubes as Green pH‐Responsive Drug Nanocarriers. ChemistrySelect 2020. [DOI: 10.1002/slct.202003281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Nahid Hemmatinejad
- Textile Engineering Department Amirkabir University of Technology Tehran Iran
| | - Seyed Hajir Bahrami
- Textile Engineering Department Amirkabir University of Technology Tehran Iran
| | - Azadeh Bashari
- Textile Engineering Department Amirkabir University of Technology Tehran Iran
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Porter SL, Coulter SM, Pentlavalli S, Laverty G. Pharmaceutical Formulation and Characterization of Dipeptide Nanotubes for Drug Delivery Applications. Macromol Biosci 2020; 20:e2000115. [PMID: 32484299 DOI: 10.1002/mabi.202000115] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/03/2020] [Indexed: 12/24/2022]
Abstract
Peptide nanotubes are promising materials for a variety of biomedical applications with ultrashort (≤7 amino acids) forms providing particular promise for clinical translation. The manufacture of peptide nanotubes has, however, been associated with toxic organic solvents restricting clinical use. The purpose of this work is to formulate dipeptide nanotubes using mild techniques easily translated to industrial upscale and to characterize their physiochemical and biological properties. Phenylalanine-phenylalanine variants can be successfully formulated using distilled water as demonstrated here. Formulations are homogenous in shape (tubular), with apparent size (50-260 nm) and a zeta potential of up to +30 mV. L-(H2 N-FF-COOH), and D-enantiomers (H2 N-ff-COOH) demonstrate no toxicity against glioblastoma cells and are explored for ability to deliver a model hydrophilic molecule, sodium fluorescein, at pH 5.5 (tumor) and 7.4 (physiological). Peptide nanotubes loaded with >85% sodium fluorescein, demonstrate burst release characteristics, fitting the Weibull model of drug release. This research provides important data contributing to the pharmaceutical formulation of peptide nanotubes as drug delivery platforms for hydrophilic drugs.
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Affiliation(s)
- Simon L Porter
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Co Antrim, Belfast, Northern Ireland, BT9 7BL, UK
| | - Sophie M Coulter
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Co Antrim, Belfast, Northern Ireland, BT9 7BL, UK
| | - Sreekanth Pentlavalli
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Co Antrim, Belfast, Northern Ireland, BT9 7BL, UK
| | - Garry Laverty
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Co Antrim, Belfast, Northern Ireland, BT9 7BL, UK
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7
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Trapani G, Caruso VCL, Cucci LM, Attanasio F, Tabbì G, Forte G, La Mendola D, Satriano C. Graphene Oxide Nanosheets Tailored With Aromatic Dipeptide Nanoassemblies for a Tuneable Interaction With Cell Membranes. Front Bioeng Biotechnol 2020; 8:427. [PMID: 32457892 PMCID: PMC7227426 DOI: 10.3389/fbioe.2020.00427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
Engineered graphene-based derivatives are attractive and promising candidates for nanomedicine applications because of their versatility as 2D nanomaterials. However, the safe application of these materials needs to solve the still unanswered issue of graphene nanotoxicity. In this work, we investigated the self-assembly of dityrosine peptides driven by graphene oxide (GO) and/or copper ions in the comparison with the more hydrophobic diphenylalanine dipeptide. To scrutinize the peptide aggregation process, in the absence or presence of GO and/or Cu2+, we used atomic force microscopy, circular dichroism, UV-visible, fluorescence and electron paramagnetic resonance spectroscopies. The perturbative effect by the hybrid nanomaterials made of peptide-decorated GO nanosheets on model cell membranes of supported lipid bilayers was investigated. In particular, quartz crystal microbalance with dissipation monitoring and fluorescence recovery after photobleaching techniques were used to track the changes in the viscoelastic properties and fluidity of the cell membrane, respectively. Also, cellular experiments with two model tumour cell lines at a short time of incubation, evidenced the high potential of this approach to set up versatile nanoplatforms for nanomedicine and theranostic applications.
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Affiliation(s)
- Giuseppe Trapani
- Scuola Superiore di Catania, University of Catania, Catania, Italy
| | | | - Lorena Maria Cucci
- Department of Chemical Sciences, Nano Hybrid BioInterfaces Lab (NHBIL), University of Catania, Catania, Italy
| | | | - Giovanni Tabbì
- Institute of Crystallography - National Council of Research, Catania, Italy
| | - Giuseppe Forte
- Department of Pharmaceutical Sciences, University of Catania, Catania, Italy
| | | | - Cristina Satriano
- Department of Chemical Sciences, Nano Hybrid BioInterfaces Lab (NHBIL), University of Catania, Catania, Italy
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8
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Tong X, Qiu Y, Zhao X, Xiong B, Liao R, Peng H, Liao Y, Xie X. Visible light-triggered gel-to-sol transition in halogen-bond-based supramolecules. SOFT MATTER 2019; 15:6411-6417. [PMID: 31334529 DOI: 10.1039/c9sm01310e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photoresponsive supramolecular gels have aroused continuous attention because of their extensive applications; however, most studies utilize UV light, which inevitably brings about some health and environmental issues. The halogen bond is an important driving force for constructing supramolecules due to its high directionality, tunable strength, good hydrophobicity, and large size of the halogen atoms. Yet, it still remains a formidable challenge to utilize halogen bonds as a driving force to fabricate a visible light responsive gel. In this work, to fabricate such a gel, azopyridine-containing Azopy-Cn (n = 8, 10, 12) was selected as a halogen bond acceptor, while 1,2-bis(2,3,5,6-tetrafluoro-4-iodophenyl)diazene (BTFIPD) was chosen as both the halogen bond donor and visible light responsive moiety. The visible light response of BTFIPD resulted from the significant separation of n-π* energy levels between trans and cis isomers due to the introduction of an electron-withdrawing group (fluorine) to azobenzene at the ortho-position. Interestingly, the gel exhibited a good gel-to-sol transition behavior upon green light irradiation. At the same time, the morphologies varied from uniform narrow flakes to broad sheets with increasing illumination time. We provide an environmentally-friendly visible light-triggered method to regulate the phase transition of supramolecular materials in applications ranging from energy conversion to information storage.
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Affiliation(s)
- Xun Tong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yuan Qiu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xiaoyu Zhao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Bijin Xiong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Rongzhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Haiyan Peng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yonggui Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China. and National Anti-counterfeit Engineering Research Center, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaolin Xie
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China. and National Anti-counterfeit Engineering Research Center, Huazhong University of Science and Technology, Wuhan 430074, China
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9
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New self-assembled archetypes in crown ether substituted $$\Delta ^\mathrm{{Z}}\hbox {Phe}$$ containing tripeptides. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1623-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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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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11
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Gour N, Kanth P. C, Koshti B, Kshtriya V, Shah D, Patel S, Agrawal-Rajput R, Pandey MK. Amyloid-like Structures Formed by Single Amino Acid Self-Assemblies of Cysteine and Methionine. ACS Chem Neurosci 2019; 10:1230-1239. [PMID: 30380833 DOI: 10.1021/acschemneuro.8b00310] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report for the very first time the discovery of amyloid-like self-assemblies formed by the nonaromatic single amino acids cysteine (Cys) and methionine (Met) under neutral aqueous conditions. The structure formation was assessed and characterized by various microscopic and spectroscopic techniques such as optical microscopy, phase contrast microscopy, scanning electron microscopy, and transmission electron microscopy. The mechanism of self-assembly and the role of hydrogen bonding and thiol interactions of Cys and Met were assessed by Fourier transform infrared spectroscopy, thermogravimetric analysis, X-ray diffraction, and solid state NMR along with various control experiments. In addition, molecular dynamics simulations were carried out to gain insight into assembly initiation. Further, Thioflavin T and Congo red binding assays with Cys and Met structures indicated that these single amino acid assemblies may have amyloid-like characteristics. To understand the biological significance of the Cys and Met structures, cytotoxicity assays of the assemblies were performed on human neuroblastoma IMR-32 cells and monkey kidney cells (COS-7). The results revealed that both Cys and Met fibers were cytotoxic. The cell viability assay further supported the hypothesis that aggregation of single amino acid may contribute to the etiology of metabolic disorders like cystinuria and hypermethioninemia. The results presented in this study are striking, and to the best of our knowledge this is the first report which demonstrates that nonaromatic amino acids like Cys and Met can undergo spontaneous self-assembly to form amyloidogenic aggregates. The results presented are also consistent with the established generic amyloid hypothesis and support a new paradigm for the study of the etiology of single amino acid initiated metabolic disorders in amyloid related diseases.
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Affiliation(s)
- Nidhi Gour
- Centre of Engineering and Enterprise, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
| | - Chandra Kanth P.
- Department of Science, School of Technology, Pandit Deendayal Petroleum University, Gandhinagar, Gujarat 382007, India
| | - Bharti Koshti
- Centre of Engineering and Enterprise, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
| | - Vivekshinh Kshtriya
- Centre of Engineering and Enterprise, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
| | - Dhruvi Shah
- School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
| | - Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai, Maharashtra 400098, India
| | - Reena Agrawal-Rajput
- School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
| | - Manoj K. Pandey
- Department of Science, School of Technology, Pandit Deendayal Petroleum University, Gandhinagar, Gujarat 382007, India
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12
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Hu H, Qiu Y, Wang J, Zhao D, Wang H, Wang Q, Liao Y, Peng H, Xie X. Photomodulated Morphologies in Halogen Bond–Driven Assembly during Gel–Sol Transition. Macromol Rapid Commun 2018; 40:e1800629. [DOI: 10.1002/marc.201800629] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/30/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Haisi Hu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Yuan Qiu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Jing Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Dongxu Zhao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Hong Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Qin Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Yonggui Liao
- Sino–US Joint Research Center on Liquid Crystal Chemistry and Physics National Anti‐counterfeit Engineering Research CenterHuazhong University of Science and Technology Wuhan 430074 China
| | - Haiyan Peng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 China
| | - Xiaolin Xie
- Sino–US Joint Research Center on Liquid Crystal Chemistry and Physics National Anti‐counterfeit Engineering Research CenterHuazhong University of Science and Technology Wuhan 430074 China
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13
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Exploring the aggregation-prone regions from structural domains of human TDP-43. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:286-296. [PMID: 30315897 DOI: 10.1016/j.bbapap.2018.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/15/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
Abstract
TDP-43 (transactive- response DNA binding protein) amazes structural biologist as its aberrant ubiquitinated cytosolic inclusions is largely involved in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). An important question in TDP-43 research is to identify the structural region mediating the formation of cytoplasmic pathological aggregates. In this study, we attempted to delineate the aggregation-prone sequences of the structural domain of TDP-43. Here, we investigated the self-assembly of peptides of TDP-43 using aggregation prediction algorithms, Zipper DB and AMYLPRED2. The three aggregation-prone peptides identified were from N-terminal domain (24GTVLLSTV31), and RNA recognition motifs, RRM1 (128GEVLMVQV135) and RRM2 (247DLIIKGIS254). Furthermore, the amyloid fibril forming propensities of these peptides were analyzed through different biophysical techniques and molecular dynamics simulation. Our study shows the different aggregation ability of conserved stretches in structural domain of TDP-43 that will possibly induce full-length aggregation of TDP-43 in vivo. The peptide form RRM2 demonstrates the higher intrinsic amyloid forming propensity and suggests that RRM2 might form the structural core of TDP-43 aggregation seen in vivo. The results of this study would help in designing peptide based inhibitors of TDP-43 aggregation.
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14
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Yin H, Dumur F, Niu Y, Ayhan MM, Grauby O, Liu W, Wang C, Siri D, Rosas R, Tonetto A, Gigmes D, Wang R, Bardelang D, Ouari O. Chameleonic Dye Adapts to Various Environments Shining on Macrocycles or Peptide and Polysaccharide Aggregates. ACS APPLIED MATERIALS & INTERFACES 2017; 9:33220-33228. [PMID: 28857543 DOI: 10.1021/acsami.7b06634] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This work describes latent fluorescence particles (LFPs) based on a new environmentally sensitive carbazole compound aggregated in water and their use as sensors for probing various cavitands and the different stages of aggregating systems. Cyclodextrins (CDs), cucurbit[n]urils (CB[n], n = 6, 7, 8), and a resorcinarene capsule were used to study the dynamic nature of the LFPs. The fluorescence was dramatically enhanced by a proposed disaggregation-induced emission enhancement (DIEE) mechanism with specific features for CB[n]. Then, the aggregated states of the dipeptides Leu-Leu, Phe-Phe, and Fmoc-Leu-Leu (vesicles, crystals, fibers) were studied by fluorescence spectroscopy and confocal fluorescence microscopy thanks to the adaptive and emissive behavior of the LFPs, allowing us to study an interesting polymorphism phenomenon. The LFPs have then been used in the sensing of the aggregation of the polysaccharide alginate, for which distinct fluorescence turn-on is detected upon stepwise biopolymer assembly, and for amylose detection. The carbazole particles not only adapt to various environments but also display multicolor fluorescent signals. They can be used for the fast probing of the aggregation propensity of newly prepared molecules or biologically relevant compounds or to accelerate the discovery of new macrocycles or of self-assembling peptides in water.
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Affiliation(s)
- Hang Yin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | | | - Yiming Niu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | - Mehmet M Ayhan
- Aix Marseille Univ , CNRS, ICR, Marseille, France
- Department of Chemistry, Gebze Technical University , P.K.:141, 41400 Gebze, Kocaeli, Turkey
| | - Olivier Grauby
- Aix Marseille Univ and CINaM , Campus de Luminy, Marseille, France
| | - Wei Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
| | - Didier Siri
- Aix Marseille Univ , CNRS, ICR, Marseille, France
| | - Roselyne Rosas
- Aix Marseille Univ , CNRS, Spectropole, FR 1739, Marseille, France
| | - Alain Tonetto
- Aix Marseille Univ , Centrale Marseille, CNRS, Fédération Sciences Chimiques Marseille (FR 1739) - PRATIM, 13331 Marseille, France
| | | | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau, China
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15
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Rajbhandary A, Nilsson BL. Investigating the effects of peptoid substitutions in self-assembly of Fmoc-diphenylalanine derivatives. Biopolymers 2017; 108. [PMID: 27696352 DOI: 10.1002/bip.22994] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/22/2016] [Indexed: 12/24/2022]
Abstract
Low molecular weight agents that undergo self-assembly into fibril networks with hydrogel properties are promising biomaterials. Most low molecular weight hydrogelators are discovered empirically or serendipitously due to imperfect understanding of the mechanisms of self-assembly, the packing structure of self-assembled materials, and how the self-assembly process corresponds to emergent hydrogelation. Herein, the mechanisms of self-assembly and hydrogelation of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-PhePhe), a well-studied low molecular weight hydrogelator, is probed by systematic comparison with derivatives in which Phe residues are replaced by corresponding N-benzyl glycine peptoid (Nphe) analogs. Peptoids are peptidomimetics that shift display of side chain functionality from the α-carbon to the terminal nitrogen. This alters the hydrogen bonding capacity, the side chain presentation geometry, amide cis/trans isomerization equilibrium, and β-sheet potential of the peptoid relative to the corresponding amino acid in the context of peptidic polymers. It was found that amino acid/peptoid hybrids Fmoc-Phe-Nphe and Fmoc-Nphe-Phe have altered fibril self-assembly propensity and reduced hydrogelation capacity relative to the parent dipeptide, and that fibril self-assembly of the dipeptoid, Fmoc-Nphe-Nphe, is completely curtailed. These findings provide insight into the potential of low molecular weight peptoids and peptide/peptoid hybrids as hydrogelation agents and illuminate the importance of hydrogen bonding and π-π interaction geometry in facilitating self-assembly of Fmoc-Phe-Phe.
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Affiliation(s)
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York
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16
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17
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Johny M, Vijayalakshmi K, Das A, Roy P, Mishra A, Dasgupta J. Modulating the Phe–Phe dipeptide aggregation landscape via covalent attachment of an azobenzene photoswitch. Chem Commun (Camb) 2017; 53:9348-9351. [DOI: 10.1039/c7cc04106c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A covalently modified trans-H-(l)AzoPhe–Phe–OH dipeptide shows reversible photo-switching between its native fibril and vesicle aggregate morphology.
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Affiliation(s)
- Melby Johny
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai
- India
| | | | - Ankita Das
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai
- India
| | - Palas Roy
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai
- India
| | - Aseem Mishra
- KIIT-Technology Business Incubator & KIIT-School of Biotechnology
- KIIT University
- Bhubaneswar
- India
| | - Jyotishman Dasgupta
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai
- India
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18
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Ely F, Cipriano TC, da Silva MO, Peressinotto VST, Alves WA. Semiconducting polymer–dipeptide nanostructures by ultrasonically-assisted self-assembling. RSC Adv 2016. [DOI: 10.1039/c6ra03013k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The preparation of bio-organic nanostructures containing dipeptides and conjugated polymers like P3HT–diphenylalanine is trigged by ultrasound energy owing the study of such hybrid materials in solution processed OFETs and beyond.
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Affiliation(s)
- Fernando Ely
- IC Packaging Lab., CTI Renato Archer
- Campinas
- Brazil
| | - Thiago C. Cipriano
- IC Packaging Lab., CTI Renato Archer
- Campinas
- Brazil
- Centro de Ciências Naturais e Humanas
- Universidade Federal do ABC
| | | | | | - Wendel A. Alves
- Centro de Ciências Naturais e Humanas
- Universidade Federal do ABC
- Santo André
- Brazil
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19
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Reddy SMM, Shanmugam G, Mandal AB. 1,1,1,3,3,3-Hexafluoro-2-propanol and 2,2,2-trifluoroethanol solvents induce self-assembly with different surface morphology in an aromatic dipeptide. Org Biomol Chem 2014; 12:6181-9. [PMID: 24999600 DOI: 10.1039/c4ob00821a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Peptide based self-assembled structures, especially those from smaller peptides, have attracted much research interest due to their potential applications as biomaterials. These structures have been produced using different solvents (one of the methods), including alcohols, except fluorinated alcohols, which are believed to support non-aggregated structures. Herein, we have studied the ability of 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) solvents to induce self-assembly of an aromatic dipeptide, namely Tyr-Phe (YF). SEM images showed that HFIP and TFE can induce self-assembly with completely different morphologies, namely microribbons and microspheres, respectively, when YF is dried on a glass surface. Optical microscopic images showed that the microribbons possess birefringence under polarized light, whereas the microspheres do not, indicating that the self-assembled structures derived from HFIP solution are more highly ordered and crystalline in nature than those derived from TFE. Spectroscopic results indicated that the YF peptide adopts completely different conformations in these solvents. Time-dependent experiments suggested that the conformation of YF in HFIP is kinetically unstable and undergoes conformational change, whereas it is more stable in TFE, demonstrating that the modes of interaction of the TFE and HFIP solvents with the peptide are dissimilar. Different self-assembled structures were observed at different time intervals when YF was incubated in neat HFIP and 10% HFIP-90% TFE, establishing that the monomeric conformation plays a dominant role in deciding the final self-assembled structure (morphology) of YF. The current results demonstrate that TFE and HFIP solvents can produce self-assembled structures with different morphologies during solvent evaporation, despite their similar properties, such as secondary structural (α-helix) induction and preserving the peptide in its monomeric conformation in solution.
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20
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Abstract
Nature produces an array of self-assembled fibres from proteins and peptides with a wide range of functionalities. This has inspired scientists to design peptides that exploit specific protein folds to form simple yet multi-functional self-assembled fibres. Of the various protein folds the most commonly used has been the β-sheet fold as it is easily accessible and produces nanoscale fibres which have a wide range of stabilities. Research has also been driven by the relationship to the various amyloid diseases, which produce β-sheet rich fibres. Here we will discuss the use of natural protein sequences as the basis of peptides that self-assemble to β-sheet rich fibres followed by peptide sequences that have been designed de novo purely based on the rules for the formation of a β-sheet. How changes in the amino acid sequence of these various peptides affects the properties of the fibres and also the macroscopic materials formed by these peptides will be discussed in each case. We will then look into how these structures have been utilized for applications as scaffolds for cell culture and tissue regeneration, followed by their use in the nanotechnology field.
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21
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Parween S, Misra A, Ramakumar S, Chauhan VS. Self-assembled dipeptide nanotubes constituted by flexible β-phenylalanine and conformationally constrained α,β-dehydrophenylalanine residues as drug delivery system. J Mater Chem B 2014; 2:3096-3106. [DOI: 10.1039/c3tb21856b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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22
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Jeon J, Mills CE, Shell MS. Molecular Insights into Diphenylalanine Nanotube Assembly: All-Atom Simulations of Oligomerization. J Phys Chem B 2013; 117:3935-43. [DOI: 10.1021/jp308280d] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joohyun Jeon
- Department
of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080, United
States
| | - Carolyn E. Mills
- Department
of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080, United
States
| | - M. Scott Shell
- Department
of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106-5080, United
States
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23
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Mahato M, Arora V, Pathak R, Gautam HK, Sharma AK. Fabrication of nanostructures through molecular self-assembly of small amphiphilic glyco-dehydropeptides. MOLECULAR BIOSYSTEMS 2012; 8:1742-9. [PMID: 22491801 DOI: 10.1039/c2mb25023c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Self-assembled peptide-based nanostructures have been the focus of research in the past decade because of their potential applications in various biological systems. Normally, small self-assembled peptide nanostructures contain hydrophobic moieties, therefore, their solubility in aqueous systems poses the important challenge in the field of molecular self-assembly in order to make effective use of these in a wide variety of applications. To improve their aqueous solubility, the self-assembled amphiphilic α,β-dehydrophenylalanine containing small glyco-dehydropeptides, Boc-Phe-ΔPhe-εAhx-GA (I) and H-Phe-ΔPhe-εAhx-GA (II) with glucosamine (GA) attached at the C-terminal through a 6-aminocaproic acid linker, were synthesized, demonstrating the formation of nanostructures in aqueous media, which were characterized by DLS, AFM and TEM. Further, nanostructure II reduced auric chloride to gold nanoparticles and formed a peptide-gold conjugate (VII). The feasibility of using the nanostructures I and II as nanovectors for drug delivery was demonstrated by loading hydrophobic molecules, eosin and N-fluoresceinyl-2-aminoethanol (FAE) dyes. Besides, these peptides displayed antimicrobial activity against Micrococcus flavus, Bacillus subtilis and Pseudomonas aeruginosa. All these results advocate the potential of these nanostructures as efficient vectors for drug delivery applications.
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Affiliation(s)
- Manohar Mahato
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
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24
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Saini A, Chauhan VS. Delineation of the core aggregation sequences of TDP-43 C-terminal fragment. Chembiochem 2011; 12:2495-501. [PMID: 21905193 DOI: 10.1002/cbic.201100427] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Indexed: 12/12/2022]
Abstract
Ubiquitinated cytoplasmic inclusions of TDP-43 and its C-terminal cleavage products are the pathological hallmarks of amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitinated inclusions. The C-terminal fragments (CTFs) of TDP-43 are increasingly considered to play an important role in its aggregation and in disease. Here, we employed a set of synthetic peptides spanning the length of the TDP-43 CTF (220-414) in order to find out its core aggregation domains. Two regions, one in the RRM-2 domain (246-255) and the other in the C-terminal domain (311-320) of TDP-43, stand out as highly aggregation prone. Studies done on recombinant purified TDP-43 CTF and its three mutants, in which these sequences were deleted individually and together, suggested that the 311-320 region has a more crucial role to play than the 246-255 in its aggregation. The study helps in defining specific peptide sequences that might form the core of TDP-43 aggregation. Identification of these sequences could help in designing peptide based inhibitors of TDP-43 aggregation.
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Affiliation(s)
- Akash Saini
- Malaria Research Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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