1
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Rangubpit W, Sungted S, Wong-Ekkabut J, Distaffen HE, Nilsson BL, Dias CL. Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar-Polar Sequence Pattern. ACS Chem Neurosci 2024. [PMID: 39172951 DOI: 10.1021/acschemneuro.4c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
One of the mechanisms accounting for the toxicity of amyloid peptides in diseases like Alzheimer's and Parkinson's is the formation of pores on the plasma membrane of neurons. Here, we perform unbiased all-atom simulations of the full membrane damaging pathway, which includes adsorption, aggregation, and perforation of the lipid bilayer accounting for pore-like structures. Simulations are performed using four peptides made with the same amino acids. Differences in the nonpolar-polar sequence pattern of these peptides prompt them to adsorb into the membrane with the extended conformations oriented either parallel [peptide labeled F1, Ac-(FKFE)2-NH2], perpendicular (F4, Ac-FFFFKKEE-NH2), or with an intermediate orientation (F2, Ac-FFKKFFEE-NH2, and F3, Ac-FFFKFEKE-NH2) in regard to the membrane surface. At the water-lipid interface, only F1 fully self-assembles into β-sheets, and F2 peptides partially fold into an α-helical structure. The β-sheets of F1 emerge as electrostatic interactions attract neighboring peptides to intermediate distances where nonpolar side chains can interact within the dry core of the bilayer. This complex interplay between electrostatic and nonpolar interactions is not observed for the other peptides. Although β-sheets of F1 peptides are mostly parallel to the membrane, some of their edges penetrate deep inside the bilayer, dragging water molecules with them. This precedes pore formation, which starts with the flow of two water layers through the membrane that expand into a stable cylindrical pore delimited by polar faces of β-sheets spanning both leaflets of the bilayer.
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Affiliation(s)
- Warin Rangubpit
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Siwaporn Sungted
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Hannah E Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627-0166, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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2
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Patkar SS, Wang B, Mosquera AM, Kiick KL. Genetically Fusing Order-Promoting and Thermoresponsive Building Blocks to Design Hybrid Biomaterials. Chemistry 2024; 30:e202400582. [PMID: 38501912 DOI: 10.1002/chem.202400582] [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] [Received: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/20/2024]
Abstract
The unique biophysical and biochemical properties of intrinsically disordered proteins (IDPs) and their recombinant derivatives, intrinsically disordered protein polymers (IDPPs) offer opportunities for producing multistimuli-responsive materials; their sequence-encoded disorder and tendency for phase separation facilitate the development of multifunctional materials. This review highlights the strategies for enhancing the structural diversity of elastin-like polypeptides (ELPs) and resilin-like polypeptides (RLPs), and their self-assembled structures via genetic fusion to ordered motifs such as helical or beta sheet domains. In particular, this review describes approaches that harness the synergistic interplay between order-promoting and thermoresponsive building blocks to design hybrid biomaterials, resulting in well-structured, stimuli-responsive supramolecular materials ordered on the nanoscale.
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Affiliation(s)
- Sai S Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
- Eli Lilly and Company, 450 Kendall Street, Cambridge, MA, 02142, United States
| | - Bin Wang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
| | - Ana Maria Mosquera
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, 19716, United States
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3
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Nilsson BL, Celebi Torabfam G, Dias CL. Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations. J Phys Chem B 2024; 128:3320-3328. [PMID: 38447080 DOI: 10.1021/acs.jpcb.3c07861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.
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Affiliation(s)
- Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627-0216, United States
| | - Gizem Celebi Torabfam
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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4
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the Nanoscale Structure of β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation-Localization Microscopy. ACS NANO 2024; 18:8798-8810. [PMID: 38478911 PMCID: PMC11025465 DOI: 10.1021/acsnano.3c11771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize by using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8L and KFE8D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) ribbon structure of both KFE8 and Aβ42 and quantifies the precise tilt of the fibrils' inner and outer backbones in relevant buffer conditions without the need for covalent labeling or sequence mutations. SMOLM also distinguishes polymorphic branched and curved morphologies of KFE8, whose backbones exhibit much more heterogeneity than those of typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross-β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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5
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Nakagawa S, Kurokawa M, Kambara O, Takei T, Daidoji K, Naito A, Takita M, Kawamoto A, Hirose M, Tamura A. Structural Analyses of Designed α-Helix and β-Sheet Peptide Nanofibers Using Solid-State Nuclear Magnetic Resonance and Cryo-Electron Microscopy and Introduction of Structure-Based Metal-Responsive Properties. Int J Mol Sci 2024; 25:1111. [PMID: 38256184 PMCID: PMC10816960 DOI: 10.3390/ijms25021111] [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] [Received: 12/16/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
The 21-residue peptide α3, which is artificially designed and consists of three repeats of 7 residues, is known to rapidly assemble into the α-helix nanofiber. However, its molecular structure within the fiber has not yet been fully elucidated. Thus, we conducted a thorough investigation of the fiber's molecular structure using solid-state NMR and other techniques. The molecules were found to be primarily composed of the α-helix structure, with some regions near the C- and N-terminal adopting a 310-helix structure. Furthermore, it was discovered that β-sheet hydrogen bonds were formed between the molecules at both ends. These intermolecular interactions caused the molecules to assemble parallelly in the same direction, forming helical fibers. In contrast, we designed two molecules, CaRP2 and βKE, that can form β-sheet intermolecular hydrogen bonds using the entire molecule instead of just the ends. Cryo-EM and other measurements confirmed that the nanofibers formed in a cross β structure, albeit at a slow rate, with the formation times ranging from 1 to 42 days. To create peptide nanofibers that instantaneously respond to changes in the external environment, we designed several molecules (HDM1-3) based on α3 by introducing metal-binding sites. One of these molecules was found to be highly responsive to the addition of metal ions, inducing α-helix formation and simultaneously assembling into nanofibers. The nanofibers lost their structure upon removal of the metal ion. The change occurred promptly and was reversible, demonstrating that the intended level of responsiveness was attained.
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Affiliation(s)
- Shota Nakagawa
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Minami Kurokawa
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Ohki Kambara
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Toshiaki Takei
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Kengo Daidoji
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan (A.N.)
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan (A.N.)
| | - Mao Takita
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan; (A.K.); (M.H.)
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan; (A.K.); (M.H.)
| | - Atsuo Tamura
- Graduate School of Science, Department of Chemistry, Kobe University, Kobe 657-8501, Japan; (S.N.); (M.K.)
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6
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Guo J, Duan Y, Jia Y, Zhao Z, Gao X, Liu P, Li F, Chen H, Ye Y, Liu Y, Zhao M, Tang Z, Liu Y. Biomimetic chiral hydrogen-bonded organic-inorganic frameworks. Nat Commun 2024; 15:139. [PMID: 38167785 PMCID: PMC10762213 DOI: 10.1038/s41467-023-43700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Assembly ubiquitously occurs in nature and gives birth to numerous functional biomaterials and sophisticated organisms. In this work, chiral hydrogen-bonded organic-inorganic frameworks (HOIFs) are synthesized via biomimicking the self-assembly process from amino acids to proteins. Enjoying the homohelical configurations analogous to α-helix, the HOIFs exhibit remarkable chiroptical activity including the chiral fluorescence (glum = 1.7 × 10-3) that is untouched among the previously reported hydrogen-bonded frameworks. Benefitting from the dynamic feature of hydrogen bonding, HOIFs enable enantio-discrimination of chiral aliphatic substrates with imperceivable steric discrepancy based on fluorescent change. Moreover, the disassembled HOIFs after recognition applications are capable of being facilely regenerated and self-purified via aprotic solvent-induced reassembly, leading to at least three consecutive cycles without losing the enantioselectivity. The underlying mechanism of chirality bias is decoded by the experimental isothermal titration calorimetry together with theoretic simulation.
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Affiliation(s)
- Jun Guo
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China.
| | - Yulong Duan
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Yunling Jia
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Zelong Zhao
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Xiaoqing Gao
- Wenzhou Key Laboratory of Biomaterials and Engineering, Wenzhou Institute, University of Chinese Academy of Sciences, 325000, Wenzhou, P. R. China
| | - Pai Liu
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Fangfang Li
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Hongli Chen
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Yutong Ye
- School of Materials Science and Engineering, Tiangong University, 300387, Tianjin, P. R. China
| | - Yujiao Liu
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China
| | - Meiting Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, Institute of Molecular Aggregation Science, Tianjin University, 300072, Tianjin, P. R. China.
| | - Zhiyong Tang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 100190, Beijing, P. R. China.
| | - Yi Liu
- State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry, Tiangong University, 300387, Tianjin, P. R. China.
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7
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Abstract
The formation of amyloid fibrils is a complex phenomenon that remains poorly understood at the atomic scale. Herein, we perform extended unbiased all-atom simulations in explicit solvent of a short amphipathic peptide to shed light on the three mechanisms accounting for fibril formation, namely, nucleation via primary and secondary mechanisms, and fibril growth. We find that primary nucleation takes place via the formation of an intermediate state made of two laminated β-sheets oriented perpendicular to each other. The amyloid fibril spine subsequently emerges from the rotation of these β-sheets to account for peptides that are parallel to each other and perpendicular to the main axis of the fibril. Growth of this spine, in turn, takes place via a dock-and-lock mechanism. We find that peptides dock onto the fibril tip either from bulk solution or after diffusing on the fibril surface. The latter docking pathway contributes significantly to populate the fibril tip with peptides. We also find that side chain interactions drive the motion of peptides in the lock phase during growth, enabling them to adopt the structure imposed by the fibril tip with atomic fidelity. Conversely, the docked peptide becomes trapped in a local free energy minimum when docked-conformations are sampled randomly. Our simulations also highlight the role played by nonpolar fibril surface patches in catalyzing and orienting the formation of small cross-β structures. More broadly, our simulations provide important new insights into the pathways and interactions accounting for primary and secondary nucleation as well as the growth of amyloid fibrils.
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Affiliation(s)
- Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Ruoyao Zhang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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8
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557571. [PMID: 37745382 PMCID: PMC10515885 DOI: 10.1101/2023.09.13.557571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils have remarkable utility as engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarity to amyloid species has been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers, KFE8L and KFE8D, and the pathological amyloid-beta peptide Aβ42. SMOLM reveals that the orientations of Nile red, as it transiently binds to both KFE8 and Aβ42, are consistent with a helical (bilayer) ribbon structure and convey the precise tilt of the fibrils' inner and outer backbones. SMOLM also finds polymorphic branched and curved morphologies of KFE8 whose backbones exhibit much more heterogeneity than those of more typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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9
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Guo J, Rich-New ST, Liu C, Huang Y, Tan W, He H, Yi M, Zhang X, Egelman EH, Wang F, Xu B. Hierarchical Assembly of Intrinsically Disordered Short Peptides. Chem 2023; 9:2530-2546. [PMID: 38094164 PMCID: PMC10715794 DOI: 10.1016/j.chempr.2023.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.
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Affiliation(s)
- Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Shane T. Rich-New
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Chen Liu
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Yimeng Huang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Xixiang Zhang
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- O’Neal Comprehensive Cancer Center University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
- Lead contact
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10
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Wu C, Zhang H, Kong N, Wu B, Lin X, Wang H. Dynamic Control of Cyclic Peptide Assembly to Form Higher-Order Assemblies. Angew Chem Int Ed Engl 2023; 62:e202303455. [PMID: 37409642 DOI: 10.1002/anie.202303455] [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: 03/08/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
Chirality correction, asymmetry, ring-chain tautomerism and hierarchical assemblies are fundamental phenomena in nature. They are geometrically related and may impact the biological roles of a protein or other supermolecules. It is challenging to study those behaviors within an artificial system due to the complexity of displaying these features. Herein, we design an alternating D,L peptide to recreate and validate the naturally occurring chirality inversion prior to cyclization in water. The resulting asymmetrical cyclic peptide containing a 4-imidazolidinone ring provides an excellent platform to study the ring-chain tautomerism, thermostability and dynamic assembly of the nanostructures. Different from traditional cyclic D,L peptides, the formation of 4-imidazolidinone promotes the formation of intertwined nanostructures. Analysis of the nanostructures confirmed the left-handedness, representing chirality induced self-assembly. This proves that a rationally designed peptide can mimic multiple natural phenomena and could promote the development of functional biomaterials, catalysts, antibiotics, and supermolecules.
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Affiliation(s)
- Chongyang Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, No. 600 Dunyu Road, Hangzhou, 310024, Zhejiang Province, China
| | - Hongyue Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, No. 600 Dunyu Road, Hangzhou, 310024, Zhejiang Province, China
| | - Nan Kong
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, No. 600 Dunyu Road, Hangzhou, 310024, Zhejiang Province, China
| | - Bihan Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, No. 600 Dunyu Road, Hangzhou, 310024, Zhejiang Province, China
| | - Xinhui Lin
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, No. 600 Dunyu Road, Hangzhou, 310024, Zhejiang Province, China
| | - Huaimin Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, No. 600 Dunyu Road, Hangzhou, 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
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11
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Guo J, Wang F, Huang Y, He H, Tan W, Yi M, Egelman EH, Xu B. Cell spheroid creation by transcytotic intercellular gelation. NATURE NANOTECHNOLOGY 2023; 18:1094-1104. [PMID: 37217766 PMCID: PMC10525029 DOI: 10.1038/s41565-023-01401-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
Cell spheroids bridge the discontinuity between in vitro systems and in vivo animal models. However, inducing cell spheroids by nanomaterials remains an inefficient and poorly understood process. Here we use cryogenic electron microscopy to determine the atomic structure of helical nanofibres self-assembled from enzyme-responsive D-peptides and fluorescent imaging to show that the transcytosis of D-peptides induces intercellular nanofibres/gels that potentially interact with fibronectin to enable cell spheroid formation. Specifically, D-phosphopeptides, being protease resistant, undergo endocytosis and endosomal dephosphorylation to generate helical nanofibres. On secretion to the cell surface, these nanofibres form intercellular gels that act as artificial matrices and facilitate the fibrillogenesis of fibronectins to induce cell spheroids. No spheroid formation occurs without endo- or exocytosis, phosphate triggers or shape switching of the peptide assemblies. This study-coupling transcytosis and morphological transformation of peptide assemblies-demonstrates a potential approach for regenerative medicine and tissue engineering.
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Affiliation(s)
- Jiaqi Guo
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Yimeng Huang
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, MA, USA.
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12
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Horváth D, Dürvanger Z, K Menyhárd D, Sulyok-Eiler M, Bencs F, Gyulai G, Horváth P, Taricska N, Perczel A. Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation. Nat Commun 2023; 14:4621. [PMID: 37528104 PMCID: PMC10394066 DOI: 10.1038/s41467-023-40294-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/21/2023] [Indexed: 08/03/2023] Open
Abstract
A large group of hormones are stored as amyloid fibrils in acidic secretion vesicles before they are released into the bloodstream and readopt their functional state. Here, we identify an evolutionarily conserved hexapeptide sequence as the major aggregation-prone region (APR) of gastrointestinal peptides of the glucagon family: xFxxWL. We determine nine polymorphic crystal structures of the APR segments of glucagon-like peptides 1 and 2, and exendin and its derivatives. We follow amyloid formation by CD, FTIR, ThT assays, and AFM. We propose that the pH-dependent changes of the protonation states of glutamate/aspartate residues of APRs initiate switching between the amyloid and the folded, monomeric forms of the hormones. We find that pH sensitivity diminishes in the absence of acidic gatekeepers and amyloid formation progresses over a broad pH range. Our results highlight the dual role of short aggregation core motifs in reversible amyloid formation and receptor binding.
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Affiliation(s)
- Dániel Horváth
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Zsolt Dürvanger
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Dóra K Menyhárd
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Máté Sulyok-Eiler
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Fruzsina Bencs
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Gergő Gyulai
- Laboratory of Interfaces and Nanostructures, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 9, Budapest, 1092, Hungary
| | - Nóra Taricska
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Perczel
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.
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13
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He X, Qu Y, Xiong S, Jiang Z, Tang Y, Yan F, Deng Y, Sun Y. Functional L-Arginine Derivative as an Efficient Vector for Intracellular Protein Delivery for Potential Cancer Therapy. J Funct Biomater 2023; 14:301. [PMID: 37367265 DOI: 10.3390/jfb14060301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The utilization of cytosolic protein delivery is a promising approach for treating various diseases by replacing dysfunctional proteins. Despite the development of various nanoparticle-based intracellular protein delivery methods, the complicated chemical synthesis of the vector, loading efficiency and endosomal escape efficiency of proteins remain a great challenge. Recently, 9-fluorenylmethyloxycarbonyl (Fmoc)-modified amino acid derivatives have been used to self-assemble into supramolecular nanomaterials for drug delivery. However, the instability of the Fmoc group in aqueous medium restricts its application. To address this issue, the Fmoc ligand neighboring arginine was substituted for dibenzocyclooctyne (DBCO) with a similar structure to Fmoc to obtain stable DBCO-functionalized L-arginine derivative (DR). Azide-modified triethylamine (crosslinker C) was combined with DR to construct self-assembled DRC via a click chemical reaction for delivering various proteins, such as BSA and saporin (SA), into the cytosol of cells. The hyaluronic-acid-coated DRC/SA was able to not only shield the cationic toxicity, but also enhance the intracellular delivery efficiency of proteins by targeting CD44 overexpression on the cell membrane. The DRC/SA/HA exhibited higher growth inhibition efficiency and lower IC50 compared to DRC/SA toward various cancer cell lines. In conclusion, DBCO-functionalized L-arginine derivative represents an excellent potential vector for protein-based cancer therapy.
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Affiliation(s)
- Xiao He
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yannv Qu
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Su Xiong
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
| | - Zhiru Jiang
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yaqin Tang
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
| | - Fei Yan
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanfei Deng
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yansun Sun
- Department of Geriatrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
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14
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Bertouille J, Kasas S, Martin C, Hennecke U, Ballet S, Willaert RG. Fast Self-Assembly Dynamics of a β-Sheet Peptide Soft Material. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206795. [PMID: 36807731 DOI: 10.1002/smll.202206795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/28/2022] [Indexed: 05/18/2023]
Abstract
Peptide-based hydrogels are promising biocompatible materials for wound healing, drug delivery, and tissue engineering applications. The physical properties of these nanostructured materials depend strongly on the morphology of the gel network. However, the self-assembly mechanism of the peptides that leads to a distinct network morphology is still a subject of ongoing debate, since complete assembly pathways have not yet been resolved. To unravel the dynamics of the hierarchical self-assembly process of the model β-sheet forming peptide KFE8 (Ac-FKFEFKFE-NH2 ), high-speed atomic force microscopy (HS-AFM) in liquid is used. It is demonstrated that a fast-growing network, based on small fibrillar aggregates, is formed at a solid-liquid interface, while in bulk solution, a distinct, more prolonged nanotube network emerges from intermediate helical ribbons. Moreover, the transformation between these morphologies has been visualized. It is expected that this new in situ and in real-time methodology will set the path for the in-depth unravelling of the dynamics of other peptide-based self-assembled soft materials, as well as gaining advanced insights into the formation of fibers involved in protein misfolding diseases.
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Affiliation(s)
- Jolien Bertouille
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Ulrich Hennecke
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, 1050, Belgium
| | - Ronnie G Willaert
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, Vrije Universiteit Brussel, Brussels, 1050, Belgium
- Research Group Structural Biology Brussels, Alliance Research Group VUB-UGent NanoMicrobiology, Vrije Universiteit Brussel, Brussels, 1050, Belgium
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15
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Yu T, Luo X, Prendergast D, Butterfoss GL, Rad B, Balsara NP, Zuckermann RN, Jiang X. Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus. ACS NANO 2023; 17:4958-4970. [PMID: 36821346 PMCID: PMC10018772 DOI: 10.1021/acsnano.2c12503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/12/2023]
Abstract
The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions (covalent and noncovalent) at the solvent-exposed N-termini have a dominant impact on the local chain ordering and hence the ability of the chains to pack into well-ordered lattices. Peptoids in pure water form fibers with limited growth in the a direction (<14 molecules in width), whereas in the presence of formamide, they grow to over microns in length in the a direction. This dependence points to the significant role of the chain terminus in determining the long-range order in the packing of peptoid lattices and provides an opportunity to modulate lattice stability and nanoscale morphology by the addition of exogenous small molecules. These findings help resolve a major challenge in the de novo structure-based design of sequence-defined biomimetic nanostructures based on crystalline domains and should accelerate the design of functional nanostructures.
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Affiliation(s)
- Tianyi Yu
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xubo Luo
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Glenn L. Butterfoss
- Center
for Genomics and Systems Biology, New York
University, Abu Dhabi, United Arab Emirates
| | - Behzad Rad
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xi Jiang
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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16
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Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022; 13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amphipathic peptides can cause biological membranes to leak either by dissolving their lipid content via a detergent-like mechanism or by forming pores on the membrane surface. These modes of membrane damage have been related to the toxicity of amyloid peptides and to the activity of antimicrobial peptides. Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. They also disturb the orientation of lipid tails in the vicinity of peptides. These distortions are minimized around pore structures. We also show that membrane-bound β-sheets become twisted with one of their extremities partially penetrating the lipid bilayer. This allows peptides on opposite leaflets to interact and form a long transmembrane β-sheet, which initiates poration. In simulations, where peptides are deposited on a single leaflet, the twist in β-sheets allows them to penetrate the membrane and form pores. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes, as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Hannah Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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17
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Kadamannil NN, Heo JM, Jang D, Zalk R, Kolusheva S, Zarivach R, Frank GA, Kim JM, Jelinek R. High-Resolution Cryo-Electron Microscopy Reveals the Unique Striated Hollow Structure of Photocatalytic Macrocyclic Polydiacetylene Nanotubes. J Am Chem Soc 2022; 144:17889-17896. [PMID: 36126329 DOI: 10.1021/jacs.2c06710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-resolution structures are crucial for understanding the functional properties of nanomaterials. We applied single-particle cryo-electron microscopy (cryo-EM), a method traditionally used for structure determination of biological macromolecules, to obtain high-resolution structures of synthetic non-biological filaments formed by photopolymerization of macrocyclic diacetylene (MDA) amphiphilic monomers. Tomographic analysis showed that the MDA monomers self-assemble into hollow nanotubes upon dispersion in water. Single-particle analysis revealed tubes consisting of six pairs of covalently bonded filaments held together by hydrophobic interactions, where each filament is composed of macrocyclic rings stacked in parallel "chair" conformations. The hollow MDA nanotube structures we found may account for the efficient scavenging of amphiphilic pollutants in water and subsequent photodegradation of the guest species.
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Affiliation(s)
| | - Jung-Moo Heo
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Daewoong Jang
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Ran Zalk
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Sofiya Kolusheva
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Raz Zarivach
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Gabriel A Frank
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Jong-Man Kim
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Raz Jelinek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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18
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Huang H, Kiick KL. Peptide-based assembled nanostructures that can direct cellular responses. Biomed Mater 2022; 17. [DOI: 10.1088/1748-605x/ac92b5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Natural originated materials have been well-studied over the past several decades owing to their higher biocompatibility compared to the traditional polymers. Peptides, consisting of amino acids, are among the most popular programable building blocks, which is becoming a growing interest in nanobiotechnology. Structures assembled using those biomimetic peptides allow the exploration of chemical sequences beyond those been routinely used in biology. In this Review, we discussed the most recent experimental discoveries on the peptide-based assembled nanostructures and their potential application at the cellular level such as drug delivery. In particular, we explored the fundamental principles of peptide self-assembly and the most recent development in improving their interactions with biological systems. We believe that as the fundamental knowledge of the peptide assemblies evolves, the more sophisticated and versatile nanostructures can be built, with promising biomedical applications.
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19
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Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
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20
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Mañas‐Torres MC, Illescas‐Lopez S, Gavira JA, de Cienfuegos LÁ, Marchesan S. Interactions Between Peptide Assemblies and Proteins for Medicine. Isr J Chem 2022. [DOI: 10.1002/ijch.202200018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mari C. Mañas‐Torres
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - Sara Illescas‐Lopez
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR) Avenida de las Palmeras 4 18100 Armilla, UEQ Granada Spain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
- Instituto de Investigación Biosanitaria ibs Granada Spain
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department University of Trieste Via L. Giorgieri 1 Trieste 34127 Italy
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21
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Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids. Proc Natl Acad Sci U S A 2022; 119:e2121586119. [PMID: 35533283 DOI: 10.1073/pnas.2121586119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phenol-soluble modulins (PSMs) are peptide-based virulence factors that play significant roles in the pathogenesis of staphylococcal strains in community-associated and hospital-associated infections. In addition to cytotoxicity, PSMs display the propensity to self-assemble into fibrillar species, which may be mediated through the formation of amphipathic conformations. Here, we analyze the self-assembly behavior of two PSMs, PSMα3 and PSMβ2, which are derived from peptides expressed by methicillin-resistant Staphylococcus aureus (MRSA), a significant human pathogen. In both cases, we observed the formation of a mixture of self-assembled species including twisted filaments, helical ribbons, and nanotubes, which can reversibly interconvert in vitro. Cryo–electron microscopy structural analysis of three PSM nanotubes, two derived from PSMα3 and one from PSMβ2, revealed that the assemblies displayed remarkably similar structures based on lateral association of cross-α amyloid protofilaments. The amphipathic helical conformations of PSMα3 and PSMβ2 enforced a bilayer arrangement within the protofilaments that defined the structures of the respective PSMα3 and PSMβ2 nanotubes. We demonstrate that, similar to amyloids based on cross-β protofilaments, cross-α amyloids derived from these PSMs display polymorphism, not only in terms of the global morphology (e.g., twisted filament, helical ribbon, and nanotube) but also with respect to the number of protofilaments within a given peptide assembly. These results suggest that the folding landscape of PSM derivatives may be more complex than originally anticipated and that the assemblies are able to sample a wide range of supramolecular structural space.
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22
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He X, Qu Y, Lin X, Sun J, Jiang Z, Wang C, Deng Y, Yan F, Sun Y. Self-assembled D-arginine derivatives based on click chemical reactions for intracellular codelivery of antigens and adjuvants for potential immunotherapy. J Mater Chem B 2022; 10:3491-3500. [PMID: 35403659 DOI: 10.1039/d2tb00346e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembled amino acid derivatives could form well-defined nanostructures which have great application value for drug delivery systems. In particular, D-amino acid derivatives possess tremendous advantages including anti-degradation and good lysosome escape compared with L-amino acid derivatives. In this work, 9-fluorenylmethyloxycarbonyl (Fmoc) neighboring D-arginine derivatives were replaced by dibenzocyclooctyne (DBCO) to extend the class of functional D-arginine derivatives, which were further reacted with various cross-linkers including azide to construct a library of self-assembled supramolecular nanovehicles and strengthen the stability of nanostructures for disease immunotherapy. Moreover, in vitro studies demonstrated that the combination of DBCO modified D-arginine derivative DR3 and cross-linker C1 not only reinforced the cellular uptake efficiency of ovalbumin (OVA) which was chosen as the model antigen, but also promoted the cytokine TNF-α release of RAW 264.7 cells after the introduction of adjuvant unmethylated cytosine-phosphate-guanine dinucleotides (CpG). Furthermore, the nanovaccine based on DR3C1 could enhance the antigen OVA and adjuvant cytosolic delivery of marrow derived dendritic cells (BMDCs), which improved the antigen-presentation cross efficiency and induced the maturation of BMDCs. Taken together, we believe that D-arginine derivatives functionalized by DBCO provide an effective strategy for disease immunotherapy and act as a great potential delivery tool.
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Affiliation(s)
- Xiao He
- Department of Geriatrics, The Shenzhen Hospital of Peking University, Shenzhen, Guangdong, 518036, China.
| | - Yannv Qu
- Department of Geriatrics, The Shenzhen Hospital of Peking University, Shenzhen, Guangdong, 518036, China.
| | - Xiaohong Lin
- Department of Infertility and Reproductive Health, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, Guangdong, 518109, China
| | - Jiapan Sun
- Department of Geriatrics, The Shenzhen Hospital of Peking University, Shenzhen, Guangdong, 518036, China.
| | - Zhiru Jiang
- Department of Geriatrics, The Shenzhen Hospital of Peking University, Shenzhen, Guangdong, 518036, China.
| | - Chaodong Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, 100053, China
| | - Yuanfei Deng
- Department of Geriatrics, The Shenzhen Hospital of Peking University, Shenzhen, Guangdong, 518036, China.
| | - Fei Yan
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China.
| | - Yansun Sun
- Department of Geriatrics, The Shenzhen Hospital of Peking University, Shenzhen, Guangdong, 518036, China.
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23
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Tan W, Zhang Q, Quiñones-Frías MC, Hsu AY, Zhang Y, Rodal A, Hong P, Luo HR, Xu B. Enzyme-Responsive Peptide Thioesters for Targeting Golgi Apparatus. J Am Chem Soc 2022; 144:6709-6713. [PMID: 35404599 PMCID: PMC9069992 DOI: 10.1021/jacs.2c02238] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Golgi apparatus (GA) is the hub of intracellular trafficking, but selectively targeting GA remains a challenge. We show an unconventional types of peptide thioesters, consisting of an aminoethyl thioester and acting as substrates of thioesterases, for instantly targeting the GA of cells. The peptide thioesters, above or below their critical micelle concentrations, enter cells mainly via caveolin-mediated endocytosis or macropinocytosis, respectively. After being hydrolyzed by GA-associated thioesterases, the resulting thiopeptides form dimers and accumulate in the GA. After saturating the GA, the thiopeptides are enriched in the endoplasmic reticulum (ER). Their buildup in ER and GA disrupts protein trafficking, thus leading to cell death via multiple pathways. The peptide thioesters target the GA of a wide variety of cells, including human, murine, and Drosophila cells. Changing d-diphenylalanine to l-diphenylalanine in the peptide maintains the GA-targeting ability. In addition, targeting GA redirects protein (e.g., NRAS) distribution. This work illustrates a thioesterase-responsive and redox-active molecular platform for targeting the GA and controlling cell fates.
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Affiliation(s)
- Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | | | - Alan Y. Hsu
- Department of Pathology, Harvard Medical School and Department of Laboratory Medicine, Children’s Hospital Boston and Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
| | - Yichi Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Avital Rodal
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA
| | - Hongbo R. Luo
- Department of Pathology, Harvard Medical School and Department of Laboratory Medicine, Children’s Hospital Boston and Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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24
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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25
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Insua I, Bergueiro J, Méndez-Ardoy A, Lostalé-Seijo I, Montenegro J. Bottom-up supramolecular assembly in two dimensions. Chem Sci 2022; 13:3057-3068. [PMID: 35414883 PMCID: PMC8926289 DOI: 10.1039/d1sc05667k] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/19/2022] [Indexed: 01/17/2023] Open
Abstract
The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. Attracted by the interesting properties of two-dimensional inorganic analogues, monomers of different chemical natures are being explored for the assembly of dynamic 2D systems. Although many important discoveries have been already achieved, great challenges are still to be addressed in this field. Hierarchical multicomponent assembly, directional non-covalent growth and internal structural control are a just a few of the examples that will be discussed in this perspective about the exciting present and the bright future of two-dimensional supramolecular assemblies. The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. This perspective discusses the main strategies to direct the supramolecular self-assembly of organic monomers in 2D.![]()
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Affiliation(s)
- Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Julian Bergueiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Alejandro Méndez-Ardoy
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Irene Lostalé-Seijo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
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26
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Criado-Gonzalez M, Espinosa-Cano E, Rojo L, Boulmedais F, Aguilar MR, Hernández R. Injectable Tripeptide/Polymer Nanoparticles Supramolecular Hydrogel: A Candidate for the Treatment of Inflammatory Pathologies. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10068-10080. [PMID: 35179869 DOI: 10.1021/acsami.1c22993] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Supramolecular peptide-based hydrogels attract great attention in several fields, i.e., biomedicine, catalysis, energy, and materials chemistry, due to the noncovalent nature of the self-assembly and functional tunable properties defined by the amino acid sequence. In this work, we developed an injectable hybrid supramolecular hydrogel whose formation was triggered by electrostatic interactions between a phosphorylated tripeptide, Fmoc-FFpY (F: phenylalanine, pY: phosphorylated tyrosine), and cationic polymer nanoparticles made of vinylimidazole and ketoprofen (poly(HKT-co-VI) NPs). Hydrogel formation was assessed through inverted tube tests, and its fibrillary structure, around polymer NPs, was observed by transmission electron microscopy. Interestingly, peptide self-assembly yields the formation of nontwisted and twisted fibers, which could be attributed to β-sheets and α-helix structures, respectively, as characterized by circular dichroism and infrared spectroscopies. An increase of the elastic modulus of the Fmoc-FFpY/polymer NPs hybrid hydrogels was observed with peptide concentration as well as its injectability property, due to its shear thinning behavior and self-healing ability. After checking their stability under physiological conditions, the cytotoxicity properties of these hybrid hydrogels were evaluated in contact with human dermal fibroblasts (FBH) and murine macrophages (RAW 264.7). Finally, the Fmoc-FFpY/polymer NPs hybrid hydrogels exhibited a great nitric oxide reduction (∼67%) up to basal values of pro-inflammatory RAW 264.7 cells, thus confirming their excellent anti-inflammatory properties for the treatment of localized inflammatory pathologies.
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Affiliation(s)
- Miryam Criado-Gonzalez
- Instituto de Ciencia y Tecnología de Polímeros (ICTP-CSIC), c/ Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Eva Espinosa-Cano
- Instituto de Ciencia y Tecnología de Polímeros (ICTP-CSIC), c/ Juan de la Cierva, 3, 28006 Madrid, Spain
- CIBER-BBN, c/ Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
| | - Luis Rojo
- Instituto de Ciencia y Tecnología de Polímeros (ICTP-CSIC), c/ Juan de la Cierva, 3, 28006 Madrid, Spain
- CIBER-BBN, c/ Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
| | - Fouzia Boulmedais
- Université de Strasbourg, CNRS, Institut Charles Sadron (UPR 22), 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
| | - María Rosa Aguilar
- Instituto de Ciencia y Tecnología de Polímeros (ICTP-CSIC), c/ Juan de la Cierva, 3, 28006 Madrid, Spain
- CIBER-BBN, c/ Monforte de Lemos 3-5, Pabellón 11, 28029 Madrid, Spain
| | - Rebeca Hernández
- Instituto de Ciencia y Tecnología de Polímeros (ICTP-CSIC), c/ Juan de la Cierva, 3, 28006 Madrid, Spain
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27
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Gatto E, Toniolo C, Venanzi M. Peptide Self-Assembled Nanostructures: From Models to Therapeutic Peptides. NANOMATERIALS 2022; 12:nano12030466. [PMID: 35159810 PMCID: PMC8838750 DOI: 10.3390/nano12030466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
Self-assembly is the most suitable approach to obtaining peptide-based materials on the nano- and mesoscopic scales. Applications span from peptide drugs for personalized therapy to light harvesting and electron conductive media for solar energy production and bioelectronics, respectively. In this study, we will discuss the self-assembly of selected model and bioactive peptides, in particular reviewing our recent work on the formation of peptide architectures of nano- and mesoscopic size in solution and on solid substrates. The hierarchical and cooperative characters of peptide self-assembly will be highlighted, focusing on the structural and dynamical properties of the peptide building blocks and on the nature of the intermolecular interactions driving the aggregation phenomena in a given environment. These results will pave the way for the understanding of the still-debated mechanism of action of an antimicrobial peptide (trichogin GA IV) and the pharmacokinetic properties of a peptide drug (semaglutide) currently in use for the therapy of type-II diabetes.
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Affiliation(s)
- Emanuela Gatto
- PEPSA-LAB, Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy;
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padua, 35131 Padua, Italy;
| | - Mariano Venanzi
- PEPSA-LAB, Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy;
- Correspondence: ; Tel.: +39-06-7259-4468
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28
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Abstract
The spectacular developments in cryoelectron microscopy involving new cameras, new microscopes, and new software make it possible today to routinely determine the atomic structures of a large range of molecular assemblies. This has allowed us to solve the atomic structure of nanotubes formed from a peptide, Lanreotide. Its gel, Somatuline, is used as a synthetic growth hormone inhibitor in the treatment of both acromegaly and cancers. The self-assembled nanotube results in a slow release form of the peptide, important pharmacologically. The nanotube structure shows an unexpected complexity and highlights the still unpredictable chemical and physicochemical determinants driving peptide self-assembly. Functional and versatile nano- and microassemblies formed by biological molecules are found at all levels of life, from cell organelles to full organisms. Understanding the chemical and physicochemical determinants guiding the formation of these assemblies is crucial not only to understand the biological processes they carry out but also to mimic nature. Among the synthetic peptides forming well-defined nanostructures, the octapeptide Lanreotide has been considered one of the best characterized, in terms of both the atomic structure and its self-assembly process. In the present work, we determined the atomic structure of Lanreotide nanotubes at 2.5-Å resolution by cryoelectron microscopy (cryo-EM). Surprisingly, the asymmetric unit in the nanotube contains eight copies of the peptide, forming two tetramers. There are thus eight different environments for the peptide, and eight different conformations in the nanotube. The structure built from the cryo-EM map is strikingly different from the molecular model, largely based on X-ray fiber diffraction, proposed 20 y ago. Comparison of the nanotube with a crystal structure at 0.83-Å resolution of a Lanreotide derivative highlights the polymorphism for this peptide family. This work shows once again that higher-order assemblies formed by even well-characterized small peptides are very difficult to predict.
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29
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Yi M, Tan W, Guo J, Xu B. Enzymatic noncovalent synthesis of peptide assemblies generates multimolecular crowding in cells for biomedical applications. Chem Commun (Camb) 2021; 57:12870-12879. [PMID: 34817487 PMCID: PMC8711086 DOI: 10.1039/d1cc05565h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic noncovalent synthesis enables the spatiotemporal control of multimolecular crowding in cells, thus offering a unique opportunity for modulating cellular functions. This article introduces some representative enzymes and molecular building blocks for generating peptide assemblies as multimolecular crowding in cells, highlights the relevant biomedical applications, such as anticancer therapy, molecular imaging, trafficking proteins, genetic engineering, artificial intracellular filaments, cell morphogenesis, and antibacterial, and briefly discusses the promises of ENS as a multistep molecular process in biology and medicine.
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Affiliation(s)
- Meihui Yi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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30
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Yi M, Guo J, He H, Tan W, Harmon N, Ghebreyessus K, Xu B. Phosphobisaromatic motifs enable rapid enzymatic self-assembly and hydrogelation of short peptides. SOFT MATTER 2021; 17:8590-8594. [PMID: 34545895 PMCID: PMC8600407 DOI: 10.1039/d1sm01221e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Enzyme-instructed self-assembly (EISA) and hydrogelation is a versatile approach for generating soft materials. Most of the substrates for alkaline phosphatase catalysed EISA utilize phosphotyrosine (pTyr) as the enzymatic trigger for EISA and hydrogelation. Here we show the first example of phosphonaphthyl (pNP) and phosphobiphenyl (pBP) motifs acting as faster enzymatic triggers than phosphotyrosine for EISA and hydrogelation. This work illustrates novel enzyme triggers for rapid enzymatic self-assembly and hydrogelation.
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Affiliation(s)
- Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
| | - Nya Harmon
- Department of Chemistry and Biochemistry, Hampton University, Hampton, VA, 23668, USA
| | - Kesete Ghebreyessus
- Department of Chemistry and Biochemistry, Hampton University, Hampton, VA, 23668, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA.
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