51
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Ni R, Chau Y. Tuning the Inter-nanofibril Interaction To Regulate the Morphology and Function of Peptide/DNA Co-assembled Viral Mimics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rong Ni
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Institute for Advanced Study; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
| | - Ying Chau
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Department of Chemical and Biomolecular Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
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52
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Ni R, Chau Y. Tuning the Inter-nanofibril Interaction To Regulate the Morphology and Function of Peptide/DNA Co-assembled Viral Mimics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201703596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Rong Ni
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Institute for Advanced Study; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
| | - Ying Chau
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Department of Chemical and Biomolecular Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
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53
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Zhou J, Li J, Du X, Xu B. Supramolecular biofunctional materials. Biomaterials 2017; 129:1-27. [PMID: 28319779 PMCID: PMC5470592 DOI: 10.1016/j.biomaterials.2017.03.014] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 12/27/2022]
Abstract
This review discusses supramolecular biofunctional materials, a novel class of biomaterials formed by small molecules that are held together via noncovalent interactions. The complexity of biology and relevant biomedical problems not only inspire, but also demand effective molecular design for functional materials. Supramolecular biofunctional materials offer (almost) unlimited possibilities and opportunities to address challenging biomedical problems. Rational molecular design of supramolecular biofunctional materials exploit powerful and versatile noncovalent interactions, which offer many advantages, such as responsiveness, reversibility, tunability, biomimicry, modularity, predictability, and, most importantly, adaptiveness. In this review, besides elaborating on the merits of supramolecular biofunctional materials (mainly in the form of hydrogels and/or nanoscale assemblies) resulting from noncovalent interactions, we also discuss the advantages of small peptides as a prevalent molecular platform to generate a wide range of supramolecular biofunctional materials for the applications in drug delivery, tissue engineering, immunology, cancer therapy, fluorescent imaging, and stem cell regulation. This review aims to provide a brief synopsis of recent achievements at the intersection of supramolecular chemistry and biomedical science in hope of contributing to the multidisciplinary research on supramolecular biofunctional materials for a wide range of applications. We envision that supramolecular biofunctional materials will contribute to the development of new therapies that will ultimately lead to a paradigm shift for developing next generation biomaterials for medicine.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jie Li
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA.
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54
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Omosun TO, Hsieh MC, Childers WS, Das D, Mehta AK, Anthony NR, Pan T, Grover MA, Berland KM, Lynn DG. Catalytic diversity in self-propagating peptide assemblies. Nat Chem 2017; 9:805-809. [DOI: 10.1038/nchem.2738] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/03/2023]
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55
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Design of multi-phase dynamic chemical networks. Nat Chem 2017; 9:799-804. [DOI: 10.1038/nchem.2737] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/19/2017] [Indexed: 01/08/2023]
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56
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Abstract
Dozens of proteins are known to convert to the aggregated amyloid state. These include fibrils associated with systemic and neurodegenerative diseases and cancer, functional amyloid fibrils in microorganisms and animals, and many denatured proteins. Amyloid fibrils can be much more stable than other protein assemblies. In contrast to globular proteins, a single protein sequence can aggregate into several distinctly different amyloid structures, termed polymorphs, and a given polymorph can reproduce itself by seeding. Amyloid polymorphs may be the molecular basis of prion strains. Whereas the Protein Data Bank contains some 100,000 globular protein and 3,000 membrane protein structures, only a few dozen amyloid protein structures have been determined, and most of these are short segments of full amyloid-forming proteins. Regardless, these amyloid structures illuminate the architecture of the amyloid state, including its stability and its capacity for formation of polymorphs.
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Affiliation(s)
- David S Eisenberg
- Howard Hughes Medical Institute and Molecular Biology Institute, University of California, Los Angeles, California 90095-1570; ,
| | - Michael R Sawaya
- Howard Hughes Medical Institute and Molecular Biology Institute, University of California, Los Angeles, California 90095-1570; ,
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57
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Nguyen PH, Sterpone F, Pouplana R, Derreumaux P, Campanera JM. Dimerization Mechanism of Alzheimer Aβ 40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J Phys Chem B 2016; 120:12111-12126. [PMID: 27933940 DOI: 10.1021/acs.jpcb.6b10722] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Amyloid beta (Aβ) oligomerization is associated with the origin and progression of Alzheimer's disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T Aβ40 dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V Aβ40 dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel β-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded β-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded β-sheet or inhibiting the formation of an interpeptide β-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of Aβ species.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Ramon Pouplana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France.,IUF (Institut Universitaire de France) , 103 Boulevard Michel, 75005 Paris, France
| | - Josep M Campanera
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain
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58
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Bleem A, Daggett V. Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering. Biotechnol Bioeng 2016; 114:7-20. [PMID: 27474784 DOI: 10.1002/bit.26059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 12/23/2022]
Abstract
Amyloids have long been associated with protein dysfunction and neurodegenerative diseases, but recent research has demonstrated that some organisms utilize the unique properties of the amyloid fold to create functional structures with important roles in biological processes. Additionally, new engineering approaches have taken advantage of amyloid structures for implementation in a wide variety of materials and devices. In this review, the role of amyloid in human disease is discussed and compared to the functional amyloids, which serve a largely structural purpose. We then consider the use of amyloid constructs in engineering applications, including their utility as building blocks for synthetic biology and molecular engineering. Biotechnol. Bioeng. 2017;114: 7-20. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alissa Bleem
- Department of Bioengineering, University of Washington, Box 355013, Seattle, Washington, 98195-5013
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Box 355013, Seattle, Washington, 98195-5013
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59
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Wang J, Liu K, Xing R, Yan X. Peptide self-assembly: thermodynamics and kinetics. Chem Soc Rev 2016; 45:5589-5604. [PMID: 27487936 DOI: 10.1039/c6cs00176a] [Citation(s) in RCA: 626] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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60
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Feng Z, Wang H, Du X, Shi J, Li J, Xu B. Minimal C-terminal modification boosts peptide self-assembling ability for necroptosis of cancer cells. Chem Commun (Camb) 2016; 52:6332-5. [PMID: 27087169 PMCID: PMC4855835 DOI: 10.1039/c6cc02282k] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Here we reported the first case in which enhancing self-assembling ability boosts anti-cancer efficacy through a simple and minimal modification of the C-terminus of a d-tripeptide. By only a 2% change of the molecular weight, this facile approach increases the inhibitory activity by over an order of magnitude (IC50 from 431 to 23 μM) towards an osteosarcoma cell line.
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Affiliation(s)
- Zhaoqianqi Feng
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA.
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61
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Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q. Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein. ACS Chem Neurosci 2016; 7:286-96. [PMID: 26815332 PMCID: PMC7842942 DOI: 10.1021/acschemneuro.5b00242] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aggregation of the copper-zinc superoxide dismutase (SOD1) protein is linked to familial amyotrophic lateral sclerosis, a progressive neurodegenerative disease. A recent experimental study has shown that the (147)GVIGIAQ(153) SOD1 C-terminal segment not only forms amyloid fibrils in isolation but also accelerates the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks its fibril formation. Amyloid formation is a nucleation-polymerization process. In this study, we investigated the oligomerization and the nucleus structure of this heptapeptide. By performing extensive replica-exchange molecular dynamics (REMD) simulations and conventional MD simulations, we found that the GVIGIAQ hexamers can adopt highly ordered bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability and results in the disappearance of bilayer β-sheet structures and the increase of disordered hexamers. We identified mixed parallel-antiparallel bilayer β-sheets in both REMD and conventional MD simulations and provided the conformational transition from the experimentally observed parallel bilayer sheets to the mixed parallel-antiparallel bilayer β-sheets. Our simulations suggest that the critical nucleus consists of six peptide chains and two additional peptide chains strongly stabilize this critical nucleus. The stabilized octamer is able to recruit additional random peptides into the β-sheet. Therefore, our simulations provide insights into the critical nucleus formation and the smallest stable nucleus of the (147)GVIGIAQ(153) peptide.
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Affiliation(s)
- Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| | - Yunxiang Sun
- Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Yuzhen Zhu
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
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62
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Li S, Mehta AK, Sidorov AN, Orlando TM, Jiang Z, Anthony NR, Lynn DG. Design of Asymmetric Peptide Bilayer Membranes. J Am Chem Soc 2016; 138:3579-86. [DOI: 10.1021/jacs.6b00977] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sha Li
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anil K. Mehta
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton N. Sidorov
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Thomas M. Orlando
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhigang Jiang
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neil R. Anthony
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David G. Lynn
- Departments
of Biology and Chemistry, ‡Emory NMR Center, ⊥Emory Integrated Cellular Imaging
Core, Emory University, Atlanta, Georgia 30322, United States
- School of Chemistry and Biochemistry and ∥School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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63
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Kapil N, Singh A, Singh M, Das D. Efficient MoS2Exfoliation by Cross-β-Amyloid Nanotubes for Multistimuli-Responsive and Biodegradable Aqueous Dispersions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509953] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nidhi Kapil
- Institute of Nano Science and Technology, Phase 10; Mohali 160062 India
| | - Ashmeet Singh
- Institute of Nano Science and Technology, Phase 10; Mohali 160062 India
| | - Manish Singh
- Institute of Nano Science and Technology, Phase 10; Mohali 160062 India
| | - Dibyendu Das
- Indian Institute of Science Education and Research (IISER) Tirupati; Andhra Pradesh 517507 India
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64
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Kapil N, Singh A, Singh M, Das D. Efficient MoS2Exfoliation by Cross-β-Amyloid Nanotubes for Multistimuli-Responsive and Biodegradable Aqueous Dispersions. Angew Chem Int Ed Engl 2016; 55:7772-6. [DOI: 10.1002/anie.201509953] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 01/03/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Nidhi Kapil
- Institute of Nano Science and Technology, Phase 10; Mohali 160062 India
| | - Ashmeet Singh
- Institute of Nano Science and Technology, Phase 10; Mohali 160062 India
| | - Manish Singh
- Institute of Nano Science and Technology, Phase 10; Mohali 160062 India
| | - Dibyendu Das
- Indian Institute of Science Education and Research (IISER) Tirupati; Andhra Pradesh 517507 India
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65
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Zhou J, Du X, Xu B. Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology. Prion 2016; 9:110-8. [PMID: 25738892 DOI: 10.1080/19336896.2015.1022021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine.
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Affiliation(s)
- Jie Zhou
- a Department of Chemistry ; Brandeis University ; Waltham , MA USA
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66
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Wang J, Shen G, Ma K, Jiao T, Liu K, Yan X. Dipeptide concave nanospheres based on interfacially controlled self-assembly: from crescent to solid. Phys Chem Chem Phys 2016; 18:30926-30930. [DOI: 10.1039/c6cp06150h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Concave nanospheres based on the self-assembly of simple dipeptides not only provide alternatives for modeling the interactions between biomacromolecules, but also present a range of applications for purification and separation, and delivery of active species.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Guizhi Shen
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Kai Ma
- Hebei Key Laboratory of Applied Chemistry
- School of Environmental and Yanshan University
- Qinhuangdao 066004
- P. R. China
| | - Tifeng Jiao
- Hebei Key Laboratory of Applied Chemistry
- School of Environmental and Yanshan University
- Qinhuangdao 066004
- P. R. China
| | - Kai Liu
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
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67
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van der Zwaag D, Pieters PA, Korevaar PA, Markvoort AJ, Spiering AJH, de Greef TFA, Meijer EW. Kinetic Analysis as a Tool to Distinguish Pathway Complexity in Molecular Assembly: An Unexpected Outcome of Structures in Competition. J Am Chem Soc 2015; 137:12677-88. [PMID: 26354151 DOI: 10.1021/jacs.5b08138] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While the sensitive dependence of the functional characteristics of self-assembled nanofibers on the molecular structure of their building blocks is well-known, the crucial influence of the dynamics of the assembly process is often overlooked. For natural protein-based fibrils, various aggregation mechanisms have been demonstrated, from simple primary nucleation to secondary nucleation and off-pathway aggregation. Similar pathway complexity has recently been described in synthetic supramolecular polymers and has been shown to be intimately linked to their morphology. We outline a general method to investigate the consequences of the presence of multiple assembly pathways, and show how kinetic analysis can be used to distinguish different assembly mechanisms. We illustrate our combined experimental and theoretical approach by studying the aggregation of chiral bipyridine-extended 1,3,5-benzenetricarboxamides (BiPy-1) in n-butanol as a model system. Our workflow consists of nonlinear least-squares analysis of steady-state spectroscopic measurements, which cannot provide conclusive mechanistic information but yields the equilibrium constants of the self-assembly process as constraints for subsequent kinetic analysis. Furthermore, kinetic nucleation-elongation models based on one and two competing pathways are used to interpret time-dependent spectroscopic measurements acquired using stop-flow and temperature-jump methods. Thus, we reveal that the sharp transition observed in the aggregation process of BiPy-1 cannot be explained by a single cooperative pathway, but can be described by a competitive two-pathway mechanism. This work provides a general tool for analyzing supramolecular polymerizations and establishing energetic landscapes, leading to mechanistic insights that at first sight may seem unexpected and counterintuitive.
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Affiliation(s)
- Daan van der Zwaag
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter A Korevaar
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Albert J Markvoort
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - A J H Spiering
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom F A de Greef
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, ‡Laboratory of Macromolecular and Organic Chemistry, and §Computational Biology Group, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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68
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Shi J, Du X, Yuan D, Haburcak R, Zhou N, Xu B. Supramolecular Detoxification of Neurotoxic Nanofibrils of Small Molecules via Morphological Switch. Bioconjug Chem 2015; 26:1879-83. [PMID: 26258500 DOI: 10.1021/acs.bioconjchem.5b00356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Insoluble amyloid plagues are likely cytoprotective, but the cellular mechanism remains less known. To model β-amyloid we use a small peptide derivative to generate cytotoxic nanofibrils that cause the death of model neuron cells (i.e., PC12). The use of supramolecular interaction effectively converts the nanofibrils to nanoparticles that are innocuous to cells. This approach also removes the cytotoxicity of the fibrils to other mammalian cells (e.g., HeLa). Preliminary mechanistic study reveals that, in contrast to the fibrils, the particles promote the expression of TNFR2, a cell survival signal, and decrease the expression of TNFR1 and DR5, two extrinsic cell death receptors. As the first use of ligand-receptor interaction to abrogate the cytotoxicity of nanoscale assemblies of small molecules, this work illustrates an effective way to use supramolecular interaction to control the morphology of supramolecular assemblies for modulating their biological activity.
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Affiliation(s)
- Junfeng Shi
- Department of Chemistry, Brandeis University , 415 South Street, MS 015, Waltham, Massachusetts 02453, United States
| | - Xuewen Du
- Department of Chemistry, Brandeis University , 415 South Street, MS 015, Waltham, Massachusetts 02453, United States
| | - Dan Yuan
- Department of Chemistry, Brandeis University , 415 South Street, MS 015, Waltham, Massachusetts 02453, United States
| | - Richard Haburcak
- Department of Chemistry, Brandeis University , 415 South Street, MS 015, Waltham, Massachusetts 02453, United States
| | - Ning Zhou
- Department of Chemistry, Brandeis University , 415 South Street, MS 015, Waltham, Massachusetts 02453, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University , 415 South Street, MS 015, Waltham, Massachusetts 02453, United States
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Yuan D, Shi J, Du X, Zhou N, Xu B. Supramolecular Glycosylation Accelerates Proteolytic Degradation of Peptide Nanofibrils. J Am Chem Soc 2015; 137:10092-5. [PMID: 26237170 PMCID: PMC4941208 DOI: 10.1021/jacs.5b05888] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Despite
the recent consensus that the oligomers of amyloid peptides
or aberrant proteins are cytotoxic species, there is still a need
for an effective way to eliminate the oligomers. Based on the fact
that normal proteins are more glycosylated than pathogenic proteins,
we show that a conjugate of nucleobase, peptide, and saccharide binds
to peptides from molecular nanofibrils and accelerates the proteolytic
degradation of the molecular nanofibrils. As the first example of
the use of supramolecular glycosylation to dissociate molecular nanofibrils
and to accelerate the degradation of peptide aggregates, this work
illustrates a new method that ultimately may lead to an effective
approach for degrading cytotoxic oligomers of peptides or aberrant
proteins.
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Affiliation(s)
- Dan Yuan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Ning Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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70
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Zhou H, Qin Y, Xu S, Sun Z. Crystallization Kinetics of Concurrent Liquid-Metastable and Metastable-Stable Transitions, and Ostwald's Step Rule. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7204-7209. [PMID: 26079145 DOI: 10.1021/acs.langmuir.5b00917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Experimental measurements of colloidal crystallization in a wide range of volume fractions of charged particles were performed to investigate the liquid-metastable-stable transition process. To fit the obtained experimental data, we developed a theoretical model to formulate the kinetics of the concurrent liquid-metastable and metastable-stable transitions. This model is well-supported by our observations. We found that when the ratio of the metastable-stable transition rate to the liquid-metastable rate is very large, the metastable state can become undetectable, although it still exists, offering a possible explanation for very few exceptions to Ostwald's step rule.
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Affiliation(s)
- Hongwei Zhou
- †Key Laboratory of Microgravity, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- ‡National Microgravity Laboratory, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Yanming Qin
- †Key Laboratory of Microgravity, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- ‡National Microgravity Laboratory, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- §College of Chemistry, Chemical Engineering and Material Science, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Shenghua Xu
- †Key Laboratory of Microgravity, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- ‡National Microgravity Laboratory, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Zhiwei Sun
- †Key Laboratory of Microgravity, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- ‡National Microgravity Laboratory, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
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71
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Smith JE, Liang C, Tseng M, Li N, Li S, Mowles AK, Mehta AK, Lynn DG. Defining the Dynamic Conformational Networks of Cross-β Peptide Assembly. Isr J Chem 2015. [DOI: 10.1002/ijch.201500012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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72
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 478] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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73
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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