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Han Q, Tao F, Yang P. Amyloid-Like Assembly to Form Film at Interfaces: Structural Transformation and Application. Macromol Biosci 2023; 23:e2300172. [PMID: 37257459 DOI: 10.1002/mabi.202300172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Protein-based biomaterials are attracting broad interest for their remarkable structural and functional properties. Disturbing the native protein's three-dimensional structural stability in vitro and controlling subsequent aggregation is an effective strategy to design and construct protein-based biomaterials. One of the recent developments in regulating protein structural transformation to ordered aggregation is amyloid assembly, which generates fibril-based 1D to 3D nanostructures as functional materials. Especially, the amyloid-like assembly to form films at interfaces has been reported, which is induced by the effective reduction of the intramolecular disulfide bond. The main contribution of this amyloid-like assembly is the large-scale formation of protein films at interfaces and excellent adhesion to target substrates. This review presents the research progress of the amyloid-like assembly to form films and related applications and thereby provides a guide to exploiting protein-based biomaterials.
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Affiliation(s)
- Qian Han
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Fei Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
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2
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Ni B, Kaplan DL, Buehler MJ. Generative design of de novo proteins based on secondary structure constraints using an attention-based diffusion model. Chem 2023; 9:1828-1849. [PMID: 37614363 PMCID: PMC10443900 DOI: 10.1016/j.chempr.2023.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
We report two generative deep learning models that predict amino acid sequences and 3D protein structures based on secondary structure design objectives via either overall content or per-residue structure. Both models are robust regarding imperfect inputs and offer de novo design capacity as they can discover new protein sequences not yet discovered from natural mechanisms or systems. The residue-level secondary structure design model generally yields higher accuracy and more diverse sequences. These findings suggest unexplored opportunities for protein designs and functional outcomes within the vast amino acid sequences beyond known proteins. Our models, based on an attention-based diffusion model and trained on a dataset extracted from experimentally known 3D protein structures, offer numerous downstream applications in conditional generative design of various biological or engineering systems. Future work may include additional conditioning, and an exploration of other functional properties of the generated proteins for various properties beyond structural objectives.
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Affiliation(s)
- Bo Ni
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Markus J. Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
- Lead contact
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3
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Gonzalez-Obeso C, Rodriguez-Cabello JC, Kaplan DL. Fast and reversible crosslinking of a silk elastin-like polymer. Acta Biomater 2022; 141:14-23. [PMID: 34971785 PMCID: PMC8898266 DOI: 10.1016/j.actbio.2021.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Elastin-like polymers (ELPs) and their chimeric subfamily the silk elastin-like polymers (SELPs) exhibit a lower critical solvation temperature (LCST) behavior in water which has been extensively studied from theoretical, computational and experimental perspectives. The inclusion of silk domains in the backbone of the ELPs effects the molecular dynamics of the elastin-like domains in response to increased temperature above its transition temperature and confers gelation ability. This response has been studied in terms of initial and long-term changes in structures, however, intermediate transition states have been less investigated. Moreover, little is known about the effects of reversible hydration on the elastin versus silk domains in the physical crosslinks. We used spectroscopic techniques to analyze initial, intermediate and long-term states of the crosslinks in SELPs. A combination of thermoanalytical and rheological measurements demonstrated that the fast reversible rehydration of the elastin motifs adjacent to the relatively small silk domains was capable of breaking the silk physical crosslinks. This feature can be exploited to tailor the dynamics of these types of crosslinks in SELPs. STATEMENT OF SIGNIFICANCE: The combination of silk and elastin in a single molecule results in synergy via their interactions to impact the protein polymer properties. The ability of the silk domains to crosslink affects the thermoresponsive properties of the elastin domains. These interactions have been studied at early and late states of the physical crosslinking, while the intermediate states were the focus of the present study to understand the reversible phase-transitions of the elastin domains over the silk physical crosslinking. The thermoresponsive properties of the elastin domains at the initial, intermediate and late states of silk crosslinking were characterized to demonstrate that reversible hydration of the elastin domains influenced the reversibility of the silk crosslinks.
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Affiliation(s)
- Constancio Gonzalez-Obeso
- Department of Biomedical Engineering Tufts University, 4, Colby St., Medford, MA, 02155, USA; BIOFORGE (Group for Advanced Materials and Nanobiotechnology), University of Valladolid-CIBER-BBN, Paseo de Belén 19, 47011, Valladolid, Spain.
| | - J C Rodriguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), University of Valladolid-CIBER-BBN, Paseo de Belén 19, 47011, Valladolid, Spain.
| | - David L Kaplan
- Department of Biomedical Engineering Tufts University, 4, Colby St., Medford, MA, 02155, USA.
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4
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Yu CH, Chen W, Chiang YH, Guo K, Martin Moldes Z, Kaplan DL, Buehler MJ. End-to-End Deep Learning Model to Predict and Design Secondary Structure Content of Structural Proteins. ACS Biomater Sci Eng 2022; 8:1156-1165. [PMID: 35129957 PMCID: PMC9347213 DOI: 10.1021/acsbiomaterials.1c01343] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural proteins are the basis of many biomaterials and key construction and functional components of all life. Further, it is well-known that the diversity of proteins' function relies on their local structures derived from their primary amino acid sequences. Here, we report a deep learning model to predict the secondary structure content of proteins directly from primary sequences, with high computational efficiency. Understanding the secondary structure content of proteins is crucial to designing proteins with targeted material functions, especially mechanical properties. Using convolutional and recurrent architectures and natural language models, our deep learning model predicts the content of two essential types of secondary structures, the α-helix and the β-sheet. The training data are collected from the Protein Data Bank and contain many existing protein geometries. We find that our model can learn the hidden features as patterns of input sequences that can then be directly related to secondary structure content. The α-helix and β-sheet content predictions show excellent agreement with training data and newly deposited protein structures that were recently identified and that were not included in the original training set. We further demonstrate the features of the model by a search for de novo protein sequences that optimize max/min α-helix/β-sheet content and compare the predictions with folded models of these sequences based on AlphaFold2. Excellent agreement is found, underscoring that our model has predictive potential for rapidly designing proteins with specific secondary structures and could be widely applied to biomedical industries, including protein biomaterial designs and regenerative medicine applications.
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Affiliation(s)
- Chi-Hua Yu
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Department of Engineering Science, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - Wei Chen
- Department of Engineering Science, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - Yu-Hsuan Chiang
- Department of Civil Engineering, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - Kai Guo
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zaira Martin Moldes
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Center for Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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5
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Li L, Zhang J, Liu M, Shi X, Zhang W, Li Y, Zhou N, Zhang Z, Zhu X. Smart supramolecular nanofibers and nanoribbons from uniform amphiphilic azobenzene oligomers. Chem Commun (Camb) 2021; 57:2192-2195. [PMID: 33527917 DOI: 10.1039/d0cc06994a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A series of self-assembled 1D nanostructures, including straight and helix nanofibers, nanoribbons, and nanobelts, were fabricated from uniform amphiphilic azobenzene oligomers with tunable molecular weight and side chain functionality, promoted by multiple and cooperative supramolecular interactions. Additionally, the morphological transformation of the nanofibers was achieved during the photoisomerization process.
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Affiliation(s)
- Lishan Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Jiandong Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Min Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Xianheng Shi
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Wei Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Yiwen Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, P. R. China.
| | - Nianchen Zhou
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, 215123, P. R. China.
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6
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Spider silk with weaker bonding resulting in higher strength and toughness through progressive unfolding and load transfer. J Mech Behav Biomed Mater 2020; 108:103773. [DOI: 10.1016/j.jmbbm.2020.103773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/27/2020] [Accepted: 04/04/2020] [Indexed: 11/20/2022]
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7
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Wongpinyochit T, Vassileiou AD, Gupta S, Mushrif SH, Johnston BF, Seib FP. Unraveling the Impact of High-Order Silk Structures on Molecular Drug Binding and Release Behaviors. J Phys Chem Lett 2019; 10:4278-4284. [PMID: 31318218 DOI: 10.1021/acs.jpclett.9b01591] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Silk continues to amaze: over the past decade, new research threads have emerged that include the use of silk fibroin for advanced pharmaceutics, including its suitability for drug delivery. Despite this ongoing interest, the details of silk fibroin structures and their subsequent drug interactions at the molecular level remain elusive, primarily because of the difficulties encountered in modeling the silk fibroin molecule. Here, we generated an atomistic silk model containing amorphous and crystalline regions. We then exploited advanced well-tempered metadynamics simulations to generate molecular conformations that we subsequently exposed to classical molecular dynamics simulations to monitor both drug binding and release. Overall, this study demonstrated the importance of the silk fibroin primary sequence, electrostatic interactions, hydrogen bonding, and higher-order conformation in the processes of drug binding and release.
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Affiliation(s)
- Thidarat Wongpinyochit
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , 161 Cathedral Street , Glasgow G4 0RE , United Kingdom
| | - Antony D Vassileiou
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , 161 Cathedral Street , Glasgow G4 0RE , United Kingdom
| | - Sukriti Gupta
- Energy Research Institute @ NTU, Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive , Singapore 637459
| | - Samir H Mushrif
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive , Singapore 637459
- Department of Chemical and Materials Engineering , University of Alberta , 9211-116 Street Northwest , Edmonton , Alberta T6G 1H9 , Canada
| | - Blair F Johnston
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , 161 Cathedral Street , Glasgow G4 0RE , United Kingdom
- National Physical Laboratory , Teddington , Middlesex TW11 0LW , United Kingdom
| | - F Philipp Seib
- Strathclyde Institute of Pharmacy and Biomedical Sciences , University of Strathclyde , 161 Cathedral Street , Glasgow G4 0RE , United Kingdom
- Leibniz Institute of Polymer Research Dresden , Max Bergmann Center of Biomaterials Dresden , Hohe Strasse 6 , 01069 Dresden , Germany
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8
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Cui M, Qi Q, Gurry T, Zhao T, An B, Pu J, Gui X, Cheng AA, Zhang S, Xun D, Becce M, Briatico-Vangosa F, Liu C, Lu TK, Zhong C. Modular genetic design of multi-domain functional amyloids: insights into self-assembly and functional properties. Chem Sci 2019; 10:4004-4014. [PMID: 31015941 PMCID: PMC6461117 DOI: 10.1039/c9sc00208a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 01/16/2023] Open
Abstract
Engineering functional amyloids through a modular genetic strategy represents new opportunities for creating multifunctional molecular materials with tailored structures and performance. Despite important advances, how fusion modules affect the self-assembly and functional properties of amyloids remains elusive. Here, using Escherichia coli curli as a model system, we systematically studied the effect of flanking domains on the structures, assembly kinetics and functions of amyloids. The designed amyloids were composed of E. coli biofilm protein CsgA (as amyloidogenic cores) and one or two flanking domains, consisting of chitin-binding domains (CBDs) from Bacillus circulans chitinase, and/or mussel foot proteins (Mfps). Incorporation of fusion domains did not disrupt the typical β-sheet structures, but indeed affected assembly rate, morphology, and stiffness of resultant fibrils. Consequently, the CsgA-fusion fibrils, particularly those containing three domains, were much shorter than the CsgA-only fibrils. Furthermore, the stiffness of the resultant fibrils was heavily affected by the structural feature of fusion domains, with β-sheet-containing domains tending to increase the Young's modulus while random coil domains decreasing the Young's modulus. In addition, fibrils containing CBD domains showed higher chitin-binding activity compared to their CBD-free counterparts. The CBD-CsgA-Mfp3 construct exhibited significantly lower binding activity than Mfp5-CsgA-CBD due to inappropriate folding of the CBD domain in the former construct, in agreement with results based upon molecular dynamics modeling. Our study provides new insights into the assembly and functional properties of designer amyloid proteins with increasing complex domain structures and lays the foundation for the future design of functional amyloid-based structures and molecular materials.
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Affiliation(s)
- Mengkui Cui
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
- University of Chinese Academy of Sciences , Beijing 100049 , China
- Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Qi Qi
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Thomas Gurry
- Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
| | - Tianxin Zhao
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
- University of Chinese Academy of Sciences , Beijing 100049 , China
- Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Bolin An
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Jiahua Pu
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Xinrui Gui
- Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
- Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Allen A Cheng
- Department of Electrical Engineering and Computer Science , Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
| | - Siyu Zhang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Dongmin Xun
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Michele Becce
- Department of Electrical Engineering and Computer Science , Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
- Dipartimento di Chimica Materiali e Ingegneria Chimica G. Natta , Politecnico di Milano , Piazza Leonardo da Vinci 32 , 20133 Milano , Italy
- Department of Materials , Imperial College London , London SW7 2AZ , UK
| | - Francesco Briatico-Vangosa
- Dipartimento di Chimica Materiali e Ingegneria Chimica G. Natta , Politecnico di Milano , Piazza Leonardo da Vinci 32 , 20133 Milano , Italy
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science , Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
| | - Chao Zhong
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
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9
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Computer Simulation of Protein Materials at Multiple Length Scales: From Single Proteins to Protein Assemblies. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42493-018-00009-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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10
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Zhang W, Yu X, Li Y, Su Z, Jandt KD, Wei G. Protein-mimetic peptide nanofibers: Motif design, self-assembly synthesis, and sequence-specific biomedical applications. Prog Polym Sci 2018. [DOI: 10.1016/j.progpolymsci.2017.12.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Choi B, Kim T, Ahn ES, Lee SW, Eom K. Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations. NANOSCALE RESEARCH LETTERS 2017; 12:228. [PMID: 28359138 PMCID: PMC5371578 DOI: 10.1186/s11671-017-1966-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 02/28/2017] [Indexed: 06/07/2023]
Abstract
Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.
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Affiliation(s)
- Bumjoon Choi
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Taehee Kim
- College of Sport Science, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Eue Soo Ahn
- College of Sport Science, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
| | - Sang Woo Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
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12
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Zhang Y, Wang A, DeBenedictis EP, Keten S. Bending energy penalty enhances the adhesive strength of functional amyloid curli to surfaces. NANOTECHNOLOGY 2017; 28:464002. [PMID: 28952462 DOI: 10.1088/1361-6528/aa8f72] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The functional amyloid curli fiber, a major proteinaceous component of biofilm extracellular matrices, plays an important role in biofilm formation and enterobacteriaceae adhesion. Curli nanofibers exhibit exceptional underwater adhesion to various surfaces, have high rigidity and strong tensile mechanical properties, and thus hold great promise in biomaterials. The mechanisms of how curli fibers strongly attach to surfaces and detach under force remain elusive. To investigate curli fiber adhesion to surfaces, we developed a coarse-grained curli fiber model, in which the protein subunit CsgA (curli specific gene A) self-assembles into the fiber. The coarse-grained model yields physiologically relevant and tunable bending rigidity and persistence length. The force-induced desorption of a single curli fiber is examined using coarse-grained modeling and theoretical analysis. We find that the bending energy penalty arising from high persistence length enhances the resistance of the curli fiber against desorption and thus strengthens the adhesion of the curli fiber to surfaces. The CsgA-surface adhesion energy and the curli fiber bending rigidity both play crucial roles in the resistance of curli fiber against desorption from surfaces. To enable the desorption process, the applied peeling force must overcome both the interfacial adhesion energy and the energy barrier for bending the curli fiber at the peeling front. We show that the energy barrier to desorption increases with the interfacial adhesion energy, however, the bending induced failure of a single curli fiber limits the work of adhesion if the proportion of the CsgA-surface adhesion energy to the CsgA-CsgA cohesive energy becomes large. These results illustrate that the optimal adhesion performance of nanofibers is dictated by the interplay between bending, surface energy and cohesive energy. Our model provides timely insight into enterobacteriaceae adhesion mechanisms as well as future designs of engineered curli fiber based adhesives.
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Affiliation(s)
- Yao Zhang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, United States of America
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13
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Yuan C, Li S, Zou Q, Ren Y, Yan X. Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly. Phys Chem Chem Phys 2017; 19:23614-23631. [DOI: 10.1039/c7cp01923h] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.
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Affiliation(s)
- Chengqian Yuan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Ying Ren
- Center for Mesoscience
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
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14
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Sintya E, Alam P. Self-assembled semi-crystallinity at parallel β -sheet nanocrystal interfaces in clustered MaSp1 (spider silk) proteins. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 58:366-71. [DOI: 10.1016/j.msec.2015.08.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/25/2015] [Accepted: 08/24/2015] [Indexed: 10/23/2022]
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15
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Landreh M, Rising A, Presto J, Jörnvall H, Johansson J. Specific chaperones and regulatory domains in control of amyloid formation. J Biol Chem 2015; 290:26430-6. [PMID: 26354437 DOI: 10.1074/jbc.r115.653097] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many proteins can form amyloid-like fibrils in vitro, but only about 30 amyloids are linked to disease, whereas some proteins form physiological amyloid-like assemblies. This raises questions of how the formation of toxic protein species during amyloidogenesis is prevented or contained in vivo. Intrinsic chaperoning or regulatory factors can control the aggregation in different protein systems, thereby preventing unwanted aggregation and enabling the biological use of amyloidogenic proteins. The molecular actions of these chaperones and regulators provide clues to the prevention of amyloid disease, as well as to the harnessing of amyloidogenic proteins in medicine and biotechnology.
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Affiliation(s)
- Michael Landreh
- From the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 5QY, United Kingdom
| | - Anna Rising
- the Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet - Novum, 141 57 Huddinge, Sweden, the Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Box 575, 751 23 Uppsala, Sweden
| | - Jenny Presto
- the Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet - Novum, 141 57 Huddinge, Sweden
| | - Hans Jörnvall
- the Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Jan Johansson
- the Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet - Novum, 141 57 Huddinge, Sweden, the Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Box 575, 751 23 Uppsala, Sweden, the Institute of Mathematics and Natural Sciences, Tallinn University, Narva mnt 25, 101 20 Tallinn, Estonia
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16
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Bortolini C, Jones NC, Hoffmann SV, Wang C, Besenbacher F, Dong M. Mechanical properties of amyloid-like fibrils defined by secondary structures. NANOSCALE 2015; 7:7745-7752. [PMID: 25839069 DOI: 10.1039/c4nr05109b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils.
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Affiliation(s)
- C Bortolini
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds 14, Building 1590, Aarhus C., Denmark.
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17
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Li Y, Sun Y, Qin M, Cao Y, Wang W. Mechanics of single peptide hydrogelator fibrils. NANOSCALE 2015; 7:5638-5642. [PMID: 25760017 DOI: 10.1039/c4nr07657e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The rigidity of peptide fibers is essential for their chemical and biological functions, despite that it remains largely unexplored. Here, we present the first direct measurement of the mechanics of individual fibers in peptide hydrogels by AFM imaging and statistical analysis and find that the intermolecular interactions play a considerable role.
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Affiliation(s)
- Ying Li
- Jiangsu Engineering Technology Research Centre of Environmental Cleaning Materials, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Joint Laboratory of Atmospheric Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, 219 Ningliu Road, Nanjing, Jiangsu 210044, P.R. China.
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18
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Demirel MC, Cetinkaya M, Pena-Francesch A, Jung H. Recent advances in nanoscale bioinspired materials. Macromol Biosci 2014; 15:300-11. [PMID: 25476469 DOI: 10.1002/mabi.201400324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Natural materials have been a fundamental part of human life since the dawn of civilization. However, due to exploitation of natural resources and cost issues, synthetic materials replaced bio-derived materials in the last century. Recent advances in bio- and nano-technologies pave the way for developing eco-friendly materials that could be produced easily from renewable resources at reduced cost and in a broad array of useful applications. This feature article highlights structural and functional characteristics of bio-derived materials, which will expedite the design fabrication and synthesis of eco-friendly and recyclable advanced nano-materials and devices.
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Affiliation(s)
- Melik C. Demirel
- Materials Research Institute; Pennsylvania State University; University Park Pennsylvania 16802 USA
- Huck Institutes of Life Sciences; Pennsylvania State University; University Park Pennsylvania 16802 USA
- College of Engineering; Pennsylvania State University; University Park Pennsylvania 16802 USA
| | | | - Abdon Pena-Francesch
- College of Engineering; Pennsylvania State University; University Park Pennsylvania 16802 USA
| | - Huihun Jung
- College of Engineering; Pennsylvania State University; University Park Pennsylvania 16802 USA
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19
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Ling S, Li C, Adamcik J, Shao Z, Chen X, Mezzenga R. Modulating materials by orthogonally oriented β-strands: composites of amyloid and silk fibroin fibrils. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:4569-74. [PMID: 24845975 DOI: 10.1002/adma.201400730] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/07/2014] [Indexed: 05/02/2023]
Abstract
Amyloid fibrils and silk fibroin (SF) fibrils are proteinaceous aggregates occurring either naturally or as artificially reconstituted fibrous systems, in which the constituent β-strands are aligned either orthogonally or parallel to the fibril main axis, conferring complementary physical properties. Here, it is shown how the combination of these two classes of protein fibrils with orthogonally oriented β-strands results in composite materials with controllable physical properties at the molecular, mesoscopic, and continuum length scales.
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Affiliation(s)
- Shengjie Ling
- Food & Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zürich, LFO23 Schmelzbergstrasse 9, 8092, Zürich, Switzerland; State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai, 200433, PR China
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