1
|
Huang H, Zheng Y, Chang M, Song J, Xia L, Wu C, Jia W, Ren H, Feng W, Chen Y. Ultrasound-Based Micro-/Nanosystems for Biomedical Applications. Chem Rev 2024. [PMID: 38924776 DOI: 10.1021/acs.chemrev.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Due to the intrinsic non-invasive nature, cost-effectiveness, high safety, and real-time capabilities, besides diagnostic imaging, ultrasound as a typical mechanical wave has been extensively developed as a physical tool for versatile biomedical applications. Especially, the prosperity of nanotechnology and nanomedicine invigorates the landscape of ultrasound-based medicine. The unprecedented surge in research enthusiasm and dedicated efforts have led to a mass of multifunctional micro-/nanosystems being applied in ultrasound biomedicine, facilitating precise diagnosis, effective treatment, and personalized theranostics. The effective deployment of versatile ultrasound-based micro-/nanosystems in biomedical applications is rooted in a profound understanding of the relationship among composition, structure, property, bioactivity, application, and performance. In this comprehensive review, we elaborate on the general principles regarding the design, synthesis, functionalization, and optimization of ultrasound-based micro-/nanosystems for abundant biomedical applications. In particular, recent advancements in ultrasound-based micro-/nanosystems for diagnostic imaging are meticulously summarized. Furthermore, we systematically elucidate state-of-the-art studies concerning recent progress in ultrasound-based micro-/nanosystems for therapeutic applications targeting various pathological abnormalities including cancer, bacterial infection, brain diseases, cardiovascular diseases, and metabolic diseases. Finally, we conclude and provide an outlook on this research field with an in-depth discussion of the challenges faced and future developments for further extensive clinical translation and application.
Collapse
Affiliation(s)
- Hui Huang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P. R. China
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Yi Zheng
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P. R. China
| | - Meiqi Chang
- Laboratory Center, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, P. R. China
| | - Jun Song
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Lili Xia
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Chenyao Wu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Wencong Jia
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Hongze Ren
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Wei Feng
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P. R. China
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Yu Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P. R. China
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| |
Collapse
|
2
|
Guo T, Wan Z, Panahi-Sarmad M, Banvillet G, Lu Y, Zargar S, Tian J, Jiang F, Mao Y, Tu Q, Rojas OJ. Chitin Nanofibers Enable the Colloidal Dispersion of Carbon Nanomaterials in Aqueous Phase and Hybrid Material Coassembly. ACS NANO 2024; 18:14954-14967. [PMID: 38820368 DOI: 10.1021/acsnano.4c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Chitin nanofibrils (ChNF) sourced from discarded marine biomass are shown as effective stabilizers of carbon nanomaterials in aqueous media. Such stabilization is evaluated for carbon nanotubes (CNT) considering spatial and temporal perspectives by using experimental (small-angle X-ray scattering, among others) and theoretical (atomistic simulation) approaches. We reveal that the coassembly of ChNF and CNT is governed by hydrophobic interactions, while electrostatic repulsion drives the colloidal stabilization of the hybrid ChNF/CNT system. Related effects are found to be transferable to multiwalled carbon nanotubes and graphene nanosheets. The observations explain the functionality of hybrid membranes obtained by aqueous phase processing, which benefit from an excellent areal mass distribution (correlated to piezoresistivity), also contributing to high electromechanical performance. The water resistance and flexibility of the ChNF/CNT membranes (along with its tensile strength at break of 190 MPa, conductivity of up to 426 S/cm, and piezoresistivity and light absorption properties) are conveniently combined in a device demonstration, a sunlight water evaporator. The latter is shown to present a high evaporation rate (as high as 1.425 kg water m-2 h-1 under one sun illumination) and recyclability.
Collapse
Affiliation(s)
- Tianyu Guo
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhangmin Wan
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mahyar Panahi-Sarmad
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
- Sustainable Functional Biomaterials Laboratory, Department of Wood Science, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gabriel Banvillet
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Yi Lu
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Shiva Zargar
- Sustainable Bioeconomy Research Group, Department of Wood Science, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1 Z4, Canada
| | - Jing Tian
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Feng Jiang
- Sustainable Functional Biomaterials Laboratory, Department of Wood Science, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yimin Mao
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Qingshi Tu
- Sustainable Bioeconomy Research Group, Department of Wood Science, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1 Z4, Canada
| | - Orlando J Rojas
- Bioproducts Institute, Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Wood Science, The University of British Columbia, 2900-2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| |
Collapse
|
3
|
Nayak K, Ghosh P, Barman S, Sudhamalla B, Theato P, De P. Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis. Bioconjug Chem 2024; 35:312-323. [PMID: 38420925 DOI: 10.1021/acs.bioconjchem.3c00509] [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: 03/02/2024]
Abstract
Developing effective amyloidosis inhibitors poses a significant challenge due to the dynamic nature of the protein structures, the complex interplay of interfaces in protein-protein interactions, and the irreversible nature of amyloid assembly. The interactions of amyloidogenic polypeptides with other peptides play a pivotal role in modulating amyloidosis and fibril formation. This study presents a novel approach for designing and synthesizing amyloid interaction surfaces using segments derived from the amyloid-promoting sequence of amyloid β-peptide [VF(Aβ(18-19)/FF(Aβ(19-20)/LVF(Aβ(17-19)/LVFF(Aβ(17-20)], where VF, FF, LVF and LVFF stands for valine phenylalanine dipeptide, phenylalanine phenylalanine dipeptide, leucine valine phenylalanine tripeptide and leucine valine phenylalanine phenylalanine tetrapeptide, respectively. These segments are conjugated with side-chain proline-based methacrylate polymers serving as potent lysozyme amyloidosis inhibitors and demonstrating reduced cytotoxicity of amyloid aggregations. Di-, tri-, and tetra-peptide conjugated chain transfer agents (CTAs) were synthesized and used for the reversible addition-fragmentation chain transfer polymerization of tert-butoxycarbonyl (Boc)-proline methacryloyloxyethyl ester (Boc-Pro-HEMA). Deprotection of Boc-groups from the side-chain proline pendants resulted in water-soluble polymers with defined peptide chain ends as peptide-polymer bioconjugates. Among them, the LVFF-conjugated polymer acted as a potent inhibitor with significantly suppressed lysozyme amyloidosis, a finding supported by comprehensive spectroscopic, microscopic, and computational analyses. These results unveil the synergistic effect between the segment-derived amyloid β-peptide and side-chain proline-based polymers, offering new prospects for targeting lysozyme amyloidosis.
Collapse
Affiliation(s)
- Kasturee Nayak
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Pooja Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
- Centre for Interdisciplinary Sciences, JIS Institute of Advanced Studies & Research (JISIASR) Kolkata, JIS University, GP Block, Sector-5, Salt Lake, Kolkata, West Bengal 700091, India
| | - Soumen Barman
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Patrick Theato
- Karlsruhe Institute of Technology (KIT), Institute for Chemical Technology and Polymer Chemistry (ITCP), Engesserstraße 18, Karlsruhe 76131, Germany
- Karlsruhe Institute of Technology (KIT), Soft Matter Synthesis Laboratory,Institute for Biological Interfaces III (IBG-3), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| |
Collapse
|
4
|
Ning S, Sanchis-Gual R, Franco C, Wendel-Garcia PD, Ye H, Veciana A, Tang Q, Sevim S, Hertle L, Llacer-Wintle J, Qin XH, Zhu C, Cai J, Chen X, Nelson BJ, Puigmartí-Luis J, Pané S. Magnetic PiezoBOTs: a microrobotic approach for targeted amyloid protein dissociation. NANOSCALE 2023; 15:14800-14808. [PMID: 37646185 PMCID: PMC10517098 DOI: 10.1039/d3nr02418k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
Piezoelectric nanomaterials have become increasingly popular in the field of biomedical applications due to their high biocompatibility and ultrasound-mediated piezocatalytic properties. In addition, the ability of these nanomaterials to disaggregate amyloid proteins, which are responsible for a range of diseases resulting from the accumulation of these proteins in body tissues and organs, has recently gained considerable attention. However, the use of nanoparticles in biomedicine poses significant challenges, including targeting and uncontrolled aggregation. To address these limitations, our study proposes to load these functional nanomaterials on a multifunctional mobile microrobot (PiezoBOT). This microrobot is designed by coating magnetic and piezoelectric barium titanate nanoparticles on helical biotemplates, allowing for the combination of magnetic navigation and ultrasound-mediated piezoelectric effects to target amyloid disaggregation. Our findings demonstrate that acoustically actuated PiezoBOTs can effectively reduce the size of aggregated amyloid proteins by over 80% in less than 10 minutes by shortening and dissociating constituent amyloid fibrils. Moreover, the PiezoBOTs can be easily magnetically manipulated to actuate the piezocatalytic nanoparticles to specific amyloidosis-affected tissues or organs, minimizing side effects. These biocompatible PiezoBOTs offer a promising non-invasive therapeutic approach for amyloidosis diseases by targeting and breaking down protein aggregates at specific organ or tissue sites.
Collapse
Affiliation(s)
- Shen Ning
- Boston University School of Medicine, Boston, MA, USA
| | - Roger Sanchis-Gual
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Carlos Franco
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Pedro D Wendel-Garcia
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Hao Ye
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Andrea Veciana
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Qiao Tang
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Semih Sevim
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Lukas Hertle
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Joaquin Llacer-Wintle
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Xiao-Hua Qin
- Institute for Biomechanics, ETH Zürich, Leopold-Ruzicka-Weg 4, CH-8093 Zürich, Switzerland
| | - Caihong Zhu
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, China
| | - Jun Cai
- School of Mechanical Engineering and Automation, Beihang University, No. 37 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xiangzhong Chen
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Bradley J Nelson
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| | - Josep Puigmartí-Luis
- Departament de Ciència dels Materials i Química Física, Institut de Química Teòrica i Computacional, University of Barcelona (UB), 08028 Barcelona, Spain.
- ICREA, Institució Catalana de Reserca i Estudis Avançats, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Salvador Pané
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zürich, Tannestrasse 3, CH-8092 Zürich, Switzerland.
| |
Collapse
|
5
|
Homma C, Tsukiiwa M, Noguchi H, Tanaka M, Okochi M, Tomizawa H, Sugizaki Y, Isobayashi A, Hayamizu Y. Designable peptides on graphene field-effect transistors for selective detection of odor molecules. Biosens Bioelectron 2023; 224:115047. [PMID: 36628827 DOI: 10.1016/j.bios.2022.115047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
Gas sensing based on graphene field-effect transistors (GFETs) has gained broad interest due to their high sensitivity. Further progress in gas sensing with GFETs requires to detection of various odor molecules for applications in the environmental monitoring, healthcare, food, and cosmetic industries. To develop the ubiquitous odor-sensing system, establishing an artificial sense of smell with electronic devices by mimicking olfactory receptors will be key. Although the application of olfactory receptors to GFETs is straightforward for odor sensing, synthetic molecules with a similar function to olfactory receptors would be desirable to realize the robust performance of sensing. In this work, we designed three new peptides consisting of two domains: a bio-probe to the target molecules and a molecular scaffold. These peptides were rationally designed based on a motif sequence in olfactory receptors and self-assembled into a molecular thin film on GFETs. Limonene, methyl salicylate, and menthol were employed as representative odor molecules of plant flavors to demonstrate the biosensing of odor molecules. The conductivity change of GFETs against the binding to odor molecules with various concentrations and the dynamic response revealed a distinct signature of three different peptides against individual species of the target molecules. The kinetic response of each peptide exhibited characteristic time constants in the adsorption and desorption process, also supported by the principal component analysis. Our demonstration of the graphene odor sensors with the designed peptides opens a way to establish future peptide-array sensors with multi-sequence of peptide, realizing an odor sensing system with higher selectivity.
Collapse
Affiliation(s)
- Chishu Homma
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, Japan
| | - Mirano Tsukiiwa
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, Japan
| | - Hironaga Noguchi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, Japan
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, Japan
| | - Hideyuki Tomizawa
- Corporate Research & Development Center, Toshiba Corporation,1, Komukai-Toshiba-Cho, Saiwai-ku, Kawasaki, 212-8582, Japan
| | - Yoshiaki Sugizaki
- Corporate Research & Development Center, Toshiba Corporation,1, Komukai-Toshiba-Cho, Saiwai-ku, Kawasaki, 212-8582, Japan
| | - Atsunobu Isobayashi
- Corporate Research & Development Center, Toshiba Corporation,1, Komukai-Toshiba-Cho, Saiwai-ku, Kawasaki, 212-8582, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, Japan.
| |
Collapse
|
6
|
Li Q, Wang Y, Zhang G, Su R, Qi W. Biomimetic mineralization based on self-assembling peptides. Chem Soc Rev 2023; 52:1549-1590. [PMID: 36602188 DOI: 10.1039/d2cs00725h] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.
Collapse
Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Gong Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou Industrial Park, Suzhou 215123, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| |
Collapse
|
7
|
Ma Y, Li X, Zhao R, Wu E, Du Q, Guo J, Wang L, Zhang F. Creating de novo peptide-based bioactivities: from assembly to origami. RSC Adv 2022; 12:25955-25961. [PMID: 36199601 PMCID: PMC9465703 DOI: 10.1039/d2ra03135c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
DNA origami has created complex structures of various spatial dimensions. However, their versatility in terms of function is limited due to the lower number of the intrinsic building blocks, i.e. nucleotides, compared with the number of amino acids. Therefore, protein origami has been proposed and demonstrated to precisely fabricate artificial functional nanostructures. Despite their hierarchical folded structures, chain-like peptides and DNA share obvious similarities in both structures and properties, especially in terms of chain hybridization; therefore, replacing DNA with peptides to create bioactivities not only has high theoretical feasibility but also provides a new bottom-up synthetic strategy. However, designing functionalities with tens to hundreds of peptide chains using the similar principle of DNA origami has not been reported, although the origami strategy holds great potential to generate more complex bioactivities. In this perspective review, we have reviewed the recent progress in and highlighted the advantages of peptide assembly and origami on the orientation of artificially created bioactivities. With the great potential of peptide origami, we appeal to develop user-friendly softwares in combination with artificial intelligence.
Collapse
Affiliation(s)
- Yuxing Ma
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College Bayannur 015000 China
| | - Xiaofang Li
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology Shanghai 200093 P. R. China
| | - Ruoyang Zhao
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
| | - Enqi Wu
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College Bayannur 015000 China
| | - Qiqige Du
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
| | - Jun Guo
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology Shanghai 200093 P. R. China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Oral Disease, Stomatology Hospital, School of Biomedical Engineering, Guangzhou Medical University Guangzhou 511436 China
| | - Liping Wang
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
| | - Feng Zhang
- Wenzhou Institute, University of Chinese Academy of Sciences Wenzhou 325001 China
- Oujiang Laboratory Wenzhou Zhejiang 325000 P. R. China
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology Shanghai 200093 P. R. China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Oral Disease, Stomatology Hospital, School of Biomedical Engineering, Guangzhou Medical University Guangzhou 511436 China
| |
Collapse
|
8
|
An H, Mamuti M, Wang X, Yao H, Wang M, Zhao L, Li L. Rationally designed modular drug delivery platform based on intracellular peptide self‐assembly. EXPLORATION 2021; 1:20210153. [PMCID: PMC10190849 DOI: 10.1002/exp.20210153] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/08/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Hong‐Wei An
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| | - Muhetaerjiang Mamuti
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| | - Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics Chinese Academy of Sciences (CAS) Beijing China
| | - Haodong Yao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics Chinese Academy of Sciences (CAS) Beijing China
| | - Man‐Di Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| | - Lina Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics Chinese Academy of Sciences (CAS) Beijing China
| | - Li‐Li Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology (NCNST) Beijing China
| |
Collapse
|
9
|
Zhu L, Gong Y, Lju H, Sun G, Zhang Q, Qian Z. Mechanisms of melatonin binding and destabilizing the protofilament and filament of tau R3-R4 domains revealed by molecular dynamics simulation. Phys Chem Chem Phys 2021; 23:20615-20626. [PMID: 34514491 DOI: 10.1039/d1cp03142b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accumulation of β-amyloid (Aβ) and tau protein is considered to be an important pathological characteristic of Alzheimer's disease (AD). Failure of medicine targeting Aβ has drawn more attention to the influence of tau protein and its fibrillization on neurodegeneration. Increasing evidence shows that melatonin (Mel) can effectively inhibit the formation of tau fibrils and disassemble preformed tau fibrils. However, the underlying mechanism is poorly understood. In this work, we investigated the kinetics of melatonin binding and destabilizing the tetrameric protofilament and octameric filament of tau R3-R4 domains by performing microsecond all-atom molecular dynamics simulations. Our results show that Mel is able to disrupt the C-shaped structure of the tau protofilament and filament, and destabilizes the association between N- and C-termini. Mel predominantly binds to β1 and β6-β8 regions and favors contact with the elongation surface, which is dominantly driven by hydrogen bonding interactions and facilitated by other interactions. The strong π-π stacking interaction of Mel with Y310 impedes the intramolecular CH-π interaction between I308 and Y310, and the cation-π interaction of Mel with R379 interferes with the formation of the D348-R379 salt bridge. Moreover, Mel occupies the protofilament surface in the tetrameric protofilament and prevents the formation of intermolecular hydrogen bonds between residues K331 and Q336 in the octameric filament. Our work provides molecular insights into Mel hindering tau fibrillization or destabilizing the protofilament and filament, and the revealed inhibitory mechanisms provide useful clues for the design of efficient anti-amyloid agents.
Collapse
Affiliation(s)
- Lili Zhu
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Yehong Gong
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China
| | - Hao Lju
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Gongwu Sun
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, China.
| |
Collapse
|
10
|
Co NT, Li MS. Effect of Surface Roughness on Aggregation of Polypeptide Chains: A Monte Carlo Study. Biomolecules 2021; 11:biom11040596. [PMID: 33919640 PMCID: PMC8072528 DOI: 10.3390/biom11040596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The self-assembly of amyloidogenic peptides and proteins into fibrillar structures has been intensively studied for several decades, because it seems to be associated with a number of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease. Therefore, understanding the molecular mechanisms of this phenomenon is important for identifying an effective therapy for the corresponding diseases. Protein aggregation in living organisms very often takes place on surfaces like membranes and the impact of a surface on this process depends not only on the surface chemistry but also on its topology. Our goal was to develop a simple lattice model for studying the role of surface roughness in the aggregation kinetics of polypeptide chains and the morphology of aggregates. We showed that, consistent with the experiment, an increase in roughness slows down the fibril formation, and this process becomes inhibited at a very highly level of roughness. We predicted a subtle catalytic effect that a slightly rough surface promotes the self-assembly of polypeptide chains but does not delay it. This effect occurs when the interaction between the surface and polypeptide chains is moderate and can be explained by taking into account the competition between energy and entropy factors.
Collapse
Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland;
| | - 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 700000, Vietnam
- Correspondence:
| |
Collapse
|
11
|
Wang Y, Guo Z, Tan T, Ji Y, Hu J, Zhang Y. The effects of nanobubbles on the assembly of glucagon amyloid fibrils. SOFT MATTER 2021; 17:3486-3493. [PMID: 33657201 DOI: 10.1039/d0sm02279a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Some recent studies have shown that the surface and interface play an important role in the assembly and aggregation of amyloid proteins. However, it is unclear how the gas-liquid interface affects the protein assembly at the nanometer scale although the presence of gas-liquid interfaces is very common in in vitro experiments. Nanobubbles have a large specific surface area, which provides a stage for interactions with various proteins and peptides on the nanometer scale. In this work, nanobubbles produced in solution were employed for studying the effects of the gas-liquid interface on the assembly of glucagon proteins. Atomic force microscopy (AFM) studies showed that nanobubble-treated glucagon solution formed fibrils with an apparent height of 4.02 ± 0.71 nm, in contrast to the fibrils formed with a height of 2.14 ± 0.53 nm in the control. Transmission electron microscopy (TEM) results also showed that nanobubbles promoted the assembly of glucagon to form more fibrils. Thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) analyses indicated that the nanobubbles induced the change of the glucagon conformation to a β-sheet structure. A mechanism that explains how nanobubbles affect the assembly of glucagon amyloid fibrils was proposed based on the above-mentioned experimental results. Given the fact that there are a considerable amount of nanobubbles existing in protein solutions, our results indicate that nanobubbles should be considered for fully understanding the protein aggregation events in vitro.
Collapse
Affiliation(s)
- Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | | | | | | | | | | |
Collapse
|
12
|
Yin XR, Yang P, Zhang HM, Zhu QJ, Yuan R, Li Y, Liang WB. Hydrophobic-Driven Electrochemiluminescence Enhancement via Target-Induced Self-Enrichment for Ultrasensitive Bioassay. Anal Chem 2020; 92:15120-15128. [DOI: 10.1021/acs.analchem.0c03394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xiao-Ru Yin
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Peng Yang
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Hao-Min Zhang
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Quan-Jing Zhu
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Ruo Yuan
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing 400038, China
| | - Wen-Bin Liang
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| |
Collapse
|
13
|
Abstract
The formation of dense, linear arrays (fibrils) by biomolecules is the hallmark of a number of degenerative diseases, such as Alzheimer's and type-2 diabetes. Protein fibrils have also attracted interest as building blocks for new materials. It has long been recognized that surfaces can affect the fibrillation process. Recent work on the model fibril forming protein human islet amyloid polypeptide (hIAPP) has shown that while the protein concentration is highest at hydrophobic surfaces, the rate of fibril formation is lower than on other surfaces. To understand this, replica exchange molecular dynamics simulations were used to investigate the conformations that hIAPP adopts on surfaces of different hydrophobicities. The hydrophobic surface stabilizes α-helical structures which are significantly different to those found on the hydrophilic surface and in bulk solution. There is also a greatly reduced conformational ensemble on the hydrophobic surface due to long-lived contacts between hydrophobic residues on the protein and the surface. This new microscopic information will help us determine the mechanism of the enhancement of fibril formation on surfaces and provides new insight into the effect of nanointerfaces and protein conformation.
Collapse
|
14
|
Jang J, Kim K, Yoon J, Park CB. Piezoelectric materials for ultrasound-driven dissociation of Alzheimer's β-amyloid aggregate structure. Biomaterials 2020; 255:120165. [PMID: 32540759 DOI: 10.1016/j.biomaterials.2020.120165] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/22/2020] [Accepted: 05/30/2020] [Indexed: 01/22/2023]
Abstract
Piezoelectric materials can evoke electrochemical reactions by transferring charge carriers to reactants upon receiving mechanical stimuli. We report a newly discovered function of piezoelectric bismuth oxychloride (BiOCl) nanosheets for dissociating Alzheimer's β-amyloid (Aβ) aggregates through ultrasound-induced redox reactions. The accumulation of Aβ aggregates (e.g., Aβ fibrils, plaques) in the central nervous system is a major pathological hallmark of Alzheimer's disease (AD). Thus, clearing Aβ aggregates is considered a key for treating AD, but the dissociation of Aβ aggregates is challenging due to their extremely robust structure consisting of β-sheets. BiOCl nanosheets are a biocompatible piezoelectric material with piezocatalytic activity in response to ultrasound. Our analyses using multiple spectroscopic and microscopic tools have revealed that BiOCl nanosheets effectively disassemble Aβ fibrils under ultrasound stimulation. Sono-activated BiOCl nanosheets produce piezo-induced oxidative stress, which effectively destabilizes the β-sheets in Aβ fibrils. In vitro evolution has also shown that sono-activated BiOCl nanosheets can effectively alleviate the neuro-toxicity of Aβ fibrils. Furthermore, ex vivo evolution demonstrated that amount of Aβ plaques in AD mouse's brain slices was drastically reduced by treatment with sono-activated BiOCl nanosheets.
Collapse
Affiliation(s)
- Jinhyeong Jang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea
| | - Kayoung Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea
| | - Jaeho Yoon
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea
| | - Chan Beum Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Science Road, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
15
|
Li Y, Li N, Wang L, Lu Q, Ji X, Zhang F. A Comparative Study on the Self-Assembly of Peptide TGV-9 by In Situ Atomic Force Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:319-325. [PMID: 32051052 DOI: 10.1017/s1431927620000082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Previous studies of amyloid diseases reported that the aggregating proteins share a similar conserved peptide sequence which can form the cross-β-sheet-containing nanostructures like nanofilaments. The template-assisted self-assembly (TASA) of peptides on inorganic substrates with different hydrophilicity could be an alternative approach to shed light on the fibrillization mechanism of proteins/peptides in vivo. To figure out the effect of interfaces on amyloid aggregation, we herein employed in situ atomic force microscopy (AFM) to investigate the self-assembling of a Parkinson disease-related core peptide sequence (TGV-9) on a hydrophobic liquid-solid interface via real-time observation of the dynamic fibrillization process. The results show that TGV-9 forms one-dimensional nanostructures on the surface of highly ordered pyrolytic graphite (HOPG) with three preferred growth orientations, which are consistent with the atomic lattice of HOPG, indicating an epitaxial growth or TASA. Conversely, the nanostructures formed in bulk solution can be free-standing nanofilaments, and the fibrillization mechanism is different from that on HOPG. These results could not only deepen the understanding of the protein/peptide aggregation mechanism but also benefit for the early diagnosis and clinic treatment of related diseases.
Collapse
Affiliation(s)
- Yaping Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Na Li
- Terahertz Technology Innovation Research Institute, Shanghai Key Laboratory of Modern Optical System, Terahertz Science Cooperative Innovation Center, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai200093, P. R. China
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, Hohhot010018, P. R. China
| | - Lei Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Qinhua Lu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Xiang Ji
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Feng Zhang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, Hohhot010018, P. R. China
- Key Laboratory of Oral Medicine, Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Institute of Oral Disease, Stomatology Hospital, Guangzhou Medical University, Guangzhou511436, P. R. China
| |
Collapse
|
16
|
Liu J, Cui X, Xie L, Huang J, Zhang L, Liu J, Wang X, Wang J, Zeng H. Probing effects of molecular-level heterogeneity of surface hydrophobicity on hydrophobic interactions in air/water/solid systems. J Colloid Interface Sci 2019; 557:438-449. [DOI: 10.1016/j.jcis.2019.09.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 11/27/2022]
|
17
|
Zheng Y, Yu L, Zou Y, Yang Y, Wang C. Steric Dependence of Chirality Effect in Surface-Mediated Peptide Assemblies Identified with Scanning Tunneling Microscopy. NANO LETTERS 2019; 19:5403-5409. [PMID: 31265784 DOI: 10.1021/acs.nanolett.9b01904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amino acid chirality has been recognized as an important driving force in constructing peptide architectures, via interactions such as chirality-induced stereochemical effect. The introduction of site-specific chiral conversion of l- and d-amino acids in peptide sequences could enable the pursuit of the chirality effects in peptide assembly. In this work, we characterized the assemblies of heptapeptides with various side chain moieties and their chiral variants using STM. Specifically, two pairs of amino acids, Gln (Q) and Asn (N), Glu (E) and Asp (D), having one methylene difference in their side chains, are selected to elucidate the steric dependence of amino acid chiral effects on surface-bound peptide assemblies. The observed heptapeptide assembly structures reveal that chirality switching of a single amino acid is able to destabilize the surface-mediated peptide assemblies, and this disturbance effect can be positively correlated with the steric hindrance of amino acid side chains. Furthermore, the strength of the impact due to chiral conversion on heptapeptide assembly structure is noticeably dependent on the mutation sites, indicative of structural heterogeneity of chiral effects. These results could contribute to the molecular insights of chirality-induced stereochemical interactions in peptide assembly.
Collapse
Affiliation(s)
- Yongfang Zheng
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Lanlan Yu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yimin Zou
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| |
Collapse
|
18
|
Inhibiting and catalysing amyloid fibrillation at dynamic lipid interfaces. J Colloid Interface Sci 2019; 543:256-262. [PMID: 30818141 DOI: 10.1016/j.jcis.2019.02.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 11/20/2022]
Abstract
Proteins are naturally exposed to diverse interfaces in living organisms, from static solid to dynamic fluid. Solid interfaces can enrich proteins as corona, and then catalyze, retard or hinder amyloid fibrillation. But fluid interfaces abundant in biology have rarely been studied for their correlation with protein fibrillation. Unsaturated fatty acids own growing essential roles in diet, whose fluid interfaces are found in vitro to catalyze amyloid fibrillation under certain physiologic conditions. It is determined by the location of double bonds within alkyl chains as well as the presence of physical shear. Docosahexaenoic acid (DHA) shows low catalysis because its unique alkyl chain does not favor to stabilize cross-β nucleus. Mixtures of different fatty acids also decelerate their catalytic activity. High catalysis poses an unprecedented approach to synthesize biologic nanofibrils as one-dimensional (1D) building blocks of functional hybrids. Fibrillation inhibition implied that appropriate diet would be a preventive strategy for amyloid-related diseases. Thus these results may find their significances in diverse fields of science as chemistry, biotechnology, nanotechnology, nutrition, amyloid pathobiology and nanomedicine.
Collapse
|
19
|
Zhang J, Zhou L, Du Q, Shen Z, Hu J, Zhang Y. Assembly of peptides in mica-graphene nanocapillaries controlled by confined water. NANOSCALE 2019; 11:8210-8218. [PMID: 30973561 DOI: 10.1039/c9nr01092k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Water in nanoscale-confined geometries has unique physicochemical properties in contrast to bulk water, and is believed to play important roles in biological processes although there is less direct information available in the literature. Here, we report the self-assembly behaviors of a neurodegenerative disease related peptide termed GAV-9 encapsulated in mica-graphene nanocapillaries interacting with water nanofilms condensed under ambient conditions, based on atomic force microscopy (AFM) imaging and molecular dynamics (MD) simulations. The results revealed that, upon increase in the humidity, the GAV-9 peptide monomers adsorbed the confined water molecules and transitioned to unexpected hydrogel-like structures. Our MD simulations also suggested that in the confined mica-graphene nanocapillaries, the GAV-9 peptide monomers would indeed form water-rich hydrogel structures instead of highly ordered nanofilaments. The interfacial water confined in the mica-graphene nanocapillary is found to be crucial for such a transition. Moreover, the distribution of confined water layers largely depended on the locations of the preformed peptide nanofilaments, and the peptide nanofilaments further assembled into nanosheets with the water layer increasing, but depolymerized to amorphous peptide assemblies with the water layer decreasing. The polymerization and depolymerization of the peptide nanofilaments could be controlled in a reversible manner. Our results have supplied a simplified model system to uncover the effects of the confined interfacial water on the biological process at the molecular level.
Collapse
Affiliation(s)
- Jinjin Zhang
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | | | | | | | | | | |
Collapse
|
20
|
Yang B, Adams DJ, Marlow M, Zelzer M. Surface-Mediated Supramolecular Self-Assembly of Protein, Peptide, and Nucleoside Derivatives: From Surface Design to the Underlying Mechanism and Tailored Functions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15109-15125. [PMID: 30032622 DOI: 10.1021/acs.langmuir.8b01165] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Among the many parameters that have been explored to exercise control over self-assembly processes, the influence of surface properties on self-assembly has been recognized as important but has received considerably less attention than other factors. This is particularly true for biomolecule-derived self-assembling molecules such as protein, peptide, and nucleobase derivatives. Because of their relevance to biomaterial and drug delivery applications, interest in these materials is increasing. As the formation of supramolecular structures from these biomolecule derivatives inevitably brings them into contact with the surfaces of surrounding materials, understanding and controlling the impact of the properties of these surfaces on the self-assembly process are important. In this feature article, we present an overview of the different surface parameters that have been used and studied for the direction of the self-assembly of protein, peptide, and nucleoside-based molecules. The current mechanistic understanding of these processes will be discussed, and potential applications of surface-mediated self-assembly will be outlined.
Collapse
Affiliation(s)
- Bin Yang
- Department of Pharmacy , University of Nottingham , Nottingham NG2 7RD , U.K
| | - Dave J Adams
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , U.K
| | - Maria Marlow
- Department of Pharmacy , University of Nottingham , Nottingham NG2 7RD , U.K
| | - Mischa Zelzer
- Department of Pharmacy , University of Nottingham , Nottingham NG2 7RD , U.K
| |
Collapse
|
21
|
Wang Y, Shen Z, Guo Z, Hu J, Zhang Y. Effects of nanobubbles on peptide self-assembly. NANOSCALE 2018; 10:20007-20012. [PMID: 30351325 DOI: 10.1039/c8nr06142d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is believed that the aggregation of amyloid proteins or peptides is promoted by the presence of an air-water interface, and substantial evidence suggests that the characteristics of the air-water interface play critical roles in foam-induced protein aggregation during foam fractionation. However, the effects of the air-water interface on the self-assembly of amyloid-like peptides have not yet been elucidated clearly at the nanometer scale. In this work, air nanobubbles produced in water solution were employed for studying interfacial effects on the self-assembly of a model amyloid peptide termed P11. An atomic force microscopy study showed that the air nanobubbles induced the formation of peptide fibrils with a 9-13 nm helix structure in the P11 solution. Thioflavin T fluorescence and circular dichroism spectroscopic analysis indicated that the nanobubbles induced the change of the peptide conformation to a β-sheet structure. Based on these observations, we have proposed a mechanism to explain how the nanobubbles affect the self-assembly of the P11 peptide at the nanometer scale. Since air nanobubbles are present in water solutions in addition to an air-water interface in normal experiments in vitro, our results indicate that nanobubbles must be taken into account to achieve a complete understanding of protein aggregation events.
Collapse
Affiliation(s)
- Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | | | | | | | | |
Collapse
|
22
|
Russell MJ. Green Rust: The Simple Organizing 'Seed' of All Life? Life (Basel) 2018; 8:E35. [PMID: 30150570 PMCID: PMC6161180 DOI: 10.3390/life8030035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023] Open
Abstract
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
Collapse
Affiliation(s)
- Michael J Russell
- Planetary Chemistry and Astrobiology, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109-8099, USA.
| |
Collapse
|
23
|
Hughes ZE, Walsh TR. Probing nano-patterned peptide self-organisation at the aqueous graphene interface. NANOSCALE 2017; 10:302-311. [PMID: 29210426 DOI: 10.1039/c7nr06441a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.
Collapse
Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
| | | |
Collapse
|
24
|
Zhou T, Zhang Z, Zhang X, Wang C, Xu G, Yang Y. Self-assembled chiral nanostructures of amphiphilic peptide: from single molecule to aggregate. J Pept Sci 2017; 23:803-809. [DOI: 10.1002/psc.3032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/19/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Ting Zhou
- College of Science; China University of Petroleum (East China); Qingdao 266580 China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology; National Center for Nanoscience and Technology; Beijing 100190 China
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education; Shandong University; Jinan 250100 China
| | - Zhiqing Zhang
- College of Science; China University of Petroleum (East China); Qingdao 266580 China
| | - Xuemei Zhang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology; National Center for Nanoscience and Technology; Beijing 100190 China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology; National Center for Nanoscience and Technology; Beijing 100190 China
| | - Guiying Xu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education; Shandong University; Jinan 250100 China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology; National Center for Nanoscience and Technology; Beijing 100190 China
| |
Collapse
|
25
|
Li N, Jang H, Yuan M, Li W, Yun X, Lee J, Du Q, Nussinov R, Hou J, Lal R, Zhang F. Graphite-Templated Amyloid Nanostructures Formed by a Potential Pentapeptide Inhibitor for Alzheimer's Disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6647-6656. [PMID: 28605901 PMCID: PMC7900909 DOI: 10.1021/acs.langmuir.7b00414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of peptides is closely related to many diseases, including Alzheimer's, Parkinson's, and prion diseases. Understanding the basic mechanism of this assembly is essential for designing ultimate cure and preventive measures. Template-assisted self-assembly (TASA) of peptides on inorganic substrates can provide fundamental understanding of substrate-dependent peptides assemble, including the role of hydrophobic interface on the peptide fibrillization. Here, we have studied the self-assembly process of a potential pentapeptide inhibitor on the surface of highly oriented pyrolytic graphite (HOPG) using real time atomic force microscopy (RT-AFM) as well as molecular dynamics (MD) simulation. Experimental and simulation results show nanofilament formation consisting of β-sheet structures and epitaxial growth on HOPG. Height analysis of the nanofilaments and MD simulation indicate that the peptides adopt a lying down configuration of double-layered antiparallel β-sheets for its epitaxial growth, and the number of nanofilament layers is concentration-dependent. These findings provide new perspective for the mechanism of peptide-based fibrillization in amyloid diseases as well as for designing well-ordered micrometrical and nanometrical structures.
Collapse
Affiliation(s)
- Na Li
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Ming Yuan
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Wanrong Li
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Xiaolin Yun
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Joon Lee
- Materials Science and Engineering Program and Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| | - Qiqige Du
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiahua Hou
- Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Ratnesh Lal
- Materials Science and Engineering Program and Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| | - Feng Zhang
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| |
Collapse
|
26
|
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
| |
Collapse
|
27
|
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
| |
Collapse
|
28
|
Kang H, Vázquez FX, Zhang L, Das P, Toledo-Sherman L, Luan B, Levitt M, Zhou R. Emerging β-Sheet Rich Conformations in Supercompact Huntingtin Exon-1 Mutant Structures. J Am Chem Soc 2017; 139:8820-8827. [PMID: 28609090 PMCID: PMC5835228 DOI: 10.1021/jacs.7b00838] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
There exists strong correlation between the extended polyglutamines (polyQ) within exon-1 of Huntingtin protein (Htt) and age onset of Huntington's disease (HD); however, the underlying molecular mechanism is still poorly understood. Here we apply extensive molecular dynamics simulations to study the folding of Htt-exon-1 across five different polyQ-lengths. We find an increase in secondary structure motifs at longer Q-lengths, including β-sheet content that seems to contribute to the formation of increasingly compact structures. More strikingly, these longer Q-lengths adopt supercompact structures as evidenced by a surprisingly small power-law scaling exponent (0.22) between the radius-of-gyration and Q-length that is substantially below expected values for compact globule structures (∼0.33) and unstructured proteins (∼0.50). Hydrogen bond analyses further revealed that the supercompact behavior of polyQ is mainly due to the "glue-like" behavior of glutamine's side chains with significantly more side chain-side chain H-bonds than regular proteins in the Protein Data Bank (PDB). The orientation of the glutamine side chains also tend to be "buried" inside, explaining why polyQ domains are insoluble on their own.
Collapse
Affiliation(s)
- Hongsuk Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Francisco X Vázquez
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Leili Zhang
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | | | - Binquan Luan
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| |
Collapse
|
29
|
Wu R, Liu J, Qiu X, Deng M. Molecular dynamics simulation of the nanofibrils formed by amyloid-based peptide amphiphiles. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1321758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rongliang Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Jun Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Xinlong Qiu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, P.R. China
| | - Manli Deng
- Key Laboratory of Colloid and Interface Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, P.R. China
| |
Collapse
|
30
|
Sorokina S, Semenyuk P, Stroylova Y, Muronetz V, Shifrina Z. Complexes between cationic pyridylphenylene dendrimers and ovine prion protein: do hydrophobic interactions matter? RSC Adv 2017. [DOI: 10.1039/c6ra26563d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
MD simulation predicted the possible binding sites for the dendrimer interactions with protein while ITC data revealed both electrostatic and hydrophobic driving forces for the complexation.
Collapse
Affiliation(s)
- S. Sorokina
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russian Federation
| | - P. Semenyuk
- Belozersky Institute of Physico-Chemical Biology
- Lomonosov Moscow State University
- Moscow
- Russian Federation
| | - Yu. Stroylova
- Belozersky Institute of Physico-Chemical Biology
- Lomonosov Moscow State University
- Moscow
- Russian Federation
| | - V. Muronetz
- Belozersky Institute of Physico-Chemical Biology
- Lomonosov Moscow State University
- Moscow
- Russian Federation
| | - Z. Shifrina
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russian Federation
| |
Collapse
|
31
|
Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
Collapse
|
32
|
Feng M, Kang H, Yang Z, Luan B, Zhou R. Potential disruption of protein-protein interactions by graphene oxide. J Chem Phys 2016; 144:225102. [PMID: 27306022 DOI: 10.1063/1.4953562] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.
Collapse
Affiliation(s)
- Mei Feng
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027, China
| | - Hongsuk Kang
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Ruhong Zhou
- Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
33
|
Thermo-responsive chiral column by scissoring motion from rigid–flexible aromatic rod assembly. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2015.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
34
|
Köhler S, Schmid F, Settanni G. Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13180-90. [PMID: 26569042 DOI: 10.1021/acs.langmuir.5b03371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fibrinogen, a blood glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin when activated. Upon adsorption on material surfaces, it also contributes to determine their biocompatibility and has been implicated in the onset of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counterion layer. Preferred adsorption orientations for the globular regions of the protein are identified. The adsorption on graphite is found to be stronger with fewer reorientation and desorption events and shows the onset of denaturation of the protein.
Collapse
Affiliation(s)
- Stephan Köhler
- Institut für Physik, ‡Graduate School Materials Science in Mainz, and §Max Planck Graduate Center, Johannes Gutenberg-Universität , Mainz 55099, Germany
| | - Friederike Schmid
- Institut für Physik, ‡Graduate School Materials Science in Mainz, and §Max Planck Graduate Center, Johannes Gutenberg-Universität , Mainz 55099, Germany
| | - Giovanni Settanni
- Institut für Physik, ‡Graduate School Materials Science in Mainz, and §Max Planck Graduate Center, Johannes Gutenberg-Universität , Mainz 55099, Germany
| |
Collapse
|
35
|
Duan G, Kang SG, Tian X, Garate JA, Zhao L, Ge C, Zhou R. Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane. NANOSCALE 2015; 7:15214-24. [PMID: 26315610 DOI: 10.1039/c5nr01839k] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many recent studies have shown that the way nanoparticles interact with cells and biological molecules can vary greatly in the serum-containing or serum-free culture medium. However, the underlying molecular mechanisms of how the so-called "protein corona" formed in serum medium affects nanoparticles' biological responses are still largely unresolved. Thus, it is critical to understand how absorbed proteins on the surfaces of nanoparticles alter their biological effects. In this work, we have demonstrated with both experimental and theoretical approaches that protein BSA coating can mitigate the cytotoxicity of graphene oxide (GO) by reducing its cell membrane penetration. Our cell viability and cellular uptake experiments showed that protein corona decreased cellular uptake of GO, thus significantly mitigating the potential cytotoxicity of GO. The electron microscopy images also confirmed that protein corona reduced the cellular morphological damage by limiting GO penetration into the cell membrane. Further molecular dynamics (MD) simulations validated the experimental results and revealed that the adsorbed BSA in effect weakened the interaction between the phospholipids and graphene surface due to a reduction of the available surface area plus an unfavorable steric effect, thus significantly reducing the graphene penetration and lipid bilayer damaging. These findings provide new insights into the underlying molecular mechanism of this important graphene protein corona interaction with cell membranes, and should have implications in future development of graphene-based biomedical applications.
Collapse
Affiliation(s)
- Guangxin Duan
- Institute of Quantitative Biology and Medicine, SRMP and RAD-X, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
| | | | | | | | | | | | | |
Collapse
|
36
|
Wang X, Weber JK, Liu L, Dong M, Zhou R, Li J. A novel form of β-strand assembly observed in Aβ(33-42) adsorbed onto graphene. NANOSCALE 2015; 7:15341-15348. [PMID: 26331805 DOI: 10.1039/c5nr00555h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted.
Collapse
Affiliation(s)
- Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
| | | | | | | | | | | |
Collapse
|
37
|
Yu Y, Yang Y, Wang C. Identification of Core Segment of Amyloidal Peptide Mediated by Chaperone Molecules by using Scanning Tunneling Microscopy. Chemphyschem 2015; 16:2995-9. [DOI: 10.1002/cphc.201500340] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/25/2015] [Indexed: 11/09/2022]
|
38
|
An D, Su J, Weber JK, Gao X, Zhou R, Li J. A Peptide-Coated Gold Nanocluster Exhibits Unique Behavior in Protein Activity Inhibition. J Am Chem Soc 2015; 137:8412-8. [DOI: 10.1021/jacs.5b00888] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Deyi An
- CAS Key Lab for
Biomedical Effects of Nanomaterials and Nanosafety, Institute of High
Energy Physics, Chinese Academy of Science, Beijing 100049, PR China
- College of Science, Yanshan University, Qinhuangdao 066004, PR China
| | - Jiguo Su
- College of Science, Yanshan University, Qinhuangdao 066004, PR China
| | - Jeffrey K. Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Xueyun Gao
- CAS Key Lab for
Biomedical Effects of Nanomaterials and Nanosafety, Institute of High
Energy Physics, Chinese Academy of Science, Beijing 100049, PR China
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Institute
of Quantitative Biology and Medicine, SRMP and RAD-X, Soochow University, Suzhou 215123, PR China
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jingyuan Li
- CAS Key Lab for
Biomedical Effects of Nanomaterials and Nanosafety, Institute of High
Energy Physics, Chinese Academy of Science, Beijing 100049, PR China
| |
Collapse
|
39
|
So CR, Liu J, Fears KP, Leary DH, Golden JP, Wahl KJ. Self-Assembly of Protein Nanofibrils Orchestrates Calcite Step Movement through Selective Nonchiral Interactions. ACS NANO 2015; 9:5782-5791. [PMID: 25970003 DOI: 10.1021/acsnano.5b01870] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The recognition of atomically distinct surface features by adsorbed biomolecules is central to the formation of surface-templated peptide or protein nanostructures. On mineral surfaces such as calcite, biomolecular recognition of, and self-assembly on, distinct atomic kinks and steps could additionally orchestrate changes to the overall shape and symmetry of a bulk crystal. In this work, we show through in situ atomic force microscopy (AFM) experiments that an acidic 20 kDa cement protein from the barnacle Megabalanus rosa (MRCP20) binds specifically to step edge atoms on {101̅4} calcite surfaces, remains bound and further assembles over time to form one-dimensional nanofibrils. Protein nanofibrils are continuous and organized at the nanoscale, exhibiting striations with a period of ca. 45 nm. These fibrils, templated by surface steps of a preferred geometry, in turn selectively dissolve underlying calcite features displaying the same atomic arrangement. To demonstrate this, we expose the protein solution to bare and fibril-associated rhombohedral etch pits to reveal that nanofibrils accelerate only the movement of fibril-forming steps when compared to undecorated steps exposed to the same solution conditions. Calcite mineralized in the presence of MRCP20 results in asymmetric crystals defined by frustrated faces with shared mirror symmetry, suggesting a similar step-selective behavior by MRCP20 in crystal growth. As shown here, selective surface interactions with step edge atoms lead to a cooperative regime of calcite modification, where templated long-range protein nanostructures shape crystals.
Collapse
Affiliation(s)
- Christopher R So
- †Chemistry Division, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Jinny Liu
- ‡Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Kenan P Fears
- †Chemistry Division, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Dagmar H Leary
- ‡Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Joel P Golden
- ‡Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| | - Kathryn J Wahl
- †Chemistry Division, US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
| |
Collapse
|
40
|
Du Q, Dai B, Hou J, Hu J, Zhang F, Zhang Y. A comparative study on the self-assembly of an amyloid-like peptide at water-solid interfaces and in bulk solutions. Microsc Res Tech 2015; 78:375-81. [DOI: 10.1002/jemt.22483] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/14/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Qiqige Du
- School of Life Sciences, Inner Mongolia Agricultural University; Hohhot 010018 China
- Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Bin Dai
- Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Jiahua Hou
- School of Life Sciences, Inner Mongolia Agricultural University; Hohhot 010018 China
| | - Jun Hu
- Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Feng Zhang
- School of Life Sciences, Inner Mongolia Agricultural University; Hohhot 010018 China
| | - Yi Zhang
- Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| |
Collapse
|
41
|
Ricci M, Spijker P, Voïtchovsky K. Water-induced correlation between single ions imaged at the solid-liquid interface. Nat Commun 2014; 5:4400. [PMID: 25027990 DOI: 10.1038/ncomms5400] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
When immersed into water, most solids develop a surface charge, which is neutralized by an accumulation of dissolved counterions at the interface. Although the density distribution of counterions perpendicular to the interface obeys well-established theories, little is known about counterions' lateral organization at the surface of the solid. Here we show, by using atomic force microscopy and computer simulations, that single hydrated metal ions can spontaneously form ordered structures at the surface of homogeneous solids in aqueous solutions. The structures are laterally stabilized only by water molecules with no need for specific interactions between the surface and the ions. The mechanism, studied here for several systems, is controlled by the hydration landscape of both the surface and the adsorbed ions. The existence of discrete ion domains could play an important role in interfacial phenomena such as charge transfer, crystal growth, nanoscale self-assembly and colloidal stability.
Collapse
Affiliation(s)
- Maria Ricci
- Department of Materials Science and Engineering, Ecole Polytechnique Fédérale de Lausanne, (EPFL), 1015 Lausanne, Switzerland
| | - Peter Spijker
- Department of Applied Physics, COMP Centre of Excellence, Aalto University, P.O. Box 11100, FI-00076 Helsinki, Finland
| | - Kislon Voïtchovsky
- 1] Department of Materials Science and Engineering, Ecole Polytechnique Fédérale de Lausanne, (EPFL), 1015 Lausanne, Switzerland [2] Department of Physics, Durham University, South Road, Durham DH1 3LE, UK
| |
Collapse
|
42
|
Russell MJ, Barge LM, Bhartia R, Bocanegra D, Bracher PJ, Branscomb E, Kidd R, McGlynn S, Meier DH, Nitschke W, Shibuya T, Vance S, White L, Kanik I. The drive to life on wet and icy worlds. ASTROBIOLOGY 2014; 14:308-43. [PMID: 24697642 PMCID: PMC3995032 DOI: 10.1089/ast.2013.1110] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/02/2014] [Indexed: 05/22/2023]
Abstract
This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).
Collapse
|
43
|
Varongchayakul N, Johnson S, Quabili T, Cappello J, Ghandehari H, Solares SDJ, Hwang W, Seog J. Direct observation of amyloid nucleation under nanomechanical stretching. ACS NANO 2013; 7:7734-7743. [PMID: 23987654 DOI: 10.1021/nn402322k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Self-assembly of amyloid nanofiber is associated with both functional biological and pathological processes such as those in neurodegenerative diseases. Despite intensive studies, the stochastic nature of the process has made it difficult to elucidate a molecular mechanism for the key amyloid nucleation event. Here we investigated nucleation of the silk-elastin-like peptide (SELP) amyloid using time-lapse lateral force microscopy (LFM). By repeated scanning of a single line on a SELP-coated mica surface, we observed a sudden stepwise height increase. This corresponds to nucleation of an amyloid fiber, which subsequently grew perpendicular to the scanning direction. The lateral force profiles followed either a worm-like chain model or an exponential function, suggesting that the atomic force microscopy (AFM) tip stretches a single or multiple SELP molecules along the scanning direction. The probability of nucleation correlated with the maximum stretching force and extension, implying that stretching of SELP molecules is a key molecular event for amyloid nucleation. The mechanically induced nucleation allows for positional and directional control of amyloid assembly in vitro, which we demonstrate by generating single nanofibers at predetermined nucleation sites.
Collapse
Affiliation(s)
- Nitinun Varongchayakul
- Department of Materials Science and Engineering, ‡Fischell Department of Bioengineering, ¶Department of Mechanical Engineering, University of Maryland , College Park, Maryland 20742, United States
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Shi T, Han Y, Li W, Zhao Y, Liu Y, Huang Z, Lu S, Zhang J. Exploring the desumoylation process of SENP1: a study combined MD simulations with QM/MM calculations on SENP1-SUMO1-RanGAP1. J Chem Inf Model 2013; 53:2360-8. [PMID: 23930863 DOI: 10.1021/ci4002487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The small ubiquitin-related modifier (SUMO)-specific protease (SENP) processes SUMOs to mature forms and deconjugates them from various modified substrates. Loss of the equilibrium from desumoylation catalyzed by abnormal SENP1 is associated with cancers and transcription factor activity. In spite of the significant role of SENP1, the molecular basis of its desumoylation remains unclear. Here, MD simulations and QM/MM methods are combined to investigate the catalytic mechanism of desumoylation. The results showed that substrate SUMO1-RanGAP1 fitted into the catalytic pocket of SENP1 by the break of internal hydrophobic interactions and the isomerization of isopeptide from trans to cis. After that, the nucleophilic sulfur anion of Cys603 in SENP1 attacked the carbonyl carbon of Gly97 of SUMO1 to trigger the reaction, and then a tetrahedral intermediate and an acyl-enzyme intermediate were generated in turn, leading to the final release of enzyme SENP1 and two products, free SUMO1 and RanGAP1. In the process, nucleophilic attack was identified as the rate-determining step with a potential energy barrier of 20.2 kcal/mol. These results are in agreement with experimental data from mutagenesis and other experiments. Our findings elucidate the catalytic mechanism of SENP1 with its substrate and may provide a better understanding of SENP desumoylation. In particular, we have identified key residues in SENP1 needed for desumoylation that might be beneficial for the design of novel inhibitors of SENP1-related diseases.
Collapse
Affiliation(s)
- Ting Shi
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine , Shanghai 200025, China
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Salts drive controllable multilayered upright assembly of amyloid-like peptides at mica/water interface. Proc Natl Acad Sci U S A 2013; 110:8543-8. [PMID: 23650355 DOI: 10.1073/pnas.1220711110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Surface-assisted self-assembly of amyloid-like peptides has received considerable interest in both amyloidosis research and nanotechnology in recent years. Despite extensive studies, some controlling factors, such as salts, are still not well understood, even though it is known that some salts can promote peptide self-assemblies through the so-called "salting-out" effect. However, they are usually noncontrollable, disordered, amorphous aggregates. Here, we show via a combined experimental and theoretical approach that a conserved consensus peptide NH2-VGGAVVAGV-CONH2 (GAV-9) (from representative amyloidogenic proteins) can self-assemble into highly ordered, multilayered nanofilaments, with surprising all-upright conformations, under high-salt concentrations. Our atomic force microscopy images also demonstrate that the vertical stacking of multiple layers is highly controllable by tuning the ionic strength, such as from 0 mM (monolayer) to 100 mM (mainly double layer), and to 250 mM MgCl2 (double, triple, quadruple, and quintuple layers). Our atomistic molecular dynamics simulations then reveal that these individual layers have very different internal nanostructures, with parallel β-sheets in the first monolayer but antiparallel β-sheets in the subsequent upper layers due to their different microenvironment. Further studies show that the growth of multilayered, all-upright nanostructures is a common phenomenon for GAV-9 at the mica/water interface, under a variety of salt types and a wide range of salt concentrations.
Collapse
|