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Huang Y, Yang G, Yu Z, Tong T, Huang Y, Zhang Q, Hong Y, Jiang J, Zhang G, Yuan Y. Amino-Acid-Encoded Bioinspired Supramolecular Self-Assembly of Multimorphological Nanocarriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311351. [PMID: 38453673 DOI: 10.1002/smll.202311351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/19/2024] [Indexed: 03/09/2024]
Abstract
Supramolecular self-assembly has emerged as an efficient tool to construct well-organized nanostructures for biomedical applications by small organic molecules. However, the physicochemical properties of self-assembled nanoarchitectures are greatly influenced by their morphologies, mechanical properties, and working mechanisms, making it challenging to design and screen ideal building blocks. Herein, using a biocompatible firefly-sourced click reaction between the cyano group of 2-cyano-benzothiazole (CBT) and the 1,2-aminothiol group of cysteine (Cys), an amino-acid-encoded supramolecular self-assembly platform Cys(SEt)-X-CBT (X represents any amino acid) is developed to incorporate both covalent and noncovalent interactions for building diverse morphologies of nanostructures with bioinspired response mechanism, providing a convenient and rapid strategy to construct site-specific nanocarriers for drug delivery, cell imaging, and enzyme encapsulation. Additionally, it is worth noting that the biodegradation of Cys(SEt)-X-CBT generated nanocarriers can be easily tracked via bioluminescence imaging. By caging either the thiol or amino groups in Cys with other stimulus-responsive sites and modifying X with probes or drugs, a variety of multi-morphological and multifunctional nanomedicines can be readily prepared for a wide range of biomedical applications.
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Affiliation(s)
- Yifan Huang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Department of Radiation Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Guokun Yang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Zian Yu
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Tong Tong
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Yan Huang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Qianzijing Zhang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yajian Hong
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Jun Jiang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Guozhen Zhang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yue Yuan
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230031, China
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2
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Adhikary R, Das A. Atomistic Pictures of Self-Assembled Helical Peptide Nanofibers. J Phys Chem B 2022; 126:9476-9492. [PMID: 36350248 DOI: 10.1021/acs.jpcb.2c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Spontaneous self-assembly of peptides has been at the forefront of supramolecular chemistry and materials science research over the last two decades. Despite the wealth of information on the morphology of the assembled objects, atomic resolution details of molecular arrangements inside them are largely unknown. In this paper, we investigated non-covalent assemblies of zwitterionic l-phenylalanine tripeptides in water using all-atom explicit-solvent molecular dynamics computer simulations. Our studies produced atomistic pictures of spontaneously assembled nanofibers composed of hundreds of peptide molecules. The dimensions of the nanofibers varied from 10 to 18 nm, with irregular helical twists along the long axes. Previously published experimental data, acquired under similar conditions, provided direct validation of the fibrous morphology and indirect support for the non-trivial helicity observed in our simulations. Quantitative analyses of peptide-water and peptide-peptide interactions revealed heterogeneous local environments of molecules across the nanometer length scales. The combination of electrostatic, hydrogen bonding, van der Waals, and hydrophobic interactions, adopted by a single molecule, was dependent on its relative position inside the fiber. Despite the presence of three hydrophobic phenyl groups, very few molecules were found to be completely shielded from the surrounding water, indicating a subtle role of the hydrophobic effect. Limited conformational flexibility of the tripeptide, along with bare electrostatic interactions, appeared to play a crucial role in the emergence of fibrous morphology of the nanostructures. Our analyses led us to formulate plausible qualitative explanations of the assembly behavior in terms of thermodynamic driving forces and kinetic considerations. We established a clear relationship between details of chemical interactions operating within few molecules and characteristics of the self-assembled states at much longer length scales.
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Affiliation(s)
- Rumela Adhikary
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Avisek Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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3
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Buell AK. Stability matters, too - the thermodynamics of amyloid fibril formation. Chem Sci 2022; 13:10177-10192. [PMID: 36277637 PMCID: PMC9473512 DOI: 10.1039/d1sc06782f] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
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Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
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Qian X, Xu X, Wu Y, Wang J, Li J, Chen S, Wen J, Li Y, Zhang Z. Strategies of engineering nanomedicines for tumor retention. J Control Release 2022; 346:193-211. [PMID: 35447297 DOI: 10.1016/j.jconrel.2022.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 01/29/2023]
Abstract
The retention of therapeutic agents in solid tumors at sufficient concentration and duration is crucial for their antitumor effects. Given the important contribution of nanomedicines to oncology, we herein summarized two major strategies of nanomedicines for tumor retention, such as transformation- and interactions-mediated strategies. The transformation-mediated retention strategy was achieved by enlarging particle size of nanomedicines or modulating the morphology into fibrous structures, while the interactions-mediated retention strategy was accomplished by modulating nanomedicines to promote their interactions with versatile cells or components in tumors. Moreover, we provide some considerations and perspectives of tumor-retaining nanomedicines for effective cancer therapy.
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Affiliation(s)
- Xindi Qian
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxuan Xu
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Wu
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jiaoying Wang
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Li
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shuo Chen
- School of Pharmacy, the University of Auckland, Auckland 1142, New Zealand
| | - Jingyuan Wen
- School of Pharmacy, the University of Auckland, Auckland 1142, New Zealand
| | - Yaping Li
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, Fudan University, Shanghai 201203, China.; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China.
| | - Zhiwen Zhang
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, Fudan University, Shanghai 201203, China.; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Zaguri D, Zimmermann MR, Meisl G, Levin A, Rencus-Lazar S, Knowles TPJ, Gazit E. Kinetic and Thermodynamic Driving Factors in the Assembly of Phenylalanine-Based Modules. ACS NANO 2021; 15:18305-18311. [PMID: 34694771 DOI: 10.1021/acsnano.1c07537] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of ordered protein and peptide assemblies is a phenomenon related to a wide range of human diseases. However, the mechanism of assembly at the molecular level remains largely unknown. Minimal models enable the exploration of the underlying interactions that are at the core of such self-assembly processes. In particular, the ability of phenylalanine, a single aromatic amino acid, to form an amyloid-like structure has challenged the previous dogma viewing a peptide backbone as a prerequisite for assembly. The driving forces controlling the nucleation and assembly in the absence of a peptide backbone remain to be identified. Here, aiming to unravel these forces, we explored the kinetics and thermodynamics of three phenylalanine-containing molecules during their assembly process: the amino acid phenylalanine, which accumulates in phenylketonuria patients, the diphenylalanine core-motif of the amyloid β peptide related to Alzheimer's disease, and the extended triphenylalanine peptide which forms a range of distinct nanostructures in vitro. We found that the aggregation propensity, regarding the critical monomer concentration, strongly increases with size, with triphenylalanine being the most aggregation-prone species under our experimental conditions. In the context of classical nucleation theory, this increase in aggregation propensity can be attributed to the larger free energy decrease upon aggregation of larger peptides and is not due to the presence/absence of a peptide bond per se. Taken together, this work provides insights into the aggregation processes of chemically simple systems and suggests that both backbone-containing peptides and backbone-lacking amino acids assemble through a similar mechanism, thus supporting the classification of amino acids in the continuum of amyloid-forming building blocks.
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Affiliation(s)
- Dor Zaguri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Manuela R Zimmermann
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sigal Rencus-Lazar
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
- BLAVATNIK CENTER for Drug Discovery for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
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Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition. Int J Mol Sci 2021; 22:ijms22168595. [PMID: 34445303 PMCID: PMC8395295 DOI: 10.3390/ijms22168595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.
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Bera S, Dong X, Krishnarjuna B, Raab SA, Hales DA, Ji W, Tang Y, Shimon LJ, Ramamoorthy A, Clemmer DE, Wei G, Gazit E. Solid-state packing dictates the unexpected solubility of aromatic peptides. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100391. [PMID: 33928264 PMCID: PMC8063180 DOI: 10.1016/j.xcrp.2021.100391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/11/2021] [Accepted: 03/12/2021] [Indexed: 05/10/2023]
Abstract
The understanding and prediction of the solubility of biomolecules, even of the simplest ones, reflect an open question and unmet need. Short aromatic tripeptides are among the most highly aggregative biomolecules. However, in marked contrast, Ala-Phe-Ala (AFA) was surprisingly found to be non-aggregative and could be solubilized at millimolar concentrations. Here, aiming to uncover the underlying molecular basis of its high solubility, we explore in detail the solubility, aggregation propensity, and atomic-level structure of the tripeptide. We demonstrate an unexpectedly high water solubility of AFA reaching 672 mM, two orders of magnitude higher than reported previously. The single crystal structure reveals an anti-parallel β sheet conformation devoid of any aromatic interactions. This study provides clear mechanistic insight into the structural basis of solubility and suggests a simple and feasible tool for its estimation, bearing implications for design of peptide drugs, peptides materials, and advancement of peptide nanotechnology.
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Affiliation(s)
- Santu Bera
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Shannon A. Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
| | - David A. Hales
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
- Department of Chemistry, Hendrix College, Conway, AR 72032, USA
| | - Wei Ji
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Linda J.W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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8
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Disassembly and reassembly of diphenylalanine crystals through evaporation of solvent. J Colloid Interface Sci 2021; 599:661-666. [PMID: 33979748 DOI: 10.1016/j.jcis.2021.04.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/21/2022]
Abstract
HYPOTHESIS Crystalline self-assemblies of diphenylalanine (FF) are since long back considered to be related to Alzheimer's disease. An improved understanding of the mechanism behind the formation of such structures can lead to strategies for investigating the dynamic processes of assembly and disassembly of FF. EXPERIMENT The assembly, disassembly and reassembly of FF crystals are influenced by the solvent composition and can be triggered by evaporation of solvent. In this work these processes are directly monitored, and the structures obtained are analyzed. FINDINGS The role of the solvent for assembly, disassembly and reassembly of diphenylalanine crystals has been demonstrated. The initial crystal structure formed via self-assembly of FF monomers can be transformed into needle-like crystals and further to hollow hexagonal microtubes through evaporation of the solvent. It is shown that all the assembly-disassembly processes are spontaneous and driven by thermodynamics. It is also found that some of the crystalline structures exhibit optical waveguiding properties.
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9
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Kitte SA, Tafese T, Xu C, Saqib M, Li H, Jin Y. Plasmon-enhanced quantum dots electrochemiluminescence aptasensor for selective and sensitive detection of cardiac troponin I. Talanta 2020; 221:121674. [PMID: 33076177 DOI: 10.1016/j.talanta.2020.121674] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
The development of highly sensitive electrochemiluminescence (ECL) immunosensors by using functional nanoparticles as signal amplifiers is a solution towards sensitive determination of many low concentration disease biomarkers. Herein, a sensitive aptamer-based, sandwich-type surface plasmon enhanced electrochemiluminescence (SPEECL) immunosensor was demonstrated for the detection of cardiac troponin I (cTnI), by means of aptamer conjugated CdS QDs and AuNPs as ECL luminophores and plasmon sources, respectively, in which Tro4 aptamer was used as a capture probe for cTnI and Tro6 aptamer as a detecting probe. The signal of the developed SPEECL system showed ~ 5-fold increment as compared to that of without AuNPs. Using this ECL platform for the detection of cTnI, a linear range and the limit of detection (LOD) were found to be 1 fg/mL - 10 ng/mL and 0.75 fg/mL, respectively.
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Affiliation(s)
- Shimeles Addisu Kitte
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; Department of Chemistry, College of Natural Sciences, Jimma University, P. O. Box 378, Jimma, Ethiopia
| | - Terefe Tafese
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Chen Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Muhammad Saqib
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China.
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Gupta S, Singh I, Sharma AK, Kumar P. Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos. Front Bioeng Biotechnol 2020; 8:504. [PMID: 32548101 PMCID: PMC7273840 DOI: 10.3389/fbioe.2020.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.
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Affiliation(s)
- Seema Gupta
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Indu Singh
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashwani K. Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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11
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The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. PLoS Comput Biol 2020; 16:e1007767. [PMID: 32365068 PMCID: PMC7282669 DOI: 10.1371/journal.pcbi.1007767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 03/02/2020] [Indexed: 11/19/2022] Open
Abstract
Many proteins have the potential to aggregate into amyloid fibrils, protein polymers associated with a wide range of human disorders such as Alzheimer’s and Parkinson’s disease. The thermodynamic stability of amyloid fibrils, in contrast to that of folded proteins, is not well understood: the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using a combination of theory, in vitro experiments, simulations of a coarse-grained protein model and meta-data analysis, we delineate the enthalpic and entropic contributions that dominate amyloid fibril elongation. Our prediction of a characteristic temperature-dependent enthalpic signature is confirmed by the performed calorimetric experiments and a meta-analysis over published data. From these results we are able to define the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability. Most proteins fold in the cell into stable, compact structures. Nevertheless, many proteins also have the ability to stick together, forming long fibrillar structures that are associated with a wide range of human disorders including Alzheimer’s and Parkinson’s disease. The exact nature of the amyloid-causing stickiness is not well understood, nevertheless amyloid fibrils show some very specific thermodynamic characteristics. Some fibrils even destabilise at low temperatures. In this work we translate hydrophobic theory previously used to model protein folding to fibril formation. We combine this theory with experimental measurements, simulations and meta-data analysis of different types of fibrils. This allowed us to unravel the nature of the stickiness in amyloid fibrils by observing the effect of temperature changes, specifically at low temperatures, on hydrophobicity.
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12
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Gupta A, Mahalakshmi R. Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49878-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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13
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Gupta A, Mahalakshmi R. Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation. J Biol Chem 2019; 295:1181-1194. [PMID: 31844019 PMCID: PMC6996891 DOI: 10.1074/jbc.ra119.011342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/11/2019] [Indexed: 11/06/2022] Open
Abstract
Ninety-five percent of all transmembrane proteins exist in kinetically trapped aggregation-prone states that have been directly linked to neurodegenerative diseases. Interestingly, the primary sequence almost invariably avoids off-pathway aggregate formation, by folding reliably into its native, thermodynamically stabilized structure. However, with the rising incidence of protein aggregation diseases, it is now important to understand the underlying mechanism(s) of membrane protein aggregation. Micromolecular physicochemical and biochemical alterations in the primary sequence that trigger the formation of macromolecular cross-β aggregates can be measured only through combinatorial spectroscopic experiments. Here, we developed spectroscopic thermal perturbation with 117 experimental variables to assess how subtle protein sequence variations drive the molecular transition of the folded protein to oligomeric aggregates. Using the Yersinia pestis outer transmembrane β-barrel Ail as a model, we delineated how a single-residue substitution that alters the membrane-anchoring ability of Ail significantly contributes to the kinetic component of Ail stability. We additionally observed a stabilizing role for interface aliphatics, and that interface aromatics physicochemically contribute to Ail self-assembly and aggregation. Moreover, our method identified the formation of structured oligomeric intermediates during Ail aggregation. We show that the self-aggregation tendency of Ail is offset by the evolution of a thermodynamically compromised primary sequence that balances folding, stability, and oligomerization. Our approach provides critical information on how subtle changes in protein primary sequence trigger cross-β fibril formation, with insights that have direct implications for deducing the molecular progression of neurodegeneration and amyloidogenesis in humans.
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Affiliation(s)
- Ankit Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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14
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Shayegan M, Tahvildari R, Metera K, Kisley L, Michnick SW, Leslie SR. Probing Inhomogeneous Diffusion in the Microenvironments of Phase-Separated Polymers under Confinement. J Am Chem Soc 2019; 141:7751-7757. [DOI: 10.1021/jacs.8b13349] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Marjan Shayegan
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Radin Tahvildari
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Kimberly Metera
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Stephen W. Michnick
- Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Sabrina R. Leslie
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
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15
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Xiong Q, Jiang Y, Cai X, Yang F, Li Z, Han W. Conformation Dependence of Diphenylalanine Self-Assembly Structures and Dynamics: Insights from Hybrid-Resolution Simulations. ACS NANO 2019; 13:4455-4468. [PMID: 30869864 DOI: 10.1021/acsnano.8b09741] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The molecular design of peptide-assembled nanostructures relies on extensive knowledge pertaining to the relationship between conformational features of peptide constituents and their behavior regarding self-assembly, and characterizing the conformational details of peptides during their self-assembly is experimentally challenging. Here, we demonstrate that a hybrid-resolution modeling method can be employed to investigate the role that conformation plays during the assembly of terminally capped diphenylalanines (FF) through microsecond simulations of hundreds or thousands of peptides. Our simulations discovered tubular or vesicular nanostructures that were consistent with experimental observation while reproducing critical self-assembly concentration and secondary structure contents in the assemblies that were measured in our experiments. The atomic details provided by our method allowed us to uncover diverse FF conformations and conformation dependence of assembled nanostructures. We found that the assembled morphologies and the molecular packing of FFs in the observed assemblies are linked closely with side-chain angle and peptide bond orientation, respectively. Of various conformations accessible to soluble FFs, only a select few are compatible with the assembled morphologies in water. A conformation resembling a FF crystal, in particular, became predominant due to its ability to permit highly ordered and energetically favorable FF packing in aqueous assemblies. Strikingly, several conformations incompatible with the assemblies arose transiently as intermediates, facilitating key steps of the assembly process. The molecular rationale behind the role of these intermediate conformations were further explained. Collectively, the structural details reported here advance the understanding of the FF self-assembly mechanism, and our method shows promise for studying peptide-assembled nanostructures and their rational design.
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Affiliation(s)
- Qinsi Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Xiang Cai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen 518055 , China
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16
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Lin Y, Penna M, Thomas MR, Wojciechowski JP, Leonardo V, Wang Y, Pashuck ET, Yarovsky I, Stevens MM. Residue-Specific Solvation-Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection. ACS NANO 2019; 13:1900-1909. [PMID: 30673202 PMCID: PMC6396410 DOI: 10.1021/acsnano.8b08117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/16/2019] [Indexed: 05/18/2023]
Abstract
Understanding the self-organization and structural transformations of molecular ensembles is important to explore the complexity of biological systems. Here, we illustrate the crucial role of cosolvents and solvation effects in thermodynamic and kinetic control over peptide association into ultrathin Janus nanosheets, elongated nanobelts, and amyloid-like fibrils. We gained further insight into the solvation-directed self-assembly (SDSA) by investigating residue-specific peptide solvation using molecular dynamics modeling. We proposed the preferential solvation of the aromatic and alkyl domains on the peptide backbone and protofibril surface, which results in volume exclusion effects and restricts the peptide association between hydrophobic walls. We explored the SDSA phenomenon in a library of cosolvents (protic and aprotic), where less polar cosolvents were found to exert a stronger influence on the energetic balance at play during peptide propagation. By tailoring cosolvent polarity, we were able to achieve precise control of the peptide nanostructures with 1D/2D shape selection. We also illustrated the complexity of the SDSA system with pathway-dependent peptide aggregation, where two self-assembly states ( i.e., thermodynamic equilibrium state and kinetically trapped state) from different sample preparation methods were obtained.
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Affiliation(s)
- Yiyang Lin
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Matthew Penna
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael R. Thomas
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jonathan P. Wojciechowski
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Vincent Leonardo
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Ye Wang
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - E. Thomas Pashuck
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
| | - Molly M. Stevens
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
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17
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Cheng DB, Wang D, Gao YJ, Wang L, Qiao ZY, Wang H. Autocatalytic Morphology Transformation Platform for Targeted Drug Accumulation. J Am Chem Soc 2019; 141:4406-4411. [DOI: 10.1021/jacs.8b13512] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Dong-Bing Cheng
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Dong Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yu-Juan Gao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Zeng-Ying Qiao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100190, China
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18
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Abstract
The aggregation of monomeric amyloid β protein (Aβ) peptide into oligomers and amyloid fibrils in the mammalian brain is associated with Alzheimer's disease. Insight into the thermodynamic stability of the Aβ peptide in different polymeric states is fundamental to defining and predicting the aggregation process. Experimental determination of Aβ thermodynamic behavior is challenging due to the transient nature of Aβ oligomers and the low peptide solubility. Furthermore, quantitative calculation of a thermodynamic phase diagram for a specific peptide requires extremely long computational times. Here, using a coarse-grained protein model, molecular dynamics (MD) simulations are performed to determine an equilibrium concentration and temperature phase diagram for the amyloidogenic peptide fragment Aβ16-22 Our results reveal that the only thermodynamically stable phases are the solution phase and the macroscopic fibrillar phase, and that there also exists a hierarchy of metastable phases. The boundary line between the solution phase and fibril phase is found by calculating the temperature-dependent solubility of a macroscopic Aβ16-22 fibril consisting of an infinite number of β-sheet layers. This in silico determination of an equilibrium (solubility) phase diagram for a real amyloid-forming peptide, Aβ16-22, over the temperature range of 277-330 K agrees well with fibrillation experiments and transmission electron microscopy (TEM) measurements of the fibril morphologies formed. This in silico approach of predicting peptide solubility is also potentially useful for optimizing biopharmaceutical production and manufacturing nanofiber scaffolds for tissue engineering.
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19
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Mason TO, Buell AK. The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:61-112. [PMID: 31713197 DOI: 10.1007/978-981-13-9791-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid β sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DTU, Lyngby, Denmark.
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20
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Argudo PG, Contreras-Montoya R, Álvarez de Cienfuegos L, Cuerva JM, Cano M, Alba-Molina D, Martín-Romero MT, Camacho L, Giner-Casares JJ. Unravelling the 2D self-assembly of Fmoc-dipeptides at fluid interfaces. SOFT MATTER 2018; 14:9343-9350. [PMID: 30307451 DOI: 10.1039/c8sm01508b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dipeptides self-assemble into supramolecular structures showing plenty of applications in the nanotechnology and biomedical fields. A set of Fmoc-dipeptides with different aminoacid sequences has been synthesized and their self-assembly at fluid interfaces has been assessed. The relevant molecular parameters for achieving an efficient 2D self-assembly process have been established. The self-assembled nanostructures of Fmoc-dipeptides displayed significant chirality and retained the chemical functionality of the aminoacids. The impact of the sequence on the final supramolecular structure has been evaluated in detail using in situ characterization techniques at air/water interfaces. This study provides a general route for the 2D self-assembly of Fmoc-dipeptides.
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Affiliation(s)
- Pablo G Argudo
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Investigación en Química Fina y Nanoquímica IUIQFN, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain.
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21
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Toprakcioglu Z, Challa PK, Levin A, Knowles TPJ. Observation of molecular self-assembly events in massively parallel microdroplet arrays. LAB ON A CHIP 2018; 18:3303-3309. [PMID: 30270398 DOI: 10.1039/c8lc00862k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The self-assembly of peptide and protein molecules into nanoscale filaments is a process associated with both biological function and malfunction. Microfluidic techniques can provide powerful tools in the study of such aggregation phenomena while providing access to exploring the role of molecular interactions in disease development. Yet, a common challenge encountered in the study of protein aggregation is the difficulty in achieving spatial and temporal control of the underlying processes. Here, we present a planar (2-D) device allowing for both the generation and confinement of 10 000 monodisperse water-in-oil droplets in an array of chambers with a trapping efficiency of 99%. Due to the specific geometry of the device, droplets can be formed and immediately trapped on the same chip, without the need for continuous flow of the oil phase. Furthermore, we demonstrate the capability of this device as a platform to study the aggregation kinetics and determine stochastic molecular nanoscale self-assembly events in a highly parallel manner for the aggregation of the dipeptide, diphenylalanine, the core recognition motif of the Aβ-42 peptide associated with Alzheimer's disease. The ability to reproducibly generate and confine monodisperse water-in-oil droplets with an extremely high trapping efficiency while maintaining entrapment under zero-flow conditions, on timescales compatible with observing molecular self-assembly events, renders it promising for numerous potential further applications in the biological and biophysical fields.
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Affiliation(s)
- Zenon Toprakcioglu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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22
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Ramer G, Ruggeri FS, Levin A, Knowles TPJ, Centrone A. Determination of Polypeptide Conformation with Nanoscale Resolution in Water. ACS NANO 2018; 12:6612-6619. [PMID: 29932670 DOI: 10.1021/acsnano.8b01425] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The folding and acquisition of proteins native structure is central to all biological processes of life. By contrast, protein misfolding can lead to toxic amyloid aggregates formation, linked to the onset of neurodegenerative disorders. To shed light on the molecular basis of protein function and malfunction, it is crucial to access structural information on single protein assemblies and aggregates under native conditions. Yet, current conformation-sensitive spectroscopic methods lack the spatial resolution and sensitivity necessary for characterizing heterogeneous protein aggregates in solution. To overcome this limitation, here we use photothermal-induced resonance to demonstrate that it is possible to acquire nanoscale infrared spectra in water with high signal-to-noise ratio (SNR). Using this approach, we probe supramolecular aggregates of diphenylalanine, the core recognition module of the Alzheimer's β-amyloid peptide, and its derivative Boc-diphenylalanine. We achieve nanoscale resolved IR spectra and maps in air and water with comparable SNR and lateral resolution, thus enabling accurate identification of the chemical and structural state of morphologically similar networks at the single aggregate ( i. e., fibril) level.
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Affiliation(s)
- Georg Ramer
- Center for Nanoscale Science and Technology , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
- Institute for Research in Electronics and Applied Physics , University of Maryland , College Park , Maryland 20742 , United States
| | | | - Aviad Levin
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , United Kingdom
- Cavendish Laboratory, Department of Physics , University of Cambridge , J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Andrea Centrone
- Center for Nanoscale Science and Technology , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
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23
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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24
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Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State. ACS Chem Neurosci 2018; 9:783-789. [PMID: 29239603 PMCID: PMC5911799 DOI: 10.1021/acschemneuro.7b00409] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
Amyloid-β
(Aβ) fibrils and plaques are one of the hallmarks
of Alzheimer’s disease. While the kinetics of fibrillar growth
of Aβ have been extensively studied, several vital questions
remain. In particular, the atomistic origins of the Arrhenius barrier
observed in experiments have not been elucidated. Employing the familiar
thermodynamic integration method, we have directly simulated the dissociation
of an Aβ(15–40) (D23N mutant) peptide from
the surface of a filament along its most probable path (MPP) using
all-atom molecular dynamics. This allows for a direct calculation
of the free energy profile along the MPP, revealing a multipeak energetic
barrier between the free peptide state and the aggregated state. By
definition of the MPP, this simulated unbinding process represents
the reverse of the physical elongation pathway, allowing us to draw
biophysically relevant conclusions from the simulation data. Analyzing
the detailed atomistic interactions along the MPP, we identify the
atomistic origins of these peaks as resulting from the dock-lock mechanism
of filament elongation. Careful analysis of the dynamics of filament
elongation could prove key to the development of novel therapeutic
strategies for amyloid-related diseases.
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Affiliation(s)
- Roberto A. Rodriguez
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Liao Y. Chen
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Germán Plascencia-Villa
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - George Perry
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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25
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Ishikawa MS, Busch C, Motzkus M, Martinho H, Buckup T. Two-step kinetic model of the self-assembly mechanism for diphenylalanine micro/nanotube formation. Phys Chem Chem Phys 2017; 19:31647-31654. [DOI: 10.1039/c7cp06611b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Formation via nucleation of FF-MNTs is based on a 2-step kinetic model and is driven by electric dipole re-orientation.
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Affiliation(s)
- M. S. Ishikawa
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
| | - C. Busch
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
| | - M. Motzkus
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
| | - H. Martinho
- Centro de Ciências Naturais e Humanas
- Universidade Federal do ABC
- Santo André-SP
- Brazil
| | - T. Buckup
- Physikalisch-Chemisches Institut
- Im Neuenheimer Feld 229
- Ruprecht-Karls-Universität
- D-69120 Heidelberg
- Germany
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