1
|
Esposito A, Leone L, De Simone A, Fusco G, Nastri F, Lombardi A. Catalytic Nanomaterials by Conjugation of an Artificial Heme-Peroxidase to Amyloid Fibrils. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39140178 DOI: 10.1021/acsami.4c10449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
The self-assembly of proteins and peptides into fibrillar amyloid aggregates is a highly promising route to define the next generation of functional nanomaterials. Amyloid fibrils, traditionally associated with neurodegenerative diseases, offer exceptional conformational and chemical stability and mechanical properties, and resistance to degradation. Here, we report the development of catalytic amyloid nanomaterials through the conjugation of a miniaturized artificial peroxidase (FeMC6*a) to a self-assembling amyloidogenic peptide derived from human transthyretin, TTR(105-115), whose sequence is YTIAALLSPYS. Our synthetic approach relies on fast and selective click ligation upon proper modification of both the peptide and FeMC6*a, leading to TTRLys108@FeMC6*a. Mixing unmodified TTR(105-115) with TTRLys108@FeMC6*a allowed the generation of enzyme-loaded amyloid fibrils, namely, FeMC6*a@fibrils. Catalytic studies, performed in aqueous solution at nearly neutral pH, using ABTS as a model substrate and H2O2 as the oxidizing agent revealed that the enzyme retains its catalytic activity. Moreover, the activity was found to depend on the TTRLys108@FeMC6*a/unmodified TTR(105-115) peptide ratio. In particular, those with the 2:100 ratio showed the highest activity in terms of initial rates and substrate conversion among the screened nanoconjugates and compared to the freely diffusing enzyme. Finally, the newly developed nanomaterials were integrated into a flow system based on a polyvinylidene difluoride membrane filter. Within this flow-reactor, multiple reaction cycles were performed, showcasing the reusability and stability of the catalytic amyloids over extended periods, thus offering significantly improved characteristics compared to the isolated FeMC6*a in the application to a number of practical scenarios.
Collapse
Affiliation(s)
- Alessandra Esposito
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| | - Alfonso De Simone
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Giuliana Fusco
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126 Naples, Italy
| |
Collapse
|
2
|
Prajapati KP, Mittal S, Ansari M, Mahato OP, Bharati S, Singh AP, Ahlawat S, Tiku AB, Anand BG, Kar K. Pleiotropic Nanostructures Built from l-Histidine Show Biologically Relevant Multicatalytic Activities. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18268-18284. [PMID: 38564419 DOI: 10.1021/acsami.3c14606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The essential amino acid histidine plays a central role in the manifestation of several metabolic processes, including protein synthesis, enzyme-catalysis, and key biomolecular interactions. However, excess accumulation of histidine causes histidinemia, which shows brain-related medical complications, and the molecular mechanism of such histidine-linked complications is largely unknown. Here, we show that histidine undergoes a self-assembly process, leading to the formation of amyloid-like cytotoxic and catalytically active nanofibers. The kinetics of histidine self-assembly was favored in the presence of Mg(II) and Co(II) ions. Molecular dynamics data showed that preferential noncovalent interactions dominated by H-bonds between histidine molecules facilitate the formation of histidine nanofibers. The histidine nanofibers induced amyloid cross-seeding reactions in several proteins and peptides including pathogenic Aβ1-42 and brain extract components. Further, the histidine nanofibers exhibited oxidase activity and enhanced the oxidation of neurotransmitters. Cell-based studies confirmed the cellular internalization of histidine nanofibers in SH-SY5Y cells and subsequent cytotoxic effects through necrosis and apoptosis-mediated cell death. Since several complications including behavioral abnormality, developmental delay, and neurological disabilities are directly linked to abnormal accumulation of histidine, our findings provide a foundational understanding of the mechanism of histidine-related complications. Further, the ability of histidine nanofibers to catalyze amyloid seeding and oxidation reactions is equally important for both biological and materials science research.
Collapse
Affiliation(s)
- Kailash Prasad Prajapati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shikha Mittal
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Masihuzzaman Ansari
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Om Prakash Mahato
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shikha Bharati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Akhilesh Pratap Singh
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shobha Ahlawat
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashu Bhan Tiku
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Bibin Gnanadhason Anand
- Biomolecular Self-Assembly Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Karunakar Kar
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
3
|
Jana AK, Güven Ö, Yaşar F. The stability and dynamics of the Aβ40/Aβ42 interlaced mixed fibrils. J Biomol Struct Dyn 2023:1-14. [PMID: 37964619 DOI: 10.1080/07391102.2023.2280765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
The accumulation of fibrillar amyloid-β (Aβ) aggregates in the brain, predominantly comprising 40- and 42-residue amyloid-β (Aβ40 and Aβ42), is a major pathological hallmark of Alzheimer's disease (AD). Aβ40 and Aβ42 naturally coexist in the brain under normal physiological conditions, and their interplay is generally considered to be a critical factor in the progression of AD. In addition to forming homogeneous oligomers and fibrils, Aβ40 and Aβ42 are also reported to co-assemble into hetero-oligomers and interlaced mixed fibrils, as evidenced by solid-state nuclear magnetic resonance spectroscopy (NMR), high molecular weight mass spectrometry and cross-seeding experiments. However, the exact molecular mechanisms underlying these processes remain unclear. In this study, we have used a recently resolved structurally uniform 1:1 mixture of Aβ40/Aβ42 interlaced mixed fibril as a prototype to gain insights into the molecular-level interactions between Aβ40 and Aβ42. We employed fully atomistic molecular dynamics simulation and compared the results with a homogeneous U-shaped Aβ40 fibrillar model. Our simulations using two different force fields provide conclusive evidence that the Aβ40/Aβ42 interlaced mixed fibril is energetically more favorable than the homogeneous Aβ40 fibrillar model. Furthermore, we also show that the increase in stability observed in the mixed model stems primarily from the packing interfaces and the stacking interfaces between C-termini. Our simulation results provide valuable mechanistic insights that are not readily accessible in experiment and could have significant implications for both the pathogenesis of AD and the development of current therapeutic strategies.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Asis K Jana
- Department of Microbiology and Biotechnology, Sister Nivedita University, Kolkata, West Bengal, India
| | - Özgür Güven
- Department of Physics Engineering, Hacettepe University, Ankara, Türkiye
| | - Fatih Yaşar
- Department of Physics Engineering, Hacettepe University, Ankara, Türkiye
| |
Collapse
|
4
|
Siddiqui KM, Durham DB, Cropp F, Ji F, Paiagua S, Ophus C, Andresen NC, Jin L, Wu J, Wang S, Zhang X, You W, Murnane M, Centurion M, Wang X, Slaughter DS, Kaindl RA, Musumeci P, Minor AM, Filippetto D. Relativistic ultrafast electron diffraction at high repetition rates. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:064302. [PMID: 38058995 PMCID: PMC10697722 DOI: 10.1063/4.0000203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
The ability to resolve the dynamics of matter on its native temporal and spatial scales constitutes a key challenge and convergent theme across chemistry, biology, and materials science. The last couple of decades have witnessed ultrafast electron diffraction (UED) emerge as one of the forefront techniques with the sensitivity to resolve atomic motions. Increasingly sophisticated UED instruments are being developed that are aimed at increasing the beam brightness in order to observe structural signatures, but so far they have been limited to low average current beams. Here, we present the technical design and capabilities of the HiRES (High Repetition-rate Electron Scattering) instrument, which blends relativistic electrons and high repetition rates to achieve orders of magnitude improvement in average beam current compared to the existing state-of-the-art instruments. The setup utilizes a novel electron source to deliver femtosecond duration electron pulses at up to MHz repetition rates for UED experiments. Instrument response function of sub-500 fs is demonstrated with < 100 fs time resolution targeted in future. We provide example cases of diffraction measurements on solid-state and gas-phase samples, including both micro- and nanodiffraction (featuring 100 nm beam size) modes, which showcase the potential of the instrument for novel UED experiments.
Collapse
Affiliation(s)
- K. M. Siddiqui
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - F. Ji
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - S. Paiagua
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA
| | - C. Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - N. C. Andresen
- Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - L. Jin
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, California 94720, USA
| | - J. Wu
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, California 94720, USA
| | - S. Wang
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - X. Zhang
- Department of Mechanical Engineering, University of California at Berkeley, Berkeley, California 94720, USA
| | - W. You
- Department of Physics and JILA, University of Colorado and NIST, Boulder, Colorado 80309, USA
| | - M. Murnane
- Department of Physics and JILA, University of Colorado and NIST, Boulder, Colorado 80309, USA
| | - M. Centurion
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - X. Wang
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - D. S. Slaughter
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA
| | | | - P. Musumeci
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
| | | | - D. Filippetto
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
5
|
Application of Amyloid-Based Hybrid Membranes in Drug Delivery. Polymers (Basel) 2023; 15:polym15061444. [PMID: 36987222 PMCID: PMC10052896 DOI: 10.3390/polym15061444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/15/2023] Open
Abstract
The properties of amyloid fibrils, e.g., unique structural characteristics and superior biocompatibility, make them a promising vehicle for drug delivery. Here, carboxymethyl cellulose (CMC) and whey protein isolate amyloid fibril (WPI-AF) were used to synthesize amyloid-based hybrid membranes as vehicles for the delivery of cationic and hydrophobic drugs (e.g., methylene blue (MB) and riboflavin (RF)). The CMC/WPI-AF membranes were synthesized via chemical crosslinking coupled with phase inversion. The zeta potential and scanning electron microscopy results revealed a negative charge and a pleated surface microstructure with a high content of WPI-AF. FTIR analysis showed that the CMC and WPI-AF were cross-linked via glutaraldehyde and the interacting forces between membrane and MB or RF was found to be electrostatic interaction and hydrogen bonding, respectively. Next, the in vitro drug release from membranes was monitored using UV-vis spectrophotometry. Additionally, two empirical models were used to analyze the drug release data and relevant rate constant and parameters were determined accordingly. Moreover, our results indicated that in vitro drug release rates depended on the drug–matrix interactions and transport mechanism, which could be controlled by altering the WPI-AF content in membrane. This research provides an excellent example of utilizing two-dimensional amyloid-based materials for drug delivery.
Collapse
|
6
|
Du DX, Simjanoska M, Fitzpatrick AWP. Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales. J Struct Biol 2023; 215:107941. [PMID: 36773734 DOI: 10.1016/j.jsb.2023.107941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
As structural determination of protein complexes approaches atomic resolution, there is an increasing focus on conformational dynamics. Here we conceptualize the combination of two techniques which have become established in recent years: microcrystal electron diffraction and ultrafast electron microscopy. We show that the extremely low dose of pulsed photoemission still enables microED due to the strength of the electron bunching from diffraction of the protein crystals. Indeed, ultrafast electron diffraction experiments on protein crystals have already been demonstrated to be effective in measuring intermolecular forces in protein microcrystals. We discuss difficulties that may arise in the acquisition and processing of data and the overall feasibility of the experiment, paying specific attention to dose and signal-to-noise ratio. In doing so, we outline a detailed workflow that may be effective in minimizing the dose on the specimen. A series of model systems that would be good candidates for initial experiments is provided.
Collapse
Affiliation(s)
- Daniel X Du
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Marija Simjanoska
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Anthony W P Fitzpatrick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.
| |
Collapse
|
7
|
Time-resolved transmission electron microscopy for nanoscale chemical dynamics. Nat Rev Chem 2023; 7:256-272. [PMID: 37117417 DOI: 10.1038/s41570-023-00469-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 02/24/2023]
Abstract
The ability of transmission electron microscopy (TEM) to image a structure ranging from millimetres to Ångströms has made it an indispensable component of the toolkit of modern chemists. TEM has enabled unprecedented understanding of the atomic structures of materials and how structure relates to properties and functions. Recent developments in TEM have advanced the technique beyond static material characterization to probing structural evolution on the nanoscale in real time. Accompanying advances in data collection have pushed the temporal resolution into the microsecond regime with the use of direct-electron detectors and down to the femtosecond regime with pump-probe microscopy. Consequently, studies have deftly applied TEM for understanding nanoscale dynamics, often in operando. In this Review, time-resolved in situ TEM techniques and their applications for probing chemical and physical processes are discussed, along with emerging directions in the TEM field.
Collapse
|
8
|
Lai YR, Lai JT, Wang SSS, Kuo YC, Lin TH. Silver nanoparticle-deposited whey protein isolate amyloid fibrils as catalysts for the reduction of methylene blue. Int J Biol Macromol 2022; 213:1098-1114. [PMID: 35688277 DOI: 10.1016/j.ijbiomac.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 11/05/2022]
Abstract
The unique structural characteristics and superior biocompatibility make the protein nanofibers promising immobilization platforms/substrates for catalysts/enzymes. Metal nanoparticles have been employed as the catalysts in industries due to their excellent catalytic activity and stability, whereas their high surface energy leads to nanoparticle aggregation, thereby hampering their catalytic performance. Here, amyloid fibril (AF) derived from whey protein isolate (WPI) was chosen as the support of silver nanoparticles (AgNP) and utilized for the catalytic reduction of methylene blue (MB). The one-dimensional amyloid-based hybrid materials (AgNP/WPI-AF) were first synthesized via chemical or photochemical route. The characterization of AgNP/WPI-AF by UV-vis spectrophotometry and electron microscopy revealed that the sizes of AgNP on WPI-AF's surface ranged from 2 to 30 nm. Next, the catalytic performances of AgNP/WPI-AF prepared by various routes for MB degradation were investigated. Additionally, the kinetic data were analyzed using two different models and the apparent rate constants and thermodynamic parameters were further determined accordingly. Moreover, the reusability of AgNP/WPI-AF was assessed by monitoring the percentage removal of MB over consecutive filtering cycles. Our results indicated that Langmuir-Hinshelwood-type mechanism better described the catalytic MB reduction using AgNP/WPI-AF. This work provides a nice example of application of nanoparticle-amyloid fibril composite materials for catalysis.
Collapse
Affiliation(s)
- You-Ren Lai
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Jinn-Tsyy Lai
- Food Industry Research and Development Institute, Hsinchu 300, Taiwan; HeySong Corporation, 178, Zhongyuan Rd., Zhongli Dist., Taoyuan City 320021, Taiwan
| | - Steven S-S Wang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yung-Chih Kuo
- Department of Chemical Engineering, National Chung Cheng University, Chia-Yi, Taiwan; Advanced Institute of Manufacturing with High-tech Innovations, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Ta-Hsien Lin
- Laboratory of Nuclear Magnetic Resonance, Medical Research Department, Taipei Veterans General Hospital, Taipei 11217, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.
| |
Collapse
|
9
|
Prajapati KP, Anand BG, Ansari M, Temgire M, Tiku AB, Kar K. Amyloid-mimicking toxic nanofibers generated via self-assembly of dopamine. NANOSCALE 2022; 14:8649-8662. [PMID: 35667124 DOI: 10.1039/d1nr07741d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular self-assembly of biologically relevant aromatic metabolites is known to generate cytotoxic nanostructures and this unique property has opened up new concepts in the molecular mechanisms of metabolite-linked disorders. Because aromaticity is intrinsic to the chemical structure of some important neuromodulators, the question of whether this property can promote their self-assembly into toxic higher order structures is highly relevant to the advancement of both fundamental and applied research. We show here that dopamine, an aromatic neuromodulator of high significance, undergoes self-assembly, under physiological buffer conditions, yielding cytotoxic supramolecular nanostructures. The oxidation of dopamine seems crucial in driving the self-assembly, and substantial inhibition effect was observed in the presence of antioxidants and acidic buffers. Strong H-bonds and π-π interactions between optimally-oriented dopamine molecules were found to stabilize the dopamine nanostructure which displayed characteristic β-structure-patterns with hydrophobic exterior and hydrophilic interior moieties. Furthermore, dopamine nanostructures were found to be highly toxic to human neuroblastoma cells, revealing apoptosis and necrosis-mediated cytotoxicity. Abnormal fluctuation in the dopamine concentration is known to predispose a multitude of neuronal complications, hence, the new findings of this study on oxidation-driven buildup of amyloid-mimicking neurotoxic dopamine assemblies may have direct relevance to the molecular origin of several dopamine related disorders.
Collapse
Affiliation(s)
| | | | - Masihuzzaman Ansari
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| | - Mayur Temgire
- Department of Chemical Engineering, Indian Institution of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ashu Bhan Tiku
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| | - Karunakar Kar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
| |
Collapse
|
10
|
Xu Z, Shan G, Hao N, Li L, Lan T, Dong Y, Wen J, Tian R, Zhang Y, Jiang L, Sui X. Structure remodeling of soy protein-derived amyloid fibrils mediated by epigallocatechin-3-gallate. Biomaterials 2022; 283:121455. [DOI: 10.1016/j.biomaterials.2022.121455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 12/18/2022]
|
11
|
Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
Collapse
Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
| |
Collapse
|
12
|
Anand BG, Prajapati KP, Ansari M, Yadav DK, Temgire M, Kar K. Genesis of Neurotoxic Hybrid Nanofibers from the Coassembly of Aromatic Amino Acids. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36722-36736. [PMID: 34327979 DOI: 10.1021/acsami.1c04161] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Considering the relevance of accumulation and self-assembly of metabolites and aftermath of biological consequences, it is important to know whether they undergo coassembly and what properties the resultant hybrid higher-order structures would exhibit. This work reveals the inherent tendency of aromatic amino acids to undergo a spontaneous coassembly process under physiologically mimicked conditions, which yields neurotoxic hybrid nanofibers. Resultant hybrid nanostructures resembled the β-structured conformers stabilized by H-bonds and π-π stacking interactions, which were highly toxic to human neuroblastoma cells. The hybrid nanofibers also showed strong cross-seeding potential that triggered in vitro aggregation of diverse globular proteins and brain extract components, converting the native structures into cross-β-rich amyloid aggregates. The heterogenic nature of the hybrid nanofibers seems crucial for their higher toxicity and faster cross-seeding potential as compared to the homogeneous amino acid nanofibers. Our findings reveal the importance of aromaticity-driven optimized intermolecular arrangements for the coassembly of aromatic amino acids, and the results may provide important clues to the fundamental understanding of metabolite accumulation-related complications.
Collapse
Affiliation(s)
- Bibin Gnanadhason Anand
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kailash Prasad Prajapati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Masihuzzaman Ansari
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepak Kumar Yadav
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mayur Temgire
- Department of Chemical Engineering, Indian Institution of Technology Bombay, Powai, Mumbai 400076, India
| | - Karunakar Kar
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
13
|
Luo M, Jin B, Luo Y, Li X. Supramicellar Nanofibrils with End-to-End Coupled Uniform Cylindrical Micelle Subunits via One-Step Assembly from a Liquid Crystalline Block Copolymer. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mingyan Luo
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Bixin Jin
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yunjun Luo
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of High Energy Density Materials, Ministry of Education, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoyu Li
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of High Energy Density Materials, Ministry of Education, Beijing Institute of Technology, Beijing 100081, China
- Experimental Centre of Advanced Materials, Beijing Institute of Technology, Beijing 100081, China
| |
Collapse
|
14
|
Adamcik J, Ruggeri FS, Berryman JT, Zhang A, Knowles TPJ, Mezzenga R. Evolution of Conformation, Nanomechanics, and Infrared Nanospectroscopy of Single Amyloid Fibrils Converting into Microcrystals. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002182. [PMID: 33511004 PMCID: PMC7816722 DOI: 10.1002/advs.202002182] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/04/2020] [Indexed: 06/12/2023]
Abstract
Nanomechanical properties of amyloid fibrils and nanocrystals depend on their secondary and quaternary structure, and the geometry of intermolecular hydrogen bonds. Advanced imaging methods based on atomic force microscopy (AFM) have unravelled the morphological and mechanical heterogeneity of amyloids, however a full understanding has been hampered by the limited resolution of conventional spectroscopic methods. Here, it is shown that single molecule nanomechanical mapping and infrared nanospectroscopy (AFM-IR) in combination with atomistic modelling enable unravelling at the single aggregate scale of the morphological, nanomechanical, chemical, and structural transition from amyloid fibrils to amyloid microcrystals in the hexapeptides, ILQINS, IFQINS, and TFQINS. Different morphologies have different Young's moduli, within 2-6 GPa, with amyloid fibrils exhibiting lower Young's moduli compared to amyloid microcrystals. The origins of this stiffening are unravelled and related to the increased content of intermolecular β-sheet and the increased lengthscale of cooperativity following the transition from twisted fibril to flat nanocrystal. Increased stiffness in Young's moduli is correlated with increased density of intermolecular hydrogen bonding and parallel β-sheet structure, which energetically stabilize crystals over the other polymorphs. These results offer additional evidence for the position of amyloid crystals in the minimum of the protein folding and aggregation landscape.
Collapse
Affiliation(s)
- Jozef Adamcik
- Department of Health Sciences and TechnologyETH ZürichZürich8092Switzerland
| | | | - Joshua T. Berryman
- University of LuxembourgDepartment of Physics and Materials Science162a Avenue de la FaïencerieLuxembourgL‐1511Luxembourg
| | - Afang Zhang
- Shanghai University Department of Polymer MaterialsNanchen Street 333Shanghai200444China
| | - Tuomas P. J. Knowles
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cavendish LaboratoryUniversity of CambridgeJ. J. Thomson AvenueCambridgeCB3 0HEUK
| | - Raffaele Mezzenga
- Department of Health Sciences and TechnologyETH ZürichZürich8092Switzerland
- Department of MaterialsETH ZürichZürich8093Switzerland
| |
Collapse
|
15
|
Wang YC, Lai YR, Wu JW, Wang SSS, Lin KS. Using palladium nanoparticle-decorated lysozyme amyloid fibrils to catalyze the reduction of methylene blue. J Taiwan Inst Chem Eng 2021. [DOI: 10.1016/j.jtice.2020.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
16
|
Atomic Force Microscopy Imaging and Nanomechanical Properties of Six Tau Isoform Assemblies. Biophys J 2020; 119:2497-2507. [PMID: 33217380 DOI: 10.1016/j.bpj.2020.10.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 11/22/2022] Open
Abstract
The amyloid fibrillar form of the protein Tau is involved in a number of neurodegenerative diseases, also known as tauopathies. In this work, six different fibrillar Tau isoforms were assembled in vitro. The morphological and nanomechanical properties of these isoforms were studied using atomic force microscopy at high resolution in air and buffer. Our results demonstrate that all Tau isoform fibrils exhibit paired-helical-filament-like structures consisting of two protofibrils separated by a shallow groove. Interestingly, whereas the N-terminal inserts do not contribute to any morphological or mechanical difference between the isoforms with the same carboxyl-terminal microtubule-binding domain repeats, isoforms with four microtubule repeats (4R) exhibited a persistence length ranging from 2.0 to 2.8 μm, almost twofold higher than those with three repeats (3R). In addition, the axial Young's modulus values derived from the persistence lengths, as well as their radial ones determined via nanoindentation experiments, were very low compared to amyloid fibrils made of other proteins. This sheds light on the weak intermolecular interaction acting between the paired β-sheets within Tau fibrils. This may play an important role in their association into high molecular weight assemblies, their dynamics, their persistence, their clearance in cells, and their propagation.
Collapse
|
17
|
Ganesan M, Paranthaman S. Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].
Collapse
Affiliation(s)
- Mahendiraprabu Ganesan
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil 626126, India
| | - Selvarengan Paranthaman
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil 626126, India
| |
Collapse
|
18
|
Deng L, Wang Y. Multiscale computational prediction of β-sheet peptide self-assembly morphology. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1738426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Li Deng
- BGI-Qingdao, Qingdao, People’s Republic of China
- State Key Laboratory of Agricultural Genomics, Shenzhen, People’s Republic of China
- China National GeneBank, Shenzhen, People’s Republic of China
| | - Yanting Wang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| |
Collapse
|
19
|
Chen B, Fu X, Lysevych M, Tan HH, Jagadish C. Four-Dimensional Probing of Phase-Reaction Dynamics in Au/GaAs Nanowires. NANO LETTERS 2019; 19:781-786. [PMID: 30677299 DOI: 10.1021/acs.nanolett.8b03870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanoeutectic phase reaction covers the fundamental study of a chemical and physical reaction of multiple phases at the nanoscale. Here, we report the direct visualization of phase-reaction dynamics in Au/GaAs nanowires (NWs) using four-dimensional (4D) electron microscopy. The NW phase reactions were initiated with a pump laser pulse, while the following dynamics in the Au/GaAs NW was probed by a precisely time-delayed electron pulse. Single-pulse imaging reveals that the cubic zinc-blende NW presents a transient length increase within the time duration of ∼150 ns, giving the appearance of intermediate phase reactions at an early stage. A final length reduction of the NW is observed after the phase reactions have fully ended. In contrast, only length reduction is seen throughout the entire process in GaAs/AlGaAs core-shell and hexagonal wurtzite GaAs NWs. The reasons for the above intriguing phenomena are discussed. The eutectic-related phenomena in both zinc-blende and wurtzite materials offer a comprehensive understanding of phase-reaction dynamics in polytypic structures commonly available in compound semiconductors.
Collapse
Affiliation(s)
- Bin Chen
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xuewen Fu
- Condensed Matter Physics & Materials Science Department , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | | | | | | |
Collapse
|
20
|
Dapson RW. Amyloid from a histochemical perspective. A review of the structure, properties and types of amyloid, and a proposed staining mechanism for Congo red staining. Biotech Histochem 2018; 93:543-556. [PMID: 30403893 DOI: 10.1080/10520295.2018.1528385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Amyloid is a diverse group of unrelated peptides or proteins that have positive functionality or are associated with various pathologies. Despite vast differences, all amyloids share several features that together uniquely define the group. 1) All amyloids possess a characteristic cross-ß pattern with X-ray diffraction typical of ß-sheet secondary protein structures. 2) All amyloids are birefringent and dichroic under polarizing microscopy after staining with Congo red, which indicates a crystalline-like (ordered) structure. 3) All amyloids cause a spectral shift in the peak wavelength of Congo red with conventional light microscopy due to perturbation of π electrons of the dye. 4) All amyloids show heightened intensity of fluorescence with Congo red, which suggests an unusual degree of packing of the dye onto the substrate. The ß portion of amyloid molecules, the only logical substrate for specific Congo red staining under histochemical conditions, consists of a stack of ß-sheets laminated by hydrophilic and hydrophobic interactions between adjacent pairs. Only the first and last ß-sheets are accessible to dyes. Each sheet is composed of numerous identical peptides running across the width of the sheet and arranged in parallel with side chains in register over the length of the fibril. Two sets of grooves are bordered by side chains. X grooves run perpendicular to the long axis of the fibril; these grooves are short (the width of the sheet) and number in the hundreds or thousands. Y grooves are parallel with the long axis. Each groove runs the entire length of the fibril, but there are very few of them. While Congo red is capable of ionic bonding with proteins via two sulfonic acid groups, physical constraints on the staining solution preclude ionic interactions. Hydrogen bonding between dye amine groups and peptide carbonyls is the most likely primary bonding mechanism, because all ß-sheets possess backbone carbonyls. Various amino acid residues may form secondary bonds to the dye via any of three van der Waals forces. It is possible that Congo red binds within the Y grooves, but that would not produce the characteristic staining features that are the diagnostic hallmarks of amyloid. Binding in the X grooves would produce a tightly packed series of dye molecules over the entire length of the fibril. This would account for the signature staining of amyloid by Congo red: dichroic birefringence, enhanced intensity of fluorescence and a shift in visible absorption wavelength.
Collapse
|
21
|
Cámara-Almirón J, Caro-Astorga J, de Vicente A, Romero D. Beyond the expected: the structural and functional diversity of bacterial amyloids. Crit Rev Microbiol 2018; 44:653-666. [PMID: 30354913 DOI: 10.1080/1040841x.2018.1491527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intense research has confirmed the formerly theoretical distribution of amyloids in nature, and studies on different systems have illustrated the role of these proteins in microbial adaptation and in interactions with the environment. Two lines of research are expanding our knowledge on functional amyloids: (i) structural studies providing insights into the molecular machineries responsible for the transition from monomer to fibers and (ii) studies showing the way in which these proteins might participate in the microbial fitness in natural settings. Much is known about how amyloids play a role in the social behavior of bacteria, or biofilm formation, and in the adhesion of bacteria to surfaces; however, we are still in the initial stages of understanding a complementary involvement of amyloids in bacteria-host interactions. This review will cover the following two topics: first, the key aspects of the microbial platforms dedicated to the assembly of the fibers, and second, the mechanisms by which bacteria utilize the morphological and biochemical variability of amyloids to modulate the immunological response of the host, plants and humans, contributing to (i) infection, in the case of pathogenic bacteria or (ii) promotion of the health of the host, in the case of beneficial bacteria.
Collapse
Affiliation(s)
- Jesús Cámara-Almirón
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Joaquin Caro-Astorga
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Antonio de Vicente
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Diego Romero
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| |
Collapse
|
22
|
Nassar R, Wong E, Bui JM, Yip CK, Li H, Gsponer J, Lamour G. Mechanical Anisotropy in GNNQQNY Amyloid Crystals. J Phys Chem Lett 2018; 9:4901-4909. [PMID: 30102541 DOI: 10.1021/acs.jpclett.8b02027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mapping the nanomechanical properties of amyloids can provide valuable insights into structure and assembly mechanisms of protein aggregates that underlie the development of various human diseases. Although it is well-known that amyloids exhibit an intrinsic stiffness comparable to that of silk (1-10 GPa), a detailed understanding of the directional dependence (anisotropy) of the stiffness of amyloids and how it relates to structural features in these protein aggregates is missing. Here we used steered molecular dynamics (SMD) simulations and amplitude modulation-frequency modulation (AM-FM) atomic force microscopy to measure the directional variation in stiffness of GNNQQNY amyloid crystals. We reveal that individual crystals display significant mechanical anisotropy and relate this anisotropy to subtle but mechanically important differences in interactions between interfaces that define the crystal architecture. Our results provide detailed insights into the structure-mechanics relationship of amyloid that may help in designing amyloid-based nanomaterials with tailored mechanical properties.
Collapse
Affiliation(s)
- Roy Nassar
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Eric Wong
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Jennifer M Bui
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Calvin K Yip
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Hongbin Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
| | - Jörg Gsponer
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Guillaume Lamour
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
| |
Collapse
|
23
|
Lee G, Lee W, Baik S, Kim YH, Eom K, Kwon T. Correlation between the hierarchical structures and nanomechanical properties of amyloid fibrils. NANOTECHNOLOGY 2018; 29:295701. [PMID: 29644980 DOI: 10.1088/1361-6528/aabd8a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amyloid fibrils have recently been highlighted due to their excellent mechanical properties, which not only play a role in their biological functions but also imply their applications in biomimetic material design. Despite recent efforts to unveil how the excellent mechanical properties of amyloid fibrils originate, it has remained elusive how the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils are determined. Here, we characterize the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils using atomic force microscopy experiments and atomistic simulations. It is shown that the hierarchical structure of amyloid fibrils plays a crucial role in determining their radial elastic property but does not make any effect on their bending elastic property. This is attributed to the role of intermolecular force acting between the filaments (constituting the fibril) on the radial elastic modulus of amyloid fibrils. Our finding illustrates how the hierarchical structure of amyloid fibrils encodes their anisotropic nanomechanical properties. Our study provides key design principles of amyloid fibrils, which endow valuable insight into the underlying mechanisms of amyloid mechanics.
Collapse
Affiliation(s)
- Gyudo Lee
- School of Public Health, Harvard University, Boston, MA 02115, United States of America
| | | | | | | | | | | |
Collapse
|
24
|
Ilie IM, den Otter WK, Briels WJ. The attachment of α-synuclein to a fiber: A coarse-grain approach. J Chem Phys 2018; 146:115102. [PMID: 28330339 DOI: 10.1063/1.4978297] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins.
Collapse
Affiliation(s)
- Ioana M Ilie
- Computational Chemical Physics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wouter K den Otter
- Computational Chemical Physics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wim J Briels
- Computational Chemical Physics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| |
Collapse
|
25
|
Semerdzhiev SA, Lindhoud S, Stefanovic A, Subramaniam V, van der Schoot P, Claessens MMAE. Hydrophobic-Interaction-Induced Stiffening of α-Synuclein Fibril Networks. PHYSICAL REVIEW LETTERS 2018; 120:208102. [PMID: 29864360 DOI: 10.1103/physrevlett.120.208102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Indexed: 05/28/2023]
Abstract
In water, networks of semiflexible fibrils of the protein α-synuclein stiffen significantly with increasing temperature. We make plausible that this reversible stiffening is a result of hydrophobic contacts between the fibrils that become more prominent with increasing temperature. The good agreement of our experimentally observed temperature dependence of the storage modulus of the network with a scaling theory linking network elasticity with reversible cross-linking enables us to quantify the endothermic binding enthalpy and estimate the effective size of hydrophobic patches on the fibril surface. Our findings may not only shed light on the role of amyloid deposits in disease conditions, but can also inspire new approaches for the design of thermoresponsive materials.
Collapse
Affiliation(s)
- Slav A Semerdzhiev
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Saskia Lindhoud
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Anja Stefanovic
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Paul van der Schoot
- Theory of Polymers and Soft Matter, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| |
Collapse
|
26
|
Sonavane S, Haider SZ, Kumar A, Ahmad B. Hemin is able to disaggregate lysozyme amyloid fibrils into monomers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1315-1325. [DOI: 10.1016/j.bbapap.2017.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/13/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
|
27
|
Riedle E, Roos MK, Thallmair S, Sailer CF, Krebs N, Fingerhut BP, de Vivie-Riedle R. Ultrafast photochemistry with two product channels: Wavepacket motion through two distinct conical intersections. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
28
|
Lamour G, Nassar R, Chan PHW, Bozkurt G, Li J, Bui JM, Yip CK, Mayor T, Li H, Wu H, Gsponer JA. Mapping the Broad Structural and Mechanical Properties of Amyloid Fibrils. Biophys J 2017; 112:584-594. [PMID: 28256219 DOI: 10.1016/j.bpj.2016.12.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022] Open
Abstract
Amyloids are fibrillar nanostructures of proteins that are assembled in several physiological processes in human cells (e.g., hormone storage) but also during the course of infectious (prion) and noninfectious (nonprion) diseases such as Creutzfeldt-Jakob and Alzheimer's diseases, respectively. How the amyloid state, a state accessible to all proteins and peptides, can be exploited for functional purposes but also have detrimental effects remains to be determined. Here, we measure the nanomechanical properties of different amyloids and link them to features found in their structure models. Specifically, we use shape fluctuation analysis and sonication-induced scission in combination with full-atom molecular dynamics simulations to reveal that the amyloid fibrils of the mammalian prion protein PrP are mechanically unstable, most likely due to a very low hydrogen bond density in the fibril structure. Interestingly, amyloid fibrils formed by HET-s, a fungal protein that can confer functional prion behavior, have a much higher Young's modulus and tensile strength than those of PrP, i.e., they are much stiffer and stronger due to a tighter packing in the fibril structure. By contrast, amyloids of the proteins RIP1/RIP3 that have been shown to be of functional use in human cells are significantly stiffer than PrP fibrils but have comparable tensile strength. Our study demonstrates that amyloids are biomaterials with a broad range of nanomechanical properties, and we provide further support for the strong link between nanomechanics and β-sheet characteristics in the amyloid core.
Collapse
Affiliation(s)
- Guillaume Lamour
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roy Nassar
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick H W Chan
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gunes Bozkurt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jixi Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jennifer M Bui
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thibault Mayor
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jörg A Gsponer
- Michael Smith Laboratories-Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
29
|
Vanacore GM, Hu J, Liang W, Bietti S, Sanguinetti S, Carbone F, Zewail AH. Ultrafast atomic-scale visualization of acoustic phonons generated by optically excited quantum dots. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044034. [PMID: 28852685 PMCID: PMC5552391 DOI: 10.1063/1.4998009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 07/28/2017] [Indexed: 05/31/2023]
Abstract
Understanding the dynamics of atomic vibrations confined in quasi-zero dimensional systems is crucial from both a fundamental point-of-view and a technological perspective. Using ultrafast electron diffraction, we monitored the lattice dynamics of GaAs quantum dots-grown by Droplet Epitaxy on AlGaAs-with sub-picosecond and sub-picometer resolutions. An ultrafast laser pulse nearly resonantly excites a confined exciton, which efficiently couples to high-energy acoustic phonons through the deformation potential mechanism. The transient behavior of the measured diffraction pattern reveals the nonequilibrium phonon dynamics both within the dots and in the region surrounding them. The experimental results are interpreted within the theoretical framework of a non-Markovian decoherence, according to which the optical excitation creates a localized polaron within the dot and a travelling phonon wavepacket that leaves the dot at the speed of sound. These findings indicate that integration of a phononic emitter in opto-electronic devices based on quantum dots for controlled communication processes can be fundamentally feasible.
Collapse
Affiliation(s)
| | | | | | - Sergio Bietti
- L-NESS and Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 53, I-20125 Milano, Italy
| | - Stefano Sanguinetti
- L-NESS and Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 53, I-20125 Milano, Italy
| | - Fabrizio Carbone
- Institute of Physics, Laboratory for Ultrafast Microscopy and Electron Scattering (LUMES), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ahmed H Zewail
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
30
|
Abdelmotilib H, Maltbie T, Delic V, Liu Z, Hu X, Fraser KB, Moehle MS, Stoyka L, Anabtawi N, Krendelchtchikova V, Volpicelli-Daley LA, West A. α-Synuclein fibril-induced inclusion spread in rats and mice correlates with dopaminergic Neurodegeneration. Neurobiol Dis 2017; 105:84-98. [PMID: 28576704 DOI: 10.1016/j.nbd.2017.05.014] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/09/2017] [Accepted: 05/29/2017] [Indexed: 01/26/2023] Open
Abstract
Proteinaceous inclusions in neurons, composed primarily of α-synuclein, define the pathology in several neurodegenerative disorders. Neurons can internalize α-synuclein fibrils that can seed new inclusions from endogenously expressed α-synuclein. The factors contributing to the spread of pathology and subsequent neurodegeneration are not fully understood, and different compositions and concentrations of fibrils have been used in different hosts. Here, we systematically vary the concentration and length of well-characterized α-synuclein fibrils and determine their relative ability to induce inclusions and neurodegeneration in different hosts (primary neurons, C57BL/6J and C3H/HeJ mice, and Sprague Dawley rats). Using dynamic-light scattering profiles and other measurements to determine fibril length and concentration, we find that femptomolar concentrations of fibrils are sufficient to induce robust inclusions in primary neurons. However, a narrow and non-linear dynamic range characterizes fibril-mediated inclusion induction in axons and the soma. In mice, the C3H/HeJ strain is more sensitive to fibril exposures than C57BL/6J counterparts, with more inclusions and dopaminergic neurodegeneration. In rats, injection of fibrils into the substantia nigra pars compacta (SNpc) results in similar inclusion spread and dopaminergic neurodegeneration as injection of the fibrils into the dorsal striatum, with prominent inclusion spread to the amygdala and several other brain areas. Inclusion spread, particularly from the SNpc to the striatum, positively correlates with dopaminergic neurodegeneration. These results define biophysical characteristics of α-synuclein fibrils that induce inclusions and neurodegeneration both in vitro and in vivo, and suggest that inclusion spread in the brain may be promoted by a loss of neurons.
Collapse
Affiliation(s)
- Hisham Abdelmotilib
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tyler Maltbie
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vedad Delic
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zhiyong Liu
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xianzhen Hu
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kyle B Fraser
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mark S Moehle
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lindsay Stoyka
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nadia Anabtawi
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Valentina Krendelchtchikova
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laura A Volpicelli-Daley
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew West
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
31
|
Shorokhov D, Zewail AH. Perspective: 4D ultrafast electron microscopy--Evolutions and revolutions. J Chem Phys 2016; 144:080901. [PMID: 26931672 DOI: 10.1063/1.4941375] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In this Perspective, the evolutionary and revolutionary developments of ultrafast electron imaging are overviewed with focus on the "single-electron concept" for probing methodology. From the first electron microscope of Knoll and Ruska [Z. Phys. 78, 318 (1932)], constructed in the 1930s, to aberration-corrected instruments and on, to four-dimensional ultrafast electron microscopy (4D UEM), the developments over eight decades have transformed humans' scope of visualization. The changes in the length and time scales involved are unimaginable, beginning with the micrometer and second domains, and now reaching the space and time dimensions of atoms in matter. With these advances, it has become possible to follow the elementary structural dynamics as it unfolds in real time and to provide the means for visualizing materials behavior and biological functions. The aim is to understand emergent phenomena in complex systems, and 4D UEM is now central for the visualization of elementary processes involved, as illustrated here with examples from past achievements and future outlook.
Collapse
Affiliation(s)
- Dmitry Shorokhov
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory for Chemical Physics, California Institute of Technology, Pasadena, California 91125, USA
| | - Ahmed H Zewail
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory for Chemical Physics, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
32
|
Abstract
Single amino acid mutations in amyloid-beta (Aβ) peptides can lead to early onset and increased severity of Alzheimer's disease. An example is the Osaka mutation (Aβ1-40E22D), which is more toxic than wild-type Aβ1-40. This mutant quickly forms early stage fibrils, one of the hallmarks of the disease, and these fibrils can even seed fibrilization of wild-type monomers. Using molecular dynamic simulations, we show that because of formation of various intra- and intermolecular salt bridges the Osaka mutant fibrils are more stable than wild-type fibrils. The mutant fibril also has a wider water channel with increased water flow than the wild type. These two observations can explain the higher toxicity and aggregation rate of the Osaka mutant over the wild type.
Collapse
Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Erik J Alred
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| |
Collapse
|
33
|
Thomas JM, Leary RK, Eggeman AS, Midgley PA. The rapidly changing face of electron microscopy. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
34
|
Hoang Viet M, Truong PM, Derreumaux P, Li MS, Roland C, Sagui C, Nguyen PH. Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study. Phys Chem Chem Phys 2015; 17:27275-80. [DOI: 10.1039/c5cp04401d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resonance between carboxylate bond vibrations and laser frequency results in melting of nanotube.
Collapse
Affiliation(s)
- Man Hoang Viet
- Department of Physics
- North Carolina State University
- Raleigh
- USA
| | - Phan Minh Truong
- Institute for Computational Science and Technology
- Quang Trung Software City
- Tan Chanh Hiep Ward
- Ho Chi Minh City
- Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique
- UPR 9080 CNRS
- IBPC
- Universite Denis Diderot
- Paris
| | - Mai Suan Li
- Institute for Computational Science and Technology
- Quang Trung Software City
- Tan Chanh Hiep Ward
- Ho Chi Minh City
- Vietnam
| | | | - Celeste Sagui
- Department of Physics
- North Carolina State University
- Raleigh
- USA
| | | |
Collapse
|