51
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Banerjee S, Holcombe B, Ringold S, Foes A, Naik T, Baghel D, Ghosh A. Nanoscale Infrared Spectroscopy Identifies Structural Heterogeneity in Individual Amyloid Fibrils and Prefibrillar Aggregates. J Phys Chem B 2022; 126:5832-5841. [PMID: 35914320 DOI: 10.1021/acs.jpcb.2c04797] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Amyloid plaques are one of the central manifestations of Alzheimer's disease pathology. Aggregation of the amyloid beta (Aβ) protein from amorphous oligomeric species to mature fibrils has been extensively studied. However, structural heterogeneities in prefibrillar species, and how that affects the structure of later-stage aggregates are not yet well understood. The integration of infrared spectroscopy with atomic force microscopy (AFM-IR) allows for identifying the signatures of individual nanoscale aggregates by spatially resolving spectra. We use AFM-IR to demonstrate that amyloid oligomers exhibit significant structural variations as evidenced in their infrared spectra. This heterogeneity is transmitted to and retained in protofibrils and fibrils. We show that amyloid fibrils do not always conform to their putative ordered structure and structurally different domains exist in the same fibril. We further demonstrate that these structural heterogeneities manifest themselves as a lack of β sheet structure in amyloid plaques in Alzheimer's tissue using infrared imaging.
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Affiliation(s)
- Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Brooke Holcombe
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Sydney Ringold
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Abigail Foes
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Tanmayee Naik
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, Alabama 35487, United States
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52
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Biswas A, Mallik BS. Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations. J Phys Chem A 2022; 126:5134-5147. [PMID: 35900106 DOI: 10.1021/acs.jpca.2c03387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.
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Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India
| | - Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502284, Telangana, India
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53
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Garg DK, Bhat R. Modulation of assembly of TDP-43 low-complexity domain by heparin: From droplets to amyloid fibrils. Biophys J 2022; 121:2568-2582. [PMID: 35644946 PMCID: PMC9300664 DOI: 10.1016/j.bpj.2022.05.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/03/2021] [Accepted: 05/25/2022] [Indexed: 11/02/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA-regulating protein that carries out many cellular functions through liquid-liquid phase separation (LLPS). The LLPS of TDP-43 is mediated by its C-terminal low-complexity domain (TDP43-LCD) corresponding to the region 267-414. In neurodegenerative disorders amyotrophic lateral sclerosis and frontotemporal dementia, pathological inclusions of the TDP-43 are found that are rich in the C-terminal fragments of ∼25 and ∼35 kDa, of which TDP43-LCD is a part. Thus, understanding the assembly process of TDP43-LCD is essential, given its involvement in the formation of both functional liquid-like assemblies and solid- or gel-like pathological aggregates. Here, we show that the solution pH and salt modulate TDP43-LCD LLPS. A gradual reduction in the pH below its isoelectric point of 9.8 results in a monotonic decrease of TDP43-LCD LLPS due to charge-charge repulsion between monomers, while at pH 6 and below no LLPS was observed. The addition of heparin to TDP43-LCD solution at pH 6, at a 1:2 heparin-to-TDP43-LCD molar ratio, promotes TDP43-LCD LLPS, while at higher concentration, it disrupts LLPS through a reentrant phase transition. Upon incubation at pH 6, TDP43-LCD undergoes gelation without phase separation. However, in the reentrant regime in the presence of a high heparin concentration, it forms thick amyloid aggregates that are significantly more SDS resistant than the gel. The results indicate that the material nature of the TDP43-LCD assembly products can be modulated by heparin which is significant in the context of liquid-to-solid phase transition observed in TDP-43 proteinopathies. Our findings are also crucial in relation to similar transitions that could occur due to alteration in the molecular level interactions among various multivalent biomolecules involving other LCDs and RNAs.
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Affiliation(s)
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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54
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Puławski W, Dzwolak W. Virtual Quasi-2D Intermediates as Building Blocks for Plausible Structural Models of Amyloid Fibrils from Proteins with Complex Topologies: A Case Study of Insulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7024-7034. [PMID: 35617668 PMCID: PMC9178918 DOI: 10.1021/acs.langmuir.2c00699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Conformational transitions of globular proteins into amyloid fibrils are complex multistage processes exceedingly challenging to simulate using molecular dynamics (MD). Slow monomer diffusion rates and rugged free energy landscapes disfavor swift self-assembly of orderly amyloid architectures within timescales accessible to all-atom MD. Here, we conduct a multiscale MD study of the amyloidogenic self-assembly of insulin: a small protein with a complex topology defined by two polypeptide chains interlinked by three disulfide bonds. To avoid kinetic traps, unconventional preplanarized insulin conformations are used as amyloid building blocks. These starting conformers generated through uniaxial compression of the native monomer in various spatial directions represent 6 distinct (out of 16 conceivable) two-dimensional (2D) topological classes varying in N-/C-terminal segments of insulin's A- and B-chains being placed inside or outside of the central loop constituted by the middle sections of both chains and Cys7A-Cys7B/Cys19B-Cys20A disulfide bonds. Simulations of the fibrillar self-assembly are initiated through a biased in-register alignment of two, three, or four layers of flat conformers belonging to a single topological class. The various starting topologies are conserved throughout the self-assembly process resulting in polymorphic amyloid fibrils varying in structural features such as helical twist, presence of cavities, and overall stability. Some of the protofilament structures obtained in this work are highly compatible with the earlier biophysical studies on insulin amyloid and high-resolution studies on insulin-derived amyloidogenic peptide models postulating the presence of steric zippers. Our approach provides in silico means to study amyloidogenic tendencies and viable amyloid architectures of larger disulfide-constrained proteins with complex topologies.
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Affiliation(s)
- Wojciech Puławski
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
| | - Wojciech Dzwolak
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
- Faculty
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland
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55
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Siu HW, Hauser K. Observation of Oligomeric States Indicates a High Structural Flexibility Required for the Onset of Polyglutamine Fibrillization. J Phys Chem Lett 2022; 13:4543-4548. [PMID: 35580015 DOI: 10.1021/acs.jpclett.2c00203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polyglutamine (polyQ) diseases are caused by misfolding and aggregation of expanded polyQ tracts in the affected protein. PolyQ fibrils have been studied in detail; however, less is known about oligomeric precursor states. By a combination of time-resolved temperature-jump (T-jump) infrared (IR) spectroscopy and an appropriately tailored polyQ model peptide, we succeeded in disentangling conformational dynamics in the heterogeneous ensemble of states evolving during aggregation. Individual structural elements could be differentiated by IR-specific signatures, i.e., hairpin monomers, β-structured oligomers, and disordered structure. Submillisecond dynamics were observed for early oligomeric states in contrast to the slow dynamics of fibril growth. We propose that a high structural flexibility of oligomers is required to initiate fibril formation, but not after a fibrillar structure has consolidated and the fibril just grows. Our study reveals that structural flexibility changes at different stages in the aggregation process, from fibril initiation to fibril growth.
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Affiliation(s)
- Ho-Wah Siu
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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56
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Mikalauskaite K, Ziaunys M, Smirnovas V. Lysozyme Amyloid Fibril Structural Variability Dependence on Initial Protein Folding State. Int J Mol Sci 2022; 23:5421. [PMID: 35628230 PMCID: PMC9141980 DOI: 10.3390/ijms23105421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 02/05/2023] Open
Abstract
Amyloid fibril formation is associated with several amyloidoses, including neurodegenerative Alzheimer's or Parkinson's diseases. The process of such fibrillar structure formation is still not fully understood, with new mechanistic insights appearing on a regular basis. This, in turn, has limited the development of potential anti-amyloid compounds, with only a handful of effective cures or treatment modalities available. One of the multiple amyloid aggregation factors that requires further examination is the ability of proteins to form multiple, structurally distinct aggregates, based on the environmental conditions. In this work, we examine how the initial folding state affects the fibrilization of lysozyme-an amyloidogenic protein, often used in protein aggregation studies. We show that there is a correlation between the initial state of the protein and the aggregate formation lag time, rate of elongation, resulting aggregate structural variability and dye-binding properties, as well as formation lag time and rate of elongation.
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Affiliation(s)
- Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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57
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Rosa E, Diaferia C, Gianolio E, Sibillano T, Gallo E, Smaldone G, Stornaiuolo M, Giannini C, Morelli G, Accardo A. Multicomponent Hydrogel Matrices of Fmoc-FF and Cationic Peptides for Application in Tissue Engineering. Macromol Biosci 2022; 22:e2200128. [PMID: 35524744 DOI: 10.1002/mabi.202200128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 11/10/2022]
Abstract
In the last years, peptide based hydrogels are being increasingly used as suitable matrices for biomedical and pharmaceutical applications, including drug delivery and tissue engineering. Recently, we decrived the synthesis and the gelation properties of a small library of cationic peptides, containing a Lys residue at the C-teminus and derivatized with a Fmoc group or with the Fmoc-diphenylalanine (FmocFF) at the N-terminus. Here, we demonstrate that the combination of these peptides with the well known hydrogelator FmocFF, in different weight/weight ratios, allows the achievement of seven novel self-sorted hydrogels, which share similar peptide organization of their supramolecular matrix. Rheological and relaxometric characterization highlighted a different mechanical rigidity and water mobility in the gels as demostrated by the storage modulus values (200 Pa<G'<35000 Pa) and by relaxometry, respectively. In vitro studied demonstrated that most of the tested mixed hydrogels do not disturb significantly the cell viability (>95%) over 72h of treatment. Moreover, in virtue to its capability to strongly favour adhesion, spreading and duplication of 3T3-L1 cells, one of the tested hydrogel may be eligible as sinthetic extracellular matrix. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Elisabetta Rosa
- Department of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, Naples, 80134, Italy
| | - Carlo Diaferia
- Department of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, Naples, 80134, Italy
| | - Eliana Gianolio
- Department of Molecular Biotechnologies and Health Science, University of Turin, Via Nizza 52, Turin, 10125, Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, Bari, 70126, Italy
| | - Enrico Gallo
- IRCCS Synlab SDN, Via E. Gianturco 113, Naples, 80143, Italy
| | | | - Mariano Stornaiuolo
- Department of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, Naples, 80134, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, Bari, 70126, Italy
| | - Giancarlo Morelli
- Department of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, Naples, 80134, Italy
| | - Antonella Accardo
- Department of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, Naples, 80134, Italy
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58
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Tempra C, Scollo F, Pannuzzo M, Lolicato F, La Rosa C. A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140767. [PMID: 35144022 DOI: 10.1016/j.bbapap.2022.140767] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Aβ peptide, which is known to form senile plaques in Alzheimer's disease; ii) α-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) functional conformations and accumulate as amyloid aggregates upon interaction with other cytosolic partners such as proteins or lipid membranes. In addition, an increasing number of reports link the toxicity of amyloid proteins to their harmful effects on membrane integrity. Still, the molecular mechanism underlying the amyloidogenic proteins transfer from the aqueous environment to the hydrocarbon core of the membrane is poorly understood. This review starts with a historical overview of the toxicity models of amyloidogenic proteins to contextualize the more recent lipid-chaperone hypothesis. Then, we report the early molecular-level events in the aggregation and ion-channel pore formation of Aβ, IAPP, and α-synuclein interacting with model membranes, emphasizing the complexity of these processes due to their different spatial-temporal resolutions. Next, we underline the need for a combined experimental and computational approach, focusing on the strengths and weaknesses of the most commonly used techniques. Finally, the last two chapters highlight the crucial role of lipid-protein complexes as molecular switches among ion-channel-like formation, detergent-like, and fibril formation mechanisms and their implication in fighting amyloidogenic diseases.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | - Federica Scollo
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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59
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Meuwly M. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?. J Phys Chem B 2022; 126:2155-2167. [PMID: 35286087 DOI: 10.1021/acs.jpcb.2c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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60
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Yu CC, Imoto S, Seki T, Chiang KY, Sun S, Bonn M, Nagata Y. Accurate molecular orientation at interfaces determined by multimode polarization-dependent heterodyne-detected sum-frequency generation spectroscopy via multidimensional orientational distribution function. J Chem Phys 2022; 156:094703. [DOI: 10.1063/5.0081209] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many essential processes occur at soft interfaces, from chemical reactions on aqueous aerosols in the atmosphere to biochemical recognition and binding at the surface of cell membranes. The spatial arrangement of molecules specifically at these interfaces is crucial for many of such processes. The accurate determination of the interfacial molecular orientation has been challenging due to the low number of molecules at interfaces and the ambiguity of their orientational distribution. Here, we combine phase- and polarization-resolved sum-frequency generation (SFG) spectroscopy to obtain the molecular orientation at the interface. We extend an exponentially decaying orientational distribution to multiple dimensions, which, in conjunction with multiple SFG datasets obtained from the different vibrational modes, allows us to determine the molecular orientation. We apply this new approach to formic acid molecules at the air–water interface. The inferred orientation of formic acid agrees very well with ab initio molecular dynamics data. The phase-resolved SFG multimode analysis scheme using the multidimensional orientational distribution thus provides a universal approach for obtaining the interfacial molecular orientation.
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Affiliation(s)
- Chun-Chieh Yu
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Sho Imoto
- Analysis Technology Center, Fujifilm R&D, 210 Nakanuma, Minamiashigara, Kanagawa 250-0123, Japan
| | - Takakazu Seki
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Kuo-Yang Chiang
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shumei Sun
- Applied Optics Beijing Area Major Laboratory, Department of Physics, Beijing Normal University, 100875 Beijing, China
| | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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61
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Corsini PM, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle CJC, Mastroianni G, Dorgan B, Sewell LM, Lynham S, Iuga D, Franks WT, Jarvis J, Carpenter GH, Curtis MA, Bernadó P, Darbari VC, Garnett JA. Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation. NPJ Biofilms Microbiomes 2022; 8:9. [PMID: 35217675 PMCID: PMC8881592 DOI: 10.1038/s41522-022-00272-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.
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Affiliation(s)
- Paula M Corsini
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Katherine Fenn
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amin Sagar
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Slobodan Sirovica
- Centre for Oral Bioengineering, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | | | - Giulia Mastroianni
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Lee M Sewell
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry, UK
| | - James Jarvis
- Randall Division of Cell and Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | - Guy H Carpenter
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Vidya C Darbari
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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62
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Wei H, Lin S, Liu W, Li Y, Li B, Yang Y. Stereostructure Dependence Phenomenon on the Self-Assembly of Ala-Ala-Ala Lipotripeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2248-2256. [PMID: 35133849 DOI: 10.1021/acs.langmuir.1c02813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A series of lipotripeptide stereoisomers based on alanine were synthesized, and their self-assembling behaviors were studied by means of circular dichroism spectra, ATR-IR, temperature-dependent 1H NMR, and X-ray diffraction patterns. In the mixed solvent of hexafluoroisopropanol/H2O (1/9, v/v), eight lipotripeptides were able to self-assembled into nanoflakes or nanoribbons driven by the hydrophobic association of alkyl chains, intermolecular hydrogen bonding among carboxyl groups at C-terminal and amide groups of alanine moieties in the peptide segment. It was found that the stacking chirality of carbonyl groups was determined by the chirality of alanine residue at C-terminal (i.e., "C-terminal determination" rule). Moreover, our research also highlighted the intermolecular hydrogen bonding on amide groups of each alanine residue, terminal carboxyl as well as the molecular packing structures can be subtly manipulated by changing the stereochemical sequence of peptide segment.
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Affiliation(s)
- He Wei
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Shuwei Lin
- Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province & Key Lab of Modern Optical Technologies of Education Ministry of China, School of Optoelectronics Science and Engineering, Soochow University, Suzhou 215123, China
| | - Wei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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63
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Price DA, Wedamulla P, Hill TD, Loth TM, Moran SD. The polarization dependence of 2D IR cross-peaks distinguishes parallel-stranded and antiparallel-stranded DNA G-quadruplexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120596. [PMID: 34801392 DOI: 10.1016/j.saa.2021.120596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Guanine-rich nucleic acid sequences have a tendency to form four-stranded non-canonical motifs known as G-quadruplexes. These motifs may adopt a wide range of structures characterized by size, strand orientation, guanine base conformation, and fold topology. Using three K+-bound model systems, we show that vibrational coupling between guanine C6 = O and ring modes varies between parallel-stranded and antiparallel-stranded G-quadruplexes, and that such structures can be distinguished by comparison of the polarization dependences of cross-peaks in their two-dimensional infrared (2D IR) spectra. Combined with previously defined vibrational frequency trends, this analysis reveals key features of a 30-nucleotide unimolecular variant of the Bcl-2 proximal promoter that are consistent with its reported structure. This study shows that 2D IR spectroscopy is a convenient method for analyzing G-quadruplex structures that can be applied to complex sequences where traditional high-resolution methods are limited by solubility and disorder.
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Affiliation(s)
- David A Price
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, IL 62901, United States
| | - Poornima Wedamulla
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, IL 62901, United States
| | - Tayler D Hill
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, IL 62901, United States
| | - Taylor M Loth
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, IL 62901, United States
| | - Sean D Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, IL 62901, United States.
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64
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Biswas A, Mallik BS. 2D IR spectra of the intrinsic vibrational probes of ionic liquid from dispersion corrected DFT-MD simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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65
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Wu L, Liu W, Li Y, Yang Y. Self-assembly driven chiral transfer from a dipeptide to the twist and stacking handedness of cyanobiphenylyl groups. NEW J CHEM 2022. [DOI: 10.1039/d2nj01259f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The chiral transfer phenomenon was studied on four Ala–Ala lipodipeptides with a cyanobiphenylyl group at the terminal alkyl chain.
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Affiliation(s)
- Lijia Wu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Wei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Key Laboratory of Polymeric Materials Design and Synthesis for Biomedical Function, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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66
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Biswas A, Mallik BS. Revisiting OD-stretching dynamics of methanol‑d4, ethanol-d6 and dilute HOD/H2O mixture with predefined potentials and wavelet transform spectra. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111385] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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67
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Trusova V, Tarabara U, Zhytniakivska O, Vus K, Gorbenko G. Fӧrster resonance energy transfer analysis of amyloid state of proteins. BBA ADVANCES 2022; 2:100059. [PMID: 37082586 PMCID: PMC10074846 DOI: 10.1016/j.bbadva.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
The Förster resonance energy transfer (FRET) is a well-established and versatile spectroscopic technique extensively used for exploring a variety of biomolecular interactions and processes. The present review is intended to cover the main results of our FRET studies focused on amyloid fibrils, a particular type of disease-associated protein aggregates. Based on the examples of several fibril-forming proteins including insulin, lysozyme and amyloidogenic variants of N-terminal fragment of apolipoprotein A-I, it was demonstrated that: (i) the two- and three-step FRET with the classical amyloid marker Thioflavin T as an input donor has a high amyloid-sensing potential and can be used to refine the amyloid detection assays; (ii) the intermolecular time-resolved and single-molecule pulse interleaved excitation FRET can give quantitative information on the nucleation of amyloid fibrils; (iii) FRET between the membrane fluorescent probes and protein-associated intrinsic or extrinsic fluorophores is suitable for monitoring the membrane binding of fibrillar proteins, exploring their location relative to lipid-water interface and restructuring on a lipid matrix; (iv) the FRET-based distance estimation between fibril-bound donor and acceptor fluorophores can serve as one of the verification criteria upon structural modeling of amyloid fibrils.
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68
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Zhang Q, Wang B, Zhang Y, Yang J, Deng B, Ding B, Zhong D. Probing Intermolecular Interactions of Amyloidogenic Fragments of SOD1 by Site-Specific Tryptophan and Its Noncanonical Derivative. J Phys Chem B 2021; 125:13088-13098. [PMID: 34812635 DOI: 10.1021/acs.jpcb.1c07175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transient amyloid intermediates are likely to be cytotoxic and play an essential role in amyloid-associated neurodegenerative diseases. Characterization of their structural and dynamic evolution is the key to elucidating the molecular mechanism of amyloid formation. Here, combining circular dichroism (CD), exciton couplet theory, and Fourier transform infrared spectroscopy with site-specific tryptophan (Trp) and its noncanonical derivative 5-cyano-tryptochan (Trp5CN), we developed a method to monitor strand-to-strand tertiary and sheet-to-sheet quaternary interactions in the aggregation cascades of an amyloidogenic fragment from protein SOD128-38 (with the sequence KVKVWGSIKGL). We found that the exciton couplet generated from the Bb band of Trp can be used as a probe for side chain interactions. Its sensitivity can be further improved by four times with the incorporation of Trp5CN. We further observed a red-shift of ∼2 cm-1 and a broadening of ∼2 cm-1 in the IR band generated from the CN stretch during the aggregation, which we attributed to the transition from a corkscrew-like structure to a cross-linked intermediate phase. We show here that the integration of optical methods with unique aromatic side chain-related probes is able to elucidate amyloid intermolecular interactions and even capture elusive transient intermediates on and off the amyloid assembling pathway.
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Affiliation(s)
- Qin Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bingyao Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Yang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bodan Deng
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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69
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Siri M, Herrera M, Moyano AJ, Celej MS. Influence of the macromolecular crowder alginate in the fibrillar organization of the functional amyloid FapC from Pseudomonas aeruginosa. Arch Biochem Biophys 2021; 713:109062. [PMID: 34688606 DOI: 10.1016/j.abb.2021.109062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Bacterial biofilms are an alternative lifestyle in which communities of bacteria are embedded in an extracellular matrix manly composed by polysaccharides, nucleic acids and proteins, being the hallmark of bacterial survival in a variety of ecological niches. Amyloid fibrils are one of the proteinaceous components of such extracellular crowded environments. FapC is the main component of the functional amyloid recently discovered in Pseudomonas species, including the opportunistic pathogen P. aeruginosa, which is a major cause of nosocomial infections and contamination of medical devices. Considering that several functional roles have been attributed to this bacterial amyloid, FapC emerged as a novel target to control Pseudomonas biofilm formation and to design new treatments against chronic infections. In this study, we used complementary biophysical techniques to evaluate conformational signatures of FapC amyloids formed in the presence of alginate, the major exopolysaccharide associated with the mucoid phenotype of P. aeruginosa strains isolated from cystic fibrosis patients. We found that the this naturally occurring macromolecular crowder leads to morphological similar yet polymorphic FapC fibrils, highlighting the importance of considering the complexity of the extracellular matrix in order to improve our understanding of microbial functional amyloids.
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Affiliation(s)
- Macarena Siri
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Melisa Herrera
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Alejandro J Moyano
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
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70
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Chelius K, Wat JH, Phadkule A, Reppert M. Distinct electrostatic frequency tuning rates for amide I and amide I' vibrations. J Chem Phys 2021; 155:195101. [PMID: 34800962 DOI: 10.1063/5.0064518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D2O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I' spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm-1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I' data. We here analyze amide I and amide I' peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I' comparison. While we find an excellent linear correlation between amide I and amide I' peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H2O/D2O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear "map" for translating between amide I and amide I' frequencies.
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Affiliation(s)
- Kevin Chelius
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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71
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Banerjee S, Ghosh A. Structurally Distinct Polymorphs of Tau Aggregates Revealed by Nanoscale Infrared Spectroscopy. J Phys Chem Lett 2021; 12:11035-11041. [PMID: 34747175 PMCID: PMC8967399 DOI: 10.1021/acs.jpclett.1c02660] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Aggregation of the tau protein plays a central role in several neurodegenerative diseases collectively known as tauopathies, including Alzheimer's and Parkinson's disease. Tau misfolds into fibrillar β sheet structures that constitute the paired helical filaments found in neurofibrillary tangles. It is known that there can be significant structural heterogeneities in tau aggregates associated with different diseases. However, while structures of mature fibrils have been studied, the structural distributions in early-stage tau aggregates is not well-understood. In the present study, we use atomic force microscopy-IR to investigate nanoscale spectra of individual tau fibrils at different stages of aggregation and demonstrate the presence of multiple fibrillar polymorphs that exhibit different secondary structures. We further show that mature fibrils contain significant amounts of antiparallel β sheets. Our results are the very first application of nanoscale infrared spectroscopy to tau aggregates and underscore the promise of spatially resolved infrared spectroscopy for investigating protein aggregation.
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Affiliation(s)
| | - Ayanjeet Ghosh
- Corresponding Author Ayanjeet Ghosh - Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35401, USA.
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72
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Tiwari D, Singh VK, Baral B, Pathak DK, Jayabalan J, Kumar R, Tapryal S, Jha HC. Indication of Neurodegenerative Cascade Initiation by Amyloid-like Aggregate-Forming EBV Proteins and Peptide in Alzheimer's Disease. ACS Chem Neurosci 2021; 12:3957-3967. [PMID: 34609141 DOI: 10.1021/acschemneuro.1c00584] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The neurotropic potential of the Epstein-Barr virus (EBV) was demonstrated quite recently; however, the mechanistic details are yet to be explored. Therefore, the effects of EBV infection in the neural milieu remain underexplored. Previous reports have suggested the potential role of virus-derived peptides in seeding the amyloid-β aggregation cascade, which lies at the center of Alzheimer's disease (AD) pathophysiology. However, no such study has been undertaken to explore the role of EBV peptides in AD. In our research, ∼100 EBV proteins were analyzed for their aggregation proclivity in silico using bioinformatic tools, followed by the prediction of 20S proteasomal cleavage sites using online algorithms NetChop ver. 3.1 and Pcleavage, thereby mimicking the cellular proteasomal cleavage activity generating short antigenic peptides of viral origin. Our study reports a high aggregate-forming tendency of a 12-amino-acid-long (146SYKHVFLSAFVY157) peptide derived from EBV glycoprotein M (EBV-gM). The in vitro analysis of aggregate formation done using Congo red and Thioflavin-S assays demonstrated dose- and time-dependent kinetics. Thereafter, Raman spectroscopy was used to validate the formation of secondary structures (α helix, β sheets) in the aggregates. Additionally, cytotoxicity assay revealed that even a low concentration of these aggregates has a lethal effect on neuroblastoma cells. The findings of this study provide insights into the mechanistic role of EBV in AD and open up new avenues to explore in the future.
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Affiliation(s)
- Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Vikas Kumar Singh
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Budhadev Baral
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Devesh Kumar Pathak
- Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Jesumony Jayabalan
- Nano Science Laboratory, MSS, Raja Ramanna Centre for Advanced Technology, Indore 452013, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Rajesh Kumar
- Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
- Centre for Advanced Electronics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Suman Tapryal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
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73
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Pachetti M, D'Amico F, Pascolo L, Pucciarelli S, Gessini A, Parisse P, Vaccari L, Masciovecchio C. UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction. Biophys J 2021; 120:4575-4589. [PMID: 34474016 PMCID: PMC8553600 DOI: 10.1016/j.bpj.2021.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 06/28/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.
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Affiliation(s)
- Maria Pachetti
- Elettra - Sincrotrone Trieste, Trieste, Italy; Department of Physics, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.
| | | | - Lorella Pascolo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Stefania Pucciarelli
- University of Camerino, School of Biosciences and Veterinary Medicine, Camerino, Italy
| | | | - Pietro Parisse
- Elettra - Sincrotrone Trieste, Trieste, Italy; Istituto Officina dei Materiali - CNR (IOM-CNR), Trieste, Italy
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74
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Confer MP, Holcombe BM, Foes AG, Holmquist JM, Walker SC, Deb S, Ghosh A. Label-Free Infrared Spectroscopic Imaging Reveals Heterogeneity of β-Sheet Aggregates in Alzheimer's Disease. J Phys Chem Lett 2021; 12:9662-9671. [PMID: 34590866 PMCID: PMC8933041 DOI: 10.1021/acs.jpclett.1c02306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aggregation of the amyloid beta (Aβ) protein into plaques is a pathological feature of Alzheimer's disease (AD). While amyloid aggregates have been extensively studied in vitro, their structural aspects and associated chemistry in the brain are not fully understood. In this report, we demonstrate, using infrared spectroscopic imaging, that Aβ plaques exhibit significant heterogeneities in terms of their secondary structure and phospholipid content. We show that the capabilities of discrete frequency infrared imaging (DFIR) are ideally suited for characterization of amyloid deposits in brain tissues and employ DFIR to identify nonplaque β-sheet aggregates distributed throughout brain tissues. We further demonstrate that phospholipid-rich β-sheet deposits exist outside of plaques in all diseased tissues, indicating their potential clinical significance. This is the very first application of DFIR toward a characterization of protein aggregates in an AD brain and provides a rapid, label-free approach that allows us to uncover β-sheet heterogeneities in the AD, which may be significant for targeted therapeutic strategies in the future.
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75
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Dai Y, Wu Y, Lan H, Ning W, Chen F, Yan G, Cai K. Structural dynamics and vibrational feature of N-Acetyl-d-glucosamine in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 259:119918. [PMID: 33991814 DOI: 10.1016/j.saa.2021.119918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/02/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.
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Affiliation(s)
- Ya'nan Dai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China
| | - Yulan Wu
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China
| | - Huaying Lan
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China
| | - Wenfeng Ning
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China
| | - Feng Chen
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, PR China
| | - Guiyang Yan
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, PR China
| | - Kaicong Cai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, PR China.
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76
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Sun C, Wang Z, Yang K, Yue L, Cheng Q, Ma YL, Lu S, Chen G, Wang R. Polyamine-Responsive Morphological Transformation of a Supramolecular Peptide for Specific Drug Accumulation and Retention in Cancer Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101139. [PMID: 34114343 DOI: 10.1002/smll.202101139] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/10/2021] [Indexed: 06/12/2023]
Abstract
The precise accumulation and extended retention of nanomedicines in the tumor tissue has been highly desired for cancer therapy. Here a novel supramolecular-peptide derived nanodrug (SPN) that can be transformed to microfibers in response to intracellular polyamine in cancer cells for significantly enhanced tumor specific accumulation and retention is developed. The supramolecular-peptide is constructed via the non-covalent interactions between cucurbit[7]uril (CB[7]) and Phe on Phe-Phe-Val-Leu-Lys-camptothecin conjugates (FFVLK-CPT, PC). The resultant amphiphilic supramolecular complex subsequently self-assembles into nanoparticles with a hydrodynamic diameter of 164.2 ± 3.7 nm. Upon internalization into spermine-overexpressed cancer cells, the CB[7]-Phe host-guest pairs can be competitively dissociated by spermine and can release free PC, which immediately form β-sheet structures and subsequently reorganize into microfibers, leading to dramatically improved accumulation, retention, and sustained release of CPT in tumor cells for highly effective cancer therapy. Accordingly, this SPN exhibit rather low toxicity against non-cancerous cells due to the morphological stability and fast exocytosis of the nanodrugs in those cells without abundant spermine. This study reports the first supramolecular peptide capable of polyamine-responsive "nanoparticle-to-microfiber" transformation for specific tumor therapy with minimal side effects. This work also offers novel insights to the design and development of stimuli-responsive nanomaterials as precision medicine.
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Affiliation(s)
- Chen Sun
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Ziyi Wang
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Kuikun Yang
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Ludan Yue
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Qian Cheng
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Yan-Long Ma
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Siyu Lu
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Guosong Chen
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR, 999078, China
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77
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Hanczyc P, Fita P. Laser Emission of Thioflavin T Uncovers Protein Aggregation in Amyloid Nucleation Phase. ACS PHOTONICS 2021; 8:2598-2609. [PMID: 34557567 PMCID: PMC8451393 DOI: 10.1021/acsphotonics.1c00082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Indexed: 05/13/2023]
Abstract
There is currently no definitive test for early detection of neurodegeneration which is linked with protein aggregation. Finding methods capable of detecting intermediate states of protein aggregates, named oligomers, is critical for the early stage diagnosis of over 30 neurodegenerative diseases including Alzheimer's or Parkinson's. Currently, fluorescence-based imaging using Thioflavin T (ThT) dye is the gold standard for detecting protein aggregation. It is used to detect aggregation in vitro and in various tissues, including the cerebrospinal fluid (CSF), whereby the disease-related protein recombinant is seeded with the patient's fluid. The major drawback of ThT is its lack of sensitivity to oligomeric forms of protein aggregates. Here, we overcome this limitation by transferring a ThT-oligomer mixture into solid state thin films and detecting fluorescence of ThT amplified in the process of stimulated emission. By monitoring the amplified spontaneous emission (ASE) we achieved a remarkable recognition sensitivity to prefibrillar oligomeric forms of insulin and lysozyme aggregates in vitro, to Aβ42 oligomers in the human protein recombinants seeded with CSF and to Aβ42 oligomers doped into brain tissue. Seeding with Alzheimer patient's CSF containing Aβ42 and Tau aggregates revealed that only Aβ42 oligomers allowed generating ASE. Thus, we demonstrated that, in contrast to the current state-of-the-art, ASE of ThT, a commonly used histological dye, can be used to detect and differentiate amyloid oligomers and evaluate the risk levels of neurodegenerative diseases to potential patients before the clinical symptoms occur.
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78
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Alperstein AM, Molnar KS, Dicke SS, Farrell KM, Makley LN, Zanni MT, Andley UP. Analysis of amyloid-like secondary structure in the Cryab-R120G knock-in mouse model of hereditary cataracts by two-dimensional infrared spectroscopy. PLoS One 2021; 16:e0257098. [PMID: 34520490 PMCID: PMC8439473 DOI: 10.1371/journal.pone.0257098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
αB-crystallin is a small heat shock protein that forms a heterooligomeric complex with αA-crystallin in the ocular lens. It is also widely distributed in tissues throughout the body and has been linked with neurodegenerative diseases such as Alzheimer's, where it is associated with amyloid fibrils. Crystallins can form amorphous aggregates in cataracts as well as more structured amyloid-like fibrils. The arginine 120 to glycine (R120G) mutation in αB-crystallin (Cryab-R120G) results in high molecular weight crystallin protein aggregates and loss of the chaperone activity of the protein in vitro, and it is associated with human hereditary cataracts and myopathy. Characterizing the amorphous (unstructured) versus the highly ordered (amyloid fibril) nature of crystallin aggregates is important in understanding their role in disease and important to developing pharmacological treatments for cataracts. We investigated protein secondary structure in wild-type (WT) and Cryab-R120G knock-in mutant mouse lenses using two-dimensional infrared (2DIR) spectroscopy, which has been used to detect amyloid-like fibrils in human lenses and measure UV radiation-induced changes in porcine lenses. Our goal was to compare the aggregated proteins in this mouse lens model to human lenses and evaluate the protein structural relevance of the Cryab-R120G knock-in mouse model to general age-related cataract disease. In the 2DIR spectra, amide I diagonal peak frequencies were red-shifted to smaller wavenumbers in mutant mouse lenses as compared to WT mouse lenses, consistent with an increase in ordered secondary structure. The cross peak frequency and intensity indicated the presence of amyloid in the mutant mouse lenses. While the diagonal and cross peak changes in location and intensity from the 2DIR spectra indicated significant structural differences between the wild type and mutant mouse lenses, these differences were smaller than those found in human lenses; thus, the Cryab-R120G knock-in mouse lenses contain less amyloid-like secondary structure than human lenses. The results of the 2DIR spectroscopy study confirm the presence of amyloid-like secondary structure in Cryab-R120G knock-in mice with cataracts and support the use of this model to study age-related cataract.
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Affiliation(s)
- Ariel M. Alperstein
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kathleen S. Molnar
- ViewPoint Therapeutics, San Francisco, California, United States of America
| | - Sidney S. Dicke
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kieran M. Farrell
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Leah N. Makley
- ViewPoint Therapeutics, San Francisco, California, United States of America
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Usha P. Andley
- Washington University School of Medicine, Department of Ophthalmology and Visual Sciences St. Louis, St. Louis, Missouri, United States of America
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79
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Najarzadeh Z, Nielsen J, Farzadfard A, Sereikaite V, Strømgaard K, Meyer RL, Otzen DE. Human Fibrinogen Inhibits Amyloid Assembly of Most Phenol-Soluble Modulins from Staphylococcus aureus. ACS OMEGA 2021; 6:21960-21970. [PMID: 34497891 PMCID: PMC8412925 DOI: 10.1021/acsomega.1c02333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Functional amyloids are highly organized protein/peptide structures that inter alia promote biofilm formation in different bacteria. One such example is provided by a family of 20-45 residue-long peptides called phenol-soluble modulins (PSMs) from Staphylococcus aureus. External components such as eukaryotic host proteins, which alter self-assembly of bacterial amyloids, can affect the biofilm matrix. Here, we studied the effect of the highly prevalent human plasma protein fibrinogen (Fg) on fibrillation of PSMs. Fg inhibits or suppresses fibrillation of most PSMs tested (PSMα1, PSMβ1, and PSMβ2) except for PSMα3, whose already rapid aggregation is accelerated even further by Fg but leads to amorphous β-rich aggregates rather than fibrils. Fg also induces PSMβ2 to form amorphous aggregates and diverts PSMα1 into off-pathway oligomers which consist of both Fg and PSMα1 and cannot seed fibrillation. Peptide arrays showed that Fg bound to the N-terminus of PSMα1, while it bound to the entire length of PSMα3 (except the C terminus) and to the C-termini of PSMβ1 and PSMβ2. The latter peptides are all positively charged, while Fg is negatively charged at physiological pH. The positive charges complement Fg's net negative charge of -7.6 at pH 7.4. Fg's ability to inhibit PSM fibrillation reveals a potential host-defense mechanism to prevent bacterial biofilm growth and infections in the human body.
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Affiliation(s)
- Zahra Najarzadeh
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Azad Farzadfard
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Vita Sereikaite
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Kristian Strømgaard
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary
Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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80
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Valentine ML, Al-Mualem ZA, Baiz CR. Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra. J Phys Chem A 2021; 125:6498-6504. [PMID: 34259508 DOI: 10.1021/acs.jpca.1c04558] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast two-dimensional infrared (2D IR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy are often performed in tandem, with FTIR typically used to interpret and provide hypotheses for 2D IR experiments. Comparisons between 2D IR and FTIR spectra can also be used to examine the structure and orientation in systems of coupled vibrational chromophores. The most common method for comparing 2D IR and FTIR lineshapes, the diagonal slice method, contains significant artifacts when applied to oscillators with low anharmonicities. Here, we introduce a new technique, the pump slice amplitude (PSA) method, for relating 2D IR lineshapes to FTIR lineshapes and compare PSAs against diagonal slices using theoretical and experimental spectra. We find that PSAs are significantly more similar to FTIR lineshapes than diagonal slices in systems with low anharmonicity.
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Affiliation(s)
- Mason L Valentine
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
| | - Ziareena A Al-Mualem
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin 78712, United States
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81
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Watson MD, Lee JC. Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells. Curr Opin Chem Biol 2021; 64:90-97. [PMID: 34186291 DOI: 10.1016/j.cbpa.2021.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 01/21/2023]
Abstract
Amyloid diseases are characterized by the aggregation of various proteins to form insoluble β-sheet-rich fibrils leading to cell death. Vibrational spectroscopies have emerged as attractive methods to study this process because of the rich structural information that can be extracted without large, perturbative probes. Importantly, specific vibrations such as the amide-I band directly report on secondary structure changes, which are key features of amyloid formation. Beyond intrinsic vibrations, the incorporation of unnatural vibrational probes can improve sensitivity for secondary structure determination (e.g. isotopic labeling), can provide residue-specific information of the surrounding polarity (e.g. unnatural amino acid), and are translatable into cellular studies. Here, we review the latest studies that have leveraged tools from chemical biology for the incorporation of novel vibrational probes into amyloidogenic proteins for both mechanistic and cellular studies.
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Affiliation(s)
- Matthew D Watson
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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82
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Christensen LFB, Alijanvand SH, Burdukiewicz M, Herbst FA, Kjeldal H, Dueholm MS, Otzen DE. Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild-type rats. Protein Sci 2021; 30:1854-1870. [PMID: 34075639 DOI: 10.1002/pro.4137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022]
Abstract
Cross seeding between amyloidogenic proteins in the gut is receiving increasing attention as a possible mechanism for initiation or acceleration of amyloid formation by aggregation-prone proteins such as αSN, which is central in the development of Parkinson's disease (PD). This is particularly pertinent in view of the growing number of functional (i.e., benign and useful) amyloid proteins discovered in bacteria. Here we identify two amyloidogenic proteins, Pr12 and Pr17, in fecal matter from PD transgenic rats and their wild type counterparts, based on their stability against dissolution by formic acid (FA). Both proteins show robust aggregation into ThT-positive aggregates that contain higher-order β-sheets and have a fibrillar morphology, indicative of amyloid proteins. In addition, Pr17 aggregates formed in vitro showed significant resistance against FA, suggesting an ability to form highly stable amyloid. Treatment with proteinase K revealed a protected core of approx. 9 kDa. Neither Pr12 nor Pr17, however, affected αSN aggregation in vitro. Thus, amyloidogenicity does not per se lead to an ability to cross-seed fibrillation of αSN. Our results support the use of proteomics and FA to identify amyloidogenic protein in complex mixtures and suggests that there may be numerous functional amyloid proteins in microbiomes.
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Affiliation(s)
- Line Friis Bakmann Christensen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Saeid Hadi Alijanvand
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Institute of Biochemistry and Biophysics (IBB), Department of Biophysics, University of Tehran, Tehran, Iran
| | - Michał Burdukiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Centre for Clinical Research, Medical University of Białystok, Białystok, Poland
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Henrik Kjeldal
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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83
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Hou YJ, Zheng X, Zhong HM, Chen F, Yan GY, Cai KC. Structural dynamics of amyloid β peptide binding to acetylcholine receptor and virtual screening for effective inhibitors. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2008150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Yan-jun Hou
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
| | - Xuan Zheng
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong-mei Zhong
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
| | - Feng Chen
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, China
| | - Gui-yang Yan
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, China
| | - Kai-cong Cai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China
- Fujian Provincial Key Laboratory of Featured Biochemical and Chemical Materials, Ningde Normal University, Ningde 352100, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
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84
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Grelich-Mucha M, Garcia AM, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Autofluorescence of Amyloids Determined by Enantiomeric Composition of Peptides. J Phys Chem B 2021; 125:5502-5510. [PMID: 34008978 PMCID: PMC8182742 DOI: 10.1021/acs.jpcb.1c00808] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Amyloid fibrils are
peptide or protein aggregates possessing a
cross-β-sheet structure. They possess intrinsic fluorescence
property, which is still not fully understood. Herein, we compare
structural and optical properties of fibrils formed from L- and D-enantiomers
of the (105–115) fragment of transthyretin (TTR) and from their
racemic mixture. Our results show that autofluorescence of fibrils
obtained from enantiomers differs from that of fibrils from the racemic
mixture. In order to elucidate the origin of observed differences,
we analyzed the structure and morphology of fibrils and showed how
variations in β-sheet organization influence optical properties
of fibrils. We clarified the contribution of aromatic rings and the
amyloid backbone to the final blue-green emission of fibrils. This
work demonstrates how enantiomeric composition of amino acids allows
us to modulate the self-assembly and final morphology of well-defined
fibrillar bionanostructures with optical properties controlled by
supramolecular organization.
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Affiliation(s)
- Manuela Grelich-Mucha
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ana M Garcia
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Vladimir Torbeev
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Bańska
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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85
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The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid. Proc Natl Acad Sci U S A 2021; 118:2014442118. [PMID: 33431675 DOI: 10.1073/pnas.2014442118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
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86
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Wong KM, Shao Q, Wang Y, Seroski DT, Liu R, Lint AH, Hudalla GA, Hall CK, Paravastu AK. CATCH Peptides Coassemble into Structurally Heterogeneous β-Sheet Nanofibers with Little Preference to β-Strand Alignment. J Phys Chem B 2021; 125:4004-4015. [PMID: 33876641 DOI: 10.1021/acs.jpcb.0c11645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Coassembling peptides offer an additional degree of freedom in the design of nanostructured biomaterials when compared to analogous self-assembling peptides. Yet, our understanding of how amino acid sequences encodes coassembled nanofiber structure is limited. Prior work on a charge-complementary pair, CATCH+ and CATCH- peptides, detected like-peptide nearest neighbors (CATCH+:CATCH+ and CATCH-:CATCH-) within coassembled β-sheet nanofibers; these self-associated peptide pairs marked a departure from an "ideal" coassembled structure. In this work, we employ solid-state NMR, isotope-edited FTIR, and coarse-grained molecular dynamics simulations to evaluate the alignment of β-strands within CATCH peptide nanofibers. Both experimental and computational results suggest that CATCH molecules coassemble into structurally heterogeneous nanofibers, which is consistent with our observations in another coassembling system, the King-Webb peptides. Within β-sheet nanofibers, β-strands were found to have nearest neighbors aligned in-register parallel, in-register antiparallel, and out-of-register. In comparison to the King-Webb peptides, CATCH nanofibers exhibit a greater degree of structural heterogeneity. By comparing the amino acid sequences of CATCH and King-Webb peptides, we can begin to unravel sequence-to-structure relationships, which may encode more precise coassembled β-sheet nanostructures.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Annabelle H Lint
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. Box 116131, Gainesville, Florida 32611, United States
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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87
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Szulc N, Burdukiewicz M, Gąsior-Głogowska M, Wojciechowski JW, Chilimoniuk J, Mackiewicz P, Šneideris T, Smirnovas V, Kotulska M. Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data. Sci Rep 2021; 11:8934. [PMID: 33903613 PMCID: PMC8076271 DOI: 10.1038/s41598-021-86530-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Several disorders are related to amyloid aggregation of proteins, for example Alzheimer's or Parkinson's diseases. Amyloid proteins form fibrils of aggregated beta structures. This is preceded by formation of oligomers-the most cytotoxic species. Determining amyloidogenicity is tedious and costly. The most reliable identification of amyloids is obtained with high resolution microscopies, such as electron microscopy or atomic force microscopy (AFM). More frequently, less expensive and faster methods are used, especially infrared (IR) spectroscopy or Thioflavin T staining. Different experimental methods are not always concurrent, especially when amyloid peptides do not readily form fibrils but oligomers. This may lead to peptide misclassification and mislabeling. Several bioinformatics methods have been proposed for in-silico identification of amyloids, many of them based on machine learning. The effectiveness of these methods heavily depends on accurate annotation of the reference training data obtained from in-vitro experiments. We study how robust are bioinformatics methods to weak supervision, encountering imperfect training data. AmyloGram and three other amyloid predictors were applied. The results proved that a certain degree of misannotation in the reference data can be eliminated by the bioinformatics tools, even if they belonged to their training set. The computational results are supported by new experiments with IR and AFM methods.
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Affiliation(s)
- Natalia Szulc
- grid.7005.20000 0000 9805 3178Department of Biomedical Engineering, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland ,grid.29172.3f0000 0001 2194 6418University of Lorraine, CNRS, 5400 Nancy, France
| | - Michał Burdukiewicz
- grid.48324.390000000122482838Medical University of Bialystok, 15-089 Białystok, Poland ,grid.413454.30000 0001 1958 0162Institute of Biochemistry and Biophysics, Polish Academy Sciences, 02-106 Warsaw, Poland
| | - Marlena Gąsior-Głogowska
- grid.7005.20000 0000 9805 3178Department of Biomedical Engineering, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Jakub W. Wojciechowski
- grid.7005.20000 0000 9805 3178Department of Biomedical Engineering, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Jarosław Chilimoniuk
- grid.8505.80000 0001 1010 5103Faculty of Biotechnology, University of Wroclaw, 50-137 Wroclaw, Poland
| | - Paweł Mackiewicz
- grid.8505.80000 0001 1010 5103Faculty of Biotechnology, University of Wroclaw, 50-137 Wroclaw, Poland
| | - Tomas Šneideris
- grid.6441.70000 0001 2243 2806Life Sciences Center, Institute of Biotechnology, Vilnius University, 01513 Vilnius, Lithuania
| | - Vytautas Smirnovas
- grid.6441.70000 0001 2243 2806Life Sciences Center, Institute of Biotechnology, Vilnius University, 01513 Vilnius, Lithuania
| | - Malgorzata Kotulska
- grid.7005.20000 0000 9805 3178Department of Biomedical Engineering, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
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88
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Pinkerton M, Ruetenik A, Bazylianska V, Nyvltova E, Barrientos A. Salvage NAD+ biosynthetic pathway enzymes moonlight as molecular chaperones to protect against proteotoxicity. Hum Mol Genet 2021; 30:672-686. [PMID: 33749726 DOI: 10.1093/hmg/ddab080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Human neurodegenerative proteinopathies are disorders associated with abnormal protein depositions in brain neurons. They include polyglutamine (polyQ) conditions such as Huntington's disease (HD) and α-synucleinopathies such as Parkinson's disease (PD). Overexpression of NMNAT/Nma1, an enzyme in the NAD+ biosynthetic salvage pathway, acts as an efficient suppressor of proteotoxicities in yeast, fly and mouse models. Screens in yeast models of HD and PD allowed us to identify three additional enzymes of the same pathway that achieve similar protection against proteotoxic stress: Npt1, Pnc1 and Qns1. The mechanism by which these proteins maintain proteostasis has not been identified. Here, we report that their ability to maintain proteostasis in yeast models of HD and PD is independent of their catalytic activity and does not require cellular protein quality control systems such as the proteasome or autophagy. Furthermore, we show that, under proteotoxic stress, the four proteins are recruited as molecular chaperones with holdase and foldase activities. The NAD+ salvage proteins act by preventing misfolding and, together with the Hsp90 chaperone, promoting the refolding of extended polyQ domains and α-synuclein (α-Syn). Our results illustrate the existence of an evolutionarily conserved strategy of repurposing or moonlighting housekeeping enzymes under stress conditions to maintain proteostasis. We conclude that the entire salvage NAD+ biosynthetic pathway links NAD+ metabolism and proteostasis and emerges as a target for therapeutics to combat age-associated neurodegenerative proteotoxicities.
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Affiliation(s)
- Meredith Pinkerton
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrea Ruetenik
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Viktoriia Bazylianska
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,MS in Biochemistry and Molecular Biology, Wayne State University, School of Medicine. Detroit, MI 48201, USA
| | - Eva Nyvltova
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine. Miami, FL 33136, USA
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89
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Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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90
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Price DA, Hill TD, Hutson KA, Rightnowar BW, Moran SD. Membrane-dependent amyloid aggregation of human BAX α9 (173-192). Protein Sci 2021; 30:1072-1080. [PMID: 33641228 DOI: 10.1002/pro.4053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/08/2021] [Accepted: 02/24/2021] [Indexed: 11/07/2022]
Abstract
Mitochondrial outer membrane permeabilization, which is a critical step in apoptosis, is initiated upon transmembrane insertion of the C-terminal α-helix (α9) of the proapoptotic Bcl-2 family protein BAX. The isolated α9 fragment (residues 173-192) is also competent to disrupt model membranes, and the structures of its membrane-associated oligomers are of interest in understanding the potential roles of this sequence in apoptosis. Here, we used ultrafast two-dimensional infrared (2D IR) spectroscopy, thioflavin T binding, and transmission electron microscopy to show that the synthetic BAX α9 peptide (α9p) forms amyloid aggregates in aqueous environments and on the surfaces of anionic small unilamellar vesicles. Its inherent amyloidogenicity was predicted by sequence analysis, and 2D IR spectra reveal that vesicles modulate the β-sheet structures of insoluble aggregates, motivating further examination of the formation or suppression of BAX amyloids in apoptosis.
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Affiliation(s)
- David A Price
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Tayler D Hill
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Kaitlyn A Hutson
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Blaze W Rightnowar
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, Carbondale, Illinois, USA
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91
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Lux J, Heyn TR, Kampen I, Schwarz K, Keppler JK, Steffen-Heins A. Amyloid aggregation of spin-labeled β-lactoglobulin. Part I: Influence of spin labeling on amyloid aggregation. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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92
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Szefczyk M, Szulc N, Gąsior-Głogowska M, Modrak-Wójcik A, Bzowska A, Majstrzyk W, Taube M, Kozak M, Gotszalk T, Rudzińska-Szostak E, Berlicki Ł. Hierarchical approach for the rational construction of helix-containing nanofibrils using α,β-peptides. NANOSCALE 2021; 13:4000-4015. [PMID: 33471005 DOI: 10.1039/d0nr04313c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The rational design of novel self-assembled nanomaterials based on peptides remains a great challenge in modern chemistry. A hierarchical approach for the construction of nanofibrils based on α,β-peptide foldamers is proposed. The incorporation of a helix-promoting trans-(1S,2S)-2-aminocyclopentanecarboxylic acid residue in the outer positions of the model coiled-coil peptide led to its increased conformational stability, which was established consistently by the results of CD, NMR and FT-IR spectroscopy. The designed oligomerization state in the solution of the studied peptides was confirmed using analytical ultracentrifugation. Moreover, the cyclopentane side chain allowed additional interactions between coiled-coil-like structures to direct the self-assembly process towards the formation of well-defined nanofibrils, as observed using AFM and TEM techniques.
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Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anna Modrak-Wójcik
- Division of Biophysics, Faculty of Physics, Institute of Experimental Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Faculty of Physics, Institute of Experimental Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Wojciech Majstrzyk
- Faculty of Microsystem Electronics and Photonics, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392 Kraków, Poland
| | - Teodor Gotszalk
- Faculty of Microsystem Electronics and Photonics, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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93
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Cai K, Zheng X, Hou Y, Chen F, Yan G, Zhuang D. Deciphering the structural preference encoded in amide-I vibrations of lysine dipeptide in gas phase and in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119066. [PMID: 33091736 DOI: 10.1016/j.saa.2020.119066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Protein's biological function is critically associated with its structural feature, which is encoded in its amino acid sequence. For evaluation of conformational fluctuation and folding mechanism, DFT calculations were performed on the model compound - lysine dipeptide (LYSD) in gas phase to demonstrate the correlation between amide-I vibrations and secondary structure. Molecular dynamics simulations were carried out for the structural dynamics of LYSD in aqueous solution. The results show that LYSD tends form C7eq, C5, β, PPII and α conformations in the gas phase and primarily presented PPII and α conformations in aqueous solution. The obtained amide-I vibrational frequencies of LYSD conformers were assigned, thus build the correlations between amide-I probes and secondary structure of LYSD. These results provide theoretical insights into the structural feature of LYSD through amide-I vibrations, and would shed light on site specific structural prediction of polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Fujian Province University, Ningde 352100, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China.
| | - Xuan Zheng
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
| | - Yanjun Hou
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
| | - Feng Chen
- Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Fujian Province University, Ningde 352100, China
| | - Guiyang Yan
- Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Fujian Province University, Ningde 352100, China
| | - Danling Zhuang
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
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94
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Vosough F, Barth A. Characterization of Homogeneous and Heterogeneous Amyloid-β42 Oligomer Preparations with Biochemical Methods and Infrared Spectroscopy Reveals a Correlation between Infrared Spectrum and Oligomer Size. ACS Chem Neurosci 2021; 12:473-488. [PMID: 33455165 PMCID: PMC8023574 DOI: 10.1021/acschemneuro.0c00642] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
![]()
Soluble oligomers of the amyloid-β(1-42)
(Aβ42) peptide,
widely considered to be among the relevant neurotoxic species involved
in Alzheimer’s disease, were characterized with a combination
of biochemical and biophysical methods. Homogeneous and stable Aβ42
oligomers were prepared by treating monomeric solutions of the peptide
with detergents. The prepared oligomeric solutions were analyzed with
blue native and sodium dodecyl sulfate polyacrylamide gel electrophoresis,
as well as with infrared (IR) spectroscopy. The IR spectra indicated
a well-defined β-sheet structure of the prepared oligomers.
We also found a relationship between the size/molecular weight of
the Aβ42 oligomers and their IR spectra: The position of the
main amide I′ band of the peptide backbone correlated with
oligomer size, with larger oligomers being associated with lower wavenumbers.
This relationship explained the time-dependent band shift observed
in time-resolved IR studies of Aβ42 aggregation in the absence
of detergents, during which the oligomer size increased. In addition,
the bandwidth of the main IR band in the amide I′ region was
found to become narrower with time in our time-resolved aggregation
experiments, indicating a more homogeneous absorption of the β-sheets
of the oligomers after several hours of aggregation. This is predominantly
due to the consumption of smaller oligomers in the aggregation process.
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Affiliation(s)
- Faraz Vosough
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
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95
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Infrared nanospectroscopy reveals the molecular interaction fingerprint of an aggregation inhibitor with single Aβ42 oligomers. Nat Commun 2021; 12:688. [PMID: 33514697 PMCID: PMC7846799 DOI: 10.1038/s41467-020-20782-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Significant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimer’s and Parkinson’s diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the structure and interaction between single Aβ42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, which is able to prevent Aβ42 aggregation in vitro and reverses its neurotoxicity in cell and animal models of Alzheimer’s disease. Our results demonstrate that the carboxyl group of this compound interacts with Aβ42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as a powerful tool in structure-based drug discovery for protein misfolding diseases. Our understanding of the molecular mechanisms underlying pathological protein aggregation remains incomplete. Here, single molecule infrared nanospectroscopy (AFM-IR) offers insight into the structure of Aβ42 oligomeric and fibrillar species and their interaction with an aggregation inhibitor, paving the way for single molecule drug discovery studies.
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96
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Basu A, Vaskevich A, Chuntonov L. Glutathione Self-Assembles into a Shell of Hydrogen-Bonded Intermolecular Aggregates on "Naked" Silver Nanoparticles. J Phys Chem B 2021; 125:895-906. [PMID: 33440116 DOI: 10.1021/acs.jpcb.0c10089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A detailed understanding of the molecular structure in nanoparticle ligand capping layers is crucial for their efficient incorporation into modern scientific and technological applications. Peptide ligands render the nanoparticles as biocompatible materials. Glutathione, a γ-ECG tripeptide, self-assembles into aggregates on the surface of ligand-free silver nanoparticles through intermolecular hydrogen bonding and forms a few nanometer-thick shells. Two-dimensional nonlinear infrared (2DIR) spectroscopy suggests that aggregates adopt a conformation resembling the β-sheet secondary structure. The shell thickness was evaluated with localized surface plasmon resonance spectroscopy and X-ray photoelectron spectroscopy. The amount of glutathione on the surface was obtained with spectrophotometry of a thiol-reactive probe. Our results suggest that the shell consists of ∼15 stacked molecular layers. These values correspond to the inter-sheet distances, which are significantly shorter than those in amyloid fibrils with relatively bulky side chains, but are comparable to glycine-rich silk fibrils, where the side chains are compact. The tight packing of the glutathione layers can be facilitated by hydrogen-bonded carboxylic acid dimers of glycine and the intermolecular salt bridges between the zwitterionic γ-glutamyl groups. The structure of the glutathione aggregates was studied by 2DIR spectroscopy of the amide-I vibrational modes using 13C isotope labeling of the cysteine carbonyl. Isotope dilution experiments revealed the coupling of modes forming vibrational excitons along the cysteine chain. The coupling along the γ-glutamyl exciton chain was estimated from these values. The obtained coupling strengths are slightly lower than those of native β-sheets, yet they appear large enough to point onto an ordered conformation of the peptides within the aggregate. Analysis of the excitons' anharmonicities and the strength of the transition dipole moments generally is in agreement with these observations.
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Affiliation(s)
- Arghyadeep Basu
- Schulich Faculty of Chemistry and Solid State Institute, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Alexander Vaskevich
- Department of Materials and Interfaces, and Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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97
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Armen JM, Schueller NR, Velankar KY, Abraham N, Palchesko RN, Fan Y, Meng WS, Gawalt ES. Chemically-Induced Cross-Linking of Peptidic Fibrils for Scaffolding Polymeric Particles and Macrophages. Macromol Biosci 2021; 21:e2000350. [PMID: 33502824 DOI: 10.1002/mabi.202000350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/04/2021] [Indexed: 11/11/2022]
Abstract
EAK16-II (EAK) is a self-assembling peptide (SAP) that forms β-sheets and β-fibrils through ionic-complementary interactions at physiological ionic strengths. The soft materials can be injected in vivo, creating depots of drugs and cells for rendering pharmacological and biological actions. The scope of the applications of EAK is sought to extend to tissues through which the flow of extracellular fluid tends to be limited. In such anatomical locales the rate and extent of the fibrilization are limited insofar as drug delivery and cellular scaffolding would be impeded. A method is generated utilizing a carbodiimide cross-linker by which EAK fibrils are pre-assembled yet remain injectable soft materials. It is hypothesized that the resulting de novo covalent linkages enhance the stacking of the β-sheet bilayers, thereby increasing the lengths of the fibrils and the extent of their cross-linking, as evidenced in Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectroscopy, scanning electron microscopy, and atomic force microscopy analyses. The cross-linked EAK (clEAK) retains polymeric microspheres with an average diameter of 1 µm. Macrophages admixed with clEAK remain viable and do not produce the inflammatory mediator interleukin-1β. These results indicate that clEAK should be investigated further as a platform for delivering particles and cells in vivo.
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Affiliation(s)
- Jennifer M Armen
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, 15282, USA
| | - Nathan R Schueller
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, 15282, USA.,University of Pittsburgh, Pittsburgh, PA, 15212, USA
| | - Ketki Y Velankar
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, 15282, USA.,University of Pittsburgh, Pittsburgh, PA, 15212, USA
| | - Nevil Abraham
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, 15282, USA.,University of Pittsburgh, Pittsburgh, PA, 15212, USA
| | - Rachelle N Palchesko
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Yong Fan
- Cellular Therapeutics Institute, Allegheny-Singer Research Institute, Allegheny Health Network, Pittsburgh, PA, 15202, USA.,The Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Wilson S Meng
- The McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15212, USA.,Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, 15282, USA.,University of Pittsburgh, Pittsburgh, PA, 15212, USA
| | - Ellen S Gawalt
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, 15282, USA.,The McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15212, USA
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98
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Linear and Non-Linear Middle Infrared Spectra of Penicillin G in the CO Stretching Mode Region. Symmetry (Basel) 2021. [DOI: 10.3390/sym13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this work we report the linear and non-linear IR spectral response characterization of the CO bonds of PenicillinG sodium salt in D2O and in DMSO−d6 solutions. In order to better characterize the spectral IR features in the CO stretching region, broadband middle infrared pump-probe spectra are recorded. The role of hydrogen bonds in determining the inhomogeneous broadening and in tuning anharmonicity of the different types of oscillators is exploited. Narrow band pump experiments, at the three central frequencies of β−lactam, amide and carboxylate CO stretching modes, identify the couplings between the different types of CO oscillators opening the possibility to gather structural dynamic information. Our results show that the strongest coupling is between the β−lactam and the carboxylate CO vibrational modes.
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99
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Zhang L, Lin S, Li Y, Li B, Yang Y. Ala–Ala dipeptides with a semi-perfluoroalkyl chain: chirality driven molecular packing difference and self-assembly driven chiral transfer. NEW J CHEM 2021. [DOI: 10.1039/d0nj05676f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The chirality of amino acids triggered the chiral molecular stacking of dipeptides and, eventually, transferred to the semi-perfluoroalkyl chain.
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Affiliation(s)
- Lianglin Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Shuwei Lin
- Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province & Key Lab of Modern Optical Technologies of Education Ministry of China
- School of Optoelectronics Science and Engineering
- Soochow University
- Suzhou 215123
- China
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
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100
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Lin S, Tong Q, Jiang P, Li B, Li Y, Yang Y. Effect of C 12H 25O– substituent position on the self-assembly behaviour of C 6H 5COO–Ala–Ala dipeptide. NEW J CHEM 2021. [DOI: 10.1039/d1nj01148k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intramolecular hydrogen bonding and steric hindrance of side chain lead the different molecular packing of dipeptides and the morphological transformation of self-assemblies’ nanostructures.
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Affiliation(s)
- Shuwei Lin
- Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province & Key Lab of Modern Optical Technologies of Education Ministry of China
- School of Optoelectronics Science and Engineering
- Soochow University
- Suzhou 215123
- China
| | - Qiyun Tong
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Pan Jiang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
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