101
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Vergara R, Berrocal T, Juárez Mejía EI, Romero-Romero S, Velázquez-López I, Pulido NO, López Sanchez HA, Silva DA, Costas M, Rodríguez-Romero A, Rodríguez-Sotres R, Sosa-Peinado A, Fernández-Velasco DA. Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding and function. FEBS J 2023; 290:4496-4512. [PMID: 37178351 DOI: 10.1111/febs.16819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
Abstract
Substrate-binding proteins (SBPs) are used by organisms from the three domains of life for transport and signalling. SBPs are composed of two domains that collectively trap ligands with high affinity and selectivity. To explore the role of the domains and the integrity of the hinge region between them in the function and conformation of SBPs, here, we describe the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. LAO is a class II SBP formed by a continuous and a discontinuous domain. Contrary to the expected behaviour based on their connectivity, the discontinuous domain shows a stable native-like structure that binds l-arginine with moderate affinity, whereas the continuous domain is barely stable and shows no detectable ligand binding. Regarding folding kinetics, studies of the entire protein revealed the presence of at least two intermediates. While the unfolding and refolding of the continuous domain exhibited only a single intermediate and simpler and faster kinetics than LAO, the folding mechanism of the discontinuous domain was complex and involved multiple intermediates. These findings suggest that in the complete protein the continuous domain nucleates folding and that its presence funnels the folding of the discontinuous domain avoiding nonproductive interactions. The strong dependence of the function, stability and folding pathway of the lobes on their covalent association is most likely the result of the coevolution of both domains as a single unit.
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Affiliation(s)
- Renan Vergara
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Tania Berrocal
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Eva Isela Juárez Mejía
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Department of Biochemistry, University of Bayreuth, Germany
| | - Isabel Velázquez-López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Nancy O Pulido
- Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Haven A López Sanchez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alejandro Sosa-Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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102
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Howard MK, Miller KR, Sohn BS, Ryan JJ, Xu A, Jackrel ME. Probing the drivers of Staphylococcus aureus biofilm protein amyloidogenesis and disrupting biofilms with engineered protein disaggregases. mBio 2023; 14:e0058723. [PMID: 37195208 PMCID: PMC10470818 DOI: 10.1128/mbio.00587-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/05/2023] [Indexed: 05/18/2023] Open
Abstract
Phenol-soluble modulins (PSMs) are the primary proteinaceous component of Staphylococcus aureus biofilms. Residence in the protective environment of biofilms allows bacteria to rapidly evolve and acquire antimicrobial resistance, which can lead to persistent infections such as those caused by methicillin-resistant S. aureus (MRSA). In their soluble form, PSMs hinder the immune response of the host and can increase the virulence potential of MRSA. PSMs also self-assemble into insoluble functional amyloids that contribute to the structural scaffold of biofilms. The specific roles of PSM peptides in biofilms remain poorly understood. Here, we report the development of a genetically tractable yeast model system for studying the properties of PSMα peptides. Expression of PSMα peptides in yeast drives the formation of toxic insoluble aggregates that adopt vesicle-like structures. Using this system, we probed the molecular drivers of PSMα aggregation to delineate key similarities and differences among the PSMs and identified a crucial residue that drives PSM features. Biofilms are a major public health threat; thus, biofilm disruption is a key goal. To solubilize aggregates comprised of a diverse range of amyloid and amyloid-like species, we have developed engineered variants of Hsp104, a hexameric AAA+ protein disaggregase from yeast. Here, we demonstrate that potentiated Hsp104 variants counter the toxicity and aggregation of PSMα peptides. Further, we demonstrate that a potentiated Hsp104 variant can drive the disassembly of preformed S. aureus biofilms. We suggest that this new yeast model can be a powerful platform for screening for agents that disrupt PSM aggregation and that Hsp104 disaggregases could be a promising tool for the safe enzymatic disruption of biofilms. IMPORTANCE Biofilms are complex mixtures secreted by bacteria that form a material in which the bacteria can become embedded. This process transforms the properties of the bacteria, and they become more resistant to removal, which can give rise to multidrug-resistant strains, such as methicillin-resistant Staphylococcus aureus (MRSA). Here, we study phenol-soluble modulins (PSMs), which are amyloidogenic proteins secreted by S. aureus, that become incorporated into biofilms. Biofilms are challenging to study, so we have developed a new genetically tractable yeast model to study the PSMs. We used our system to learn about several key features of the PSMs. We also demonstrate that variants of an amyloid disaggregase, Hsp104, can disrupt the PSMs and, more importantly, dissolve preformed S. aureus biofilms. We propose that our system can be a powerful screening tool and that Hsp104 disaggregases may be a new avenue to explore for biofilm disruption agents.
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Affiliation(s)
- Matthew K. Howard
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Karlie R. Miller
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Brian S. Sohn
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Jeremy J. Ryan
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
| | - Andy Xu
- Department of Chemistry, Washington University, St. Louis, Missouri, USA
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103
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Khan JM, Malik A, Sharma P, Fatima S. Anionic surfactant causes dual conformational changes in insulin. Int J Biol Macromol 2023; 247:125790. [PMID: 37451378 DOI: 10.1016/j.ijbiomac.2023.125790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/30/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Amyloid fibrillation is a process by which proteins aggregate and form insoluble fibrils that are implicated in several neurodegenerative diseases. In n this study, we aimed to investigate the impact of the negatively charged detergent sodium dodecyl sulfate (SDS) on insulin amyloid fibrillation at pH 7.4 and 2.0, as SDS has been linked to the acceleration of amyloid fibrillation in vitro, but the underlying molecular mechanism is not fully understood. Our findings show that insulin forms amyloid-like aggregates in the presence of SDS at concentrations ranging from 0.05 to 1.8 mM at pH 2.0, while no aggregates were observed at SDS concentrations greater than 1.8 mM, and insulin remained soluble. However, at pH 7.4, insulin remained soluble regardless of the concentration of SDS. Interestingly, the aggregated insulin had a cross-β sheet secondary structure, and when incubated with higher SDS concentrations, it gained more alpha-helix. The electrostatics and hydrophobic interaction of SDS and insulin may contribute to amyloid induction. Moreover, the SDS-induced aggregation was not affected by the presence of salts. Furthermore, as the concentration of SDS increased, the preformed insulin amyloid induced by SDS began to disintegrate. Overall, our study sheds light on the mechanism of surfactant-induced amyloid fibrillation in insulin protein.
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Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Prerna Sharma
- Geisinger Commonwealth School of Medicine, Scranton, PA 18509, USA
| | - Sadaf Fatima
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
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104
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Ali R, Wu Y. Enantioselective transport of chiral spheres using focused femtosecond laser pulses. OPTICS EXPRESS 2023; 31:29716-29729. [PMID: 37710766 DOI: 10.1364/oe.497468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
Optical tweezers are commonly used for manipulating chiral particles by tailoring the properties of the electromagnetic field or of the particles themselves. Non-linearity provides additional degree of freedom to control the manipulation by changing the trapping conditions. In this work, we leverage the nonlinear optical properties of a medium by illuminating it with a circularly polarized laser pulse, enabling single particle enantioselection for the chiral spheres immersed in it. By adjusting the power of the laser pulses, we demonstrate stable trapping of chiral spheres with one handedness near the focal region, while spheres with the opposite handedness are repelled. This enables the chiral resolution of racemic mixtures. Additionally, we perturbed the stable equilibrium position of the trap by driving the sample stage, leading to the emergence of a new stable equilibrium position achieved under the action of the Stokes force. Here we show that the chirality of each individually trapped particle can also be characterized by the rotation of the equilibrium position. Since the power of the laser pulses can be experimentally controlled, this scheme is practical to perform enantioselection, chiral characterization, and chiral resolution of a single chiral sphere with arbitrarily small chirality parameters.
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105
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Singh NK, Bhardwaj P, Radhakrishna M. Hydrophobicity─A Single Parameter for the Accurate Prediction of Disordered Regions in Proteins. J Chem Inf Model 2023; 63:5375-5383. [PMID: 37581491 DOI: 10.1021/acs.jcim.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The prediction of disordered regions in proteins is crucial for understanding their functions, dynamics, and interactions. Intrinsically disordered proteins (IDPs) play a key role in many biological processes like cell signaling, recognition, and regulation, but experimentally determining these regions can be challenging due to their high mobility. To address this challenge, we present an algorithm called HydroDisPred (HDP). HDP uses a single parameter, the fraction of hydrophobicity (λ) in each segment of the protein, to accurately predict disordered regions. The algorithm was validated using experimental data from the DisProt database and was found to be on par and, in some cases, more effective than the existing algorithms. HDP is a simple and effective method for identifying disordered regions in proteins, and its prediction is not affected by the availability of training data, unlike other ML approaches. The application is housed in the web server and can be accessed through the URL https://proseqanalyser.iitgn.ac.in/hydrodispred/.
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Affiliation(s)
- Nitin Kumar Singh
- Discipline of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Pratyasha Bhardwaj
- Discipline of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Mithun Radhakrishna
- Discipline of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
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106
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Rajput S, Pollak R, Huber K, Ebbinghaus S, Nayar D. Ethylene glycol energetically disfavours oligomerization of pseudoisocyanine dyestuffs at crowded concentrations. SOFT MATTER 2023; 19:6399-6413. [PMID: 37580997 DOI: 10.1039/d3sm00564j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The intriguing role of the intracellular crowded environment in regulating protein aggregation remains elusive. The convolution of several factors such as the protein sequence-dependence, crowder's shape and size and diverse intermolecular interactions makes it complex to identify systematic trends. One of the ways to simplify the problem is to study a synthetic model for self-assembling proteins. In this study, we examine the aggregation behaviour of the cationic pseudoisocyanine chloride (PIC) dyestuff which is known to self-assemble and form fibril-like J-aggregates in aqueous solutions, similar to those formed by amyloid-forming proteins. Prior experimental studies have shown that polyethylene glycol impedes and Ficoll-400 promotes the self-assembly of PIC dyes. To achieve molecular insights, we examine the effect of crowding by ethylene glycol on the solvation thermodynamics of oligomerization of dyes into H-type and J-type oligomers using extensive molecular dynamics simulations. The binding free energy calculations show that the formation of J-oligomers is more favourable than that of H-oligomers in water. The stability of H- and J- tetramers and pentamers decreases in crowded solutions. The formation of oligomers is supported by the favourable change in dye-solvent interaction energy in both pure water and aqueous ethylene glycol solution although it is opposed by the reduced dye-solvent entropy. Ethylene glycol, as a molecular crowder, disfavours the H- as well as J-oligomerization via preferential binding to the dye oligomers. An unfavourable change in dye-crowder and dye-dye interaction energy on dye association makes the H-oligomer formation less favourable in crowded solution than in pure water solution. In the case of J-oligomers, however, the unfavourable change in dye-crowder interaction energy primarily contributes to making total dye-solvent energy unfavourable. The results are supported by isothermal titration calorimetry measurements where the binding of ethylene glycol to PIC molecules is found to be endothermic. The results provide an emerging view that a crowded environment can disfavour self-assembly of PIC dyes by interactions with the oligomeric states. The findings have implications in understanding the role of a crowded environment in shaping the free energy landscapes of proteins.
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Affiliation(s)
- Satyendra Rajput
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Roland Pollak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38196 Braunschweig, Germany
| | - Klaus Huber
- Department of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38196 Braunschweig, Germany
| | - Divya Nayar
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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107
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Kaygisiz K, Rauch-Wirth L, Dutta A, Yu X, Nagata Y, Bereau T, Münch J, Synatschke CV, Weil T. Data-mining unveils structure-property-activity correlation of viral infectivity enhancing self-assembling peptides. Nat Commun 2023; 14:5121. [PMID: 37612273 PMCID: PMC10447463 DOI: 10.1038/s41467-023-40663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure-function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure-property-activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining-even for small datasets-enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Lena Rauch-Wirth
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Arghya Dutta
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Xiaoqing Yu
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Yuki Nagata
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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108
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Vadukul D, Papp M, Thrush RJ, Wang J, Jin Y, Arosio P, Aprile FA. α-Synuclein Aggregation Is Triggered by Oligomeric Amyloid-β 42 via Heterogeneous Primary Nucleation. J Am Chem Soc 2023; 145:18276-18285. [PMID: 37556728 PMCID: PMC10450681 DOI: 10.1021/jacs.3c03212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 08/11/2023]
Abstract
An increasing number of cases where amyloids of different proteins are found in the same patient are being reported. This observation complicates diagnosis and clinical intervention. Amyloids of the amyloid-β peptide or the protein α-synuclein are traditionally considered hallmarks of Alzheimer's and Parkinson's diseases, respectively. However, the co-occurrence of amyloids of these proteins has also been reported in patients diagnosed with either disease. Here, we show that soluble species containing amyloid-β can induce the aggregation of α-synuclein. Fibrils formed under these conditions are solely composed of α-synuclein to which amyloid-β can be found associated but not as part of the core of the fibrils. Importantly, by global kinetic analysis, we found that the aggregation of α-synuclein under these conditions occurs via heterogeneous primary nucleation, triggered by soluble aggregates containing amyloid-β.
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Affiliation(s)
- Devkee
M. Vadukul
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Marcell Papp
- Department
of Chemistry and Applied Biosciences, Institute
for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Rebecca J. Thrush
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Jielei Wang
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Yiyun Jin
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Paolo Arosio
- Department
of Chemistry and Applied Biosciences, Institute
for Chemical and Bioengineering, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Francesco A. Aprile
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
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109
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Chen S, Puri A, Bell B, Fritsche J, Palacios H, Balch M, Sprunger M, Howard M, Patterson J, Patti G, Davis A, Jackrel M. HtrA1 prevents and reverses α-synuclein aggregation, rendering it non-toxic and seeding incompetent. RESEARCH SQUARE 2023:rs.3.rs-2570571. [PMID: 37674720 PMCID: PMC10479434 DOI: 10.21203/rs.3.rs-2570571/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Parkinson disease (PD) is closely linked to the misfolding and accumulation of α-synuclein (α-syn) into Lewy bodies. HtrA1 is a PDZ serine protease that degrades fibrillar tau, which is associated with Alzheimer disease (AD). Further, inactivating mutations to mitochondrial HtrA2 have been implicated in PD. Here, we establish that HtrA1 inhibits the aggregation of α-syn as well as FUS and TDP-43, which are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We demonstrate that the protease domain of HtrA1 is necessary and sufficient for inhibition of aggregation, yet this activity is independent of HtrA1 proteolytic activity. Further, we find that HtrA1 also disaggregates preformed α-syn fibrils, which may promote their clearance. Treatment of α-syn fibrils with HtrA1 renders α-syn incapable of seeding the aggregation of endogenous α-syn in mammalian biosensor cells. We find that HtrA1 remodels α-syn by specifically targeting the NAC domain, which is the key domain that catalyzes α-syn oligomerization and fibrillization. Finally, in a primary neuron model of α-syn aggregation, we show that HtrA1 and its proteolytically inactive form both detoxify α-syn and prevent the formation of hyperphosphorylated α-syn accumulations. Our findings suggest that HtrA1 prevents aggregation and promotes disaggregation of multiple disease-associated proteins, and may be a therapeutic target for treating a range of neurodegenerative disorders.
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110
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Ogi S, Takamatsu A, Matsumoto K, Hasegawa S, Yamaguchi S. Biomimetic Design of a Robustly Stabilized Folded State Enabling Seed-Initiated Supramolecular Polymerization under Microfluidic Mixing. Angew Chem Int Ed Engl 2023; 62:e202306428. [PMID: 37332181 DOI: 10.1002/anie.202306428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/20/2023]
Abstract
We have investigated the folding and assembly behavior of a cystine-based dimeric diamide bearing pyrene units and solubilizing alkyl chains. In low-polarity solvents, it forms a 14-membered ring through double intramolecular hydrogen bonds between two diamide units. The spectroscopic studies revealed that the folded state is thermodynamically unstable and eventually transforms into more energetically stable helical supramolecular polymers that show an enhanced chiral excitonic coupling between the transition dipoles of the pyrene units. Importantly, compared to an alanine-based monomeric diamide, the dimeric diamide exhibits a superior kinetic stability in the metastable folded state, as well as an increased thermodynamic stability in the aggregated state. Accordingly, the initiation of supramolecular polymerization can be regulated using a seeding method even under microfluidic mixing conditions. Furthermore, taking advantage of a self-sorting behavior observed in a mixture of l-cysteine- and d-cysteine-based dimeric diamides, a two-step supramolecular polymerization was achieved by stepwise addition of the corresponding seeds.
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Affiliation(s)
- Soichiro Ogi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
- Integrated Research Consortium on Chemical Science (IRCCS), Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
| | - Aiko Takamatsu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
| | - Kentaro Matsumoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
| | - Shintaro Hasegawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
| | - Shigehiro Yamaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
- Integrated Research Consortium on Chemical Science (IRCCS), Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya, 464-8602, Japan
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111
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Li Z, Zheng Y, Yan J, Yan Y, Peng C, Wang Z, Liu H, Liu Y, Zhou Y, Ding M. Self-Assembly of Poly(Amino Acid)s Mediated by Secondary Conformations. Chembiochem 2023; 24:e202300132. [PMID: 37340829 DOI: 10.1002/cbic.202300132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
Self-assembly of block copolymers has recently drawn great attention due to its remarkable performance and wide variety of applications in biomedicine, biomaterials, microelectronics, photoelectric materials, catalysts, etc. Poly(amino acid)s (PAAs), formed by introducing synthetic amino acids into copolymer backbones, are able to fold into different secondary conformations when compared with traditional amphiphilic copolymers. Apart from changing the chemical composition and degree of polymerization of copolymers, the self-assembly behaviors of PAAs could be controlled by their secondary conformations, which are more flexible and adjustable for fine structure tailoring. In this article, we summarize the latest findings on the variables that influence secondary conformations, in particular the regulation of order-to-order conformational changes and the approaches used to manage the self-assembly behaviors of PAAs. These strategies include controlling pH, redox reactions, coordination, light, temperature, and so on. Hopefully, we can provide valuable perspectives that will be useful for the future development and use of synthetic PAAs.
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Affiliation(s)
- Zifen Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yi Zheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Jingyue Yan
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yue Yan
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Chuan Peng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Zuojie Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Hang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yeqiang Zhou
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Mingming Ding
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
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112
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Ghorbani M, Brooks BR, Klauda JB. Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics. J Phys Chem B 2023; 127:6887-6895. [PMID: 37527428 DOI: 10.1021/acs.jpcb.3c02473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Conformational dynamics in proteins can give rise to aggregation prone states during folding, and these kinetically stable states could form oligomers and aggregates. In this study, we investigate the intermediate states and near-folded states of β2-microglobulin and their physico-chemical properties using molecular dynamics and Markov state modeling. Analysis of hundreds of microseconds simulation show the importance of the edge strands in the misfolded states that give rise to a high exposure of hydrophobic residues in the core of the protein that could initiate oligomerization and aggregate formation. Our study sheds light on the first step of aggregation of β2m monomers and gave a better picture of the landscape of protein misfolding and aggregation.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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113
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Ndjomatchoua FT, Gninzanlong CL, Djomo TLMM, Kepnang Pebeu MF, Tchawoua C. Diversity-enhanced stability. Phys Rev E 2023; 108:024206. [PMID: 37723729 DOI: 10.1103/physreve.108.024206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/11/2023] [Indexed: 09/20/2023]
Abstract
We give compelling evidence that diversity, represented by a quenched disorder, can produce a resonant collective transition between two unsteady states in a network of coupled oscillators. The stability of a metastable state is optimized and the mean first-passage time maximized at an intermediate value of diversity. This finding shows that a system can benefit from inherent heterogeneity by allowing it to maximize the transition time from one state to another at the appropriate degree of heterogeneity.
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Affiliation(s)
- Frank Thomas Ndjomatchoua
- Department of Physics, Faculty of Science, University of Yaoundé 1, P.O. Box 812, Ngoa Ekelle, Yaoundé, Cameroon
| | - Carlos Lawrence Gninzanlong
- Department of Physics, Faculty of Science, University of Yaoundé 1, P.O. Box 812, Ngoa Ekelle, Yaoundé, Cameroon
| | - Thierry Landry Michel Mbong Djomo
- Department of Civil Engineering, National Higher Polytechnic Institute, University of Bamenda, P.O. Box 39, Bambili, Bamenda, Cameroon
| | - Maxime Fabrice Kepnang Pebeu
- Department of Physics, Faculty of Science, University of Yaoundé 1, P.O. Box 812, Ngoa Ekelle, Yaoundé, Cameroon
| | - Clément Tchawoua
- Department of Physics, Faculty of Science, University of Yaoundé 1, P.O. Box 812, Ngoa Ekelle, Yaoundé, Cameroon
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114
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Okada S, Matsumoto Y, Takahashi R, Arai K, Kanemura S, Okumura M, Muraoka T. Semi-enzymatic acceleration of oxidative protein folding by N-methylated heteroaromatic thiols. Chem Sci 2023; 14:7630-7636. [PMID: 37476727 PMCID: PMC10355094 DOI: 10.1039/d3sc01540h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
We report the first example of a synthetic thiol-based compound that promotes oxidative protein folding upon 1-equivalent loading to the disulfide bonds in the client protein to afford the native form in over 70% yield. N-Methylation is a central post-translational processing of proteins in vivo for regulating functions including chaperone activities. Despite the universally observed biochemical reactions in nature, N-methylation has hardly been utilized in the design, functionalization, and switching of synthetic bioregulatory agents, particularly folding promotors. As a biomimetic approach, we developed pyridinylmethanethiols to investigate the effects of N-methylation on the promotion of oxidative protein folding. For a comprehensive study on the geometrical effects, constitutional isomers of pyridinylmethanethiols with ortho-, meta-, and para-substitutions have been synthesized. Among the constitutional isomers, para-substituted pyridinylmethanethiol showed the fastest disulfide-bond formation of the client proteins to afford the native forms most efficiently. N-Methylation drastically increased the acidity and enhanced the oxidizability of the thiol groups in the pyridinylmethanethiols to enhance the folding promotion efficiencies. Among the isomers, para-substituted N-methylated pyridinylmethanethiol accelerated the oxidative protein folding reactions with the highest efficiency, allowing for protein folding promotion by 1-equivalent loading as a semi-enzymatic activity. This study will offer a novel bioinspired molecular design of synthetic biofunctional agents that are semi-enzymatically effective for the promotion of oxidative protein folding including biopharmaceuticals such as insulin in vitro by minimum loading.
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Affiliation(s)
- Shunsuke Okada
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Yosuke Matsumoto
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Rikana Takahashi
- Department of Chemistry, School of Science, Tokai University Kitakaname Hiratsuka-shi Kanagawa 259-1292 Japan
| | - Kenta Arai
- Department of Chemistry, School of Science, Tokai University Kitakaname Hiratsuka-shi Kanagawa 259-1292 Japan
- Institute of Advanced Biosciences, Tokai University Kitakaname Hiratsuka-shi Kanagawa 259-1292 Japan
| | - Shingo Kanemura
- School of Science, Kwansei Gakuin University 1 Gakuen Uegahara Sanda Hyogo 669-1330 Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University 6-3 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 3-8-1 Harumi-cho Fuchu Tokyo 183-8538 Japan
- Kanagawa Institute of Industrial Science and Technology 3-2-1 Sakato, Takatsu-ku Kawasaki Kanagawa 213-0012 Japan
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115
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Mou HZ, Zhao CL, Song J, Xing L, Chen HY, Xu JJ. Ambient Temperature Affects Protein Self-Assembly by Interfering with the Interfacial Aggregation Behavior. ACS OMEGA 2023; 8:24999-25008. [PMID: 37483188 PMCID: PMC10357426 DOI: 10.1021/acsomega.3c01606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023]
Abstract
Amyloid fibrillation is known to be associated with degenerative diseases, and mature fibrils are also considered as valuable biomedical materials. Thus, the mechanism and influencing factors of fibrillation have always been the focus of research. However, in vitro studies are always plagued by low reproducibility of kinetics and the molecular mechanism of amyloid fibrillation is under debate until now. Here, we identified the ambient temperature (AT) as a non-negligible interfering factor in in vitro self-assembly of globular protein hen egg-white lysozyme for the first time. By multimodal molecular spectroscopy methods, not only the effect of ATs on the kinetics of protein aggregation was described but also the conformational changes of the molecular structure with different ATs were captured. Through investigating the dependence of interfacial area and catalysis, the reason for this influence was construed by the various aggregation behaviors of protein molecules in the two-phase interface. The results suggest that in vitro mechanism research on protein fibrillation needs to first clarify the AT for a more accurate comparative analysis. The proposal of this concept will provide a new clue for a deeper understanding of the mechanism of protein self-assembly and may have an impact on evaluating the efficiency of amyloid accelerators or inhibitors based on the comparative analysis of protein self-assembly.
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116
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Ghosh N, Kundu LM. Cyclic di-peptide in situ inhibited protein-aggregation. Bioorg Med Chem Lett 2023; 91:129379. [PMID: 37331639 DOI: 10.1016/j.bmcl.2023.129379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Abstract
An increasing number of neurodegenerative diseases seem to be associated with protein misfolding that often leads to misfolded protein aggregates with a β-sheet conformation and accumulation in the brain which directly contributes to or modulates the associated pathology. Protein aggregation diseases like Huntington's disease results from the deposition of aggregated huntingtin proteins within the nucleus, transmissible prion encephalopathies occur due to extracellular deposition of pathogenic prion proteins whereas Alzheimer's disease from the accumulation of both extracellular β-amyloid and intracellular hyperphosphorylated tau protein aggregates. In the generalized purpose, we have taken the core sequence of amyloid-β (responsible for its aggregation) as the aggregating peptide (AP). Among the various emerging therapeutic approaches against aggregation-related degenerative diseases such as diminishing the monomeric precursor protein, inhibiting aggregation, or blocking aggregation-induced cellular toxicity pathways, we focussed on the strategy based on the inhibition of protein aggregation using rationally designed peptide inhibitors comprising both the recognition and β-breaking component in the sequence. The "O → N acyl migration" concept was used to form cyclic peptide in situ for the generation of a bent unit which may act as disruption moiety for the inhibition process. The kinetics of aggregation was characterized by various biophysical tools (ThT-assay, TEM, CD, and FTIR). Results implied that the designed inhibitor peptides (IP) might be valuable to inhibit all the related aggregated peptides.
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Affiliation(s)
- Nibedita Ghosh
- Centre for the Environment, IIT Guwahati, Assam 781039, India; Symbol Discovery Ltd, Hyderabad 500046, India.
| | - Lal Mohan Kundu
- Centre for the Environment, IIT Guwahati, Assam 781039, India; Department of Chemistry, Indian Institute of Technology Guwahati, 781039, India
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117
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Wang J, Yang D, Qi K, Lai S, Li X, Ju X, Liu W, He C, Wang D, Zhao Y, Ke Y, Xu H. Effect of Achiral Glycine Residue on the Handedness of Surfactant-Like Short Peptide Self-Assembly Nanofibers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37402318 DOI: 10.1021/acs.langmuir.3c01165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Surfactant-like short peptides are a kind of ideal model for the study of chiral self-assembly. At present, there are few studies on the chiral self-assembly of multicharged surfactant-like peptides. In this study, we adopted a series of short peptides of Ac-I4KGK-NH2 with different combinations of L-lysine and D-lysine residues as the model molecules. TEM, AFM and SANS results showed that Ac-I4LKGLK-NH2, Ac-I4LKGDK-NH2, and Ac-I4DKGLK-NH2 formed the morphologies of nanofibers, and Ac-I4DKGDK-NH2 formed nanoribbons. All the self-assembled nanofibers, including the intermediate nanofibers of Ac-I4DKGDK-NH2 nanoribbons, showed the chirality of left handedness. Based on the molecular simulation results, it has been demonstrated that the supramolecular chirality was directly dictated by the orientation of single β strand. The insertion of glycine residue demolished the effect of lysine residues on the single strand conformation due to its high conformational flexibility. The replacement of L-isoleucine with Da-isoleucine also confirmed that the isoleucine residues involved in the β-sheet determined the supramolecular handedness. This study provides a profound mechanism of the chiral self-assembly of short peptides. We hope that it will improve the regulation of chiral molecular self-assembly with achiral glycine, as well.
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Affiliation(s)
- Jiqian Wang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Debo Yang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Kai Qi
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Shike Lai
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaohan Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Xinfeng Ju
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Wenliang Liu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Chunyong He
- Spallation Neutron Source Science Center, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Yubin Ke
- Spallation Neutron Source Science Center, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
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118
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Wijker S, Palmans ARA. Protein-Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water. Chempluschem 2023; 88:e202300260. [PMID: 37417828 DOI: 10.1002/cplu.202300260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
The folding of proteins into functional nanoparticles with defined 3D structures has inspired chemists to create simple synthetic systems mimicking protein properties. The folding of polymers into nanoparticles in water proceeds via different strategies, resulting in the global compaction of the polymer chain. Herein, we review the different methods available to control the conformation of synthetic polymers and collapse/fold them into structured, functional nanoparticles, such as hydrophobic collapse, supramolecular self-assembly, and covalent cross-linking. A comparison is made between the design principles of protein folding to synthetic polymer folding and the formation of structured nanocompartments in water, highlighting similarities and differences in design and function. We also focus on the importance of structure for functional stability and diverse applications in complex media and cellular environments.
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Affiliation(s)
- Stefan Wijker
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems, Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
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119
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Chandrasekhar G, Pengyong H, Pravallika G, Hailei L, Caixia X, Rajasekaran R. Defensin-based therapeutic peptide design in attenuating V30M TTR-induced Familial Amyloid Polyneuropathy. 3 Biotech 2023; 13:227. [PMID: 37304406 PMCID: PMC10250285 DOI: 10.1007/s13205-023-03646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
In the present study, we aimed to formulate an effective therapeutic candidate against V30M mutant transthyretin (TTR) protein to hinder its pathogenic misfolding. Nicotiana alata Defensin 1 (NaD1) Antimicrobial Peptide (AMP) was availed due to its tendency to aggregate, which may compete for aggregation-prone regions of pathogenic TTR protein. Based on NaD1's potential to bind to V30M TTR, we proposed NaD1-derived tetra peptides: CKTE and SKIL to be initial therapeutic candidates. Based on their association with mutant TTR protein, CKTE tetra peptide showed considerable interaction and curative potential as compared to SKIL tetra peptide. Further analyses from discrete molecular dynamics simulation corroborate CKTE tetra peptide's effectiveness as a 'beta-sheet breaker' against V30M TTR. Various post-simulation trajectory analyses suggested that CKTE tetra peptide alters the structural dynamics of pathogenic V30M TTR protein, thereby potentially attenuating its beta-sheets and impeding its aggregation. Normal mode analysis simulation corroborated that V30M TTR conformation is altered upon its interaction with CKTE peptide. Moreover, simulated thermal denaturation findings suggested that CKTE-V30M TTR complex is more susceptible to simulated denaturation, relative to pathogenic V30M TTR; further substantiating CKTE peptide's potential to alter V30M TTR's pathogenic conformation. Moreover, the residual frustration analysis augmented CKTE tetra peptide's proclivity in reorienting the conformation of V30M TTR. Therefore, we predicted that the tetra peptide, CKTE could be a promising therapeutic candidate in mitigating the amyloidogenic detrimental effects of V30M TTR-mediated familial amyloid polyneuropathy (FAP). Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03646-4.
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Affiliation(s)
- G. Chandrasekhar
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
| | - H. Pengyong
- Changzhi Medical College, Changzhi, 046000 China
| | - G. Pravallika
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
| | - L. Hailei
- Changzhi Medical College, Changzhi, 046000 China
| | - X. Caixia
- Changzhi Medical College, Changzhi, 046000 China
| | - R. Rajasekaran
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
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120
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Ji YM, Hou M, Zhou W, Ning ZW, Zhang Y, Xing GW. An AIE-Active NIR Fluorescent Probe with Good Water Solubility for the Detection of Aβ 1-42 Aggregates in Alzheimer's Disease. Molecules 2023; 28:5110. [PMID: 37446772 DOI: 10.3390/molecules28135110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Alzheimer's disease (AD), an amyloid-related disease, seriously endangers the health of elderly individuals. According to current research, its main pathogenic factor is the amyloid protein, which is a kind of fibrillar aggregate formed by noncovalent self-assembly of proteins. Based on the characteristics of aggregation-induced emission (AIE), a bislactosyl-decorated tetraphenylethylene (TPE) molecule TMNL (TPE + malononitrile + lactose), bearing two malononitrile substituents, was designed and synthesized in this work. The amphiphilic TMNL could self-assemble into fluorescent organic nanoparticles (FONs) with near-infrared (NIR) fluorescence emission in physiological PBS (phosphate buffered saline), achieving excellent fluorescent enhancement (47-fold) upon its combination with Aβ1-42 fibrils. TMNL was successfully applied to image Aβ1-42 plaques in the brain tissue of AD transgenic mice, and due to the AIE properties of TMNL, no additional rinsing process was necessary. It is believed that the probe reported in this work should be useful for the sensitive detection and accurate localization mapping of Aβ1-42 aggregates related to Alzheimer's disease.
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Affiliation(s)
- Yan-Ming Ji
- Center of Safety Production and Testing Technology, China Academy of Safety Science and Technology, Beijing 100012, China
| | - Min Hou
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhang-Wei Ning
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yuan Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Energy Conversion and Storage Materials, Beijing Normal University, Beijing 100875, China
| | - Guo-Wen Xing
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, Beijing Normal University, Beijing 100875, China
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121
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Xia Z, Wu Y, Lam JYL, Zhang Z, Burke M, Fertan E, Ranasinghe RT, Hidari E, Danial JS, Klenerman D. A computational suite for the structural and functional characterization of amyloid aggregates. CELL REPORTS METHODS 2023; 3:100499. [PMID: 37426747 PMCID: PMC10326375 DOI: 10.1016/j.crmeth.2023.100499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/11/2023] [Accepted: 05/17/2023] [Indexed: 07/11/2023]
Abstract
We developed the aggregate characterization toolkit (ACT), a fully automated computational suite based on existing and widely used core algorithms to measure the number, size, and permeabilizing activity of recombinant and human-derived aggregates imaged with diffraction-limited and super-resolution microscopy methods at high throughput. We have validated ACT on simulated ground-truth images of aggregates mimicking those from diffraction-limited and super-resolution microscopies and showcased its use in characterizing protein aggregates from Alzheimer's disease. ACT is developed for high-throughput batch processing of images collected from multiple samples and is available as an open-source code. Given its accuracy, speed, and accessibility, ACT is expected to be a fundamental tool in studying human and non-human amyloid intermediates, developing early disease stage diagnostics, and screening for antibodies that bind toxic and heterogeneous human amyloid aggregates.
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Affiliation(s)
- Zengjie Xia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Jeff Yui Long Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Ziwei Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Melanie Burke
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Emre Fertan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Rohan T. Ranasinghe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Eric Hidari
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - John S.H. Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
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122
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Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023; 158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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123
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202215785. [PMID: 38515735 PMCID: PMC10952214 DOI: 10.1002/ange.202215785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 03/08/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. Angew Chem Int Ed Engl 2023; 62:e202215785. [PMID: 36876912 PMCID: PMC10953358 DOI: 10.1002/anie.202215785] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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125
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Avni A, Joshi A, Mukhopadhyay S. Hydrogen-Deuterium Exchange Vibrational Raman Spectroscopy Distinguishes Distinct Amyloid Polymorphs Comprising Altered Core Architecture. J Phys Chem Lett 2023:5592-5601. [PMID: 37307286 DOI: 10.1021/acs.jpclett.3c01086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibrils are ordered protein aggregates comprising a hydrogen-bonded central cross-β core displaying a structural diversity in their supramolecular packing arrangements within the core. Such an altered packing results in amyloid polymorphism that gives rise to morphological and biological strain diversities. Here, we show that vibrational Raman spectroscopy coupled with hydrogen/deuterium (H/D) exchange discerns the key structural features that are responsible for yielding diverse amyloid polymorphs. Such a noninvasive and label-free methodology allows us to structurally distinguish distinct amyloid polymorphs displaying altered hydrogen bonding and supramolecular packing within the cross-β structural motif. By using quantitative molecular fingerprinting and multivariate statistical analysis, we analyze key Raman bands for the protein backbone and side chains that allow us to capture the conformational heterogeneity and structural distributions within distinct amyloid polymorphs. Our results delineate the key molecular factors governing the structural diversity in amyloid polymorphs and can potentially simplify studying amyloid remodeling by small molecules.
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Buzzo BB, Giuliatti S, Pereira PAM, Gomes-Pepe ES, Lemos EGDM. Molecular Docking of Lac_CB10: Highlighting the Great Potential for Bioremediation of Recalcitrant Chemical Compounds by One Predicted Bacteroidetes CopA-Laccase. Int J Mol Sci 2023; 24:9785. [PMID: 37372934 DOI: 10.3390/ijms24129785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Laccases are multicopper oxidases (MCOs) with a broad application spectrum, particularly in second-generation ethanol biotechnology and the bioremediation of xenobiotics and other highly recalcitrant compounds. Synthetic pesticides are xenobiotics with long environmental persistence, and the search for their effective bioremediation has mobilized the scientific community. Antibiotics, in turn, can pose severe risks for the emergence of multidrug-resistant microorganisms, as their frequent use for medical and veterinary purposes can generate constant selective pressure on the microbiota of urban and agricultural effluents. In the search for more efficient industrial processes, some bacterial laccases stand out for their tolerance to extreme physicochemical conditions and their fast generation cycles. Accordingly, to expand the range of effective approaches for the bioremediation of environmentally important compounds, the prospection of bacterial laccases was carried out from a custom genomic database. The best hit found in the genome of Chitinophaga sp. CB10, a Bacteroidetes isolate obtained from a biomass-degrading bacterial consortium, was subjected to in silico prediction, molecular docking, and molecular dynamics simulation analyses. The putative laccase CB10_180.4889 (Lac_CB10), composed of 728 amino acids, with theoretical molecular mass values of approximately 84 kDa and a pI of 6.51, was predicted to be a new CopA with three cupredoxin domains and four conserved motifs linking MCOs to copper sites that assist in catalytic reactions. Molecular docking studies revealed that Lac_CB10 had a high affinity for the molecules evaluated, and the affinity profiles with multiple catalytic pockets predicted the following order of decreasing thermodynamically favorable values: tetracycline (-8 kcal/mol) > ABTS (-6.9 kcal/mol) > sulfisoxazole (-6.7 kcal/mol) > benzidine (-6.4 kcal/mol) > trimethoprim (-6.1 kcal/mol) > 2,4-dichlorophenol (-5.9 kcal/mol) mol. Finally, the molecular dynamics analysis suggests that Lac_CB10 is more likely to be effective against sulfisoxazole-like compounds, as the sulfisoxazole-Lac_CB10 complex exhibited RMSD values lower than 0.2 nm, and sulfisoxazole remained bound to the binding site for the entire 100 ns evaluation period. These findings corroborate that LacCB10 has a high potential for the bioremediation of this molecule.
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Affiliation(s)
- Bárbara Bonfá Buzzo
- Department of Agricultural and Environmental Biotechnology, Faculty of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil
- Graduate Program in Agricultural and Livestock Microbiology, UNESP, Jaboticabal 14884-900, SP, Brazil
| | - Silvana Giuliatti
- Department of Genetics, Faculty of Medicine of Ribeirao Preto, Ribeirao Preto 13566-590, SP, Brazil
| | | | - Elisângela Soares Gomes-Pepe
- Department of Agricultural and Environmental Biotechnology, Faculty of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Department of Agricultural and Environmental Biotechnology, Faculty of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil
- Molecular Biology Laboratory, Institute for Research in Bioenergy (IPBEN), Jaboticabal 14884-900, SP, Brazil
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127
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Vendruscolo M. Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation. Expert Opin Drug Discov 2023:1-11. [PMID: 37276120 DOI: 10.1080/17460441.2023.2221024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. AREAS COVERED We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. EXPERT OPINION There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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128
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Rao A, Roy S, Jain V, Pillai PP. Nanoparticle Self-Assembly: From Design Principles to Complex Matter to Functional Materials. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25248-25274. [PMID: 35715224 DOI: 10.1021/acsami.2c05378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The creation of matter with varying degrees of complexities and desired functions is one of the ultimate targets of self-assembly. The ability to regulate the complex interactions between the individual components is essential in achieving this target. In this direction, the initial success of controlling the pathways and final thermodynamic states of a self-assembly process is promising. Despite the progress made in the field, there has been a growing interest in pushing the limits of self-assembly processes. The main inception of this interest is that the intended self-assembled state, with varying complexities, may not be "at equilibrium (or at global minimum)", rendering free energy minimization unsuitable to form the desired product. Thus, we believe that a thorough understanding of the design principles as well as the ability to predict the outcome of a self-assembly process is essential to form a collection of the next generation of complex matter. The present review highlights the potent role of finely tuned interparticle interactions in nanomaterials to achieve the preferred self-assembled structures with the desired properties. We believe that bringing the design and prediction to nanoparticle self-assembly processes will have a similar effect as retrosynthesis had on the logic of chemical synthesis. Along with the guiding principles, the review gives a summary of the different types of products created from nanoparticle assemblies and the functional properties emerging from them. Finally, we highlight the reasonable expectations from the field and the challenges lying ahead in the creation of complex and evolvable matter.
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Affiliation(s)
- Anish Rao
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Sumit Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Vanshika Jain
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
| | - Pramod P Pillai
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411 008, India
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Pieper T, Roth KDR, Glaser V, Riet T, Buitrago-Molina LE, Hagedorn M, Lieber M, Hust M, Noyan F, Jaeckel E, Hardtke-Wolenski M. Generation of Chimeric Antigen Receptors against Tetraspanin 7. Cells 2023; 12:1453. [PMID: 37296574 PMCID: PMC10252682 DOI: 10.3390/cells12111453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Adoptive transfer of antigen-specific regulatory T cells (Tregs) has shown promising results in the treatment of autoimmune diseases; however, the use of polyspecific Tregs has limited effects. However, obtaining a sufficient number of antigen-specific Tregs from patients with autoimmune disorders remains challenging. Chimeric antigen receptors (CARs) provide an alternative source of T cells for novel immunotherapies that redirect T cells independently of the MHC. In this study, we aimed to generate antibody-like single-chain variable fragments (scFv) and subsequent CARs against tetraspanin 7 (TSPAN7), a membrane protein highly expressed on the surface of pancreatic beta cells, using phage display technology. We established two methods for generating scFvs against TSPAN7 and other target structures. Moreover, we established novel assays to analyze and quantify their binding abilities. The resulting CARs were functional and activated specifically by the target structure, but could not recognize TSPAN7 on the surface of beta cells. Despite this, this study demonstrates that CAR technology is a powerful tool for generating antigen-specific T cells and provides new approaches for generating functional CARs.
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Affiliation(s)
- Tom Pieper
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Medizinische Biotechnologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Viktor Glaser
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Tobias Riet
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
- Department I of Internal Medicine, Tumor Genetics, University Hospital of Cologne, Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50933 Cologne, Germany
| | - Laura Elisa Buitrago-Molina
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Maike Hagedorn
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Maren Lieber
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Medizinische Biotechnologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Fatih Noyan
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
| | - Elmar Jaeckel
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
- Department of Liver Transplantation, Multi Organ Transplant Program, University Health Network, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Matthias Hardtke-Wolenski
- Department of Gastroenterology, Hepatology, Infectious Diseases & Endocrinology, Hannover Medical School, 30625 Hannover, Germany
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, 47057 Essen, Germany
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130
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Santos TP, Calabrese V, Boehm MW, Baier SK, Shen AQ. Flow-induced alignment of protein nanofibril dispersions. J Colloid Interface Sci 2023; 638:487-497. [PMID: 36758259 DOI: 10.1016/j.jcis.2023.01.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 02/05/2023]
Abstract
HYPOTHESIS Protein nanofibrils (PNF) resulting from the self-assembly of proteins or peptides can present structural ordering triggered by numerous factors, including the shear flow. We hypothesize that i) depending on the contour length of the PNF and the magnitude of the shear rate applied to the PNF dispersion, they exhibit specific orientation, and ii) it is possible to predict the alignment of PNF by establishing a flow-alignment relationship. Understanding such a relationship is pivotal to improving the fundamental knowledge and application of fibril systems. EXPERIMENTS We use β-lactoglobulin PNF aqueous dispersions with different average contour lengths but equal persistence lengths. We employ simple shear-dominated microfluidic devices with state-of-the-art imaging techniques: flow-induced birefringence (FIB) and micro-particle image velocimetry (μ-PIV), to probe the effect of shear flow on PNF alignment. FINDINGS We provide an empirical relationship connecting the birefringence Δn (quantifying the extent of PNF alignment), and the Péclet number Pe (correlating the shear rate of the flow relative to the rotational diffusion of PNF) to understand the flow-alignment behavior of PNF under shear-dominated flows. Furthermore, we assess the alignment and flow profile of PNF at both high and low flow rates. The length of PNF emerges as a controlling parameter capable of modulating PNF alignment at specific shear rates. Our results shed new insights into the hydrodynamic behavior of PNF, which is highly relevant to various industrial processes involving the fibril systems.
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Affiliation(s)
- Tatiana P Santos
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
| | - Vincenzo Calabrese
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | | | - Stefan K Baier
- Motif FoodWorks, Inc., Boston, MA, USA; The University of Queensland School of Chemical Engineering, St. Lucia, Queensland, Australia
| | - Amy Q Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
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131
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Priyadarshi A, Devi HM, Swaminathan R. Disruption of Spatial Proximities among Charged Groups in Equilibrium-Denatured States of Proteins Tracked Using Protein Charge Transfer Spectra. Biochemistry 2023. [PMID: 37162303 DOI: 10.1021/acs.biochem.3c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The absorption and luminescence originating from protein charge transfer spectra (ProCharTS) depend on the proximity between multiple charged groups in a protein. This makes ProCharTS absorbance/luminescence intensity a sensitive probe for detecting changes in the protein structure, which alter the proximity among charged groups in the protein. In this work, ProCharTS absorbance of charge-rich proteins like human serum albumin (HSA), α3C, and α3W was used to monitor structural changes upon chemical denaturant-induced protein unfolding under equilibrium conditions. The denaturation midpoints were estimated using nonlinear regression analysis. For HSA, absorbance at 325 and 340 nm estimated the GdnHCl-induced denaturation midpoints to be 0.80 and 0.61 M, respectively. A similar analysis of α3C and α3W ProCharTS absorbance yielded denaturation midpoints of 0.88 and 0.86 M at 325 nm and 0.96 and 0.66 M at 340 nm, respectively. A previously reported molten globule-like state in the GdnHCl-induced HSA unfolding pathway was detected by the increase in HSA ProCharTS absorbance at 0.5 M GdnHCl. To validate the above results, protein unfolding was additionally monitored using conventional methods like circular dichroism (CD), Trp, and dansyl fluorescence. Our results suggest that disruption of charged amino acid sidechain contacts as revealed by ProCharTS occurs at lower denaturant concentrations compared to the loss of secondary/folded structure monitored by CD and fluorescence. Further, HSA ProCharTS absorbance at 315-340 nm revealed that tertiary contacts among charged residues were disrupted at lower GdnHCl concentrations compared to sequence adjacent contacts. Our data underscore the utility of ProCharTS as a novel label-free tool to track unfolding in charge-rich proteins.
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Affiliation(s)
- Anurag Priyadarshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Himanshi Maniram Devi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
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132
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Vila JA. Rethinking the protein folding problem from a new perspective. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023:10.1007/s00249-023-01657-w. [PMID: 37165178 DOI: 10.1007/s00249-023-01657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/16/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
One of the main concerns of Anfinsen was to reveal the connection between the amino-acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins fold and how a sequence encodes its folding. As to the why, he proposes a plausible answer, namely, the thermodynamic hypothesis. As to the how, this remains an unsolved challenge. Consequently, the protein folding problem is examined here from a new perspective, namely, as an 'analytic whole'. Conceiving the protein folding in this way enabled us to (i) examine in detail why the force-field-based approaches have failed, among other purposes, in their ability to predict the three-dimensional structure of a protein accurately; (ii) propose how to redefine them to prevent these shortcomings, and (iii) conjecture on the origin of the state-of-the-art numerical-methods success to predict the tridimensional structure of proteins accurately.
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Affiliation(s)
- Jorge A Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700, San Luis, Argentina.
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133
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Fischbach A, Johns A, Schneider KL, Hao X, Tessarz P, Nyström T. Artificial Hsp104-mediated systems for re-localizing protein aggregates. Nat Commun 2023; 14:2663. [PMID: 37160881 PMCID: PMC10169802 DOI: 10.1038/s41467-023-37706-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Spatial Protein Quality Control (sPQC) sequesters misfolded proteins into specific, organelle-associated inclusions within the cell to control their toxicity. To approach the role of sPQC in cellular fitness, neurodegenerative diseases and aging, we report on the construction of Hsp100-based systems in budding yeast cells, which can artificially target protein aggregates to non-canonical locations. We demonstrate that aggregates of mutant huntingtin (mHtt), the disease-causing agent of Huntington's disease can be artificially targeted to daughter cells as well as to eisosomes and endosomes with this approach. We find that the artificial removal of mHtt inclusions from mother cells protects them from cell death suggesting that even large mHtt inclusions may be cytotoxic, a trait that has been widely debated. In contrast, removing inclusions of endogenous age-associated misfolded proteins does not significantly affect the lifespan of mother cells. We demonstrate also that this approach is able to manipulate mHtt inclusion formation in human cells and has the potential to be useful as an alternative, complementary approach to study the role of sPQC, for example in aging and neurodegenerative disease.
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Affiliation(s)
- Arthur Fischbach
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Angela Johns
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Kara L Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Peter Tessarz
- Max-Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), Cologne, Germany
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg, Sweden.
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134
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Gibertini S, Ruggieri A, Cheli M, Maggi L. Protein Aggregates and Aggrephagy in Myopathies. Int J Mol Sci 2023; 24:ijms24098456. [PMID: 37176163 PMCID: PMC10179229 DOI: 10.3390/ijms24098456] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
A number of muscular disorders are hallmarked by the aggregation of misfolded proteins within muscle fibers. A specialized form of macroautophagy, termed aggrephagy, is designated to remove and degrade protein aggregates. This review aims to summarize what has been studied so far about the direct involvement of aggrephagy and the activation of the key players, among others, p62, NBR1, Alfy, Tollip, Optineurin, TAX1BP1 and CCT2 in muscular diseases. In the first part of the review, we describe the aggrephagy pathway with the involved proteins; then, we illustrate the muscular disorder histologically characterized by protein aggregates, highlighting the role of aggrephagy pathway abnormalities in these muscular disorders.
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Affiliation(s)
- Sara Gibertini
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Alessandra Ruggieri
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Marta Cheli
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Lorenzo Maggi
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
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135
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Hosseini AN, van der Spoel D. Simulations of Amyloid-Forming Peptides in the Crystal State. Protein J 2023:10.1007/s10930-023-10119-3. [PMID: 37145206 DOI: 10.1007/s10930-023-10119-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
There still is little treatment available for amyloid diseases, despite their significant impact on individuals and the social and economic implications for society. One reason for this is that the physical nature of amyloid formation is not understood sufficiently well. Therefore, fundamental research at the molecular level remains necessary to support the development of therapeutics. A few structures of short peptides from amyloid-forming proteins have been determined. These can in principle be used as scaffolds for designing aggregation inhibitors. Attempts to this end have often used the tools of computational chemistry, in particular molecular simulation. However, few simulation studies of these peptides in the crystal state have been presented so far. Hence, to validate the capability of common force fields (AMBER19SB, CHARMM36m, and OPLS-AA/M) to yield insight into the dynamics and structural stability of amyloid peptide aggregates, we have performed molecular dynamics simulations of twelve different peptide crystals at two different temperatures. From the simulations, we evaluate the hydrogen bonding patterns, the isotropic B-factors, the change in energy, the Ramachandran plots, and the unit cell parameters and compare the results with the crystal structures. Most crystals are stable in the simulations but for all force fields there is at least one that deviates from the experimental crystal, suggesting more work is needed on these models.
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Affiliation(s)
- A Najla Hosseini
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE, 75124, Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE, 75124, Uppsala, Sweden.
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136
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Iorio A, Timr Š, Chiodo L, Derreumaux P, Sterpone F. Evolution of large Aβ16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events. Proteins 2023. [PMID: 37139594 DOI: 10.1002/prot.26500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 05/05/2023]
Abstract
Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from β-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aβ16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 μs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aβ sequences.
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Affiliation(s)
- Antonio Iorio
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
| | - Štěpán Timr
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Letizia Chiodo
- Research Unit in Non Linear Physics and Mathematical Modeling Engineering Department of Campus Bio-Medico, University of Rome, Rome, Italy
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
- Institut Universitaire de France, Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
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137
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Mitra A, Sarkar N. Elucidating the inhibitory effects of rationally designed novel hexapeptide against hen egg white lysozyme fibrillation at acidic and physiological pH. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140899. [PMID: 36693516 DOI: 10.1016/j.bbapap.2023.140899] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/23/2023]
Abstract
Inhibition of highly ordered cross-β-sheet-rich aggregates of misfolded amyloid proteins using rationally designed sequence-based short peptides is a promising therapeutic strategy for the treatment of neurodegenerative diseases. Here, we have explored the anti-amyloidogenic potency of a rationally designed hexapeptide (Tyr-Pro-Gln-Ile-Pro-Asn) on in vitro hen egg white lysozyme (HEWL) amyloid fibril formation at acidic pH and physiological pH using computational docking as well as various biophysical techniques such as fluorescence spectroscopy, UV-vis spectroscopy, FTIR spectroscopy, confocal microscopy and TEM. The peptide was designed based on the aggregation-prone region (APR) of HEWL and thus referred to as SqP1 (Sequence-based Peptide 1). SqP1 showed over 70% inhibition of HEWL amyloid formation at pH 2.2 and approximately 50% inhibition at pH 7.5. We propose that SqP1 binds to the APR of HEWL and interacts strongly with the Trp62/Trp63, ultimately stabilizing monomeric HEWL at both the pH conditions and preventing conformation changes in the structure of HEWL, leading to the formation of amyloidogenic fibrillar structures. A sequence-based peptide inhibitor of HEWL amyloid formation was not reported previously, making this a critical study that will further emphasize the importance of short synthetic peptides as amyloid inhibitors.
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Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela 769008, Odisha, India.
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138
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Chen Z, Wang X, Chen X, Huang J, Wang C, Wang J, Wang Z. Accelerating therapeutic protein design with computational approaches toward the clinical stage. Comput Struct Biotechnol J 2023; 21:2909-2926. [PMID: 38213894 PMCID: PMC10781723 DOI: 10.1016/j.csbj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 01/13/2024] Open
Abstract
Therapeutic protein, represented by antibodies, is of increasing interest in human medicine. However, clinical translation of therapeutic protein is still largely hindered by different aspects of developability, including affinity and selectivity, stability and aggregation prevention, solubility and viscosity reduction, and deimmunization. Conventional optimization of the developability with widely used methods, like display technologies and library screening approaches, is a time and cost-intensive endeavor, and the efficiency in finding suitable solutions is still not enough to meet clinical needs. In recent years, the accelerated advancement of computational methodologies has ushered in a transformative era in the field of therapeutic protein design. Owing to their remarkable capabilities in feature extraction and modeling, the integration of cutting-edge computational strategies with conventional techniques presents a promising avenue to accelerate the progression of therapeutic protein design and optimization toward clinical implementation. Here, we compared the differences between therapeutic protein and small molecules in developability and provided an overview of the computational approaches applicable to the design or optimization of therapeutic protein in several developability issues.
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Affiliation(s)
- Zhidong Chen
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Juyang Huang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Chenglin Wang
- Shenzhen Qiyu Biotechnology Co., Ltd, Shenzhen 518107, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
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139
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Menon S, Mondal J. Conformational Plasticity in α-Synuclein and How Crowded Environment Modulates It. J Phys Chem B 2023; 127:4032-4049. [PMID: 37114769 DOI: 10.1021/acs.jpcb.3c00982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
A 140-residue intrinsically disordered protein (IDP), α-synuclein (αS), is known to adopt conformations that are vastly plastic and susceptible to environmental cues and crowders. However, the inherently heterogeneous nature of αS has precluded a clear demarcation of its monomeric precursor between aggregation-prone and functionally relevant aggregation-resistant states and how a crowded environment could modulate their mutual dynamic equilibrium. Here, we identify an optimal set of distinct metastable states of αS in aqueous media by dissecting a 73 μs-long molecular dynamics ensemble via building a comprehensive Markov state model (MSM). Notably, the most populated metastable state corroborates with the dimension obtained from PRE-NMR studies of αS monomer, and it undergoes kinetic transition at diverse time scales with a weakly populated random-coil-like ensemble and a globular protein-like state. However, subjecting αS to a crowded environment results in a nonmonotonic compaction of these metastable conformations, thereby skewing the ensemble by either introducing new tertiary contacts or by reinforcing the innate contacts. The early stage of dimerization process is found to be considerably expedited in the presence of crowders, albeit promoting nonspecific interactions. Together with this, using an extensively sampled ensemble of αS, this exposition demonstrates that crowded environments can potentially modulate the conformational preferences of IDP that can either promote or inhibit aggregation events.
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Affiliation(s)
- Sneha Menon
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
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140
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Adhav VA, Shelke SS, Balanarayan P, Saikrishnan K. Sulfur-mediated chalcogen versus hydrogen bonds in proteins: a see-saw effect in the conformational space. QRB DISCOVERY 2023; 4:e5. [PMID: 37564297 PMCID: PMC10411326 DOI: 10.1017/qrd.2023.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 08/12/2023] Open
Abstract
Divalent sulfur (S) forms a chalcogen bond (Ch-bond) via its σ-holes and a hydrogen bond (H-bond) via its lone pairs. The relevance of these interactions and their interplay for protein structure and function is unclear. Based on the analyses of the crystal structures of small organic/organometallic molecules and proteins and their molecular electrostatic surface potential, we show that the reciprocity of the substituent-dependent strength of the σ-holes and lone pairs correlates with the formation of either Ch-bond or H-bond. In proteins, cystines preferentially form Ch-bonds, metal-chelated cysteines form H-bonds, while methionines form either of them with comparable frequencies. This has implications for the positioning of these residues and their role in protein structure and function. Computational analyses reveal that the S-mediated interactions stabilise protein secondary structures by mechanisms such as helix capping and protecting free β-sheet edges by negative design. The study highlights the importance of S-mediated Ch-bond and H-bond for understanding protein folding and function, the development of improved strategies for protein/peptide structure prediction and design and structure-based drug discovery.
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Affiliation(s)
| | - Sanket Satish Shelke
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Pananghat Balanarayan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
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141
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Rani R, Syngkli S, Nongkhlaw J, Das B. Expression and characterisation of human glycerol kinase: the role of solubilising agents and molecular chaperones. Biosci Rep 2023; 43:BSR20222258. [PMID: 37021775 PMCID: PMC10130975 DOI: 10.1042/bsr20222258] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/11/2023] [Accepted: 04/06/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Glycerol kinase (GK; EC 2.7.1.30) facilitates the entry of glycerol into pathways of glucose and triglyceride metabolism and may play a potential role in Type 2 diabetes mellitus (T2DM). However, the detailed regulatory mechanisms and structure of the human GK are unknown. METHODS The human GK gene was cloned into the pET-24a(+) vector and over-expressed in Escherichia coli BL21 (DE3). Since the protein was expressed as inclusion bodies (IBs), various culture parameters and solubilising agents were used but they did not produce bioactive His-GK; however, co-expression of His-GK with molecular chaperones, specifically pKJE7, achieved expression of bioactive His-GK. The overexpressed bioactive His-GK was purified using coloumn chromatography and characterised using enzyme kinetics. RESULTS The overexpressed bioactive His-GK was purified apparently to homogeneity (∼295-fold) and characterised. The native His-GK was a dimer with a monomeric molecular weight of ∼55 kDa. Optimal enzyme activity was observed in TEA buffer (50 mM) at 7.5 pH. K+ (40 mM) and Mg2+ (2.0 mM) emerged as prefered metal ions for His-GK activity with specific activity 0.780 U/mg protein. The purified His-GK obeyed standard Michaelis-Menten kinetics with Km value of 5.022 µM (R2=0.927) for its substrate glycerol; whereas, that for ATP and PEP was 0.767 mM (R2=0.928) and 0.223 mM (R2=0.967), respectively. Other optimal parameters for the substrate and co-factors were also determined. CONCLUSION The present study demonstrates that co-expression of molecular chaperones assists with the expression of bioactive human GK for its characterisation.
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Affiliation(s)
- Riva Mary Rani
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India
| | - Superior Syngkli
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India
| | - Joplin Nongkhlaw
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India
| | - Bidyadhar Das
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India
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142
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Rey F, Berardo C, Maghraby E, Mauri A, Messa L, Esposito L, Casili G, Ottolenghi S, Bonaventura E, Cuzzocrea S, Zuccotti G, Tonduti D, Esposito E, Paterniti I, Cereda C, Carelli S. Redox Imbalance in Neurological Disorders in Adults and Children. Antioxidants (Basel) 2023; 12:antiox12040965. [PMID: 37107340 PMCID: PMC10135575 DOI: 10.3390/antiox12040965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Oxygen is a central molecule for numerous metabolic and cytophysiological processes, and, indeed, its imbalance can lead to numerous pathological consequences. In the human body, the brain is an aerobic organ and for this reason, it is very sensitive to oxygen equilibrium. The consequences of oxygen imbalance are especially devastating when occurring in this organ. Indeed, oxygen imbalance can lead to hypoxia, hyperoxia, protein misfolding, mitochondria dysfunction, alterations in heme metabolism and neuroinflammation. Consequently, these dysfunctions can cause numerous neurological alterations, both in the pediatric life and in the adult ages. These disorders share numerous common pathways, most of which are consequent to redox imbalance. In this review, we will focus on the dysfunctions present in neurodegenerative disorders (specifically Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis) and pediatric neurological disorders (X-adrenoleukodystrophies, spinal muscular atrophy, mucopolysaccharidoses and Pelizaeus-Merzbacher Disease), highlighting their underlining dysfunction in redox and identifying potential therapeutic strategies.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Erika Maghraby
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Giovanna Casili
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Sara Ottolenghi
- Department of Medicine and Surgery, University of Milano Bicocca, 20126 Milano, Italy
| | - Eleonora Bonaventura
- Child Neurology Unit, Buzzi Children's Hospital, 20154 Milano, Italy
- Center for Diagnosis and Treatment of Leukodystrophies and Genetic Leukoencephalopathies (COALA), Buzzi Children's Hospital, 20154 Milano, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Davide Tonduti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Child Neurology Unit, Buzzi Children's Hospital, 20154 Milano, Italy
- Center for Diagnosis and Treatment of Leukodystrophies and Genetic Leukoencephalopathies (COALA), Buzzi Children's Hospital, 20154 Milano, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
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143
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Limbocker R, Cremades N, Cascella R, Tessier PM, Vendruscolo M, Chiti F. Characterization of Pairs of Toxic and Nontoxic Misfolded Protein Oligomers Elucidates the Structural Determinants of Oligomer Toxicity in Protein Misfolding Diseases. Acc Chem Res 2023. [PMID: 37071750 DOI: 10.1021/acs.accounts.3c00045] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
ConspectusThe aberrant misfolding and aggregation of peptides and proteins into amyloid aggregates occurs in over 50 largely incurable protein misfolding diseases. These pathologies include Alzheimer's and Parkinson's diseases, which are global medical emergencies owing to their prevalence in increasingly aging populations worldwide. Although the presence of mature amyloid aggregates is a hallmark of such neurodegenerative diseases, misfolded protein oligomers are increasingly recognized as of central importance in the pathogenesis of many of these maladies. These oligomers are small, diffusible species that can form as intermediates in the amyloid fibril formation process or be released by mature fibrils after they are formed. They have been closely associated with the induction of neuronal dysfunction and cell death. It has proven rather challenging to study these oligomeric species because of their short lifetimes, low concentrations, extensive structural heterogeneity, and challenges associated with producing stable, homogeneous, and reproducible populations. Despite these difficulties, investigators have developed protocols to produce kinetically, chemically, or structurally stabilized homogeneous populations of protein misfolded oligomers from several amyloidogenic peptides and proteins at experimentally ameneable concentrations. Furthermore, procedures have been established to produce morphologically similar but structurally distinct oligomers from the same protein sequence that are either toxic or nontoxic to cells. These tools offer unique opportunities to identify and investigate the structural determinants of oligomer toxicity by a close comparative inspection of their structures and the mechanisms of action through which they cause cell dysfunction.This Account reviews multidisciplinary results, including from our own groups, obtained by combining chemistry, physics, biochemistry, cell biology, and animal models for pairs of toxic and nontoxic oligomers. We describe oligomers comprised of the amyloid-β peptide, which underlie Alzheimer's disease, and α-synuclein, which are associated with Parkinson's disease and other related neurodegenerative pathologies, collectively known as synucleinopathies. Furthermore, we also discuss oligomers formed by the 91-residue N-terminal domain of [NiFe]-hydrogenase maturation factor from E. coli, which we use as a model non-disease-related protein, and by an amyloid stretch of Sup35 prion protein from yeast. These oligomeric pairs have become highly useful experimental tools for studying the molecular determinants of toxicity characteristic of protein misfolding diseases. Key properties have been identified that differentiate toxic from nontoxic oligomers in their ability to induce cellular dysfunction. These characteristics include solvent-exposed hydrophobic regions, interactions with membranes, insertion into lipid bilayers, and disruption of plasma membrane integrity. By using these properties, it has been possible to rationalize in model systems the responses to pairs of toxic and nontoxic oligomers. Collectively, these studies provide guidance for the development of efficacious therapeutic strategies to target rationally the cytotoxicity of misfolded protein oligomers in neurodegenerative conditions.
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Affiliation(s)
- Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York 10996, United States
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza 50009, Spain
| | - Roberta Cascella
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Peter M Tessier
- Departments of Chemical Engineering, Pharmaceutical Sciences, and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
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144
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Zhang C, Bye JW, Lui LH, Zhang H, Hales J, Brocchini S, Curtis RA, Dalby PA. Enhanced Thermal Stability and Reduced Aggregation in an Antibody Fab Fragment at Elevated Concentrations. Mol Pharm 2023; 20:2650-2661. [PMID: 37040431 PMCID: PMC10155210 DOI: 10.1021/acs.molpharmaceut.3c00081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The aggregation of protein therapeutics such as antibodies remains a major challenge in the biopharmaceutical industry. The present study aimed to characterize the impact of the protein concentration on the mechanisms and potential pathways for aggregation, using the antibody Fab fragment A33 as the model protein. Aggregation kinetics were determined for 0.05 to 100 mg/mL Fab A33, at 65 °C. A surprising trend was observed whereby increasing the concentration decreased the relative aggregation rate, ln(v) (% day-1), from 8.5 at 0.05 mg/mL to 4.4 at 100 mg/mL. The absolute aggregation rate (mol L-1 h-1) increased with the concentration following a rate order of approximately 1 up to a concentration of 25 mg/mL. Above this concentration, there was a transition to an apparently negative rate order of -1.1 up to 100 mg/mL. Several potential mechanisms were examined as possible explanations. A greater apparent conformational stability at 100 mg/mL was observed from an increase in the thermal transition midpoint (Tm) by 7-9 °C, relative to those at 1-4 mg/mL. The associated change in unfolding entropy (△Svh) also increased by 14-18% at 25-100 mg/mL, relative to those at 1-4 mg/mL, indicating reduced conformational flexibility in the native ensemble. Addition of Tween or the crowding agents Ficoll and dextran, showed that neither surface adsorption, diffusion limitations nor simple volume crowding affected the aggregation rate. Fitting of kinetic data to a wide range of mechanistic models implied a reversible two-state conformational switch mechanism from aggregation-prone monomers (N*) into non-aggregating native forms (N) at higher concentrations. kD measurements from DLS data also suggested a weak self-attraction while remaining colloidally stable, consistent with macromolecular self-crowding within weakly associated reversible oligomers. Such a model is also consistent with compaction of the native ensemble observed through changes in Tm and △Svh.
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Affiliation(s)
- Cheng Zhang
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Jordan W Bye
- School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, U.K
| | - Lok H Lui
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Hongyu Zhang
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - John Hales
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
| | - Steve Brocchini
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Robin A Curtis
- School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, U.K
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, U.K
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145
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Pandey SP, P K, Dutta T, Chakraborty B, Koner AL, Singh PK. Mitochondria-Directing Fluorogenic Probe: An Efficient Amyloid Marker for Imaging Lipid Metabolite-Induced Protein Aggregation in Live Cells and Caenorhabditis elegans. Anal Chem 2023; 95:6341-6350. [PMID: 37014217 DOI: 10.1021/acs.analchem.2c05466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
The design and development of optical probes for sensing neurotoxic amyloid fibrils are active and important areas of research and are undergoing continuous advancements. In this paper, we have synthesized a red emissive styryl chromone-based fluorophore (SC1) for fluorescence-based detection of amyloid fibrils. SC1 records exceptional modulation in its photophysical properties in the presence of amyloid fibrils, which has been attributed to the extreme sensitivity of its photophysical properties toward the immediate microenvironment of the probe in the fibrillar matrix. SC1 also shows very high selectivity toward the amyloid-aggregated form of the protein as compared to its native form. The probe is also able to monitor the kinetic progression of the fibrillation process, with comparable efficiency as that of the most popular amyloid probe, Thioflavin-T. Moreover, the performance of SC1 is least sensitive to the ionic strength of the medium, which is an advantage over Thioflavin-T. In addition, the molecular level interaction forces between the probe and the fibrillar matrix have been interrogated by molecular docking calculations which suggest the binding of the probe to the exterior channel of the fibrils. The probe has also been demonstrated to sense protein aggregates from the Aβ-40 protein, which is known to be responsible for Alzheimer's disease. Moreover, SC1 exhibited excellent biocompatibility and exclusive accumulation at mitochondria which allowed us to successfully demonstrate the applicability of this probe to detect mitochondrial-aggregated protein induced by an oxidative stress indicator molecule 4-hydroxy-2-nonenal (4-HNE) in A549 cell lines as well as in a simple animal model like Caenorhabditis elegans. Overall, the styryl chromone-based probe presents a potentially exciting alternative for the sensing of neurotoxic protein aggregation species both in vitro as well as in vivo.
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Affiliation(s)
- Shrishti P Pandey
- Department of Biotechnology, Mithibai College of Arts, Chauhan Institute of Science and Amrutben Jivanlal College of Commerce and Economics, Vile Parle (W) 400056, India
| | - Kavyashree P
- Bionanotechnology Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Tanoy Dutta
- Bionanotechnology Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Barsha Chakraborty
- Bionanotechnology Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Apurba Lal Koner
- Bionanotechnology Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Prabhat K Singh
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India
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146
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Morfino P, Aimo A, Vergaro G, Sanguinetti C, Castiglione V, Franzini M, Perrone MA, Emdin M. Transthyretin Stabilizers and Seeding Inhibitors as Therapies for Amyloid Transthyretin Cardiomyopathy. Pharmaceutics 2023; 15:pharmaceutics15041129. [PMID: 37111614 PMCID: PMC10143494 DOI: 10.3390/pharmaceutics15041129] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/15/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Transthyretin (TTR) amyloid cardiomyopathy (ATTR-CM) is a progressive and increasingly recognized cause of heart failure which is associated with high mortality and morbidity. ATTR-CM is characterized by the misfolding of TTR monomers and their deposition within the myocardium as amyloid fibrils. The standard of care for ATTR-CM consists of TTR-stabilizing ligands, such as tafamidis, which aim at maintaining the native structure of TTR tetramers, thus preventing amyloid aggregation. However, their efficacy in advanced-staged disease and after long-term treatment is still a source of concern, suggesting the existence of other pathogenetic factors. Indeed, pre-formed fibrils present in the tissue can further accelerate amyloid aggregation in a self-propagating process known as “amyloid seeding”. The inhibition of amyloidogenesis through TTR stabilizers combined with anti-seeding peptides may represent a novel strategy with additional benefits over current therapies. Finally, the role of stabilizing ligands needs to be reassessed in view of the promising results derived from trials which have evaluated alternative strategies, such as TTR silencers and immunological amyloid disruptors.
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Affiliation(s)
- Paolo Morfino
- Interdisciplinary Center for Health Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Alberto Aimo
- Interdisciplinary Center for Health Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, 56124 Pisa, Italy
| | - Giuseppe Vergaro
- Interdisciplinary Center for Health Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, 56124 Pisa, Italy
| | - Chiara Sanguinetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Vincenzo Castiglione
- Interdisciplinary Center for Health Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, 56124 Pisa, Italy
| | - Maria Franzini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Marco Alfonso Perrone
- Division of Cardiology and CardioLab, Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Michele Emdin
- Interdisciplinary Center for Health Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
- Cardiology Division, Fondazione Toscana Gabriele Monasterio, 56124 Pisa, Italy
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147
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Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
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148
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Wei Z, Dai S, Huang J, Hu X, Ge C, Zhang X, Yang K, Shao P, Sun P, Xiang N. Soy Protein Amyloid Fibril Scaffold for Cultivated Meat Application. ACS APPLIED MATERIALS & INTERFACES 2023; 15:15108-15119. [PMID: 36916732 DOI: 10.1021/acsami.2c21702] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
It is important to have sustainable and edible scaffolds to produce cultivated meat. In this research, three-dimensional (3D) porous scaffolds were developed by soy protein amyloid fibrils for cultivated meat applications. Food-safe biological and physical cross-linking methods using microbial transglutaminase and temperature-controlled water vapor annealing technique were employed to crosslink soy protein amyloid fibrils, resulting in the production of 3D scaffolds. The generated 3D scaffolds had pores with sizes ranging from 50 to 250 μm, porosities of 72-83%, and compressive moduli of 3.8-4.2 kPa, depending on the type of soy protein used in the process (β-conglycinin (7S), glycinin (11S) and soy protein isolate (SPI)). When present with pepsin, these scaffolds can degrade within an hour but remain stable in phosphate-buffered saline for at least 30 days. The soy protein amyloid fibril scaffolds enabled C2C12 mouse skeletal myoblasts proliferate and differentiate without adding cell adhesive proteins or other coatings. The results demonstrate the potential of abundant and inexpensive soy protein amyloid fibrils to be utilized as scaffold materials for cultivated meat in the food industry.
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Affiliation(s)
- Zhengxun Wei
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
| | - Siqing Dai
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
| | - Jiayi Huang
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
| | - Xinyu Hu
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
| | - Chengxin Ge
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
| | - Ximing Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Kai Yang
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
| | - Ping Shao
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
- Key Laboratory of Food Macromolecular Resources Processing Technology Research, China National Light Industry, Zhejiang University of Technology, Hangzhou 310014, China
| | - Peilong Sun
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
- Key Laboratory of Food Macromolecular Resources Processing Technology Research, China National Light Industry, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ning Xiang
- Department of Food Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People's Republic of China
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149
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Nakama T, Rossen A, Ebihara R, Yagi-Utsumi M, Fujita D, Kato K, Sato S, Fujita M. Hysteresis behavior in the unfolding/refolding processes of a protein trapped in metallo-cages. Chem Sci 2023; 14:2910-2914. [PMID: 36937586 PMCID: PMC10016334 DOI: 10.1039/d2sc05879k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Confinement of molecules in a synthetic host can physically isolate even their unstable temporary structures, which has potential for application to protein transient structure analysis. Here we report the NMR snapshot observation of protein unfolding and refolding processes by confining a target protein in a self-assembled coordination cage. With increasing acetonitrile content in CD3CN/H2O media (50 to 90 vol%), the folding structure of a protein sharply denatured at 83 vol%, clearly revealing the regions of initial unfolding. Unfavorable aggregation of the protein leading to irreversible precipitation is completely prevented because of the spatial isolation of the single protein molecule in the cage. When the acetonitrile content reversed (84 to 70 vol%), the once-denatured protein started to regain its original folded structure at 80 vol%, showing that the protein folding/unfolding process can be referred to as a phase transition with hysteresis behavior.
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Affiliation(s)
- Takahiro Nakama
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Anouk Rossen
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Risa Ebihara
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya 467-8603 Japan
| | - Daishi Fujita
- Institute for Integrated Cell-Material Sciences (iCeMS), Institute for Advanced Study, Kyoto University Yoshida, Sakyo-ku Kyoto 606-8501 Japan
| | - Koichi Kato
- Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya 467-8603 Japan
| | - Sota Sato
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
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150
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Application of Amyloid-Based Hybrid Membranes in Drug Delivery. Polymers (Basel) 2023; 15:polym15061444. [PMID: 36987222 PMCID: PMC10052896 DOI: 10.3390/polym15061444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/15/2023] Open
Abstract
The properties of amyloid fibrils, e.g., unique structural characteristics and superior biocompatibility, make them a promising vehicle for drug delivery. Here, carboxymethyl cellulose (CMC) and whey protein isolate amyloid fibril (WPI-AF) were used to synthesize amyloid-based hybrid membranes as vehicles for the delivery of cationic and hydrophobic drugs (e.g., methylene blue (MB) and riboflavin (RF)). The CMC/WPI-AF membranes were synthesized via chemical crosslinking coupled with phase inversion. The zeta potential and scanning electron microscopy results revealed a negative charge and a pleated surface microstructure with a high content of WPI-AF. FTIR analysis showed that the CMC and WPI-AF were cross-linked via glutaraldehyde and the interacting forces between membrane and MB or RF was found to be electrostatic interaction and hydrogen bonding, respectively. Next, the in vitro drug release from membranes was monitored using UV-vis spectrophotometry. Additionally, two empirical models were used to analyze the drug release data and relevant rate constant and parameters were determined accordingly. Moreover, our results indicated that in vitro drug release rates depended on the drug–matrix interactions and transport mechanism, which could be controlled by altering the WPI-AF content in membrane. This research provides an excellent example of utilizing two-dimensional amyloid-based materials for drug delivery.
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