1
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Namba N, Ohgita T, Tamagaki-Asahina H, Nishitsuji K, Shimanouchi T, Sato T, Saito H. Amyloidogenic 60-71 deletion/ValThr insertion mutation of apolipoprotein A-I generates a new aggregation-prone segment that promotes nucleation through entropic effects. Sci Rep 2023; 13:18514. [PMID: 37898709 PMCID: PMC10613298 DOI: 10.1038/s41598-023-45803-y] [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: 07/31/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023] Open
Abstract
The N-terminal fragment of apolipoprotein A-I (apoA-I), comprising residues 1-83, contains three segments prone to aggregation: residues 14-22, 53-58, and 67-72. We previously demonstrated that residues 14-22 are critical in apoA-I fibril formation while residues 53-58 entropically drove the nucleation process. Here, we investigated the impact of amyloidogenic mutations (Δ60-71/VT, Δ70-72, and F71Y) located around residues 67-72 on fibril formation by the apoA-I 1-83 fragment. Thioflavin T fluorescence assay demonstrated that the Δ60-71/VT mutation significantly enhances both nucleation and fibril elongation rates, whereas the Δ70-72 and F71Y mutations had minimal effects. Circular dichroism measurements and microscopic observations revealed that all variant fragments formed straight fibrils, transitioning from random coils to β-sheet structures. Kinetic analysis demonstrated that primary nucleation is the dominant step in fibril formation, with fibril elongation reaching saturation at high protein concentrations. Thermodynamically, both nucleation and fibril elongation were enthalpically and entropically unfavorable in all apoA-I 1-83 variants, in which the entropic barrier of nucleation was almost eliminated for the Δ60-71/VT variant. Taken together, our results suggest the presence of new aggregation-prone segment in the Δ60-71/VT variant that promotes nucleation through entropic effects.
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Affiliation(s)
- Norihiro Namba
- Laboratory of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Takashi Ohgita
- Laboratory of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Hiroko Tamagaki-Asahina
- Division of Liberal Arts Sciences, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Kazuchika Nishitsuji
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
| | - Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takeshi Sato
- Division of Liberal Arts Sciences, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Hiroyuki Saito
- Laboratory of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan.
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2
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Temperature dependent aggregation mechanism and pathway of lysozyme: By all atom and coarse grained molecular dynamics simulation. J Mol Graph Model 2020; 103:107816. [PMID: 33291026 DOI: 10.1016/j.jmgm.2020.107816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 11/21/2022]
Abstract
Aggregation of protein causes various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. It was found that aggregation of protein depends on many factors like temperature, pH, salt type, salt concentration, ionic strength, protein concentration, co solutes. Here we have tried to capture the aggregation mechanism and pathway of hen egg white lysozyme using molecular dynamics simulations at two different temperatures; 300 K and 340 K. Along with the all atom simulations to get the atomistic details of aggregation mechanism, we have used coarse grained simulation with MARTINI force field to monitor the aggregation for longer duration. Our results suggest that due to the aggregation, changes in the conformation of lysozyme are more at 340 K than at 300 K. The change in the conformation of the lysozyme at 300 K is mainly due to aggregation where at 340 K change in conformation of lysozyme is due to both aggregation and temperature. Also, a more compact aggregated system is formed at 340 K.
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3
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Seifi B, Aina A, Wallin S. Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH. Proteins 2020; 89:289-300. [PMID: 32996201 DOI: 10.1002/prot.26014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 08/31/2020] [Indexed: 01/08/2023]
Abstract
RfaH is a compact two-domain bacterial transcription factor that functions both as a regulator of transcription and an enhancer of translation. Underpinning the dual functional roles of RfaH is a partial but dramatic fold switch, which completely transforms the ~50-amino acid C-terminal domain (CTD) from an all-α state to an all-β state. The fold switch of the CTD occurs when RfaH binds to RNA polymerase (RNAP), however, the details of how this structural transformation is triggered is not well understood. Here we use all-atom Monte Carlo simulations to characterize structural fluctuations and mechanical stability properties of the full-length RfaH and the CTD as an isolated fragment. In agreement with experiments, we find that interdomain contacts are crucial for maintaining a stable, all-α CTD in free RfaH. To probe mechanical properties, we use pulling simulations to measure the work required to inflict local deformations at different positions along the chain. The resulting mechanical stability profile reveals that free RfaH can be divided into a "rigid" part and a "soft" part, with a boundary that nearly coincides with the boundary between the two domains. We discuss the potential role of this feature for how fold switching may be triggered by interaction with RNAP.
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Affiliation(s)
- Bahman Seifi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
| | - Adekunle Aina
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
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4
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Petrlova J, Petruk G, Huber RG, McBurnie EW, van der Plas MJA, Bond PJ, Puthia M, Schmidtchen A. Thrombin-derived C-terminal fragments aggregate and scavenge bacteria and their proinflammatory products. J Biol Chem 2020; 295:3417-3430. [PMID: 32034093 PMCID: PMC7076200 DOI: 10.1074/jbc.ra120.012741] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
Thrombin-derived C-terminal peptides (TCPs), including a major 11-kDa fragment (TCP96), are produced through cleavage by human neutrophil elastase and aggregate lipopolysaccharide (LPS) and the Gram-negative bacterium Escherichia coli. However, the physiological roles of TCP96 in controlling bacterial infections and reducing LPS-induced inflammation are unclear. Here, using various biophysical methods, in silico molecular modeling, microbiological and cellular assays, and animal models, we examined the structural features and functional roles of recombinant TCP96 (rTCP96) in the aggregation of multiple bacteria and the Toll-like receptor (TLR) agonists they produce. We found that rTCP96 aggregates both Gram-negative and Gram-positive bacteria, including Staphylococcus aureus and Pseudomonas aeruginosa, and their cell-wall components LPS, lipid A, and lipoteichoic acid (LTA). The Gram-negative bacteria E. coli and P. aeruginosa were particularly sensitive to aggregation-induced bacterial permeabilization and killing. As a proof of concept, we show that rTCP96 reduces LPS-induced NF-κB activation in human monocytes, as well as in mouse models of LPS-induced subcutaneous inflammation. Moreover, in a mouse model of subcutaneous inoculation with P. aeruginosa, rTCP96 reduced bacterial levels. Together, these results link TCP-mediated aggregation of endotoxins and bacteria in vitro to attenuation of inflammation and bacterial levels in vivo.
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Affiliation(s)
- Jitka Petrlova
- Department of Clinical Sciences, Division of Dermatology and Venereology, Lund University, Lund SE-22184, Sweden.
| | - Ganna Petruk
- Department of Clinical Sciences, Division of Dermatology and Venereology, Lund University, Lund SE-22184, Sweden
| | | | - Eilish W McBurnie
- Bioinformatics Institute (A*STAR), Singapore SG-138671; Department of Chemistry, University of Southampton, Southampton UK-SO17 1BJ, United Kingdom
| | - Mariena J A van der Plas
- Department of Clinical Sciences, Division of Dermatology and Venereology, Lund University, Lund SE-22184, Sweden; Department of Pharmacy, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore SG-138671; Department of Biological Sciences, National University of Singapore, Singapore SG-117558
| | - Manoj Puthia
- Department of Clinical Sciences, Division of Dermatology and Venereology, Lund University, Lund SE-22184, Sweden
| | - Artur Schmidtchen
- Department of Clinical Sciences, Division of Dermatology and Venereology, Lund University, Lund SE-22184, Sweden; Department of Biomedical Sciences, Copenhagen Wound Healing Center, Bispebjerg Hospital, University of Copenhagen, Copenhagen DK-2400, Denmark
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5
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Churchill CDM, Healey MA, Preto J, Tuszynski JA, Woodside MT. Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments. Biophys J 2019; 117:1125-1135. [PMID: 31477241 DOI: 10.1016/j.bpj.2019.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/21/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins often play an important role in protein aggregation. However, it is challenging to determine the structures and interactions that drive the early stages of aggregation because they are transient and obscured in a heterogeneous mixture of disordered states. Even computational methods are limited because the lack of ordered structure makes it difficult to ensure that the relevant conformations are sampled. We address these challenges by integrating atomistic simulations with high-resolution single-molecule measurements reported previously, using the measurements to help discern which parts of the disordered ensemble of structures in the simulations are most probable while using the simulations to identify residues and interactions that are important for oligomer stability. This approach was applied to α-synuclein, an intrinsically disordered protein that aggregates in the context of Parkinson's disease. We simulated single-molecule pulling experiments on dimers, the minimal oligomer, and compared them to force spectroscopy measurements. Force-extension curves were simulated starting from a set of 66 structures with substantial structured content selected from the ensemble of dimer structures generated at zero force via Monte Carlo simulations. The pattern of contour length changes as the structures unfolded through intermediate states was compared to the results from optical trapping measurements on the same dimer to discern likely structures occurring in the measurements. Simulated pulling curves were generally consistent with experimental data but with a larger number of transient intermediates. We identified an ensemble of β-rich dimer structures consistent with the experimental data from which dimer interfaces could be deduced. These results suggest specific druggable targets in the structural motifs of α-synuclein that may help prevent the earliest steps of oligomerization.
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Affiliation(s)
| | - Mark A Healey
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Jordane Preto
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
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6
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Bille A, Jensen KS, Mohanty S, Akke M, Irbäck A. Stability and Local Unfolding of SOD1 in the Presence of Protein Crowders. J Phys Chem B 2019; 123:1920-1930. [PMID: 30753785 DOI: 10.1021/acs.jpcb.8b10774] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Using NMR and Monte Carlo (MC) methods, we investigate the stability and dynamics of superoxide dismutase 1 (SOD1) in homogeneous crowding environments, where either bovine pancreatic trypsin inhibitor (BPTI) or the B1 domain of streptococcal protein G (PGB1) serves as a crowding agent. By NMR, we show that both crowders, and especially BPTI, cause a drastic loss in the overall stability of SOD1 in its apo monomeric form. Additionally, we determine chemical shift perturbations indicating that SOD1 interacts with the crowder proteins in a residue-specific manner that further depends on the identity of the crowding protein. Furthermore, the specificity of SOD1-crowder interactions is reciprocal: chemical shift perturbations on BPTI and PGB1 identify regions that interact preferentially with SOD1. By MC simulations, we investigate the local unfolding of SOD1 in the absence and presence of the crowders. We find that the crowders primarily interact with the long flexible loops of the folded SOD1 monomer. The basic mechanisms by which the SOD1 β-barrel core unfolds remain unchanged when adding the crowders. In particular, both with and without the crowders, the second β-sheet of the barrel is more dynamic and unfolding-prone than the first. Notably, the MC simulations (exploring the early stages of SOD1 unfolding) and the NMR experiments (under equilibrium conditions) identify largely the same set of PGB1 and BPTI residues as prone to form SOD1 contacts. Thus, contacts stabilizing the unfolded state of SOD1 in many cases appear to form early in the unfolding reaction.
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Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics , Lund University , Sölvegatan 14A , SE-223 62 Lund , Sweden
| | - Kristine Steen Jensen
- Department of Biophysical Chemistry, Center for Molecular Protein Science , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Sandipan Mohanty
- Institute for Advanced Simulation, Jülich Supercomputing Centre , Forschungszentrum Jülich , D-52425 Jülich , Germany
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics , Lund University , Sölvegatan 14A , SE-223 62 Lund , Sweden
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7
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Nilsson D, Mohanty S, Irbäck A. Markov modeling of peptide folding in the presence of protein crowders. J Chem Phys 2018; 148:055101. [PMID: 29421894 DOI: 10.1063/1.5017031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use Markov state models (MSMs) to analyze the dynamics of a β-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major free-energy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders has a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate ku, while the folding rate kf is left largely unchanged.
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Affiliation(s)
- Daniel Nilsson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Sandipan Mohanty
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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8
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Zhu L, Petrlova J, Gysbers P, Hebert H, Wallin S, Jegerschöld C, Lagerstedt JO. Structures of apolipoprotein A-I in high density lipoprotein generated by electron microscopy and biased simulations. Biochim Biophys Acta Gen Subj 2017; 1861:2726-2738. [DOI: 10.1016/j.bbagen.2017.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/18/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
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9
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Petrlova J, Hansen FC, van der Plas MJA, Huber RG, Mörgelin M, Malmsten M, Bond PJ, Schmidtchen A. Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism. Proc Natl Acad Sci U S A 2017; 114:E4213-E4222. [PMID: 28473418 PMCID: PMC5448181 DOI: 10.1073/pnas.1619609114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Effective control of endotoxins and bacteria is crucial for normal wound healing. During injury, the key enzyme thrombin is formed, leading to generation of fibrin. Here, we show that human neutrophil elastase cleaves thrombin, generating 11-kDa thrombin-derived C-terminal peptides (TCPs), which bind to and form amorphous amyloid-like aggregates with both bacterial lipopolysaccharide (LPS) and gram-negative bacteria. In silico molecular modeling using atomic resolution and coarse-grained simulations corroborates our experimental observations, altogether indicating increased aggregation through LPS-mediated intermolecular contacts between clusters of TCP molecules. Upon bacterial aggregation, recombinantly produced TCPs induce permeabilization of Escherichia coli and phagocytic uptake. TCPs of about 11 kDa are present in acute wound fluids as well as in fibrin sloughs from patients with infected wounds. We noted aggregation and colocalization of LPS with TCPs in such fibrin material, which indicates the presence of TCP-LPS aggregates under physiological conditions. Apart from identifying a function of proteolyzed thrombin and its fragments, our findings provide an interesting link between the coagulation system, innate immunity, LPS scavenging, and protein aggregation/amyloid formation.
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Affiliation(s)
- Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden;
| | - Finja C Hansen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Mariena J A van der Plas
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | | | - Matthias Mörgelin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Martin Malmsten
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 138671 Singapore
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
- Dermatology, Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore
- Dermatology, Skane University Hospital, SE-22185 Lund, Sweden
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10
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Lucato CM, Lupton CJ, Halls ML, Ellisdon AM. Amyloidogenicity at a Distance: How Distal Protein Regions Modulate Aggregation in Disease. J Mol Biol 2017; 429:1289-1304. [PMID: 28342736 DOI: 10.1016/j.jmb.2017.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022]
Abstract
The misfolding of proteins to form amyloid is a key pathological feature of several progressive, and currently incurable, diseases. A mechanistic understanding of the pathway from soluble, native protein to insoluble amyloid is crucial for therapeutic design, and recent efforts have helped to elucidate the key molecular events that trigger protein misfolding. Generally, either global or local structural perturbations occur early in amyloidogenesis to expose aggregation-prone regions of the protein that can then self-associate to form toxic oligomers. Surprisingly, these initiating structural changes are often caused or influenced by protein regions distal to the classically amyloidogenic sequences. Understanding the importance of these distal regions in the pathogenic process has highlighted many remaining knowledge gaps regarding the precise molecular events that occur in classic aggregation pathways. In this review, we discuss how these distal regions can influence aggregation in disease and the recent technical and conceptual advances that have allowed this insight.
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Affiliation(s)
- Christina M Lucato
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher J Lupton
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew M Ellisdon
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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11
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Townsend D, Hughes E, Hussain R, Siligardi G, Baldock S, Madine J, Middleton DA. Heparin and Methionine Oxidation Promote the Formation of Apolipoprotein A-I Amyloid Comprising α-Helical and β-Sheet Structures. Biochemistry 2017; 56:1632-1644. [DOI: 10.1021/acs.biochem.6b01120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David Townsend
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Eleri Hughes
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Rohanah Hussain
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, Oxon, England
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot OX11 0DE, Oxon, England
| | - Sarah Baldock
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Jillian Madine
- Department of Biochemistry, Institute
of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David A. Middleton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
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12
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Bille A, Mohanty S, Irbäck A. Peptide folding in the presence of interacting protein crowders. J Chem Phys 2016; 144:175105. [PMID: 27155657 DOI: 10.1063/1.4948462] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.
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Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Sandipan Mohanty
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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13
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Bille A, Linse B, Mohanty S, Irbäck A. Equilibrium simulation of trp-cage in the presence of protein crowders. J Chem Phys 2015; 143:175102. [DOI: 10.1063/1.4934997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Björn Linse
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Sandipan Mohanty
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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14
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Mizuguchi C, Ogata F, Mikawa S, Tsuji K, Baba T, Shigenaga A, Shimanouchi T, Okuhira K, Otaka A, Saito H. Amyloidogenic Mutation Promotes Fibril Formation of the N-terminal Apolipoprotein A-I on Lipid Membranes. J Biol Chem 2015; 290:20947-20959. [PMID: 26175149 DOI: 10.1074/jbc.m115.664227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Indexed: 02/01/2023] Open
Abstract
The N-terminal amino acid 1-83 fragment of apolipoprotein A-I (apoA-I) has a strong propensity to form amyloid fibrils at physiological neutral pH. Because apoA-I has an ability to bind to lipid membranes, we examined the effects of the lipid environment on fibril-forming properties of the N-terminal fragment of apoA-I variants. Thioflavin T fluorescence assay as well as fluorescence and transmission microscopies revealed that upon lipid binding, fibril formation by apoA-I 1-83 is strongly inhibited, whereas the G26R mutant still retains the ability to form fibrils. Such distinct effects of lipid binding on fibril formation were also observed for the amyloidogenic prone region-containing peptides, apoA-I 8-33 and 8-33/G26R. This amyloidogenic region shifts from random coil to α-helical structure upon lipid binding. The G26R mutation appears to prevent this helix transition because lower helical propensity and more solvent-exposed conformation of the G26R variant upon lipid binding were observed in the apoA-I 1-83 fragment and 8-33 peptide. With a partially α-helical conformation induced by the presence of 2,2,2-trifluoroethanol, fibril formation by apoA-I 1-83 was strongly inhibited, whereas the G26R variant can form amyloid fibrils. These findings suggest a new possible pathway for amyloid fibril formation by the N-terminal fragment of apoA-I variants: the amyloidogenic mutations partially destabilize the α-helical structure formed upon association with lipid membranes, resulting in physiologically relevant conformations that allow fibril formation.
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Affiliation(s)
- Chiharu Mizuguchi
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Fuka Ogata
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Shiho Mikawa
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Kohei Tsuji
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Teruhiko Baba
- Research Center for Stem Cell Engineering (SCRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
| | - Akira Shigenaga
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Keiichiro Okuhira
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Hiroyuki Saito
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan.
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