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Polańska O, Szulc N, Stottko R, Olek M, Nadwodna J, Gąsior-Głogowska M, Szefczyk M. Challenges in Peptide Solubilization - Amyloids Case Study. CHEM REC 2024; 24:e202400053. [PMID: 39023378 DOI: 10.1002/tcr.202400053] [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: 03/18/2024] [Revised: 05/23/2024] [Indexed: 07/20/2024]
Abstract
Peptide science has been a rapidly growing research field because of the enormous potential application of these biocompatible and bioactive molecules. However, many factors limit the widespread use of peptides in medicine, and low solubility is among the most common problems that hamper drug development in the early stages of research. Solubility is a crucial, albeit poorly understood, feature that determines peptide behavior. Several different solubility predictors have been proposed, and many strategies and protocols have been reported to dissolve peptides, but none of them is a one-size-fits-all method for solubilization of even the same peptide. In this review, we look for the reasons behind the difficulties in dissolving peptides, analyze the factors influencing peptide aggregation, conduct a critical analysis of solubilization strategies and protocols available in the literature, and give some tips on how to deal with the so-called difficult sequences. We focus on amyloids, which are particularly difficult to dissolve and handle such as amyloid beta (Aβ), insulin, and phenol-soluble modulins (PSMs).
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Affiliation(s)
- Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Natalia Szulc
- Department of Physics and Biophysics, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Rafał Stottko
- Faculty of Chemistry, Wrocław University of Science and Technology, Gdanska 7/9, 50-344, Wrocław, Poland
| | - Mateusz Olek
- Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Traugutta 2, 41-800 Zabrze, Poland
| | - Julita Nadwodna
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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2
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Suladze S, Sarkar R, Rodina N, Bokvist K, Krewinkel M, Scheps D, Nagel N, Bardiaux B, Reif B. Atomic resolution structure of full-length human insulin fibrils. Proc Natl Acad Sci U S A 2024; 121:e2401458121. [PMID: 38809711 PMCID: PMC11161806 DOI: 10.1073/pnas.2401458121] [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: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Patients with type 1 diabetes mellitus who are dependent on an external supply of insulin develop insulin-derived amyloidosis at the sites of insulin injection. A major component of these plaques is identified as full-length insulin consisting of the two chains A and B. While there have been several reports that characterize insulin misfolding and the biophysical properties of the fibrils, atomic-level information on the insulin fibril architecture remains elusive. We present here an atomic resolution structure of a monomorphic insulin amyloid fibril that has been determined using magic angle spinning solid-state NMR spectroscopy. The structure of the insulin monomer yields a U-shaped fold in which the two chains A and B are arranged in parallel to each other and are oriented perpendicular to the fibril axis. Each chain contains two β-strands. We identify two hydrophobic clusters that together with the three preserved disulfide bridges define the amyloid core structure. The surface of the monomeric amyloid unit cell is hydrophobic implicating a potential dimerization and oligomerization interface for the assembly of several protofilaments in the mature fibril. The structure provides a starting point for the development of drugs that bind to the fibril surface and disrupt secondary nucleation as well as for other therapeutic approaches to attenuate insulin aggregation.
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Affiliation(s)
- Saba Suladze
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology, Neuherberg85764, Germany
| | - Riddhiman Sarkar
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology, Neuherberg85764, Germany
| | - Natalia Rodina
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
| | - Krister Bokvist
- Sanofi-Aventis Deutschland GmbH, Diabetes Research, Industriepark Höchst, Frankfurt65926, Germany
| | - Manuel Krewinkel
- Sanofi-Aventis Deutschland GmbH, Manufacturing Science and Technology, Industriepark Höchst, Frankfurt65926, Germany
| | - Daniel Scheps
- Chemistry Manufacturing & Controls Microbial Platform, Sanofi-Aventis Deutschland GmbH, Microbial Platform, Industriepark Höchst, Frankfurt65926, Germany
| | - Norbert Nagel
- Sanofi-Aventis Deutschland GmbH, Tides Platform, Industriepark Höchst, Frankfurt65926, Germany
| | - Benjamin Bardiaux
- Institut Pasteur, Department of Structural Biology and Chemistry, Structural Bioinformatics Unit, CNRS UMR 3528, Université Paris Cité, Paris75015, France
- Institut Pasteur, Department of Structural Biology and Chemistry, Bacterial Transmembrane Systems Unit, CNRS UMR 3528, Université Paris Cité, Paris75015, France
| | - Bernd Reif
- Bavarian Nuclear Magnetic Resonance Center at the Department of Biosciences, School of Natural Sciences, Technische Universität München, Garching85747, Germany
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology, Neuherberg85764, Germany
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3
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Bassotti E, Gabrielli S, Paradossi G, Chiessi E, Telling M. An experimentally representative in-silico protocol for dynamical studies of lyophilised and weakly hydrated amorphous proteins. Commun Chem 2024; 7:83. [PMID: 38609466 PMCID: PMC11014950 DOI: 10.1038/s42004-024-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Characterization of biopolymers in both dry and weakly hydrated amorphous states has implications for the pharmaceutical industry since it provides understanding of the effect of lyophilisation on stability and biological activity. Atomistic Molecular Dynamics (MD) simulations probe structural and dynamical features related to system functionality. However, while simulations in homogenous aqueous environments are routine, dehydrated model assemblies are a challenge with systems investigated in-silico needing careful consideration; simulated systems potentially differing markedly despite seemingly negligible changes in procedure. Here we propose an in-silico protocol to model proteins in lyophilised and weakly hydrated amorphous states that is both more experimentally representative and routinely applicable. Since the outputs from MD align directly with those accessed by neutron scattering, the efficacy of the simulation protocol proposed is shown by validating against experimental neutron data for apoferritin and insulin. This work also highlights that without cooperative experimental and simulative data, development of simulative procedures using MD alone would prove most challenging.
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Affiliation(s)
- Elisa Bassotti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Sara Gabrielli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Gaio Paradossi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy.
| | - Mark Telling
- STFC, ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11OQX, UK.
- Department of Materials, University of Oxford, Parks Road, Oxford, UK.
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4
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Thiel A, Speranza MJ, Jadhav S, Stevens LL, Unruh DK, Ren P, Ponder JW, Shen J, Schnieders MJ. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2024; 20:2921-2933. [PMID: 38507252 PMCID: PMC11008096 DOI: 10.1021/acs.jctc.3c01180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024]
Abstract
Accurately predicting protein behavior across diverse pH environments remains a significant challenge in biomolecular simulations. Existing constant-pH molecular dynamics (CpHMD) algorithms are limited to fixed-charge force fields, hindering their application to biomolecular systems described by permanent atomic multipoles or induced dipoles. This work overcomes these limitations by introducing the first polarizable CpHMD algorithm in the context of the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. Additionally, our implementation in the open-source Force Field X (FFX) software has the unique ability to handle titration state changes for crystalline systems including flexible support for all 230 space groups. The evaluation of constant-pH molecular dynamics (CpHMD) with the AMOEBA force field was performed on 11 crystalline peptide systems that span the titrating amino acids (Asp, Glu, His, Lys, and Cys). Titration states were correctly predicted for 15 out of the 16 amino acids present in the 11 systems, including for the coordination of Zn2+ by cysteines. The lone exception was for a HIS-ALA peptide where CpHMD predicted both neutral histidine tautomers to be equally populated, whereas the experimental model did not consider multiple conformers and diffraction data are unavailable for rerefinement. This work demonstrates the promise polarizable CpHMD simulations for pKa predictions, the study of biochemical mechanisms such as the catalytic triad of proteases, and for improved protein-ligand binding affinity accuracy in the context of pharmaceutical lead optimization.
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Affiliation(s)
- Andrew
C. Thiel
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Matthew J. Speranza
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
| | - Sanika Jadhav
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Lewis L. Stevens
- Department
of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Daniel K. Unruh
- Office
of the Vice President for Research, University
of Iowa, Iowa City, Iowa 52242, United
States
| | - Pengyu Ren
- Department
of Biomedical Engineering, University of
Texas, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Michael J. Schnieders
- Department
of Biomedical Engineering, University of
Iowa, Iowa City, Iowa 52242, United States
- Department
of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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5
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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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6
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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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7
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Khan JM, Malik A, Alresaini SM. Molecular mechanism of insulin aggregation in the presence of a cationic surfactant. Int J Biol Macromol 2023; 230:123370. [PMID: 36693606 DOI: 10.1016/j.ijbiomac.2023.123370] [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: 11/14/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Protein aggregation and amyloid fibrillation are connected with neurodegenerative disorders. Insulin, a small molecular weight protein related to type II diabetes, has been shown to self-assemble to form protein aggregates. In this work, we investigated the effects of cetyltrimethylammonium bromide (CTAB) of insulin on the in vitro aggregation process at pH 7.4 and 2.0. The aggregation tendency of insulin was measured using a variety of biophysical approaches, including turbidity measurements, light scattering, far UV-CD, ThT dye binding, and transmission electron microscopy. The turbidity results demonstrated that at pH 7.4, a low concentration of CTAB (30-180 μM) causes insulin aggregation but at higer concentration (>180 μM) aggregation was not seen. However, at pH 2.0, both low as well as high concentrations of CTAB were unable to promote insulin aggregation. The ThT dye binding and far-UV CD data suggest that aggregation induced by CTAB is not having an ordered structure. Insulin treated with higher concentrations (>180 μM) of CTAB, the insulin gained a secondary structure. The possible cause of inducing aggregation in insulin is electrostatic and hydrophobic interaction because insulin contains a net negative charge at pH 7.4 and no aggregation at pH 2.0 due to electrostatic repulsion.
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Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition, College 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
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8
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Acharya N, Jha SK. Dry Molten Globule-Like Intermediates in Protein Folding, Function, and Disease. J Phys Chem B 2022; 126:8614-8622. [PMID: 36286394 DOI: 10.1021/acs.jpcb.2c04991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The performance of a protein depends on its correct folding to the final functional native form. Hence, understanding the process of protein folding has remained an important field of research for the scientific community for the past five decades. Two important intermediate states, namely, wet molten globule (WMG) and dry molten globule (DMG), have emerged as critical milestones during protein folding-unfolding reactions. While much has been discussed about WMGs as a common unfolding intermediate, the evidence for DMGs has remained elusive owing to their near-native features, which makes them difficult to probe using global structural probes. This Review puts together the available literature and new evidence on DMGs to give a broader perspective on the universality of DMGs and discuss their significance in protein folding, function, and disease.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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9
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Abstract
Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer's and Parkinson's diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.
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10
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Gorai B, Vashisth H. Progress in Simulation Studies of Insulin Structure and Function. Front Endocrinol (Lausanne) 2022; 13:908724. [PMID: 35795141 PMCID: PMC9252437 DOI: 10.3389/fendo.2022.908724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 01/02/2023] Open
Abstract
Insulin is a peptide hormone known for chiefly regulating glucose level in blood among several other metabolic processes. Insulin remains the most effective drug for treating diabetes mellitus. Insulin is synthesized in the pancreatic β-cells where it exists in a compact hexameric architecture although its biologically active form is monomeric. Insulin exhibits a sequence of conformational variations during the transition from the hexamer state to its biologically-active monomer state. The structural transitions and the mechanism of action of insulin have been investigated using several experimental and computational methods. This review primarily highlights the contributions of molecular dynamics (MD) simulations in elucidating the atomic-level details of conformational dynamics in insulin, where the structure of the hormone has been probed as a monomer, dimer, and hexamer. The effect of solvent, pH, temperature, and pressure have been probed at the microscopic scale. Given the focus of this review on the structure of the hormone, simulation studies involving interactions between the hormone and its receptor are only briefly highlighted, and studies on other related peptides (e.g., insulin-like growth factors) are not discussed. However, the review highlights conformational dynamics underlying the activities of reported insulin analogs and mimetics. The future prospects for computational methods in developing promising synthetic insulin analogs are also briefly highlighted.
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Affiliation(s)
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, United States
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11
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Das A, Shah M, Saraogi I. Molecular Aspects of Insulin Aggregation and Various Therapeutic Interventions. ACS BIO & MED CHEM AU 2022; 2:205-221. [PMID: 37101572 PMCID: PMC10114644 DOI: 10.1021/acsbiomedchemau.1c00054] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Protein aggregation leading to the formation of amyloid fibrils has various adverse effects on human health ranging from fatigue and numbness to organ failure and death in extreme cases. Insulin, a peptide hormone commonly used to treat diabetes, undergoes aggregation at the site of repeated injections in diabetic patients as well as during its industrial production and transport. The reduced bioavailability of insulin due to aggregation hinders the proper control of glucose levels in diabetic patients. Thus, it is necessary to develop rational approaches for inhibiting insulin aggregation, which in turn requires a detailed understanding of the mechanism of fibrillation. Given the relative simplicity of insulin and ease of access, insulin has also served as a model system for studying amyloids. Approaches to inhibit insulin aggregation have included the use of natural molecules, synthetic peptides or small molecules, and bacterial chaperone machinery. This review focuses on insulin aggregation with an emphasis on its mechanism, the structural features of insulin fibrils, and the reported inhibitors that act at different stages in the aggregation pathway. We discuss molecules that can serve as leads for improved inhibitors for use in commercial insulin formulations. We also discuss the aggregation propensity of fast- and slow-acting insulin biosimilars, commonly administered to diabetic patients. The development of better insulin aggregation inhibitors and insights into their mechanism of action will not only aid diabetic therapies, but also enhance our knowledge of protein amyloidosis.
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Affiliation(s)
- Anirban Das
- Department
of Chemistry and Department of Biological Sciences, Indian
Institute of Science Education and Research
Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Mosami Shah
- Department
of Chemistry and Department of Biological Sciences, Indian
Institute of Science Education and Research
Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department
of Chemistry and Department of Biological Sciences, Indian
Institute of Science Education and Research
Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
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12
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Bardhan M, Dolui S, Chaudhuri S, Paul U, Bhattacharjee G, Ghosal M, Maiti NC, Mukhopadhyay D, Senapati D. Impact of porous nanomaterials on inhibiting protein aggregation behaviour. RSC Adv 2021; 11:3354-3362. [PMID: 35424305 PMCID: PMC8693984 DOI: 10.1039/d0ra10927d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Aggregation of intrinsically disordered as well as the ordered proteins under certain premises or physiological conditions leads to pathological disorder. Here we have presented a detailed investigation on the effect of a porous metallic (Au) and a non-metallic (Si) nanomaterial on the formation of ordered (fiber-like/amyloid) and disordered (amorphous) aggregates of proteins. Porous nanogold (PNG) was found to reduce the amyloid aggregation of insulin but does not have much impact on the lag phase in the aggregation kinetics, whereas porous nano-silica (PNS) was found both to decrease the amount of aggregation as well as prolong the lag phase of amyloid fiber formation from insulin. On the other hand, both the porous nanoparticles are found to decrease the extent of amorphous aggregation (with slight improvement for PNS) of pathogenic huntingtin (Htt) protein in Huntington's disease cell model. This is a noted direct observation in controlling and understanding protein aggregation diseases which may help us to formulate nanotherapeutic drugs for future clinical applications. Aggregation of intrinsically disordered as well as the ordered proteins under certain premises or physiological conditions leads to pathological disorder.![]()
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Affiliation(s)
- Munmun Bardhan
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Sandip Dolui
- Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Siddhi Chaudhuri
- Biophysics and Structural Genomics Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Uttam Paul
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | | | - Manorama Ghosal
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Nakul C. Maiti
- Biophysics and Structural Genomics Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Dulal Senapati
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
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13
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Lam YPY, Chiu CKC, Wootton CA, Hands-Portman I, Li M, Barrow MP, O'Connor PB. Does deamidation affect inhibitory mechanisms towards amyloid protein aggregation? Chem Commun (Camb) 2020; 56:9787-9790. [PMID: 32748913 DOI: 10.1039/d0cc03548c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deamidated amyloid proteins have been shown to accelerate fibril formation. Herein, the results show the inhibition performance and the interaction site between site-specific inhibitor and amyloid protein are significantly influenced by deamidation; while the inhibition mechanism of non-site specific inhibitor shows no significant disruption caused by amyloid protein deamidation.
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Affiliation(s)
- Yuko P Y Lam
- Department of Chemistry, University of Warwick, Coventry, UK.
| | | | | | | | - Meng Li
- Department of Chemistry, University of Warwick, Coventry, UK.
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, UK.
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14
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The Environment Is a Key Factor in Determining the Anti-Amyloid Efficacy of EGCG. Biomolecules 2019; 9:biom9120855. [PMID: 31835741 PMCID: PMC6995563 DOI: 10.3390/biom9120855] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/06/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Millions of people around the world suffer from amyloid-related disorders, including Alzheimer's and Parkinson's diseases. Despite significant and sustained efforts, there are still no disease-modifying drugs available for the majority of amyloid-related disorders, and the overall failure rate in clinical trials is very high, even for compounds that show promising anti-amyloid activity in vitro. In this study, we demonstrate that even small changes in the chemical environment can strongly modulate the inhibitory effects of anti-amyloid compounds. Using one of the best-established amyloid inhibitory compounds, epigallocatechin-3-gallate (EGCG), as an example, and two amyloid-forming proteins, insulin and Parkinson's disease-related α -synuclein, we shed light on the previously unexplored sensitivity to solution conditions of the action of this compound on amyloid fibril formation. In the case of insulin, we show that the classification of EGCG as an amyloid inhibitor depends on the experimental conditions select, on the method used for the evaluation of the efficacy, and on whether or not EGCG is allowed to oxidise before the experiment. For α -synuclein, we show that a small change in pH value, from 7 to 6, transforms EGCG from an efficient inhibitor to completely ineffective, and we were able to explain this behaviour by the increased stability of EGCG against oxidation at pH 6.
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15
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Quantifying Na(I)-insulin and K(I)-insulin non-covalent complexes by ESI–MS method and calculation of their equilibrium constants. Int J Biol Macromol 2017; 103:910-918. [DOI: 10.1016/j.ijbiomac.2017.05.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/05/2017] [Accepted: 05/25/2017] [Indexed: 01/10/2023]
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16
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Singh R, Bansal R, Rathore AS, Goel G. Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics. Biophys J 2017; 112:1571-1585. [PMID: 28445749 DOI: 10.1016/j.bpj.2017.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 03/03/2017] [Accepted: 03/20/2017] [Indexed: 12/29/2022] Open
Abstract
Earliest events in the aggregation process, such as single molecule reconfiguration, are extremely important and the most difficult to characterize in experiments. To this end, we have used well-tempered bias exchange metadynamics simulations to determine the equilibrium ensembles of an insulin molecule under amyloidogenic conditions of low pH and high temperature. A bin-based clustering method that uses statistics accumulated in bias exchange metadynamics trajectories was employed to construct a detailed thermodynamic and kinetic model of insulin folding. The highest lifetime, lowest free-energy ensemble identified consisted of native conformations adopted by a folded insulin monomer in solution, namely, the R-, the Rf-, and the T-states of insulin. The lowest free-energy structure had a root mean square deviation of only 0.15 nm from native x-ray structure. The second longest-lived metastable state was an unfolded, compact monomer with little similarity to the native structure. We have identified three additional long-lived, metastable states from the bin-based model. We then carried out an exhaustive structural characterization of metastable states on the basis of tertiary contact maps and per-residue accessible surface areas. We have also determined the lowest free-energy path between two longest-lived metastable states and confirm earlier findings of non-two-state folding for insulin through a folding intermediate. The ensemble containing the monomeric intermediate retained 58% of native hydrophobic contacts, however, accompanied by a complete loss of native secondary structure. We have discussed the relative importance of nativelike versus nonnative tertiary contacts for the folding transition. We also provide a simple measure to determine the importance of an individual residue for folding transition. Finally, we have compared and contrasted this intermediate with experimental data obtained in spectroscopic, crystallographic, and calorimetric measurements during early stages of insulin aggregation. We have also determined stability of monomeric insulin by incubation at a very low concentration to isolate protein-protein interaction effects.
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Affiliation(s)
- Richa Singh
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Rohit Bansal
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Anurag Singh Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India.
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17
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Das S, Bhattacharyya D. Destabilization of Human Insulin Fibrils by Peptides of Fruit Bromelain Derived From Ananas comosus (Pineapple). J Cell Biochem 2017; 118:4881-4896. [PMID: 28548677 DOI: 10.1002/jcb.26173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/25/2017] [Indexed: 12/20/2022]
Abstract
Deposition of insulin aggregates in human body leads to dysfunctioning of several organs. Effectiveness of fruit bromelain from pineapple in prevention of insulin aggregate was investigated. Proteolyses of bromelain was done as par human digestive system and the pool of small peptides was separated from larger peptides and proteins. Under conditions of growth of insulin aggregates from its monomers, this pool of peptides restricted the reaction upto formation of oligomers of limited size. These peptides also destabilized preformed insulin aggregates to oligomers. These processes were followed fluorimetrically using Thioflavin T and 1-ANS, size-exclusion HPLC, dynamic light scattering, atomic force microscopy, and transmission electron microscopy. Sequences of insulin (A and B chains) and bromelain were aligned using Clustal W software to predict most probable sites of interactions. Synthetic tripeptides corresponding to the hydrophobic interactive sites of bromelain showed disaggregation of insulin suggesting specificity of interactions. The peptides GG and AAA serving as negative controls showed no potency in destabilization of aggregates. Disaggregation potency of the peptides was also observed when insulin was deposited on HepG2 liver cells where no formation of toxic oligomers occurred. Amyloidogenic des-octapeptide (B23-B30 of insulin) incapable of cell signaling showed cytotoxicity similar to insulin. This toxicity could be neutralized by bromelain derived peptides. FT-IR and far-UV circular dichroism analysis indicated that disaggregated insulin had structure distinctly different from that of its hexameric (native) or monomeric states. Based on the stoichiometry of interaction and irreversibility of disaggregation, the mechanism/s of the peptides and insulin interactions has been proposed. J. Cell. Biochem. 118: 4881-4896, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sromona Das
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032, India
| | - Debasish Bhattacharyya
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032, India
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18
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Donnini S, Ullmann RT, Groenhof G, Grubmüller H. Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer. J Chem Theory Comput 2016; 12:1040-51. [PMID: 26881315 DOI: 10.1021/acs.jctc.5b01160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.
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Affiliation(s)
- Serena Donnini
- Nanoscience Center and Department of Biological and Environmental Sciences, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylä, Finland
| | - R Thomas Ullmann
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä , P. O. Box 35, 40014 Jyväskylä, Finland
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Faßberg 11, 37077 Göttingen, Germany
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19
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Mishra NK, Krishna Deepak RNV, Sankararamakrishnan R, Verma S. Controlling in Vitro Insulin Amyloidosis with Stable Peptide Conjugates: A Combined Experimental and Computational Study. J Phys Chem B 2015; 119:15395-406. [DOI: 10.1021/acs.jpcb.5b08215] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Narendra Kumar Mishra
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
| | - R. N. V. Krishna Deepak
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
| | - Ramasubbu Sankararamakrishnan
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
| | - Sandeep Verma
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
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20
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Felice B, Prabhakaran MP, Zamani M, Rodríguez AP, Ramakrishna S. Electrosprayed poly(vinyl alcohol) particles: preparation and evaluation of their drug release profile. POLYM INT 2015. [DOI: 10.1002/pi.4972] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Betiana Felice
- Laboratorio de Medios e Interfases (LAMEIN), Departamento de Bioingeniería; Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán; Tucumán Argentina
- Instituto Superior de Investigaciones Biológicas (INSIBIO); CONICET 4000 Tucumán Argentina
- START - Thrust 3, Create Research Wing 03-08, 1 Create Way; National University of Singapore; Singapore 138602
| | - Molamma P Prabhakaran
- START - Thrust 3, Create Research Wing 03-08, 1 Create Way; National University of Singapore; Singapore 138602
- Department of Mechanical Engineering; National University of Singapore; Singapore
| | - Maedeh Zamani
- START - Thrust 3, Create Research Wing 03-08, 1 Create Way; National University of Singapore; Singapore 138602
- Department of Mechanical Engineering; National University of Singapore; Singapore
| | - Andrea P Rodríguez
- Laboratorio de Medios e Interfases (LAMEIN), Departamento de Bioingeniería; Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán; Tucumán Argentina
- Instituto Superior de Investigaciones Biológicas (INSIBIO); CONICET 4000 Tucumán Argentina
| | - Seeram Ramakrishna
- START - Thrust 3, Create Research Wing 03-08, 1 Create Way; National University of Singapore; Singapore 138602
- Department of Mechanical Engineering; National University of Singapore; Singapore
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21
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Van Vuong Q, Bednarikova Z, Antosova A, Huy PDQ, Siposova K, Tuan NA, Li MS, Gazova Z. Inhibition of insulin amyloid fibrillization by glyco-acridines: an in vitro and in silico study. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00004a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of glyco-acridines determines their impact on insulin amyloid aggregation and newly introduced geometrical descriptors allow us to distinguish different binding affinities.
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Affiliation(s)
- Quan Van Vuong
- Institute for Computational Science and Technology
- Ho Chi Minh City
- Vietnam
| | - Zuzana Bednarikova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | - Andrea Antosova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | - Pham Dinh Quoc Huy
- Institute for Computational Science and Technology
- Ho Chi Minh City
- Vietnam
- Institute of Physics
- Polish Academy of Sciences
| | - Katarina Siposova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | | | - Mai Suan Li
- Institute for Computational Science and Technology
- Ho Chi Minh City
- Vietnam
- Institute of Physics
- Polish Academy of Sciences
| | - Zuzana Gazova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
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22
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Das A, Chakrabarti A, Das PK. Suppression of protein aggregation by gold nanoparticles: a new way to store and transport proteins. RSC Adv 2015. [DOI: 10.1039/c4ra17026a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Suppression of protein aggregation by gold nanoparticles under physiological conditions and its dependence on the nanoparticle size.
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Affiliation(s)
- Anindita Das
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 560012
- India
| | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - Puspendu K. Das
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 560012
- India
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23
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Gladytz A, Lugovoy E, Charvat A, Häupl T, Siefermann KR, Abel B. Intermediates caught in the act: tracing insulin amyloid fibril formation in time by combined optical spectroscopy, light scattering, mass spectrometry and microscopy. Phys Chem Chem Phys 2015; 17:918-27. [DOI: 10.1039/c4cp03072a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Insulin under acidic conditions. PDB-Databank structure visualized with VMD.
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Affiliation(s)
- A. Gladytz
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
| | - E. Lugovoy
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
| | - A. Charvat
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
| | - T. Häupl
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- 04103 Leipzig
- Germany
| | - K. R. Siefermann
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
| | - B. Abel
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig
- Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
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24
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Batzli KM, Love BJ. Formation of platinum-coated templates of insulin nanowires used in reducing 4-nitrophenol. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 48:103-11. [PMID: 25579902 DOI: 10.1016/j.msec.2014.11.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/10/2014] [Accepted: 11/22/2014] [Indexed: 10/24/2022]
Abstract
Modern technology demands ever smaller and more efficient nanoparticles, wires and networks. The natural tendency for amyloid proteins to form fibrillar structures is leveraged in creating high aspect ratio, nano-sized protein fibers as scaffolds for metallized nanowires. The morphology of fibrils is influenced by induced strain during denaturing and early aggregation and subsequent fibril deposition with platinum leads to controlled catalyst surfaces based on the initial protein precipitate. Here we have created insulin fibrils with varying morphologies produced in the presence of heat and strain and investigated their metallization with platinum by TEM. The catalytic activity of the metal-coated protein fibrils was resolved by tracking the reaction kinetics of the conversion of 4-nitrophenol to 4-aminophenol in the presence of the produced nanowires using UV-Vis spectroscopy. The effects of fibril morphology and temperature on the pseudo-first-order kinetics of conversion are investigated. Conversion to 4-aminophenol occurs on the order of minutes and is independent of temperature in the range tested (7 to 20°C). Two regimes of conversion are identified, an early higher rate, followed by a slower later rate.
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Affiliation(s)
- Kiersten M Batzli
- Department of Materials Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109, United States
| | - Brian J Love
- Department of Materials Science and Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109, United States; Macromolecular Science and Engineering Research Center, University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109, United States; Department of Biomedical Engineering and Biologic and Materials Sciences (Dentistry), University of Michigan, 2300 Hayward St, Ann Arbor, MI 48109, United States.
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25
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Batzli KM, Love BJ. Agitation of amyloid proteins to speed aggregation measured by ThT fluorescence: a call for standardization. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 48:359-64. [PMID: 25579934 DOI: 10.1016/j.msec.2014.09.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
This retrospective study of protein aggregation measured by Thioflavin T (ThT) fluorescence assay in published literature has assessed protein sensitivity to denaturing conditions that include elevated temperatures, fluctuations in pH, and concentration and, in particular, agitation to induce amyloid structure formation. The dynamic tracking of fluorescence shows a sigmoidal evolution as aggregates form; the resulting kinetics of association have been analyzed to explore the range of aggregation behavior which occurs based on environmental parameters. Comparisons between the experimental results of different groups have been historically difficult due to subtleties of experimental procedures including denaturing temperature, protein type and concentration, formulation differences, and how agitation is achieved. While it is clear that agitation has a strong influence on the driving force for aggregation, the use of magnetic stirring bar or shaker table rotational speed is insufficient to characterize the degree of turbulence produced during shear. The pathway forward in resolving dependence of aggregate formation on shear may require alternative methodologies or better standardization of the experimental protocols.
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Affiliation(s)
- Kiersten M Batzli
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Brian J Love
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Macromolecular Science and Engineering Research Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering and Biologic and Materials Sciences (Dentistry), University of Michigan, Ann Arbor, MI 48109, USA.
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26
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Matthes D, Daebel V, Meyenberg K, Riedel D, Heim G, Diederichsen U, Lange A, de Groot BL. Spontaneous Aggregation of the Insulin-Derived Steric Zipper Peptide VEALYL Results in Different Aggregation Forms with Common Features. J Mol Biol 2014; 426:362-76. [DOI: 10.1016/j.jmb.2013.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 10/09/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
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27
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Foderà V, Zaccone A, Lattuada M, Donald AM. Electrostatics controls the formation of amyloid superstructures in protein aggregation. PHYSICAL REVIEW LETTERS 2013; 111:108105. [PMID: 25166715 DOI: 10.1103/physrevlett.111.108105] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Indexed: 05/23/2023]
Abstract
The possibility for proteins to aggregate in different superstructures, i.e. large-scale polymorphism, has been widely observed, but an understanding of the physicochemical mechanisms behind it is still out of reach. Here we present a theoretical model for the description of a generic aggregate formed from an ensemble of charged proteins. The model predicts the formation of multifractal structures with the geometry of the growth determined by the electrostatic interactions between single proteins. The model predictions are successfully verified in comparison with experimental curves for aggregate growth allowing us to reveal the mechanism of formation of such complex structures. The model is general and is able to predict aggregate morphologies occurring both in vivo and in vitro. Our findings provide a framework where the physical interactions between single proteins, the aggregate morphology, and the growth kinetics are connected into a single model in agreement with the experimental data.
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Affiliation(s)
- Vito Foderà
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alessio Zaccone
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom and Theory of Condensed Matter, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Marco Lattuada
- ETH Institute for Chemical and Bioengineering, HCI F135, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
| | - Athene M Donald
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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28
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Shaking and stirring: Comparison of controlled laboratory stress conditions applied to the human growth hormone. Process Biochem 2013. [DOI: 10.1016/j.procbio.2012.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Surmacz-Chwedoruk W, Nieznańska H, Wójcik S, Dzwolak W. Cross-seeding of fibrils from two types of insulin induces new amyloid strains. Biochemistry 2012; 51:9460-9. [PMID: 23127165 DOI: 10.1021/bi301144d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The irreversibility and autocatalytic character of amyloidogenesis and the polymorphism of amyloid fibrils underlie the phenomenon of self-propagating strains, wherein the mother seed, rather than the seeding environment, determines the properties of daughter fibrils. Here we study the formation of amyloid fibrils from bovine insulin and the recombinant Lys(B31)-Arg(B32) human insulin analog. The two polypeptides are similar enough to cross-seed but, upon spontaneous aggregation, form amyloid fibrils with distinct spectral features in the infrared amide I' band region. When bovine insulin is cross-seeded with the analog amyloid (and vice versa), the shape, absorption maximum, and even fine fingerprint features of the amide I' band are passed from the mother to daughter fibrils with a high degree of fidelity. Although the differences in primary structure between bovine insulin and the Lys(B31)-Arg(B32) analog of human insulin lie outside of the polypeptide's critical amyloidogenic regions, they affect the secondary structure of fibrils, possibly the formation of intermolecular salt bridges, and the susceptibility to dissection and denaturation with dimethyl sulfoxide (DMSO). All these phenotypic features of mother fibrils are imprinted in daughter amyloid upon cross-seeding. Analysis of noncooperative DMSO-induced denaturation of daughter fibrils suggests that the self-propagating polymorphism underlying the emergence of new amyloid strains is encoded on the level of secondary structure. Our findings have been discussed in the context of polymorphism of fibrils, amyloid strains, and possible implications for mechanisms of amyloidogenesis.
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30
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Factors affecting the formation of insulin amyloid spherulites. Colloids Surf B Biointerfaces 2012; 89:216-22. [DOI: 10.1016/j.colsurfb.2011.09.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 09/04/2011] [Accepted: 09/10/2011] [Indexed: 11/20/2022]
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31
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Liu Y, Burger SK, Ayers PW, Vöhringer-Martinez E. Computational Study of the Binding Modes of Caffeine to the Adenosine A2A Receptor. J Phys Chem B 2011; 115:13880-90. [PMID: 21970461 DOI: 10.1021/jp2022049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yuli Liu
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4M1, Canada
| | - Steven K. Burger
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4M1, Canada
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4M1, Canada
| | - Esteban Vöhringer-Martinez
- Laboratorio de Química Teórica Computacional (QTC), Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
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Heldt CL, Kurouski D, Sorci M, Grafeld E, Lednev IK, Belfort G. Isolating toxic insulin amyloid reactive species that lack β-sheets and have wide pH stability. Biophys J 2011; 100:2792-800. [PMID: 21641325 DOI: 10.1016/j.bpj.2011.04.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/05/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022] Open
Abstract
Amyloid diseases, including Alzheimer's disease, are characterized by aggregation of normally functioning proteins or peptides into ordered, β-sheet rich fibrils. Most of the theories on amyloid toxicity focus on the nuclei or oligomers in the fibril formation process. The nuclei and oligomers are transient species, making their full characterization difficult. We have isolated toxic protein species that act like an oligomer and may provide the first evidence of a stable reactive species created by disaggregation of amyloid fibrils. This reactive species was isolated by dissolving amyloid fibrils at high pH and it has a mass >100 kDa and a diameter of 48 ± 15 nm. It seeds the formation of fibrils in a dose dependent manner, but using circular dichroism and deep ultraviolet resonance Raman spectroscopy, the reactive species was found to not have a β-sheet rich structure. We hypothesize that the reactive species does not decompose at high pH and maintains its structure in solution. The remaining disaggregated insulin, excluding the toxic reactive species that elongated the fibrils, returned to native structured insulin. This is the first time, to our knowledge, that a stable reactive species of an amyloid reaction has been separated and characterized by disaggregation of amyloid fibrils.
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Affiliation(s)
- Caryn L Heldt
- Howard P. Isermann Department of Chemical and Biological Engineering and The Center of Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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Donnini S, Tegeler F, Groenhof G, Grubmüller H. Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. J Chem Theory Comput 2011; 7:1962-1978. [PMID: 21687785 PMCID: PMC3114466 DOI: 10.1021/ct200061r] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Indexed: 12/22/2022]
Abstract
pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach. In the latter, the dynamics of the titration coordinate λ, which interpolates between the protonated and deprotonated states, is driven by generalized forces between the protonated and deprotonated states. The hydration free energy, as a function of pH, is included to facilitate constant pH simulations. The protonation states of titratable groups are allowed to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH. The accuracy of the method is tested against titration curves of single amino acids and a dipeptide in explicit solvent.
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Affiliation(s)
- Serena Donnini
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Gerrit Groenhof
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Matthes D, Gapsys V, Daebel V, de Groot BL. Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization. PLoS One 2011; 6:e19129. [PMID: 21559277 PMCID: PMC3086902 DOI: 10.1371/journal.pone.0019129] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 03/16/2011] [Indexed: 11/19/2022] Open
Abstract
The process of protein misfolding and self-assembly into various, polymorphic aggregates is associated with a number of important neurodegenerative diseases. Only recently, crystal structures of several short peptides have provided detailed structural insights into -sheet rich aggregates, known as amyloid fibrils. Knowledge about early events of the formation and interconversion of small oligomeric states, an inevitable step in the cascade of peptide self-assembly, however, remains still limited. We employ molecular dynamics simulations in explicit solvent to study the spontaneous aggregation process of steric zipper peptide segments from the tau protein and insulin in atomistic detail. Starting from separated chains with random conformations, we find a rapid formation of structurally heterogeneous, -sheet rich oligomers, emerging from multiple bimolecular association steps and diverse assembly pathways. Furthermore, our study provides evidence that aggregate intermediates as small as dimers can be kinetically trapped and thus affect the structural evolution of larger oligomers. Alternative aggregate structures are found for both peptide sequences in the different independent simulations, some of which feature characteristics of the known steric zipper conformation (e.g., -sheet bilayers with a dry interface). The final aggregates interconvert with topologically distinct oligomeric states exclusively via internal rearrangements. The peptide oligomerization was analyzed through the perspective of a minimal oligomer, i.e., the dimer. Thereby all observed multimeric aggregates can be consistently mapped onto a space of reduced dimensionality. This novel method of conformational mapping reveals heterogeneous association and reorganization dynamics that are governed by the characteristics of peptide sequence and oligomer size.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Venita Daebel
- Solid-State NMR, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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Heldt CL, Sorci M, Posada D, Hirsa A, Belfort G. Detection and reduction of microaggregates in insulin preparations. Biotechnol Bioeng 2010; 108:237-41. [DOI: 10.1002/bit.22902] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Helmreich EJ. Ways and means of coping with uncertainties of the relationship of the genetic blue print to protein structure and function in the cell. Cell Commun Signal 2010; 8:26. [PMID: 20849616 PMCID: PMC2954850 DOI: 10.1186/1478-811x-8-26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/17/2010] [Indexed: 11/24/2022] Open
Abstract
As one of the disciplines of systems biology, proteomics is central to enabling the elucidation of protein function within the cell; furthermore, the question of how to deduce protein structure and function from the genetic readout has gained new significance. This problem is of particular relevance for proteins engaged in cell signalling. In dealing with this question, I shall critically comment on the reliability and predictability of transmission and translation of the genetic blue print into the phenotype, the protein. Based on this information, I will then evaluate the intentions and goals of today's proteomics and gene-networking and appraise their chances of success. Some of the themes commented on in this publication are explored in greater detail with particular emphasis on the historical roots of concepts and techniques in my forthcoming book, published in German: Von Molekülen zu Zellen. 100 Jahre experimentelle Biologie. Betrachtungen eines Biochemikers.
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Hensen U, Grubmüller H, Lange OF. Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:011913. [PMID: 19658735 DOI: 10.1103/physreve.80.011913] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2008] [Revised: 03/19/2009] [Indexed: 05/28/2023]
Abstract
The quasiharmonic approximation is the most widely used estimate for the configurational entropy of macromolecules from configurational ensembles generated from atomistic simulations. This method, however, rests on two assumptions that severely limit its applicability, (i) that a principal component analysis yields sufficiently uncorrelated modes and (ii) that configurational densities can be well approximated by Gaussian functions. In this paper we introduce a nonparametric density estimation method which rests on adaptive anisotropic kernels. It is shown that this method provides accurate configurational entropies for up to 45 dimensions thus improving on the quasiharmonic approximation. When embedded in the minimally coupled subspace framework, large macromolecules of biological interest become accessible, as demonstrated for the 67-residue coldshock protein.
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Affiliation(s)
- Ulf Hensen
- Department of Theoretical Biophysics, Max-Planck Institut für biophysikalische Chemie, 37070 Göttingen, Germany
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