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Danielsson A, Samsonov SA, Liwo A, Sieradzan AK. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. J Chem Theory Comput 2023; 19:6023-6036. [PMID: 37587433 PMCID: PMC10500997 DOI: 10.1021/acs.jctc.3c00511] [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: 05/17/2023] [Indexed: 08/18/2023]
Abstract
Heparin is an unbranched periodic polysaccharide composed of negatively charged monomers and involved in key biological processes, including anticoagulation, angiogenesis, and inflammation. Its structure and dynamics have been studied extensively using experimental as well as theoretical approaches. The conventional approach of computational chemistry applied to the analysis of biomolecules is all-atom molecular dynamics, which captures the interactions of individual atoms by solving Newton's equation of motion. An alternative is molecular dynamics simulations using coarse-grained models of biomacromolecules, which offer a reduction of the representation and consequently enable us to extend the time and size scale of simulations by orders of magnitude. In this work, we extend the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules developed in our laboratory to heparin. We carried out extensive tests to estimate the optimal weights of energy terms of the effective energy function as well as the optimal Debye-Hückel screening factor for electrostatic interactions. We applied the model to study unbound heparin molecules of polymerization degree ranging from 6 to 68 residues. We compare the obtained coarse-grained heparin conformations with models obtained from X-ray diffraction studies of heparin. The SUGRES-1P force field was able to accurately predict the general shape and global characteristics of heparin molecules.
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Affiliation(s)
- Annemarie Danielsson
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A. Samsonov
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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2
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Leimu L, Haavisto O, Nesati V, Holm P, Haapalinna A, Salbo R, Pesonen U. Development of an in vitro aggregation assay for long synthetic polypeptide, amyloidogenic gelsolin fragment AGelD187N 173-242. PLoS One 2023; 18:e0290179. [PMID: 37590229 PMCID: PMC10434866 DOI: 10.1371/journal.pone.0290179] [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: 04/11/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Aggregation of the gelsolin protein fragment is the hallmark of the hereditary systemic disease gelsolin amyloidosis. As with other protein misfolding diseases, there is an urgent need for efficient disease-modifying treatment for gelsolin amyloidosis. The formation of amyloids can be reproduced by incubating the disease-causing amyloidogenic 8 kDa polypeptide, 70-residue gelsolin protein fragment, AGelD187N 173-242, in vitro and monitoring the process by thioflavin T dye. However, for screening of potential aggregation inhibitors, the required protein amounts are large and the biotechnological production of amyloidogenic proteins has many challenges. Conversely, use of shorter synthetic regions of AGelD187N 173-242 does not mimic the in vivo aggregation kinetics of full-length fragment as they have different aggregation propensity. In this study, we present an in vitro aggregation assay for full-length AGelD187N 173-242 that has been produced by solid-phase chemical synthesis and after that monomerized carefully. Chemical synthesis allows us to produce high quantities of full-length fragment efficiently and at low cost. We demonstrate that the generated aggregates are fibrillar in nature and how the purity, terminal modification, initial aggregates and seeding affect the aggregation kinetics of a synthetic gelsolin fragment. We also present sufficient quality criteria for the initial monomerized synthetic polypeptide.
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Affiliation(s)
- Laura Leimu
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Oskar Haavisto
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Victor Nesati
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | | | - Rune Salbo
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
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3
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Khurshid B, Rehman AU, Luo R, Khan A, Wadood A, Anwar J. Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. ACS OMEGA 2022; 7:15132-15144. [PMID: 35572757 PMCID: PMC9089684 DOI: 10.1021/acsomega.2c01034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 05/14/2023]
Abstract
Glycosaminoglycans (GAGs), in particular, heparan sulfate and heparin, are found colocalized with Aβ amyloid. They have been shown to enhance fibril formation, suggesting a possible pathological connection. We have investigated heparin's assembly of the KLVFFA peptide fragment using molecular dynamics simulation, to gain a molecular-level mechanistic understanding of how GAGs enhance fibril formation. The simulations reveal an exquisite process wherein heparin accelerates peptide assembly by first "gathering" the peptide molecules and then assembling them. Heparin does not act as a mere template but is tightly coupled to the peptides, yielding a composite protofilament structure. The strong intermolecular interactions suggest composite formation to be a general feature of heparin's interaction with peptides. Heparin's chain flexibility is found to be essential to its fibril promotion activity, and the need for optimal heparin chain length and concentration has been rationalized. These insights yield design rules (flexibility; chain-length) and protocol guidance (heparin:peptide molar ratio) for developing effective heparin mimetics and other functional GAGs.
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Affiliation(s)
- Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Ray Luo
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Alamzeb Khan
- Department
of Pediatrics, Yale School of Medicine, Yale University, New Haven, Connecticut 06511, United States
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Jamshed Anwar
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, United Kingdom
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4
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Ahanger I, Parray ZA, Nasreen K, Ahmad F, Hassan MI, Islam A, Sharma A. Heparin Accelerates the Protein Aggregation via the Downhill Polymerization Mechanism: Multi-Spectroscopic Studies to Delineate the Implications on Proteinopathies. ACS OMEGA 2021; 6:2328-2339. [PMID: 33521471 PMCID: PMC7841943 DOI: 10.1021/acsomega.0c05638] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Heparin is one of the members of the glycosaminoglycan (GAG) family, which has been associated with protein aggregation diseases including Alzheimer's disease, Parkinson's disease, and prion diseases. Here, we investigate heparin-induced aggregation of bovine serum albumin (BSA) using different spectroscopic techniques [absorption, 8-anilino-1-naphthalene sulfonic acid (ANS) and thioflavin T (ThT) fluorescence binding, and far- and near-UV circular dichroism]. Kinetic measurements revealed that heparin is involved in the significant enhancement of aggregation of BSA. The outcomes showed dearth of the lag phase and a considerable change in rate constant, which provides conclusive evidence, that is, heparin-induced BSA aggregation involves the pathway of the downhill polymerization mechanism. Heparin also causes enhancement of fluorescence intensity of BSA significantly. Moreover, heparin was observed to form amyloids and amorphous aggregates of BSA which were confirmed by ThT and ANS fluorescence, respectively. Circular dichroism measurements exhibit a considerable change in the secondary and tertiary structure of the protein due to heparin. In addition, binding studies of heparin with BSA to know the cause of aggregation, isothermal titration calorimetry measurements were exploited, from which heparin was observed to promote the aggregation of BSA by virtue of electrostatic interactions between positively charged amino acid residues of protein and negatively charged groups of GAG. The nature of binding of heparin with BSA is very much apparent with an appreciable heat of interaction and is largely exothermic in nature. Moreover, the Gibbs free energy change (ΔG) is negative, which indicates spontaneous nature of binding, and the enthalpy change (ΔH) and entropy change (ΔS) are also largely negative, which suggest that the interaction is driven by hydrogen bonding.
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Affiliation(s)
- Ishfaq
Ahmad Ahanger
- Department
of Chemistry, Biochemistry and Forensic Science, Amity School of Applied
Sciences, Amity University Haryana, Gurugram 122 413, India
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Khalida Nasreen
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anurag Sharma
- Department
of Chemistry, Biochemistry and Forensic Science, Amity School of Applied
Sciences, Amity University Haryana, Gurugram 122 413, India
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5
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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6
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Sharma K, Mehra S, Sawner AS, Markam PS, Panigrahi R, Navalkar A, Chatterjee D, Kumar R, Kadu P, Patel K, Ray S, Kumar A, Maji SK. Effect of Disease-Associated P123H and V70M Mutations on β-Synuclein Fibrillation. ACS Chem Neurosci 2020; 11:2836-2848. [PMID: 32833434 DOI: 10.1021/acschemneuro.0c00405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Synucleinopathies are a class of neurodegenerative diseases, including Parkinson's disease (PD), Dementia with Lewy bodies (DLB), and Multiple System Atrophy (MSA). The common pathological hallmark of synucleinopathies is the filamentous α-synuclein (α-Syn) aggregates along with membrane components in cytoplasmic inclusions in the brain. β-Synuclein (β-Syn), an isoform of α-Syn, inhibits α-Syn aggregation and prevents its neurotoxicity, suggesting the neuroprotective nature of β-Syn. However, this notion changed with the discovery of disease-associated β-Syn mutations, V70M and P123H, in patients with DLB. It is still unclear how these missense mutations alter the structural and amyloidogenic properties of β-Syn, leading to neurodegeneration. Here, we characterized the biophysical properties and investigated the effect of mutations on β-Syn fibrillation under different conditions. V70M and P123H show high membrane binding affinity compared to wild-type β-Syn, suggesting their potential role in membrane interactions. β-Syn and its mutants do not aggregate under normal physiological conditions; however, the proteins undergo self-polymerization in a slightly acidic microenvironment and/or in the presence of an inducer, forming long unbranched amyloid fibrils similar to α-Syn. Strikingly, V70M and P123H mutants exhibit accelerated fibrillation compared to native β-Syn under these conditions. NMR study further revealed that these point mutations induce local perturbations at the site of mutation in β-Syn. Overall, our data provide insight into the biophysical properties of disease-associated β-Syn mutations and demonstrate that these mutants make the native protein more susceptible to aggregation in an altered microenvironment.
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Affiliation(s)
- Karan Sharma
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Ajay S. Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Pratap S. Markam
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India 400076
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7
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Pande M, Srivastava R. Molecular and clinical insights into protein misfolding and associated amyloidosis. Eur J Med Chem 2019; 184:111753. [PMID: 31622853 DOI: 10.1016/j.ejmech.2019.111753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022]
Abstract
The misfolding of normally soluble proteins causes their aggregation and deposition in the tissues which disrupts the normal structure and function of the corresponding organs. The proteins with high β-sheet contents are more prone to form amyloids as they exhibit high propensity of self-aggregation. The self aggregated misfolded proteins act as template for further aggregation that leads to formation of protofilaments and eventually amyloid fibrils. More than 30 different types of proteins are known to be associated with amyloidosis related diseases. Several aspects of the amyloidogenic behavior of proteins remain elusive. The exact reason that causes misfolding of the protein and its association into amyloid fibrils is not known. These misfolded intermediates surpass the over engaged quality control system of the cell which clears the misfolded intermediates. This promotes the self-aggregation, accumulation and deposition of these misfolded species in the form of amyloids in the different parts of the body. The amyloid deposition can be localized as in Alzheimer disease or systemic as reported in most of the amyloidosis. The amyloidosis can be of acquired type or familial. The current review aims at bringing together recent updates and comprehensive information about protein amyloidosis and associated diseases at one place.
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Affiliation(s)
- Monu Pande
- Department of Biochemistry, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ragini Srivastava
- Department of Biochemistry, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India.
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8
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Protein Nanofibrils as Storage Forms of Peptide Drugs and Hormones. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:265-290. [PMID: 31713202 DOI: 10.1007/978-981-13-9791-2_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amyloids are highly organized cross β-sheet protein nanofibrils that are associated with both diseases and functions. Thermodynamically amyloids are stable structures as they represent the lowest free energy state that proteins can attain. However, recent studies suggest that amyloid fibrils can be dissociated by a change in environmental parameters such as pH and ionic strength. This reversibility of amyloids can not only be associated with disease, but function as well. In disease-associated amyloids, fibrils can act as reservoirs of cytotoxic oligomers. Recently, in higher organisms such as mammals, hormones were found to be stored in amyloid-like state, where these were reported to act as a reservoir of functional monomers. These hormone amyloids can dissociate to monomers upon release from the secretory granules, and subsequently bind to their respective receptors and perform their functions. In this book chapter, we describe in detail how these protein nanofibrils represent the densest possible peptide packing and are suitable for long-term storage. Thus, mimicking the feature of amyloids to release functional monomers, it is possible to formulate amyloid-based peptide/protein drugs, which can be used for sustained release.
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9
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Heparan sulfate S-domains and extracellular sulfatases (Sulfs): their possible roles in protein aggregation diseases. Glycoconj J 2018; 35:387-396. [PMID: 30003471 DOI: 10.1007/s10719-018-9833-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/25/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
Abstract
Highly sulfated domains of heparan sulfate (HS), also known as HS S-domains, consist of repeated trisulfated disaccharide units [iduronic acid (2S)-glucosamine (NS, 6S)-]. The expression of HS S-domains at the cell surface is determined by two mechanisms: tightly regulated biosynthetic machinery and enzymatic remodeling by extracellular endoglucosamine 6-sulfatases, Sulf-1 and Sulf-2. Intracellular or extracellular deposits of misfolded and aggregated proteins are characteristic of protein aggregation diseases. Although proteins can aggregate alone, deposits of protein aggregates in vivo contain a number of proteinaceous and non-protein components. HS S-domains are one non-protein component of these aggregated deposits. HS S-domains are considered to be critical for signal transduction of several growth factors and several disease conditions, such as tumor progression, but their roles in protein aggregation diseases are not yet fully understood. This review summarizes the current understanding of the possible roles of HS S-domains and Sulfs in the formation and cytotoxicity of protein aggregates.
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10
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Pentamethinium salts as ligands for cancer: Sulfated polysaccharide co-receptors as possible therapeutic target. Bioorg Chem 2018; 82:74-85. [PMID: 30273836 DOI: 10.1016/j.bioorg.2018.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 12/11/2022]
Abstract
A series of pentamethinium salts with benzothiazolium and indolium side units comprising one or two positive charges were designed and synthesized to determine the relationships among the molecular structure, charge density, affinity to sulfated polysaccharides, and biological activity. Firstly, it was found that the affinity of the pentamethinium salts to sulfated polysaccharides correlated with their biological activity. Secondly, the side heteroaromates displayed a strong effect on the cytotoxicity and selectivity towards cancer cells. Finally, doubly charged pentamethinium salts possessing benzothiazolium side units exhibited remarkably high efficacy against a taxol-resistant cancer cell line.
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11
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Dharmadana D, Reynolds NP, Conn CE, Valéry C. Molecular interactions of amyloid nanofibrils with biological aggregation modifiers: implications for cytotoxicity mechanisms and biomaterial design. Interface Focus 2017; 7:20160160. [PMID: 28630679 PMCID: PMC5474041 DOI: 10.1098/rsfs.2016.0160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Amyloid nanofibrils are ubiquitous biological protein fibrous aggregates, with a wide range of either toxic or beneficial activities that are relevant to human disease and normal biology. Protein amyloid fibrillization occurs via nucleated polymerization, through non-covalent interactions. As such, protein nanofibril formation is based on a complex interplay between kinetic and thermodynamic factors. The process entails metastable oligomeric species and a highly thermodynamically favoured end state. The kinetics, and the reaction pathway itself, can be influenced by third party moieties, either molecules or surfaces. Specifically, in the biological context, different classes of biomolecules are known to act as catalysts, inhibitors or modifiers of the generic protein fibrillization process. The biological aggregation modifiers reviewed here include lipid membranes of varying composition, glycosaminoglycans and metal ions, with a final word on xenobiotic compounds. The corresponding molecular interactions are critically analysed and placed in the context of the mechanisms of cytotoxicity of the amyloids involved in diverse pathologies and the non-toxicity of functional amyloids (at least towards their biological host). Finally, the utilization of this knowledge towards the design of bio-inspired and biocompatible nanomaterials is explored.
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Affiliation(s)
- Durga Dharmadana
- School of Health and Biomedical Sciences, Discipline of Pharmaceutical Sciences, RMIT University, Bundoora, Melbourne, Victoria 3083, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3001, Australia
| | - Nicholas P. Reynolds
- ARC Training Centre for Biodevices, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Charlotte E. Conn
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3001, Australia
| | - Céline Valéry
- School of Health and Biomedical Sciences, Discipline of Pharmaceutical Sciences, RMIT University, Bundoora, Melbourne, Victoria 3083, Australia
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12
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Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. Biophys J 2017; 112:868-880. [PMID: 28297646 DOI: 10.1016/j.bpj.2017.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 11/23/2022] Open
Abstract
Amyloid formation is implicated in a number of human diseases, and is thought to proceed via a nucleation-dependent polymerization mechanism. Experimenters often wish to relate changes in amyloid formation kinetics, for example, in response to small molecules to specific mechanistic steps along this pathway. However, fitting kinetic fibril formation data to a complex model including explicit rate constants results in an ill-posed problem with a vast number of potential solutions. The levels of uncertainty remaining in parameters calculated from these models, arising both from experimental noise and high levels of degeneracy or codependency in parameters, is often unclear. Here, we demonstrate that a combination of explicit mathematical models with an approximate Bayesian computation approach can be used to assign the mechanistic effects of modulators on amyloid fibril formation. We show that even when exact rate constants cannot be extracted, parameters derived from these rate constants can be recovered and used to assign mechanistic effects and their relative magnitudes with a great deal of confidence. Furthermore, approximate Bayesian computation provides a robust method for visualizing uncertainty remaining in the model parameters, regardless of its origin. We apply these methods to the problem of heparin-mediated tau polymerization, which displays complex kinetic behavior not amenable to analysis by more traditional methods. Our analysis indicates that the role of heparin cannot be explained by enhancement of nucleation alone, as has been previously proposed. The methods described here are applicable to a wide range of systems, as models can be easily adapted to account for new reactions and reversibility.
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13
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Stewart KL, Hughes E, Yates EA, Middleton DA, Radford SE. Molecular Origins of the Compatibility between Glycosaminoglycans and Aβ40 Amyloid Fibrils. J Mol Biol 2017; 429:2449-2462. [PMID: 28697887 PMCID: PMC5548265 DOI: 10.1016/j.jmb.2017.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022]
Abstract
The Aβ peptide forms extracellular plaques associated with Alzheimer's disease. In addition to protein fibrils, amyloid plaques also contain non-proteinaceous components, including glycosaminoglycans (GAGs). We have shown previously that the GAG low-molecular-weight heparin (LMWH) binds to Aβ40 fibrils with a three-fold-symmetric (3Q) morphology with higher affinity than Aβ40 fibrils in alternative structures, Aβ42 fibrils, or amyloid fibrils formed from other sequences. Solid-state NMR analysis of the GAG-3Q fibril complex revealed an interaction site at the corners of the 3Q fibril structure, but the origin of the binding specificity remained obscure. Here, using a library of short heparin polysaccharides modified at specific sites, we show that the N-sulfate or 6-O-sulfate of glucosamine, but not the 2-O-sulfate of iduronate within heparin is required for 3Q binding, indicating selectivity in the interactions of the GAG with the fibril that extends beyond general electrostatic complementarity. By creating 3Q fibrils containing point substitutions in the amino acid sequence, we also show that charged residues at the fibril three-fold apices provide the majority of the binding free energy, while charged residues elsewhere are less critical for binding. The results indicate, therefore, that LMWH binding to 3Q fibrils requires a precise molecular complementarity of the sulfate moieties on the GAG and charged residues displayed on the fibril surface. Differences in GAG binding to fibrils with distinct sequence and/or structure may thus contribute to the diverse etiology and progression of amyloid diseases.
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Affiliation(s)
- Katie L Stewart
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Eleri Hughes
- Department of Chemistry, University of Lancaster, Lancaster LA1 4YB, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - David A Middleton
- Department of Chemistry, University of Lancaster, Lancaster LA1 4YB, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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14
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Quittot N, Sebastiao M, Bourgault S. Modulation of amyloid assembly by glycosaminoglycans: from mechanism to biological significance. Biochem Cell Biol 2017; 95:329-337. [DOI: 10.1139/bcb-2016-0236] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Glycosaminoglycans (GAGs) are long and unbranched polysaccharides that are abundant in the extracellular matrix and basement membrane of multicellular organisms. These linear polyanionic macromolecules are involved in many physiological functions from cell adhesion to cellular signaling. Interestingly, amyloid fibrils extracted from patients afflicted with protein misfolding diseases are virtually always associated with GAGs. Amyloid fibrils are highly organized nanostructures that have been historically associated with pathological states, such as Alzheimer’s disease and systemic amyloidoses. However, recent studies have identified functional amyloids that accomplish crucial physiological roles in almost all living organisms, from bacteria to insects and mammals. Over the last 2 decades, numerous reports have revealed that sulfated GAGs accelerate and (or) promote the self-assembly of a large diversity of proteins, both inherently amyloidogenic and non-aggregation prone. Despite the fact that many studies have investigated the molecular mechanism(s) by which GAGs induce amyloid assembly, the mechanistic elucidation of GAG-mediated amyloidogenesis still remains the subject of active research. In this review, we expose the contribution of GAGs in amyloid assembly, and we discuss the pathophysiological and functional significance of GAG-mediated fibrillization. Finally, we propose mechanistic models of the unique and potent ability of sulfated GAGs to hasten amyloid fibril formation.
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Affiliation(s)
- Noé Quittot
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
| | - Mathew Sebastiao
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
| | - Steve Bourgault
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
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15
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Li Y, Wang L, Lu T, Wei Y, Li F. The effects of chondroitin sulfate and serum albumin on the fibrillation of human islet amyloid polypeptide at phospholipid membranes. Phys Chem Chem Phys 2017; 18:12000-8. [PMID: 27067251 DOI: 10.1039/c5cp07642k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycosaminoglycans and serum albumin are important cellular components that regulate the fibril formation of proteins. Whereas the effects of cellular components on the fibrillation of amyloid proteins in bulk solution are widely studied, less attention has been paid to the effects of cellular components on amyloidogenesis occurring at cellular membranes. In this study, we focus on the impacts of chondroitin sulfate A (CSA) and bovine serum albumin (BSA) on the amyloidogenic behaviors of human islet amyloid polypeptide (hIAPP) at phospholipid membranes consisting of neutral POPC and anionic POPG. Using the thioflavin T fluorescence assay, atomic force microscopy, circular dichroism and nuclear magnetic resonance measurements, we demonstrate that CSA has an intensive promotion effect on the fibrillation of hIAPP at the POPC membrane, which is larger than the total effect of CSA alone and POPC alone. The further enhanced promotion of the fibrillation of hIAPP by CSA at the neutral membrane is associated with a specific interaction of CSA with POPC. In contrast, the activity of BSA as an inhibitor of hIAPP fibrillation observed in bulk solution decreases dramatically in the presence of POPG vesicles. The dramatic loss of the inhibition efficiency of BSA arises essentially from a specific interaction with the POPG component, but not simply from suppression by an opposite effect of the anionic membrane. The findings in this study suggest that the interactions between membranes and cellular components may have a significant effect on the activity of the cellular components in regulating the fibrillation of hIAPP.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun 130012, P. R. China.
| | - Li Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun 130012, P. R. China.
| | - Tong Lu
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun 130012, P. R. China.
| | - Ying Wei
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun 130012, P. R. China.
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Avenue, Changchun 130012, P. R. China.
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16
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Probing amylin fibrillation at an early stage via a tetracysteine-recognising fluorophore. Talanta 2017; 173:44-50. [PMID: 28602190 DOI: 10.1016/j.talanta.2017.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 11/23/2022]
Abstract
Amyloid fibrillation is a nucleation-dependent process known be involved in the development of more than 20 progressive and chronic diseases. The detection of amyloid formation at the nucleation stage can greatly advance early diagnoses and treatment of diseases. In this work, we developed a new assay for the early detection of amylin fibrillation using the biarsenical dye 4,5-bis(1,3,2-dithiarsolan-2-yl)fluorescein (FlAsH), which could recognise tetracysteine motifs and transform from non-fluorescent form into strongly fluorescent complexes. Due to the close proximity of two cysteine residues within the hydrophilic domain of amylin, a non-contiguous tetracysteine motif can form upon amylin dimerisation or oligomerisation, which can be recognised by FlAsH and emit strong fluorescence. This enables us to report the nucleation-growth process of amylin without modification of the protein sequence. We showed that the use of this assay not only allowed the tracking of initial nucleation events, but also enabled imaging of amyloid fibrils and investigation of the effects of amyloid inhibitor/modulator toward amylin fibrillation.
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17
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Nishitsuji K, Uchimura K. Sulfated glycosaminoglycans in protein aggregation diseases. Glycoconj J 2017; 34:453-466. [DOI: 10.1007/s10719-017-9769-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/06/2017] [Accepted: 03/27/2017] [Indexed: 01/01/2023]
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18
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Pihlamaa T, Suominen S, Kiuru-Enari S, Tanskanen M. Increasing amount of amyloid are associated with the severity of clinical features in hereditary gelsolin (AGel) amyloidosis. Amyloid 2016; 23:225-233. [PMID: 27879149 DOI: 10.1080/13506129.2016.1238355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Patients with hereditary gelsolin (AGel) amyloidosis (HGA) present with hanging skin (cutis laxa) and bilateral cranial neuropathy, and require symptomatic plastic surgery. Our clinical observation of tissue fragility prompted us to design a prospective study. METHODS Twenty-nine patients with HGA undergoing surgery were interviewed and clinically examined. The height and thickness of skin folds in standard anatomical localizations were measured. The presence and distribution of amyloid in skin samples were analyzed using Congo red staining and immunohistochemistry using antibodies against gelsolin amyloid (AGel) subunit. RESULTS The measured skin folds stretched more in patients with HGA (e.g. skin over olecranon, p < 0.001). The skin folds were thinner in patients with HGA (e.g. forehead skin, p < 0.001). The skin and subcutaneous fat were abnormally fragile during surgery. The total amount of AGel amyloid, and its presence in the deep layers of the skin and subcutaneous fat correlated with the measurements of skin folds, age and extent of cranial neuropathy. CONCLUSIONS The AGel amyloid in the skin and subcutis, together with morphologic changes in the dermal stroma and skin adnexa contribute to the atrophied and fragile structure of HGA skin. This is the first study to demonstrate the correlation between AGel amyloid accumulation and clinical disease severity.
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Affiliation(s)
- Tiia Pihlamaa
- a Department of Plastic and Reconstructive Surgery , Helsinki University Hospital , Helsinki , Finland
| | - Sinikka Suominen
- a Department of Plastic and Reconstructive Surgery , Helsinki University Hospital , Helsinki , Finland
| | - Sari Kiuru-Enari
- b Department of Neurology , Clinical Neurosciences, University of Helsinki , Helsinki , Finland , and
| | - Maarit Tanskanen
- c Department of Pathology , University of Helsinki and HUSLAB , Helsinki , Finland
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19
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Jangholi A, Ashrafi-Kooshk MR, Arab SS, Riazi G, Mokhtari F, Poorebrahim M, Mahdiuni H, Kurganov BI, Moosavi-Movahedi AA, Khodarahmi R. Appraisal of role of the polyanionic inducer length on amyloid formation by 412-residue 1N4R Tau protein: A comparative study. Arch Biochem Biophys 2016; 609:1-19. [DOI: 10.1016/j.abb.2016.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
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20
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Mikawa S, Mizuguchi C, Nishitsuji K, Baba T, Shigenaga A, Shimanouchi T, Sakashita N, Otaka A, Akaji K, Saito H. Heparin promotes fibril formation by the N-terminal fragment of amyloidogenic apolipoprotein A-I. FEBS Lett 2016; 590:3492-3500. [DOI: 10.1002/1873-3468.12426] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/05/2016] [Accepted: 09/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Shiho Mikawa
- Department of Biophysical Chemistry; Kyoto Pharmaceutical University; Japan
- Institute of Biomedical Sciences; Graduate School of Pharmaceutical Sciences; Tokushima University; Japan
| | - Chiharu Mizuguchi
- Department of Biophysical Chemistry; Kyoto Pharmaceutical University; Japan
- Institute of Biomedical Sciences; Graduate School of Pharmaceutical Sciences; Tokushima University; Japan
| | - Kazuchika Nishitsuji
- Department of Molecular Pathology; Institute of Biomedical Sciences; Tokushima University Graduate School; Japan
| | - Teruhiko Baba
- Biotechnology Research Institute for Drug Discovery; National Institute of Advanced Industrial Science and Technology (AIST); Tsukuba Japan
| | - Akira Shigenaga
- Institute of Biomedical Sciences; Graduate School of Pharmaceutical Sciences; Tokushima University; Japan
| | | | - Naomi Sakashita
- Department of Molecular Pathology; Institute of Biomedical Sciences; Tokushima University Graduate School; Japan
| | - Akira Otaka
- Institute of Biomedical Sciences; Graduate School of Pharmaceutical Sciences; Tokushima University; Japan
| | - Kenichi Akaji
- Department of Medicinal Chemistry; Kyoto Pharmaceutical University; Japan
| | - Hiroyuki Saito
- Department of Biophysical Chemistry; Kyoto Pharmaceutical University; Japan
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21
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Takase H, Tanaka M, Yamamoto A, Watanabe S, Takahashi S, Nadanaka S, Kitagawa H, Yamada T, Mukai T. Structural requirements of glycosaminoglycans for facilitating amyloid fibril formation of human serum amyloid A. Amyloid 2016; 23:67-75. [PMID: 27097047 DOI: 10.3109/13506129.2016.1168292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Serum amyloid A (SAA) is a precursor protein of amyloid fibrils. Given that heparan sulfate (HS), a glycosaminoglycan (GAG), is detected in amyloid deposits, it has been suggested that GAG is a key component of amyloid fibril formation. We previously reported that heparin (an analog of HS) facilitates the fibril formation of SAA, but the structural requirements remain unknown. In the present study, we investigated the structural requirements of GAGs for facilitating the amyloid fibril formation of SAA. Spectroscopic analyses using structurally diverse GAG analogs suggested that the fibril formation of SAA was facilitated irrespective of the backbone structure of GAGs; however, the facilitating effect was strongly correlated with the degree of sulfation. Microscopic analyses revealed that the morphologies of SAA aggregates were modulated by the GAGs. The HS molecule, which is less sulfated than heparin but contains highly sulfated domains, exhibited a relatively high potential to facilitate fibril formation compared to other GAGs. The length dependence of fragmented heparins on the facilitating effect suggested that a high density of sulfate groups is also required. These results indicate that not only the degree of sulfation but also the lengths of sulfated domains in GAG play important roles in fibril formation of SAA.
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Affiliation(s)
- Hiroka Takase
- a Department of Biophysical Chemistry , Kobe Pharmaceutical University , Kobe , Japan
| | - Masafumi Tanaka
- a Department of Biophysical Chemistry , Kobe Pharmaceutical University , Kobe , Japan
| | - Aki Yamamoto
- a Department of Biophysical Chemistry , Kobe Pharmaceutical University , Kobe , Japan
| | - Shiori Watanabe
- a Department of Biophysical Chemistry , Kobe Pharmaceutical University , Kobe , Japan
| | - Sanae Takahashi
- a Department of Biophysical Chemistry , Kobe Pharmaceutical University , Kobe , Japan
| | - Satomi Nadanaka
- b Department of Biochemistry , Kobe Pharmaceutical University , Kobe , Japan , and
| | - Hiroshi Kitagawa
- b Department of Biochemistry , Kobe Pharmaceutical University , Kobe , Japan , and
| | - Toshiyuki Yamada
- c Department of Clinical Laboratory Medicine , Jichi Medical University , Shimotsuke , Japan
| | - Takahiro Mukai
- a Department of Biophysical Chemistry , Kobe Pharmaceutical University , Kobe , Japan
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22
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Koskelainen S, Pihlamaa T, Suominen S, Zhao F, Salo T, Risteli J, Baumann M, Kalimo H, Kiuru-Enari S. Gelsolin amyloid angiopathy causes severe disruption of the arterial wall. APMIS 2016; 124:639-48. [PMID: 27198069 DOI: 10.1111/apm.12554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/18/2016] [Indexed: 11/26/2022]
Abstract
Hereditary gelsolin amyloidosis (HGA) is a dominantly inherited systemic disease reported worldwide. HGA is characterized by ophthalmological, neurological, and dermatological manifestations. AGel amyloid accumulates at basal lamina of epithelial and muscle cells, thus amyloid angiopathy is encountered in nearly every organ. HGA patients have cardiovascular, hemorrhagic, and potentially vascularly induced neurological problems. To clarify pathomechanisms of AGel angiopathy, we performed histological, immunohistochemical, and electron microscopic analyses on facial temporal artery branches from 8 HGA patients and 13 control subjects. We demonstrate major pathological changes in arteries: disruption of the tunica media, disorganization of vascular smooth muscle cells, and accumulation of AGel fibrils in arterial walls, where they associate with the lamina elastica interna, which becomes fragmented and diminished. We also provide evidence of abnormal accumulation and localization of collagen types I and III and an increase of collagen type I degradation product in the tunica media. Vascular smooth muscle cells appear to be morphologically and semi-quantitatively normal, only their basal lamina is often thickened. In conclusion, angiopathy in HGA results in severe disruption of arterial walls, characterized by prominent AGel deposition, collagen derangement and severe elastolysis, and it may be responsible for several, particularly hemorrhagic, disease manifestations in HGA.
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Affiliation(s)
- Susanna Koskelainen
- Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiia Pihlamaa
- Department of Plastic Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Sinikka Suominen
- Department of Plastic Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Fang Zhao
- Advanced Microscopy Unit, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tuula Salo
- Research Group of Cancer and Translational Medicine, Medical Faculty, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Juha Risteli
- Research Group of Cancer and Translational Medicine, Medical Faculty, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Marc Baumann
- Meilahti Clinical Proteomics Core Facility, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hannu Kalimo
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Forensic Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sari Kiuru-Enari
- Clinical Neurosciences, Neurology, University of Helsinki, Helsinki, Finland
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23
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Stenvang M, Christiansen G, Otzen DE. Epigallocatechin Gallate Remodels Fibrils of Lattice Corneal Dystrophy Protein, Facilitating Proteolytic Degradation and Preventing Formation of Membrane-Permeabilizing Species. Biochemistry 2016; 55:2344-57. [DOI: 10.1021/acs.biochem.6b00063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marcel Stenvang
- Interdisciplinary
Nanoscience Center
(iNANO), Department of Molecular Biology and Genetics, Center for
Insoluble Protein Structures (inSPIN), Aarhus University, Aarhus, Denmark
| | | | - Daniel E. Otzen
- Interdisciplinary
Nanoscience Center
(iNANO), Department of Molecular Biology and Genetics, Center for
Insoluble Protein Structures (inSPIN), Aarhus University, Aarhus, Denmark
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24
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Li JP, Kusche-Gullberg M. Heparan Sulfate: Biosynthesis, Structure, and Function. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:215-73. [PMID: 27241222 DOI: 10.1016/bs.ircmb.2016.02.009] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Heparan sulfate (HS) proteoglycans (PGs) are ubiquitously expressed on cell surfaces and in the extracellular matrix of most animal tissues, having essential functions in development and homeostasis, as well as playing various roles in disease processes. The functions of HSPGs are mainly dependent on interactions between the HS-side chains with a variety of proteins including cytokines, growth factors, and their receptors. In a given HS polysaccharide, negatively charged sulfate and carboxylate groups are arranged in various types of domains, generated through strictly regulated biosynthetic reactions and with enormous potential for structural variability. The mode of HS-protein interactions is assessed through binding experiments using saccharides of defined composition in vitro, signaling assays in cell models where HS structures are manipulated, and targeted disruption of genes for biosynthetic enzymes in animals (mouse, zebrafish, Drosophila, and Caenorhabditis elegans) followed by phenotype analysis. Whereas some protein ligands appear to require strictly defined HS structure, others bind to variable saccharide domains without apparent dependence on distinct saccharide sequence. These findings raise intriguing questions concerning the functional significance of regulation in HS biosynthesis and the potential for development of therapeutics targeting HS-protein interactions.
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Affiliation(s)
- J-P Li
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden; SciLifeLab, University of Uppsala, Uppsala, Sweden.
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25
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Liu H, Ojha B, Morris C, Jiang M, Wojcikiewicz EP, Rao PPN, Du D. Positively Charged Chitosan and N-Trimethyl Chitosan Inhibit Aβ40 Fibrillogenesis. Biomacromolecules 2015; 16:2363-73. [DOI: 10.1021/acs.biomac.5b00603] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | | | | | | | - Praveen P. N. Rao
- School
of Pharmacy, Health Sciences Campus, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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26
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Singh PK, Ghosh D, Tewari D, Mohite GM, Carvalho E, Jha NN, Jacob RS, Sahay S, Banerjee R, Bera AK, Maji SK. Cytotoxic helix-rich oligomer formation by melittin and pancreatic polypeptide. PLoS One 2015; 10:e0120346. [PMID: 25803428 PMCID: PMC4372375 DOI: 10.1371/journal.pone.0120346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/21/2015] [Indexed: 12/20/2022] Open
Abstract
Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail.
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Affiliation(s)
- Pradeep K. Singh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Debanjan Tewari
- Department of Biotechnology, IIT Madras, Chennai, Tamil Nadu, India
| | - Ganesh M. Mohite
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Edmund Carvalho
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Narendra Nath Jha
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Reeba S. Jacob
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Shruti Sahay
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Rinti Banerjee
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Amal K. Bera
- Department of Biotechnology, IIT Madras, Chennai, Tamil Nadu, India
| | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
- * E-mail:
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27
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Iannuzzi C, Irace G, Sirangelo I. The effect of glycosaminoglycans (GAGs) on amyloid aggregation and toxicity. Molecules 2015; 20:2510-28. [PMID: 25648594 PMCID: PMC6272481 DOI: 10.3390/molecules20022510] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/29/2015] [Indexed: 01/15/2023] Open
Abstract
Amyloidosis is a protein folding disorder in which normally soluble proteins are deposited extracellularly as insoluble fibrils, impairing tissue structure and function. Charged polyelectrolytes such as glycosaminoglycans (GAGs) are frequently found associated with the proteinaceous deposits in tissues of patients affected by amyloid diseases. Experimental evidence indicate that they can play an active role in favoring amyloid fibril formation and stabilization. Binding of GAGs to amyloid fibrils occurs mainly through electrostatic interactions involving the negative polyelectrolyte charges and positively charged side chains residues of aggregating protein. Similarly to catalyst for reactions, GAGs favor aggregation, nucleation and amyloid fibril formation functioning as a structural templates for the self-assembly of highly cytotoxic oligomeric precursors, rich in β-sheets, into harmless amyloid fibrils. Moreover, the GAGs amyloid promoting activity can be facilitated through specific interactions via consensus binding sites between amyloid polypeptide and GAGs molecules. We review the effect of GAGs on amyloid deposition as well as proteins not strictly related to diseases. In addition, we consider the potential of the GAGs therapy in amyloidosis.
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Affiliation(s)
- Clara Iannuzzi
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Via L. De Crecchio 7, Napoli 80138, Italy.
| | - Gaetano Irace
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Via L. De Crecchio 7, Napoli 80138, Italy.
| | - Ivana Sirangelo
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Via L. De Crecchio 7, Napoli 80138, Italy.
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28
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Nguyen PT, Andraka N, De Carufel CA, Bourgault S. Mechanistic Contributions of Biological Cofactors in Islet Amyloid Polypeptide Amyloidogenesis. J Diabetes Res 2015; 2015:515307. [PMID: 26576436 PMCID: PMC4630397 DOI: 10.1155/2015/515307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/26/2015] [Accepted: 02/09/2015] [Indexed: 01/24/2023] Open
Abstract
Type II diabetes mellitus is associated with the deposition of fibrillar aggregates in pancreatic islets. The major protein component of islet amyloids is the glucomodulatory hormone islet amyloid polypeptide (IAPP). Islet amyloid fibrils are virtually always associated with several biomolecules, including apolipoprotein E, metals, glycosaminoglycans, and various lipids. IAPP amyloidogenesis has been originally perceived as a self-assembly homogeneous process in which the inherent aggregation propensity of the peptide and its local concentration constitute the major driving forces to fibrillization. However, over the last two decades, numerous studies have shown a prominent role of amyloid cofactors in IAPP fibrillogenesis associated with the etiology of type II diabetes. It is increasingly evident that the biochemical microenvironment in which IAPP amyloid formation occurs and the interactions of the polypeptide with various biomolecules not only modulate the rate and extent of aggregation, but could also remodel the amyloidogenesis process as well as the structure, toxicity, and stability of the resulting fibrils.
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Affiliation(s)
- Phuong Trang Nguyen
- Department of Chemistry, Pharmaqam, University of Quebec in Montreal, Montreal, QC, Canada H3C 3P8
- Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Canada
| | - Nagore Andraka
- Department of Chemistry, Pharmaqam, University of Quebec in Montreal, Montreal, QC, Canada H3C 3P8
- Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Canada
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, 48080 Bilbao, Spain
| | - Carole Anne De Carufel
- Department of Chemistry, Pharmaqam, University of Quebec in Montreal, Montreal, QC, Canada H3C 3P8
- Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Canada
| | - Steve Bourgault
- Department of Chemistry, Pharmaqam, University of Quebec in Montreal, Montreal, QC, Canada H3C 3P8
- Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Canada
- *Steve Bourgault:
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29
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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30
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Yamada M, Hara S, Yamada T, Katagiri F, Hozumi K, Nomizu M. Double-stranded DNA stereoselectively promotes aggregation of amyloid-like fibrils and generates peptide/DNA matrices. Biopolymers 2014; 102:465-72. [DOI: 10.1002/bip.22571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/22/2014] [Accepted: 09/27/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Masanori Yamada
- Department of Chemistry, Faculty of Science; Okayama University of Science; Ridaicho, Kita-ku Okayama 700-0005 Japan
| | - Sachiko Hara
- Department of Chemistry, Faculty of Science; Okayama University of Science; Ridaicho, Kita-ku Okayama 700-0005 Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture; Hokkaido University; Sapporo 060-8589 Japan
| | - Fumihiko Katagiri
- School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Hachioji Tokyo 192-0392 Japan
| | - Kentaro Hozumi
- School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Hachioji Tokyo 192-0392 Japan
| | - Motoyoshi Nomizu
- School of Pharmacy; Tokyo University of Pharmacy and Life Sciences; Hachioji Tokyo 192-0392 Japan
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31
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Zhao D, Zhang S, Meng Y, Xiongwei D, Zhang D, Liang Y, Wang L, Liu C. Polyanion binding accelerates the formation of stable and low-toxic aggregates of ALS-linked SOD1 mutant A4V. Proteins 2014; 82:3356-72. [PMID: 25220364 DOI: 10.1002/prot.24691] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 12/16/2022]
Abstract
The toxic property thus far shared by both ALS-linked SOD1 variants and wild-type SOD1 is an increased propensity to aggregation. However, whether SOD1 oligomers or aggregates are toxic to cells remains to be well defined. Moreover, how the toxic SOD1 species are removed from intra- and extracellular environments also needs to be further explored. The DNA binding has been shown to be capable of accelerating the aggregatio\n of wild-type and oxidized SOD1 forms under acidic and neutral conditions. In this study, we explore the binding of DNA and heparin, two types of essential life polyanions, to A4V, an ALS-linked SOD1 mutant, under acidic conditions, and its consequences. The polyanion binding alters the A4V conformation, neutralizes its local positive charges, and increases its local concentrations along the polyanion chain, which are sufficient to lead to acceleration of the pH-dependent A4V aggregation. The accelerated aggregation, which is ascribed to the polyanion binding-mediated removal or shortening of the lag phase in aggregation, contributes to the formation of amorphous A4V nanoparticles. The prolonged incubation with polyanions not only results in the complete conversion of likely soluble toxic A4V oligomers into non- and low-toxic SDS-resistant aggregates, but also increases their stability. Although this is only an initial step toward reducing the toxicity of SOD1 mutants, the accelerating role of polyanions in protein aggregation might become one of the rapid pathways that remove toxic forms of SOD1 mutants from intra- and extracellular environments.
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Affiliation(s)
- Dan Zhao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
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32
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Aguilera JJ, Zhang F, Beaudet JM, Linhardt RJ, Colón W. Divergent effect of glycosaminoglycans on the in vitro aggregation of serum amyloid A. Biochimie 2014; 104:70-80. [PMID: 24878279 DOI: 10.1016/j.biochi.2014.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/12/2014] [Indexed: 11/25/2022]
Abstract
Serum amyloid A (SAA) is an apolipoprotein involved in poorly understood roles in inflammation. Upon trauma, hepatic expression of SAA rises 1000 times the basal levels. In the case of inflammatory diseases like rheumatoid arthritis, there is a risk for deposition of SAA fibrils in various organs leading to Amyloid A (AA) amyloidosis. Although the amyloid deposits in AA amyloidosis accumulate with the glycosaminoglycan (GAG) heparan sulfate, the role GAGs play in the function and pathology of SAA is an enigma. It has been shown that GAG sulfation is a contributing factor in protein fibrillation and for co-aggregating with a plethora of amyloidogenic proteins. Herein, the effects of heparin, heparan sulfate, hyaluronic acid, chondroitin sulfate A, and heparosan on the oligomerization and aggregation properties of pathogenic mouse SAA1.1 were investigated. Delipidated SAA was used to better understand the interactions between SAA and GAGs without the complicating involvement of lipids. The results revealed-to varying degrees-that all GAGs accelerated SAA1.1 aggregation, but had variable effects on its fibrillation. Heparan sulfate, hyaluronic acid, and heparosan did not affect much the fibrillation of SAA1.1. In contrast, chondroitin sulfate A blocked SAA fibril formation and facilitated the formation of spherical aggregates of various sizes. Interestingly, heparin caused formation of spherical SAA1.1 aggregates of various sizes, vast amounts of thin protofibrils, and few long fibrils of various heights. These results suggest that GAGs may have an intrinsic and divergent influence on the aggregation and fibrillation of HDL-free SAA1.1 in vivo, with functional and pathological implications.
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Affiliation(s)
- J Javier Aguilera
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Julie M Beaudet
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Wilfredo Colón
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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33
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Wang H, Raleigh DP. The ability of insulin to inhibit the formation of amyloid by pro-islet amyloid polypeptide processing intermediates is significantly reduced in the presence of sulfated glycosaminoglycans. Biochemistry 2014; 53:2605-14. [PMID: 24654599 PMCID: PMC4010284 DOI: 10.1021/bi4015488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
Islet
amyloid polypeptide (IAPP) is responsible for amyloid deposition
in type 2 diabetes and plays an important role in the loss of β-cell
mass associated with the disease and in the failure of islet transplants, but the mechanism of islet amyloid formation is not understood. The
incorrect processing of proIAPP to produce partially processed forms
of the peptide has been proposed to play a role in the initiation
of islet amyloid in vivo by promoting interactions
with proteoglycans of the extracellular matrix. Insulin is a potent
inhibitor of the formation of amyloid by IAPP in vitro in a homogeneous solution; however, its ability to inhibit IAPP
in the presence of proteoglycans has not been tested, nor has its
effect on the formation of amyloid by proIAPP processing intermediates
been examined. Here we show that insulin is a much less effective
amyloid inhibitor of both IAPP and proIAPP processing intermediates in vitro in the presence of model glycosaminoglycans, but
does inhibit the formation of amyloid by proIAPP processing intermediates
in a homogeneous solution. This highlights another mechanism by which
sulfated proteoglycans could enhance islet amyloid formation in vivo. Interactions with sulfated proteoglycans can directly
promote amyloid formation and can also significantly reduce the effectiveness
of natural inhibitors.
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Affiliation(s)
- Hui Wang
- Department of Chemistry, State University of New York at Stony Brook , Stony Brook, New York 11794-3400, United States
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34
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Ghosh D, Dutta P, Chakraborty C, Singh PK, Anoop A, Jha NN, Jacob RS, Mondal M, Mankar S, Das S, Malik S, Maji SK. Complexation of amyloid fibrils with charged conjugated polymers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3775-3786. [PMID: 24678792 DOI: 10.1021/la404739f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
It has been suggested that conjugated charged polymers are amyloid imaging agents and promising therapeutic candidates for neurological disorders. However, very less is known about their efficacy in modulating the amyloid aggregation pathway. Here, we studied the modulation of Parkinson's disease associated α-synuclein (AS) amyloid assembly kinetics using conjugated polyfluorene polymers (PF, cationic; PFS, anionic). We also explored the complexation of these charged polymers with the various AS aggregated species including amyloid fibrils and oligomers using multidisciplinary biophysical techniques. Our data suggests that both polymers irrespective of their different charges in the side chains increase the fibrilization kinetics of AS and also remarkably change the morphology of the resultant amyloid fibrils. Both polymers were incorporated/aligned onto the AS amyloid fibrils as evident from electron microscopy (EM) and atomic force microscopy (AFM), and the resultant complexes were structurally distinct from their pristine form of both polymers and AS supported by FTIR study. Additionally, we observed that the mechanism of interactions between the polymers with different species of AS aggregates were markedly different.
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Affiliation(s)
- Dhiman Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, Maharashtra, Mumbai 400076, India
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35
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Bucciantini M, Rigacci S, Stefani M. Amyloid Aggregation: Role of Biological Membranes and the Aggregate-Membrane System. J Phys Chem Lett 2014; 5:517-27. [PMID: 26276603 DOI: 10.1021/jz4024354] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Several human degenerative diseases involve amyloidogenic peptides/proteins with high conformational plasticity and propensity to self-aggregate into polymeric fibrillar assemblies sharing the cross-β structure and endowed with cytotoxic potential. Although the mechanisms of amyloid growth and toxicity are not fully understood, a common property of amyloids is their ability to interact with lipid bilayers disturbing membrane integrity. Lipid bilayers can also act as conformational catalysts, favoring protein misfolding and inducing the growth of aggregation nuclei, early oligomers, and mature fibrils with specific biophysical, structural, and toxicity features. This Perspective will highlight these effects in the context of a membrane-oligomer system where the conformational/biophysical features of either component affect those of the other. In this context, we will highlight the modulation of the protein-cell surface interaction by the content of membrane cholesterol and gangliosides, notably GM1. In particular, we will discuss data that indicate how these interactions affect the structural and stability properties of both protein and bilayers as well as the final cytotoxic effect. Our goal is to propose shared membrane-based mechanisms that could apply to any amyloidogenic peptide/protein, providing a biochemical background for amyloid growth and toxicity.
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Affiliation(s)
- Monica Bucciantini
- †Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, V.le Morgagni 50, 50134 Florence, Italy
| | - Stefania Rigacci
- †Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, V.le Morgagni 50, 50134 Florence, Italy
| | - Massimo Stefani
- †Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, V.le Morgagni 50, 50134 Florence, Italy
- ‡National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome, Italy
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36
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Minsky BB, Zheng B, Dubin PL. Inhibition of antithrombin and bovine serum albumin native state aggregation by heparin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:278-287. [PMID: 24313340 DOI: 10.1021/la4039232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein native state aggregation, a major problem in pharmaceutical and biological processes, has been addressed pharmacologically by the addition of protein-binding excipients. Heparin (Hp), a highly sulfated polysaccharide, interacts with numerous proteins with moderate to high affinity, but reports about its effect on protein aggregation are contradictory. We studied the pH dependence of the aggregation of antithrombin (AT) and bovine serum albumin (BSA) in the presence and absence of heparin. High-precision turbidimetry showed strong aggregation for both AT and BSA in I = 10 mM NaCl, conditions at which electrostatically driven Hp binding and aggregation both occur, with more obvious aggregation of heparin-free AT appearing as larger aggregate size. Aggregation of AT was dramatically inhibited at Hp: protein 6:1 (mole ratio); however, the effect at 0.5:1 Hp:protein was greater for BSA. Frontal analysis capillary electrophoresis showed a much larger equilibrium association constant Kobs between Hp and AT, in accord with the onset of Hp binding at a higher pH; both effects are explained by the higher charge density of the positive domain for AT as revealed by modeling with DelPhi. The corresponding modeling images showed that these domains persist at high salt only for AT, consistent with the 160-fold drop in Kobs at 100 mM salt for BSA-Hp binding. The smaller inhibition effect for AT arises from the tendency of its uncomplexed monomer to form larger aggregates more rapidly, but the stronger binding of Hp to AT does not facilitate Hp-induced aggregate dissolution which occurs more readily for BSA. This can be attributed to the higher density of AT aggregates evidenced by higher fractal dimensions. Differences between inhibition and reversal by Hp arise because the former may depend on the stage at which Hp enters the aggregation process and the latter on aggregate size and morphology.
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Affiliation(s)
- Burcu Baykal Minsky
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts, 01003, United States
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37
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Luminescence response of an osmium(II) complex to macromolecular polyanions for the detection of heparin and chondroitin sulfate in biomedical preparations. Anal Chim Acta 2013; 804:221-7. [DOI: 10.1016/j.aca.2013.10.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 11/20/2022]
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38
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De Carufel CA, Nguyen PT, Sahnouni S, Bourgault S. New insights into the roles of sulfated glycosaminoglycans in islet amyloid polypeptide amyloidogenesis and cytotoxicity. Biopolymers 2013; 100:645-55. [DOI: 10.1002/bip.22243] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/11/2013] [Accepted: 03/17/2013] [Indexed: 01/16/2023]
Affiliation(s)
| | - Phuong Trang Nguyen
- Department of Chemistry; University of Québec in Montreal; Montreal QC H3C 3P8 Canada
| | - Sabrina Sahnouni
- Department of Chemistry; University of Québec in Montreal; Montreal QC H3C 3P8 Canada
| | - Steve Bourgault
- Department of Chemistry; University of Québec in Montreal; Montreal QC H3C 3P8 Canada
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39
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Jha NN, Anoop A, Ranganathan S, Mohite GM, Padinhateeri R, Maji SK. Characterization of Amyloid Formation by Glucagon-Like Peptides: Role of Basic Residues in Heparin-Mediated Aggregation. Biochemistry 2013; 52:8800-10. [DOI: 10.1021/bi401398k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Narendra Nath Jha
- Department
of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - A. Anoop
- Department
of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | | | - Ganesh M. Mohite
- Department
of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | | | - Samir K. Maji
- Department
of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
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40
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Ojha B, Liu H, Dutta S, Rao PPN, Wojcikiewicz EP, Du D. Poly(4-styrenesulfonate) as an Inhibitor of Aβ40 Amyloid Fibril Formation. J Phys Chem B 2013; 117:13975-84. [DOI: 10.1021/jp4065467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | - Praveen P. N. Rao
- School
of Pharmacy, Health Sciences Campus, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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41
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Cecchi C, Stefani M. The amyloid-cell membrane system. The interplay between the biophysical features of oligomers/fibrils and cell membrane defines amyloid toxicity. Biophys Chem 2013; 182:30-43. [PMID: 23820236 DOI: 10.1016/j.bpc.2013.06.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 12/14/2022]
Abstract
Amyloid cytotoxicity, structure and polymorphisms are themes of increasing importance. Present knowledge considers any peptide/protein able to undergo misfolding and aggregation generating intrinsically cytotoxic amyloids. It also describes growth and structure of amyloid fibrils and their possible disassembly, whereas reduced information is available on oligomer structure. Recent research has highlighted the importance of the environmental conditions as determinants of the amyloid polymorphisms and cytotoxicity. Another body of evidence describes chemical or biological surfaces as key sites of protein misfolding and aggregation or of interaction with amyloids and the resulting biochemical modifications inducing cell functional/viability impairment. In particular, the membrane lipid composition appears to modulate cell response to toxic amyloids, thus contributing to explain the variable vulnerability to the same amyloids of different cell types. Finally, a recent view describes amyloid toxicity as an emerging property dependent on a complex interplay between the biophysical features of early aggregates and the interacting cell membranes taken as a whole system.
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Affiliation(s)
- Cristina Cecchi
- Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, Florence, Italy
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42
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Tan S, Lu L, Li L, Liu J, Oksov Y, Lu H, Jiang S, Liu S. Polyanionic candidate microbicides accelerate the formation of semen-derived amyloid fibrils to enhance HIV-1 infection. PLoS One 2013; 8:e59777. [PMID: 23544097 PMCID: PMC3609764 DOI: 10.1371/journal.pone.0059777] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/18/2013] [Indexed: 12/21/2022] Open
Abstract
Polyanionic candidate microbicides, including cellulose sulfate, carrageenan, PRO 2000, were proven ineffective in preventing HIV-1 transmission and even cellulose sulfate showed increased risk of HIV acquisition in the Phase III efficacy trials. Semen plays critical roles in HIV-1 sexual transmission. Specifically, amyloid fibrils formed by fragments of prostatic acidic phosphatase (PAP) in semen termed semen-derived enhancer of virus infection (SEVI) could drastically enhance HIV-1 infection. Here we investigated the interaction between polyanions and PAP248-286, a prototype peptide of SEVI, to understand the possible cause of polyanionic candidate microbicides to fail in clinical trials. We found anionic polymers could efficiently promote SEVI fibril formation, most likely mediated by the natural electrostatic interaction between polyanions and PAP248-286, as revealed by acid native PAGE and Western blot. The overall anti-HIV-1 activity of polyanions in the presence or absence of PAP248-286 or semen was evaluated. In the viral infection assay, the supernatants of polyanions/PAP248-286 or polyanions/semen mixtures containing the free, unbound polyanionic molecules showed a general reduction in antiviral efficacy, while the pellets containing amyloid fibrils formed by the polyanion-bound PAP248-286 showed aggravated enhancement of viral infection. Collectively, from the point of drug-host protein interaction, our study revealed that polyanions facilitate SEVI fibril formation to promote HIV-1 infection, thus highlighting a molecular mechanism underlying the failure of polyanions in clinical trials and the importance of drug-semen interaction in evaluating the anti-HIV-1 efficacy of candidate microbicides.
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Affiliation(s)
- Suiyi Tan
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of Ministries of Education & Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Lin Li
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jixiang Liu
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Yelena Oksov
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Hong Lu
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
| | - Shibo Jiang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Key Laboratory of Medical Molecular Virology of Ministries of Education & Health, Shanghai Medical College and Institute of Medical Microbiology, Fudan University, Shanghai, China
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
- * E-mail: (SJ); (SL)
| | - Shuwen Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- * E-mail: (SJ); (SL)
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43
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Abstract
Hereditary gelsolin amyloidosis (HGA) is an autosomally dominantly inherited form of systemic amyloidosis, characterized mainly by cranial and sensory peripheral neuropathy, corneal lattice dystrophy, and cutis laxa. HGA, originally reported from Finland and now increasingly from other countries in Europe, North and South America, and Asia, may still be underdiagnosed worldwide. It is the first and so-far only known disorder caused by a gelsolin gene defect, namely a G654A or G654T mutation. Gelsolin is a principal actin-modulating protein, implicated in multiple biological processes, also in the nervous system, e.g. axonal transport, myelination, neurite outgrowth, and neuroprotection. The gelsolin gene defect causes expression of variant gelsolin, followed by systemic deposition of gelsolin amyloid (AGel) in HGA patients and even other consequences on the metabolism and function of gelsolin. In HGA, specific therapy is not yet available but correct diagnosis enables adequate symptomatic treatment which decisively improves the quality of life in these patients. A transgenic murine model of HGA expressing AGel is available, in anticipation of new treatment options targeted toward this slowly progressive but devastating amyloidosis. Present and future lessons learned from HGA may be applicable even in diagnosis and treatment of other hereditary and sporadic amyloidoses.
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Affiliation(s)
- Sari Kiuru-Enari
- Department of Neurology, Unit for Neuromuscular Diseases, Helsinki University Central Hospital, Helsinki, Finland.
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44
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Structural features and cytotoxicity of amyloid oligomers: Implications in Alzheimer's disease and other diseases with amyloid deposits. Prog Neurobiol 2012; 99:226-45. [DOI: 10.1016/j.pneurobio.2012.03.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 12/22/2022]
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45
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Salt Anions Promote the Conversion of HypF-N into Amyloid-Like Oligomers and Modulate the Structure of the Oligomers and the Monomeric Precursor State. J Mol Biol 2012; 424:132-49. [DOI: 10.1016/j.jmb.2012.09.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 09/11/2012] [Accepted: 09/26/2012] [Indexed: 11/17/2022]
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46
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Shahbazi MA, Hamidi M. The impact of preparation parameters on typical attributes of chitosan-heparin nanohydrogels: particle size, loading efficiency, and drug release. Drug Dev Ind Pharm 2012; 39:1774-82. [DOI: 10.3109/03639045.2012.736518] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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47
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A zinc complex of heparan sulfate destabilises lysozyme and alters its conformation. Biochem Biophys Res Commun 2012; 425:794-9. [PMID: 22884801 DOI: 10.1016/j.bbrc.2012.07.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/27/2012] [Indexed: 11/22/2022]
Abstract
The naturally occurring anionic cell surface polysaccharide heparan sulfate is involved in key biological activities and is implicated in amyloid formation. Following addition of Zn-heparan sulfate, hen lysozyme, a model amyloid forming protein, resembled β-rich amyloid by far UV circular dichroism (increased β-sheet: +25%), with a significantly reduced melting temperature (from 68 to 58 °C) by fluorescence shift assay. Secondary structure stability of the Zn-heparan sulfate complex with lysozyme was also distinct from that with heparan sulfate, under stronger denaturation conditions using synchrotron radiation circular dichroism. Changing the cation associated with heparan sulfate is sufficient to alter the conformation and stability of complexes formed between heparan sulfate and lysozyme, substantially reducing the stability of the protein. Complexes of heparan sulfate and cations, such as Zn, which are abundant in the brain, may provide alternative folding routes for proteins.
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48
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Multiple Roles of Heparin in the Aggregation of p25α. J Mol Biol 2012; 421:601-15. [DOI: 10.1016/j.jmb.2012.01.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/29/2011] [Accepted: 01/30/2012] [Indexed: 11/17/2022]
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49
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Arosio P, Jaquet B, Wu H, Morbidelli M. On the role of salt type and concentration on the stability behavior of a monoclonal antibody solution. Biophys Chem 2012; 168-169:19-27. [DOI: 10.1016/j.bpc.2012.05.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/23/2012] [Accepted: 05/25/2012] [Indexed: 11/27/2022]
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50
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Amyloid-Like Fibril Formation by Tachykinin Neuropeptides and Its Relevance to Amyloid β-Protein Aggregation and Toxicity. Cell Biochem Biophys 2012; 64:29-44. [DOI: 10.1007/s12013-012-9364-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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