1
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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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Tanaka M, Takarada T, Nadanaka S, Kojima R, Hosoi K, Machiba Y, Kitagawa H, Yamada T. Influences of amino-terminal modifications on amyloid fibril formation of human serum amyloid A. Arch Biochem Biophys 2023; 742:109615. [PMID: 37105512 DOI: 10.1016/j.abb.2023.109615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023]
Abstract
Human serum amyloid A (SAA) is a precursor protein involved in AA amyloidosis. The N-terminal region of the SAA molecule is crucial for amyloid fibril formation, and therefore modifications in this region are considered to influence the pathogenesis of AA amyloidosis. In the present study, using the N-terminal peptide corresponding to the putative first helix region of the SAA molecule, we investigated the influences of N-terminal modifications on amyloid fibril formation. Spectroscopic analyses revealed that carbamoylation of the N-terminal amino group delayed the onset of amyloid fibril formation. From transmission electron microscopic observations, the N-terminal carbamoylated aggregate showed remarkably different morphologies from the unmodified control. In contrast, acetylation of the N-terminal amino group or truncation of N-terminal amino acid(s) considerably diminished amyloidogenic properties. Furthermore, we also tested the cell toxicity of each peptide aggregate on cultured cells by two cytotoxic assays. Irrespective of carbamoylation or acetylation, MTT assay revealed that SAA peptides reduced the reductive activity of MTT on cells, whereas no apparent increase in LDH release was observed during an LDH assay. In contrast, N-terminal truncation did not affect either MTT reduction or LDH release. These results suggest that N-terminal modification of SAA molecules can act as a switch to regulate susceptibility to AA amyloidosis.
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Affiliation(s)
- Masafumi Tanaka
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan.
| | - Toru Takarada
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Satomi Nadanaka
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Risa Kojima
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Kimiko Hosoi
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Yuki Machiba
- Laboratory of Functional Molecular Chemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Hiroshi Kitagawa
- Laboratory of Biochemistry, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Toshiyuki Yamada
- Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke, 329-0498, Japan
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3
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Shintani-Domoto Y, Sugiura Y, Ogawa M, Sugiyama E, Abe H, Sakatani T, Ohashi R, Ushiku T, Fukayama M. N-terminal peptide fragment constitutes core of amyloid deposition of serum amyloid A: An imaging mass spectrometry study. PLoS One 2022; 17:e0275993. [PMID: 36240260 PMCID: PMC9565386 DOI: 10.1371/journal.pone.0275993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Serum amyloid A (SAA) is an acute phase protein, which undergoes structural changes and deposits in the extracellular matrix, causing organ damage. Systemic AA amyloidosis is a relatively common amyloid subtype among the more than 30 amyloid subtypes, but the mechanism of amyloid fibril formation remains unclear. In this study, we investigated the tissue distribution of SAA derived peptides in formalin-fixed paraffin embedded (FFPE) specimens of human myocardium with amyloidosis using matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS). In the whole SAA protein, four trypsin-digested peptides in the range of SAA2-67 were visualized and the N-terminal peptide; SAA2-15, was selectively localized in the Congo red-positive region. The C-terminal peptides; SAA47-62, SAA48-62, and SAA63-67 were detected not only in the Congo red-positive region but also in the surrounding negative region. Our results demonstrate that the N-terminal SAA2-15 plays a critical role in the formation of AA amyloid fibril, as previously reported. Roles of the C-terminal peptides require further investigation.
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Affiliation(s)
- Yukako Shintani-Domoto
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Diagnostic Pathology, Nippon Medical School Hospital, Tokyo, Japan
- * E-mail:
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Makiko Ogawa
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eiji Sugiyama
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Sakatani
- Department of Diagnostic Pathology, Nippon Medical School Hospital, Tokyo, Japan
| | - Ryuji Ohashi
- Department of Diagnostic Pathology, Nippon Medical School Hospital, Tokyo, Japan
- Department of Integrated Diagnostic Pathology, Nippon Medical School, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Asahi Tele Pathology Center, Asahi General Hospital, Asahi-City, Chiba, Japan
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4
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Jana AK, Greenwood AB, Hansmann UHE. Small Peptides for Inhibiting Serum Amyloid A Aggregation. ACS Med Chem Lett 2021; 12:1613-1621. [PMID: 34676044 DOI: 10.1021/acsmedchemlett.1c00456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/01/2021] [Indexed: 12/18/2022] Open
Abstract
Deposition of human serum amyloid A (SAA) amyloids in blood vessels, causing inflammation, thrombosis, and eventually organ damage, is commonly seen as a consequence of certain cancers and inflammatory diseases and may also be a risk after SARS-COV-2 infections. Several attempts have been made to develop peptide-based drugs that inhibit or at least slow down SAA amyloidosis. We use extensive all-atom molecular dynamic simulations to compare three of these drug candidates for their ability to destabilize SAA fibrils and to propose for the best candidate, the N-terminal sequence SAA1-5, a mechanism for inhibition. As the lifetime of peptide drugs can be increased by replacing l-amino acids with their mirror d-amino acids, we have also studied corresponding d-peptides. We find that DRI-SAA1-5, formed of d-amino acids with the sequence of the peptide reversed, has similar inhibitory properties compared to the original l-peptide and therefore may be a promising candidate for drugs targeting SAA amyloidosis.
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Affiliation(s)
- Asis K. Jana
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Augustus B. Greenwood
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H. E. Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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5
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Jana AK, Greenwood AB, Hansmann UHE. Presence of a SARS-CoV-2 Protein Enhances Amyloid Formation of Serum Amyloid A. J Phys Chem B 2021; 125:9155-9167. [PMID: 34370466 PMCID: PMC8369982 DOI: 10.1021/acs.jpcb.1c04871] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A marker for the severeness and disease progress of COVID-19 is overexpression of serum amyloid A (SAA) to levels that in other diseases are associated with a risk for SAA amyloidosis. To understand whether SAA amyloidosis could also be a long-term risk of SARS-CoV-2 infections, we have used long all-atom molecular dynamic simulations to study the effect of a SARS-CoV-2 protein segment on SAA amyloid formation. Sampling over 40 μs, we find that the presence of the nine-residue segment SK9, located at the C-terminus of the envelope protein, increases the propensity for SAA fibril formation by three mechanisms: it reduces the stability of the lipid-transporting hexamer shifting the equilibrium toward monomers, it increases the frequency of aggregation-prone configurations in the resulting chains, and it raises the stability of SAA fibrils. Our results therefore suggest that SAA amyloidosis and related pathologies may be a long-term risk of SARS-CoV-2 infections.
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Affiliation(s)
- Asis K Jana
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Augustus B Greenwood
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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6
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Maszota-Zieleniak M, Danielsson A, Samsonov SA. The potential role of glycosaminoglycans in serum amyloid A fibril formation by in silico approaches. Matrix Biol Plus 2021; 12:100080. [PMID: 34401710 PMCID: PMC8350538 DOI: 10.1016/j.mbplus.2021.100080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/10/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
SAA dimer binds GAGs stronger than its monomer. Due to its net negative charge SAA prefers to bind short GAG sequences. GAG binding by SAA is electrostatics-driven and rather unspecific. GAG binding site is constituted predominantly by the N-terminal helix residues. GAG binding could potenitally attenuate unfolding of the N-terminal helix.
Serum amyloid A (SAA) is actively involved in such pathological processes as atherosclerosis, rheumatoid arthritis, cancer and Alzheimer's disease by its aggregation. One of the factors that can attenuate its aggregation and so affects its physiological role is its interactions with glycosminoglycans (GAGs), linear anionic periodic polysaccharides. These molecules located in the extracellular matrix of the cell are highly variable in their chemical composition and sulfation patterns. Despite the available experimental evidence of SAA-GAG interactions, no mechanistic details at atomic level have been reported for these systems so far. In our work we aimed to apply diverse computational tools to characterize SAA-GAG complexes formation and to answer questions about their potential specificity, energetic patterns, particular SAA residues involved in these interactions, favourable oligomeric state of the protein and the potential influence of GAGs on SAA aggregation. Molecular docking, conventional and replica exchange molecular dynamics approaches were applied to corroborate the experimental knowledge and to propose the corresponding molecular models. SAA-GAG complex formation was found to be electrostatics-driven and rather unspecific of a GAG sulfation pattern, more favorable for the dimer than for the monomer when binding to a short GAG oligosaccharide through its N-terminal helix, potentially contributing to the unfolding of this helix, which could lead to the promotion of the protein aggregation. The data obtained add to the specific knowledge on SAA-GAG systems and deepen the general understanding of protein-GAG interactions that is of a considerable value for the development of GAG-based approaches in a broad theurapeutic context.
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Affiliation(s)
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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7
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Wang W, Khatua P, Hansmann UHE. Cleavage, Downregulation, and Aggregation of Serum Amyloid A. J Phys Chem B 2020; 124:1009-1019. [PMID: 31955564 DOI: 10.1021/acs.jpcb.9b10843] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Various diseases cause overexpression of the serum amyloid A (SAA) protein, which in some cases, but not in all cases, leads to amyloidosis as a secondary disease. Response to the overexpression involves dissociation of the SAA hexamer and subsequent cleavage of the released monomers, most commonly yielding fragments SAA1-76 of the full-sized SAA1-104. We report results from molecular dynamic simulations that probe the role of this cleavage for downregulating the activity and concentration of SAA. We propose a mechanism that relies on two elements. First, the probability to assemble into hexamers is lower for the fragments than it is for the full-sized protein. Second, unlike other fragments, SAA1-76 can switch between two distinct configurations. The first kind is easy to proteolyse (allowing a fast reduction of the SAA concentration) but prone to aggregation, whereas the situation is opposite for the second kind. If the time scale for amyloid formation is longer than the one for proteolysis, the aggregation-prone species dominates. However, if environmental conditions such as low pH increases the risk of amyloid formation, the ensemble shifts toward the more protected form. We speculate that SAA amyloidosis is a failure of this switching mechanism leading to accumulation of the aggregation-prone species and subsequent amyloid formation.
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Affiliation(s)
- Wenhua Wang
- Department of Chemistry & Biochemistry , University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Prabir Khatua
- Department of Chemistry & Biochemistry , University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry , University of Oklahoma , Norman , Oklahoma 73019 , United States
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8
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Skibiszewska S, Żaczek S, Dybala-Defratyka A, Jędrzejewska K, Jankowska E. Influence of short peptides with aromatic amino acid residues on aggregation properties of serum amyloid A and its fragments. Arch Biochem Biophys 2020; 681:108264. [PMID: 31945312 DOI: 10.1016/j.abb.2020.108264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 12/20/2022]
Abstract
Serum amyloid A variant 1.1 (SAA1.1) is an acute phase protein. In response to injury, inflammation or infection its production increases highly, which may lead to aggregation of the protein and accumulation of its deposits in various organs. Due to the cellular toxicity of the aggregates, as well as the fact that accumulated deposits are a burden that obstructs proper functioning of the affected tissues, it is vital to find a way to suppress the process of pathological aggregates formation. To make this possible, it is necessary to investigate thoroughly the oligomerization process and recognize factors that may influence its course. Some previous studies showed that aromatic interactions are important to the potential of an inhibitor to suppress the aggregation process. In our research we had proved that a five-residue peptide RSFFS (saa1-5) is an efficient inhibitor of aggregation of the most amyloidogenic fragment of SAA1.1, SAA1-12. In the present work the oligomerization and aggregation propensity of SAA1-12 was compared to that of SAA1-27, in order to determine the contribution of the sequence which extends beyond the most amyloidogenic region but encompasses residues reportedly involved in the stabilization of the SAA native conformation. Thioflavin T fluorescence assay, quantitative chromatographic analysis of the insoluble fraction and transmission electron microscopy allowed for a deeper insight into the SAA aggregation process and the morphology of aggregates. Substitutions of Phe3 and/or Phe4 residues in saa1-5 sequence with tryptophan, tyrosine, homophenylalanine, naphthylalanine and β,β-diphenylalanine allowed to study the influence of different aromatic systems on the aggregation of SAA1-12 and SAA1-27, and evaluate these results in relation to hSAA1.1 protein. Our results indicate that compounds with aromatic moieties can affect the course of the aggregation process and change the ratio between the soluble and insoluble aggregates.
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Affiliation(s)
- Sandra Skibiszewska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Łódź, Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924, Łódź, Poland
| | - Katarzyna Jędrzejewska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Elżbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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9
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Jin L, Syrovets T, Scheller JS, Zhang X, Simmet T. Comparative Study on Hyaluronic Acid Binding to Murine SAA1.1 and SAA2.2. ACS OMEGA 2019; 4:13388-13399. [PMID: 31460467 PMCID: PMC6704436 DOI: 10.1021/acsomega.9b01590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Persistently high plasma levels of serum amyloid A (SAA) may induce AA amyloidosis in various organs causing their dysfunction. Although SAA isoforms share a high degree of homology, only the SAA1.1 isoform is found in amyloid deposits. SAA1.1 misfolding is a nucleation-dependent process with dimer and trimer formation playing a major role in SAA fibril formation through self-catalyzed recruitment of native SAA molecules. Yet, a structural model of initial SAA oligomerization is still missing. In this study, we constructed a loosely associated model for murine SAA1.1 and SAA2.2 dimers in the presence or absence of hyaluronic acid as an exemplary glycosaminoglycan, a factor known to facilitate SAA fibril formation. Molecular dynamics simulations predicted that hyaluronic acid finally stabilized in a different binding pocket of the pathogenic SAA1.1 dimer compared to the nonpathogenic SAA2.2 dimer. Besides, Markov state modeling points to dynamic behavioral differences between the linker region of SAA1.1 and SAA2.2 and identifies a state unique to pathogenic SAA1.1 while bound to hyaluronic acid. The presence or absence of hyaluronic acid, as well as the dimer interface switch, affects dynamic behavior and possible oligomeric states, proposing a conceivable clue to the deviant pathogenicity of the two SAA isoforms.
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Affiliation(s)
- Lu Jin
- Institute
of Pharmacology of Natural Products & Clinical Pharmacology, Ulm University, Helmholtzstr. 20, 89081 Ulm, Germany
| | - Tatiana Syrovets
- Institute
of Pharmacology of Natural Products & Clinical Pharmacology, Ulm University, Helmholtzstr. 20, 89081 Ulm, Germany
| | - Judith S. Scheller
- Institute
of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Xinlei Zhang
- Department
of Medicinal Chemistry, School of Pharmacy, Fourth Military Medical University, 710032 Xi’an, P. R. China
| | - Thomas Simmet
- Institute
of Pharmacology of Natural Products & Clinical Pharmacology, Ulm University, Helmholtzstr. 20, 89081 Ulm, Germany
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10
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Guryanov I, Real-Fernández F, Sabatino G, Prisco N, Korzhikov-Vlakh V, Biondi B, Papini AM, Korzhikova-Vlakh E, Rovero P, Tennikova T. Modeling interaction between gp120 HIV protein and CCR5 receptor. J Pept Sci 2019; 25:e3142. [PMID: 30680875 DOI: 10.1002/psc.3142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023]
Abstract
The study of the process of HIV entry into the host cell and the creation of biomimetic nanosystems that are able to selectively bind viral particles and proteins is a high priority research area for the development of novel diagnostic tools and treatment of HIV infection. Recently, we described multilayer nanoparticles (nanotraps) with heparin surface and cationic peptides comprising the N-terminal tail (Nt) and the second extracellular loop (ECL2) of CCR5 receptor, which could bind with high affinity some inflammatory chemokines, in particular, Rantes. Because of the similarity of the binding determinants in CCR5 structure, both for chemokines and gp120 HIV protein, here we expand this approach to the study of the interactions of these biomimetic nanosystems and their components with the peptide representing the V3 loop of the activated form of gp120. According to surface plasmon resonance results, a conformational rearrangement is involved in the process of V3 and CCR5 fragments binding. As in the case of Rantes, ECL2 peptide showed much higher affinity to V3 peptide than Nt (KD = 3.72 × 10-8 and 1.10 × 10-6 M, respectively). Heparin-covered nanoparticles bearing CCR5 peptides effectively bound V3 as well. The presence of both heparin and the peptides in the structure of the nanotraps was shown to be crucial for the interaction with the V3 loop. Thus, short cationic peptides ECL2 and Nt proved to be excellent candidates for the design of CCR5 receptor mimetics.
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Affiliation(s)
- I Guryanov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
| | - F Real-Fernández
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Italy
| | - G Sabatino
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Italy.,CNR Istituto di Biostrutture e Bioimmagini, 95126, Catania, Italy
| | - N Prisco
- Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, 50019, Sesto Fiorentino, Italy
| | - V Korzhikov-Vlakh
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
| | - B Biondi
- CNR-ICB, Padova Unit, Department of Chemistry, University of Padova, 35131, Padova, Italy
| | - A M Papini
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino, Italy.,PeptLab@UCP Platform and Laboratory of Chemical Biology EA4505, University Paris-Seine, 95031, Cergy-Pontoise CEDEX, France
| | - E Korzhikova-Vlakh
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
| | - P Rovero
- CNR Istituto di Biostrutture e Bioimmagini, 95126, Catania, Italy.,Laboratory of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, 50019, Sesto Fiorentino, Italy
| | - T Tennikova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, 198504, Russia
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11
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Wang W, Xi W, Hansmann UHE. Stability of the N-Terminal Helix and Its Role in Amyloid Formation of Serum Amyloid A. ACS OMEGA 2018; 3:16184-16190. [PMID: 30533585 PMCID: PMC6275945 DOI: 10.1021/acsomega.8b02377] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/16/2018] [Indexed: 05/03/2023]
Abstract
Colonic amyloidosis is the result of overexpression of the serum amyloid A (SAA) protein in inflammatory bowel disease or colon cancer. Crucial for amyloid formation are the first ten N-terminal residues, which in the crystal structure are a part of a 27-residue long helix. Here, we study this 27-residue N-terminal region of SAA by a multiexchange variant of replica exchange molecular dynamics. An ensemble of configurations is observed, dominated by three motifs: the single helix of the crystal structure, a helix-turn-helix configurations, and such where the residues 14-27 are the part of a helix but the first 13 residues form an extended and disordered segment that is prone to aggregation. The single point mutation E9A shifts the equilibrium to the latter motif, indicating the importance of interactions involving this residue for the stability of the SAA protein.
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12
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Tanaka M, Kawakami T, Okino N, Sasaki K, Nakanishi K, Takase H, Yamada T, Mukai T. Acceleration of amyloid fibril formation by carboxyl-terminal truncation of human serum amyloid A. Arch Biochem Biophys 2018; 639:9-15. [DOI: 10.1016/j.abb.2017.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/12/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022]
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13
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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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14
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Tanaka M, Nishimura A, Takeshita H, Takase H, Yamada T, Mukai T. Effect of lipid environment on amyloid fibril formation of human serum amyloid A. Chem Phys Lipids 2017; 202:6-12. [DOI: 10.1016/j.chemphyslip.2016.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
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15
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Bernhardt NA, Xi W, Wang W, Hansmann UHE. Simulating Protein Fold Switching by Replica Exchange with Tunneling. J Chem Theory Comput 2016; 12:5656-5666. [PMID: 27767301 DOI: 10.1021/acs.jctc.6b00826] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms that are essential for its function or are important during folding or association. These various forms populate a multifunnel folding and association landscape where mutations, changes in environment, or interaction with other molecules switch between the encoded folds. We introduce replica exchange with tunneling as a way to efficiently simulate switching between distinct folds of proteins and protein aggregates. The correctness and efficiency of our approach are demonstrated in a series of simulations covering a wide range of proteins, from a small 11-residue large designed peptide to two 56-residue large mutants of the A and B domains of protein G.
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Affiliation(s)
- Nathan A Bernhardt
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Wenhui Xi
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Wei Wang
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
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16
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Mass spectrometric immunoassays for discovery, screening and quantification of clinically relevant proteoforms. Bioanalysis 2016; 8:1623-1633. [PMID: 27396364 DOI: 10.4155/bio-2016-0060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human proteins can exist as multiple proteoforms with potential diagnostic or prognostic significance. MS top-down approaches are ideally suited for proteoforms identification because there is no prerequisite for a priori knowledge of the specific proteoform. One such top-down approach, termed mass spectrometric immunoassay utilizes antibody-derivatized microcolumns for rapid and contained proteoforms isolation and detection via MALDI-TOF MS. The mass spectrometric immunoassay can also provide quantitative measurement of the proteoforms through inclusion of an internal reference standard into the analytical sample, serving as normalizer for all sample processing and data acquisition steps. Reviewed here are recent developments and results from the application of mass spectrometric immunoassays for discovery of clinical correlations of specific proteoforms for the protein biomarkers RANTES, retinol binding protein, serum amyloid A and apolipoprotein C-III.
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17
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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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18
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Digre A, Nan J, Frank M, Li JP. Heparin interactions with apoA1 and SAA in inflammation-associated HDL. Biochem Biophys Res Commun 2016; 474:309-314. [PMID: 27105909 DOI: 10.1016/j.bbrc.2016.04.092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/18/2016] [Indexed: 12/23/2022]
Abstract
Apolipoprotein A1 (apoA1) is the main protein component responsible for transportation of cholesterol on high-density lipoprotein (HDL). Serum amyloid A (SAA) is an acute phase protein associated with HDL. Apart from their physiological functions, both apoA1 and SAA have been identified as 'amyloidogenic peptides'. We report herein that the polysaccharide heparin interacts with both apoA1 and SAA in HDL isolated from plasma of inflamed mice. The reaction is rapid, forming complex aggregates composed of heparin, apoA1 and SAA as revealed by gel electrophoresis. This interaction is dependent on the size and concentration of added heparin. Mass spectrometry analysis of peptides derived from chemically crosslinked HDL-SAA particles detected multiple crosslinks between apoA1 and SAA, indicating close proximity (within 25 Å) of these two proteins on the HDL surface, providing a molecular and structural mechanism for the simultaneous binding of heparin to apoA1 and SAA.
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Affiliation(s)
- Andreas Digre
- Department of Medical Biochemistry and Microbiology/SciLifeLab, University of Uppsala, The Biomedical Center, Box 582, SE-751 23 Uppsala, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden
| | | | - Jin-Ping Li
- Department of Medical Biochemistry and Microbiology/SciLifeLab, University of Uppsala, The Biomedical Center, Box 582, SE-751 23 Uppsala, Sweden.
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19
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Yassine HN, Trenchevska O, He H, Borges CR, Nedelkov D, Mack W, Kono N, Koska J, Reaven PD, Nelson RW. Serum amyloid a truncations in type 2 diabetes mellitus. PLoS One 2015; 10:e0115320. [PMID: 25607823 PMCID: PMC4301920 DOI: 10.1371/journal.pone.0115320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/21/2014] [Indexed: 12/16/2022] Open
Abstract
Serum Amyloid A (SAA) is an acute phase protein complex consisting of several abundant isoforms. The N- terminus of SAA is critical to its function in amyloid formation. SAA is frequently truncated, either missing an arginine or an arginine-serine dipeptide, resulting in isoforms that may influence the capacity to form amyloid. However, the relative abundance of truncated SAA in diabetes and chronic kidney disease is not known.
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Affiliation(s)
- Hussein N Yassine
- University of Southern California, Los Angeles, CA, United States of America
| | | | - Huijuan He
- University of Southern California, Los Angeles, CA, United States of America
| | - Chad R Borges
- Arizona State University, Tempe, AZ, United States of America
| | - Dobrin Nedelkov
- Arizona State University, Tempe, AZ, United States of America
| | - Wendy Mack
- University of Southern California, Los Angeles, CA, United States of America
| | - Naoko Kono
- University of Southern California, Los Angeles, CA, United States of America
| | - Juraj Koska
- Phoenix VA Health Care System, Phoenix, AZ, United States of America
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, United States of America
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20
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Amyloid-Forming Properties of Human Apolipoproteins: Sequence Analyses and Structural Insights. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:175-211. [PMID: 26149931 DOI: 10.1007/978-3-319-17344-3_8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Apolipoproteins are protein constituents of lipoproteins that transport cholesterol and fat in circulation and are central to cardiovascular health and disease. Soluble apolipoproteins can transiently dissociate from the lipoprotein surface in a labile free form that can misfold, potentially leading to amyloid disease. Misfolding of apoA-I, apoA-II, and serum amyloid A (SAA) causes systemic amyloidoses, apoE4 is a critical risk factor in Alzheimer's disease, and apolipoprotein misfolding is also implicated in cardiovascular disease. To explain why apolipoproteins are over-represented in amyloidoses, it was proposed that the amphipathic α-helices, which form the lipid surface-binding motif in this protein family, have high amyloid-forming propensity. Here, we use 12 sequence-based bioinformatics approaches to assess amyloid-forming potential of human apolipoproteins and to identify segments that are likely to initiate β-aggregation. Mapping such segments on the available atomic structures of apolipoproteins helps explain why some of them readily form amyloid while others do not. Our analysis shows that nearly all amyloidogenic segments: (i) are largely hydrophobic, (ii) are located in the lipid-binding amphipathic α-helices in the native structures of soluble apolipoproteins, (iii) are predicted in both native α-helices and β-sheets in the insoluble apoB, and (iv) are predicted to form parallel in-register β-sheet in amyloid. Most of these predictions have been verified experimentally for apoC-II, apoA-I, apoA-II and SAA. Surprisingly, the rank order of the amino acid sequence propensity to form amyloid (apoB>apoA-II>apoC-II≥apoA-I, apoC-III, SAA, apoC-I>apoA-IV, apoA-V, apoE) does not correlate with the proteins' involvement in amyloidosis. Rather, it correlates directly with the strength of the protein-lipid association, which increases with increasing protein hydrophobicity. Therefore, the lipid surface-binding function and the amyloid-forming propensity are both rooted in apolipoproteins' hydrophobicity, suggesting that functional constraints make it difficult to completely eliminate pathogenic apolipoprotein misfolding. We propose that apolipoproteins have evolved protective mechanisms against misfolding, such as the sequestration of the amyloidogenic segments via the native protein-lipid and protein-protein interactions involving amphipathic α-helices and, in case of apoB, β-sheets.
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Colón W, Aguilera JJ, Srinivasan S. Intrinsic Stability, Oligomerization, and Amyloidogenicity of HDL-Free Serum Amyloid A. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:117-34. [PMID: 26149928 DOI: 10.1007/978-3-319-17344-3_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Serum amyloid A (SAA) is an acute-phase reactant protein predominantly bound to high-density lipoprotein in serum and presumed to play various biological and pathological roles. Upon tissue trauma or infection, hepatic expression of SAA increases up to 1,000 times the basal levels. Prolonged increased levels of SAA may lead to amyloid A (AA) amyloidosis, a usually fatal systemic disease in which the amyloid deposits are mostly comprised of the N-terminal 1-76 fragment of SAA. SAA isoforms may differ across species in their ability to cause AA amyloidosis, and the mechanism of pathogenicity remains poorly understood. In vitro studies have shown that SAA is a marginally stable protein that folds into various oligomeric species at 4 °C. However, SAA is largely disordered at 37 °C, reminiscent of intrinsically disordered proteins. Non-pathogenic murine (m)SAA2.2 spontaneously forms amyloid fibrils in vitro at 37 °C whereas pathogenic mSAA1.1 has a long lag (nucleation) phase, and eventually forms fibrils of different morphology than mSAA2.2. Remarkably, human SAA1.1 does not form mature fibrils in vitro. Thus, it appears that the intrinsic amyloidogenicity of SAA is not a key determinant of pathogenicity, and that other factors, including fibrillation kinetics, ligand binding effects, fibril stability, nucleation efficiency, and SAA degradation may play key roles. This chapter will focus on the known structural and biophysical properties of SAA and discuss how these properties may help better understand the molecular mechanism of AA amyloidosis.
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Affiliation(s)
- Wilfredo Colón
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,
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22
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Westermark GT, Fändrich M, Westermark P. AA amyloidosis: pathogenesis and targeted therapy. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2014; 10:321-44. [PMID: 25387054 DOI: 10.1146/annurev-pathol-020712-163913] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The understanding of why and how proteins misfold and aggregate into amyloid fibrils has increased considerably during recent years. Central to amyloid formation is an increase in the frequency of the β-sheet structure, leading to hydrogen bonding between misfolded monomers and creating a fibril that is comparably resistant to degradation. Generation of amyloid fibrils is nucleation dependent, and once formed, fibrils recruit and catalyze the conversion of native molecules. In AA amyloidosis, the expression of cytokines, particularly interleukin 6, leads to overproduction of serum amyloid A (SAA) by the liver. A chronically high plasma concentration of SAA results in the aggregation of amyloid into cross-β-sheet fibrillar deposits by mechanisms not fully understood. Therefore, AA amyloidosis can be thought of as a consequence of long-standing inflammatory disease. This review summarizes current knowledge about AA amyloidosis. The systemic amyloidoses have been regarded as intractable conditions, but improvements in the understanding of fibril composition and pathogenesis over the past decade have led to the development of a number of different therapeutic approaches with promising results.
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23
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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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24
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Takase H, Tanaka M, Miyagawa S, Yamada T, Mukai T. Effect of amino acid variations in the central region of human serum amyloid A on the amyloidogenic properties. Biochem Biophys Res Commun 2014; 444:92-7. [PMID: 24440699 DOI: 10.1016/j.bbrc.2014.01.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Human serum amyloid A (SAA) is a precursor protein of the amyloid fibrils that are responsible for AA amyloidosis. Of the four human SAA genotypes, SAA1 is most commonly associated with AA amyloidosis. Furthermore, SAA1 has three major isoforms (SAA1.1, 1.3, and 1.5) that differ by single amino acid variations at two sites in their 104-amino acid sequences. In the present study, we examined the effect of amino acid variations in human SAA1 isoforms on the amyloidogenic properties. All SAA1 isoforms adopted α-helix structures at 4°C, but were unstructured at 37°C. Heparin-induced amyloid fibril formation of SAA1 was observed at 37°C, as evidenced by the increased thioflavin T (ThT) fluorescence and β-sheet structure formation. Despite a comparable increase in ThT fluorescence, SAA1 molecules retained their α-helix structures at 4°C. At both temperatures, no essential differences in ThT fluorescence and secondary structures were observed among the SAA1 isoforms. However, the fibril morphologies appeared to differ; SAA1.1 formed long and curly fibrils, whereas SAA1.3 formed thin and straight fibrils. The peptides corresponding to the central regions of the SAA1 isoforms containing amino acid variations showed distinct amyloidogenicities, reflecting their direct effects on amyloid fibril formation. These findings may provide novel insights into the influence of amino acid variations in human SAA on the pathogenesis of AA amyloidosis.
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Affiliation(s)
- Hiroka Takase
- Department of Biophysical Chemistry, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Masafumi Tanaka
- Department of Biophysical Chemistry, Kobe Pharmaceutical University, Kobe 658-8558, Japan.
| | - Sachiko Miyagawa
- Department of Biophysical Chemistry, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Toshiyuki Yamada
- Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Takahiro Mukai
- Department of Biophysical Chemistry, Kobe Pharmaceutical University, Kobe 658-8558, Japan
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25
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Katagiri F, Takeyama K, Hozumi K, Kikkawa Y, Nomizu M. Structural requirement of fibrogenic laminin-derived peptide A119 (LSNIDYILIKAS) for amyloid-like fibril formation and cellular activity. Biochemistry 2012; 51:8218-25. [PMID: 23013455 DOI: 10.1021/bi300822d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A119 peptide (LSNIDYILIKAS), derived from the mouse laminin α1 chain sequence (residues 1321-1332), promotes cell attachment, neurite outgrowth, and amyloid-like fibril formation. In this study, we evaluated the structural requirements of A119 for biological activities and amyloid-like fibril formation. The attachment of the cell to A119 was inhibited by heparin, and using syndecan- and glypican-overexpressed cells, it was determined that A119 specifically binds to syndecans. We also evaluated the critical residues for A119 activities using a set of alanine-substituted peptides. Cell attachment activity was significantly reduced in the Leu(1)-, Ser(2)-, Asn(3)-, Ile(4)-, Ile(7)-, Ile(9)-, and Lys(10)-substituted alanine peptides. Residues Ile(4), Ile(7), Ile(9), and Lys(10) were important for neurite outgrowth activity. Congo red staining and electron microscopic examination revealed that the Ile(4), Ile(7), Ile(9), and Ser(12) residues of A119 were required for amyloid-like fibril formation. These data suggest that the Ile residues are critical for the amyloid-like fibril formation, cell attachment, and neurite outgrowth activity of A119. Furthermore, an enantiomer of A119 showed similar amyloid-like fibril formation and increased levels of cell attachment and FAK signal transduction. These findings shed light on the mechanism of amyloid-like fibril formation and demonstrate a relationship between the ability to form amyloid-like fibrils and cell behavior.
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Affiliation(s)
- Fumihiko Katagiri
- Laboratory of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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Nordling E, Abraham-Nordling M. Colonic amyloidosis, computational analysis of the major amyloidogenic species, Serum Amyloid A. Comput Biol Chem 2012; 39:29-34. [PMID: 22885776 DOI: 10.1016/j.compbiolchem.2012.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 06/25/2012] [Accepted: 06/26/2012] [Indexed: 12/20/2022]
Abstract
Amyloidosis is characterized by misfolding of proteins. The clinical gastrointestinal manifestations of amyloidosis may mimic other disease, such as inflammatory bowel disease or colonic cancer. As these patients have a high risk for bleeding and poor wound healing following surgery it is important to diagnose them correctly and do a careful preoperative assessment. The most common form of colonic amyloidosis is caused by Serum Amyloid A (SAA), an acute phase protein of unknown function. It is expressed in response to inflammation and the increased levels may lead to amyloidosis. The main treatment is to suppress the acute phase response and thereby reduce production of SAA. As no structure for SAA is available we aim to perform an in silico assessment of its structural and fibrillation properties. In the paper we propose an ab initio model of the structure of SAA, which consists of a five membered helical bundle with a fold related to the tetratricopeptide repeat domain. As there are uncertainties relating to the packing of the helices, each helical region is subjected to triplicate molecular dynamics simulations to assess the integrity of the structural region. The first helix, stretching from residues 1 to 13, is the least stable according to the simulations; almost all of the helical conformation is lost during the 10 ns simulations, whereas the other helices maintain portions that remain in an helical conformation in at least 80% of the simulations. All helices are also subjected to a single 100 ns simulation to investigate how the secondary structure develops over time. In them helix 1 adopts a β-hairpin structure similar to other fibril forming proteins. The β-hairpin can in turn multimerise and form a mature fibril structure. The mechanism behind the conformational transition appears to be driven by interactions of side chains of charged residues, particularly Arginine 1. It exchanges interaction partners in the simulation and stabilizes intermediate conformations on the folding pathway to the final β-hairpin.
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Affiliation(s)
- Erik Nordling
- IFM Bioinformatics, Linköping University, Linköping, Sweden
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