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Osetrina DA, Kusova AM, Bikmullin AG, Klochkova EA, Yulmetov AR, Semenova EA, Mukhametzyanov TA, Usachev KS, Klochkov VV, Blokhin DS. Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation. Int J Mol Sci 2023; 24:ijms24108949. [PMID: 37240295 DOI: 10.3390/ijms24108949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86-107), SEM1(68-107), SEM1(49-107) and SEM1(45-107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45-107) and SEM1(49-107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45-107) starts immediately after purification, which is not observed for SEM1(49-107). Seeing that the peptide amino acid sequence of SEM1(45-107) differs from SEM1(49-107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45-67) and SEM1(49-67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45-67) and SEM1(49-67). However, SEM1(45-67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides' (SEM1(45-107) and SEM1(49-107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45-107) N-terminus, which contributes to an increased rate of amyloid formation.
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Affiliation(s)
- Daria A Osetrina
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Aleksandra M Kusova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan 420111, Russia
| | - Aydar G Bikmullin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Evelina A Klochkova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Aydar R Yulmetov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Evgenia A Semenova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Timur A Mukhametzyanov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Konstantin S Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan 420111, Russia
| | - Vladimir V Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Dmitriy S Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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Agrawal N, Parisini E. Early Stages of Misfolding of PAP248-286 at two different pH values: An Insight from Molecular Dynamics Simulations. Comput Struct Biotechnol J 2022; 20:4892-4901. [PMID: 36147683 PMCID: PMC9474323 DOI: 10.1016/j.csbj.2022.08.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 01/01/2023] Open
Abstract
PAP248-286 peptides, which are highly abundant in human semen, aggregate and form amyloid fibrils that enhance HIV infection. Previous experimental studies have shown that the infection-promoting activity of PAP248-286 begins to increase well before amyloid formation takes place and that pH plays a key role in the enhancement of PAP248-286-related infection. Hence, understanding the early stages of misfolding of the PAP2482-86 peptide is crucial. To this end, we have performed 60 independent MD simulations for a total of 24 µs at two different pH values (4.2 and 7.2). Our data shows that early stages of misfolding of the PAP248-286 peptide is a multistage process and that the first step of the process is a transition from an “I-shaped” structure to a “U-shaped” structure. We further observed that the structure of PAP248-286 at the two different pH values shows significantly different features. At pH 4.2, the peptide has less intra-molecular H-bonds and a reduced α-helical content than at pH 7.2. Moreover, differences in intra-peptide residues contacts are also observed at the two pH values. Finally, free energy landscape analysis shows that there are more local minima in the energy surface of the peptide at pH 7.2 than at pH 4.2. Overall, the present study elucidates the early stages of misfolding of the PAP248-286 peptide at the atomic level, thus possibly opening new avenues in structure-based drug discovery against HIV infection.
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Affiliation(s)
- Nikhil Agrawal
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Corresponding authors at: Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia.
| | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Bologna, Italy
- Corresponding authors at: Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia.
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Kusova A, Abramova M, Skvortsova P, Yulmetov A, Mukhametzyanov T, Klochkov V, Blokhin D. Structure of amyloidogenic PAP(85-120) peptide by high-resolution NMR spectroscopy. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mohapatra S, Viswanathan GKK, Wettstein L, Arad E, Paul A, Kumar V, Jelinek R, Münch J, Segal D. Dual concentration-dependent effect of ascorbic acid on PAP(248-286) amyloid formation and SEVI-mediated HIV infection. RSC Chem Biol 2021; 2:1534-1545. [PMID: 34704058 PMCID: PMC8496042 DOI: 10.1039/d1cb00084e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/08/2021] [Indexed: 12/20/2022] Open
Abstract
Human semen contains various amyloidogenic peptides derived from Prostatic Acid Phosphatase (PAP) and Semenogelin proteins that are capable of enhancing HIV-1 infection when assembled into fibrils. The best characterized among them is a 39 amino acid peptide PAP(248–286), which forms amyloid fibrils termed SEVI (semen-derived enhancer of viral infection) that increase the infectivity of HIV-1 by orders of magnitude. Inhibiting amyloid formation by PAP(248–286) may mitigate the sexual transmission of HIV-1. Several vitamins have been shown to reduce the aggregation of amyloids such as Aβ, α-Synuclein, and Tau, which are associated with neurodegenerative diseases. Since ascorbic acid (AA, vitamin C) is the most abundant vitamin in semen with average concentrations of 0.4 mM, we here examined how AA affects PAP(248–286) aggregation in vitro. Using ThT binding assays, transmission electron microscopy, and circular dichroism spectroscopy, a dual and concentration-dependent behavior of AA in modulating PAP(248–286) fibril formation was observed. We found that low molar ratios of AA:PAP(248–286) promoted whereas high molar ratios inhibited PAP(248–286) fibril formation. Accordingly, PAP(248–286) aggregated in the presence of low amounts of AA enhanced HIV-1 infection, whereas excess amounts of AA during aggregation reduced the infectivity enhancing effect in cell culture. Collectively, this work provides a biophysical insight into the effect of AA, an important seminal component, on SEVI fibrillation which might impact amyloid formation kinetics, thereby modulating the biological activity of semen amyloids. Human semen contains various amyloidogenic peptides derived from Prostatic Acid Phosphatase (PAP) and Semenogelin proteins that are capable of enhancing HIV-1 infection when assembled into fibrils.![]()
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Affiliation(s)
- Satabdee Mohapatra
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv 69978 Israel
| | - Guru Krishna Kumar Viswanathan
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv 69978 Israel
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center Ulm 89081 Germany
| | - Elad Arad
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev Beer Sheva 8410501 Israel
| | - Ashim Paul
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv 69978 Israel
| | - Vijay Kumar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv 69978 Israel
| | - Raz Jelinek
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev Beer Sheva 8410501 Israel
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center Ulm 89081 Germany
| | - Daniel Segal
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv 69978 Israel
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Li M, Dong X, Liu Y, Sun Y. Brazilin Inhibits Prostatic Acidic Phosphatase Fibrillogenesis and Decreases its Cytotoxicity. Chem Asian J 2017; 12:1062-1068. [PMID: 28303660 DOI: 10.1002/asia.201700058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/24/2017] [Indexed: 11/06/2022]
Abstract
A 39-amino acid peptide fragment that is derived from prostatic acidic phosphatase (PAP), PAP248-286 , is secreted in large amounts in human semen and forms amyloid fibrils. These fibrils can capture HIV virions and increase the attachment of virions to target cells; as such, they are called a "semen-derived enhancer of virus infection" (SEVI). Therefore, the inhibition of the formation of PAP248-286 amyloid fibrils is of great significance. Herein, we demonstrate that brazilin effectively inhibits PAP248-286 aggregation. The inhibitory effect increases with increasing brazilin concentration. Thioflavin T fluorescence assays and TEM observations confirmed that a few fibrils formed when brazilin was present with PAP248-286 in an equimolar concentration. Circular dichroism spectroscopy indicated that brazilin inhibited the secondary structural transitions from α-helices and random coils into β-sheets. Cytotoxicity assays showed that brazilin significantly decreased the cytotoxicity of the fibrils at 0.01 mmol L-1 . Isothermal titration calorimetry revealed that hydrophobic interactions were the main driving force for the binding of brazilin to the PAP248-286 monomer (dissociation constant, 4.03 μmol L-1 ), and that the binding affinity of brazilin for the fibrils was at least three orders of magnitude lower than that for the monomer. These results indicate that brazilin holds great potential as a small-molecule agent against SEVIs.
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Affiliation(s)
- Ming Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300354, P. R. China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300354, P. R. China
| | - Yang Liu
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, Guangdong, 515063, P. R. China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300354, P. R. China
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Khodov IA, Maltceva OV, Klochkov VV, Koifman OI, Mamardashvili NZ. N-Confused porphyrins: complexation and 1H NMR studies. NEW J CHEM 2017. [DOI: 10.1039/c7nj01814b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complexation of 2-aza-21-carba-tetraphenylporphyrin and 2-aza-2-methyl-5,10,15,20-tetraphenyl-21-carbaporphyrin with nickel and zinc acetates in organic solvents has been investigated by UV-Vis spectroscopy and 1H NMR.
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Affiliation(s)
- Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
- Kazan Federal University
- Kazan
| | - Olga V. Maltceva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
| | | | - Oscar I. Koifman
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
- Research Institute of Macroheterocycles
- Ivanovo State University of Chemistry and Technology
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Efimov S, Khodov I, Ratkova E, Kiselev M, Berger S, Klochkov V. Detailed NOESY/T-ROESY analysis as an effective method for eliminating spin diffusion from 2D NOE spectra of small flexible molecules. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.09.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Blokhin DS, Fayzullina AR, Filippov AV, Karataeva FK, Klochkov VV. Spatial structure of fibrinopeptide B in water solution with DPC micelles by NMR spectroscopy. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.08.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Usachev KS, Efimov SV, Kolosova OA, Filippov AV, Klochkov VV. High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles. JOURNAL OF BIOMOLECULAR NMR 2015; 61:227-34. [PMID: 25430060 DOI: 10.1007/s10858-014-9885-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/20/2014] [Indexed: 05/22/2023]
Abstract
PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel β-sheet when it binds to DPC micelles.
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Affiliation(s)
- K S Usachev
- Kazan Federal University, Kremlevskaya, 18, Kazan, 420008, Russian Federation,
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Usachev K, Filippov A, Khairutdinov B, Antzutkin O, Klochkov V. NMR structure of the Arctic mutation of the Alzheimer’s Aβ(1–40) peptide docked to SDS micelles. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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