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Khrustalev VV, Stojarov AN, Akunevich AA, Baranov OE, Popinako AV, Samoilovich EO, Yermalovich MA, Semeiko GV, Sapon EG, Cheprasova VI, Shalygo NV, Poboinev VV, Khrustaleva TA, Khrustaleva OV. Structural Shifts of the Parvovirus B19 Capsid Receptor-binding Domain: A Peptide Study. Protein Pept Lett 2024; 31:128-140. [PMID: 38053353 DOI: 10.2174/0109298665272845231121064717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/25/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Binding appropriate cellular receptors is a crucial step of a lifecycle for any virus. Structure of receptor-binding domain for a viral surface protein has to be determined before the start of future drug design projects. OBJECTIVES Investigation of pH-induced changes in the secondary structure for a capsid peptide with loss of function mutation can shed some light on the mechanism of entrance. METHODS Spectroscopic methods were accompanied by electrophoresis, ultrafiltration, and computational biochemistry. RESULTS In this study, we showed that a peptide from the receptor-binding domain of Parvovirus B19 VP1 capsid (residues 13-31) is beta-structural at pH=7.4 in 0.01 M phosphate buffer, but alpha- helical at pH=5.0, according to the circular dichroism (CD) spectroscopy results. Results of infra- red (IR) spectroscopy showed that the same peptide exists in both alpha-helical and beta-structural conformations in partial dehydration conditions both at pH=7.4 and pH=5.0. In contrast, the peptide with Y20W mutation, which is known to block the internalization of the virus, forms mostly alpha-helical conformation in partial dehydration conditions at pH=7.4. According to our hypothesis, an intermolecular antiparallel beta structure formed by the wild-type peptide in its tetramers at pH=7.4 is the prototype of the similar intermolecular antiparallel beta structure formed by the corresponding part of Parvovirus B19 receptor-binding domain with its cellular receptor (AXL). CONCLUSION Loss of function Y20W substitution in VP1 capsid protein prevents the shift into the beta-structural state by the way of alpha helix stabilization and the decrease of its ability to turn into the disordered state.
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Affiliation(s)
| | | | | | - Oleg Evgenyevich Baranov
- Bach Institute of Biochemistry, Shared-Access Equipment Centre "Industrial Biotechnology" of Russian Academy of Science, Leninskiy prospect, 33/2, Moscow, 119071, Russian Federation
| | - Anna Vladimirovna Popinako
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy prospect, 33/2, Moscow, 119071, Russian Federation
| | - Elena Olegovna Samoilovich
- Laboratory of Vaccine-controlled Infections, Republican Research and Practical Center for Epidemiology and Microbiology, Filimonova 23, Minsk, 220114, Belarus
| | - Marina Anatolyevna Yermalovich
- Laboratory of Vaccine-controlled Infections, Republican Research and Practical Center for Epidemiology and Microbiology, Filimonova 23, Minsk, 220114, Belarus
| | - Galina Valeryevna Semeiko
- Laboratory of Vaccine-controlled Infections, Republican Research and Practical Center for Epidemiology and Microbiology, Filimonova 23, Minsk, 220114, Belarus
| | - Egor Gennadyevich Sapon
- Laboratory of infra-red spectroscopy and infra-red microscopy, Belarusian State Technological University, Sverdlova 13a, Minsk, 220006, Belarus
| | - Victoria Igorevna Cheprasova
- Laboratory of infra-red spectroscopy and infra-red microscopy, Belarusian State Technological University, Sverdlova 13a, Minsk, 220006, Belarus
| | | | - Victor Vitoldovich Poboinev
- Department of General Chemistry, Belarusian State Medical University, Dzerzhinskogo 83, Minsk, 220045, Belarus
| | - Tatyana Aleksandrovna Khrustaleva
- Laboratory of Biomedical Technologies and Medical Rehabilitation, Institute of Physiology of the National Academy of Sciences of Belarus, Academicheskaya 28, Minsk, 220072; Belarus
| | - Olga Victorovna Khrustaleva
- Department of General Chemistry, Belarusian State Medical University, Dzerzhinskogo 83, Minsk, 220045, Belarus
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Poboinev VV, Khrustalev VV, Akunevich AA, Shalygo NV, Stojarov AN, Khrustaleva TA, Kordyukova LV. Peptide Models of the Cytoplasmic Tail of Influenza A/H1N1 Virus Hemagglutinin Expand Understanding its pH-Dependent Modes of Interaction with Matrix Protein M1. Protein J 2023:10.1007/s10930-023-10101-z. [PMID: 36952102 PMCID: PMC10034248 DOI: 10.1007/s10930-023-10101-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly conserved cysteines. We recently proposed a model of HA CT of Influenza A/H1N1 virus possessing an antiparallel beta structure based on the experimental secondary structure analysis of four 14-15 amino acid long synthetic peptides, corresponding to the HA CT sequence, with free or acetaminomethylated cysteines. To dispel doubts about possible non-specific "amyloid-like" aggregation of those synthetic peptides in phosphate buffer solution, we have determined the order of oligomers based on blue native gel electrophoresis, membrane filtration, fluorescence spectroscopy and molecular modeling approaches. We have found that unmodified peptides form only low molecular weight oligomers, while modified peptides form both oligomers of low order similar to those found for unmodified peptides and high order conglomerates, which however are not of beta-amyloid-like fold. This study confirms that the beta structure previously detected by circular dichroism spectroscopy analysis is more likely the result of intrinsic propensity of the HA CT amino acid sequence than the consequence of aggregation. The structures of low order oligomers of the synthetic peptides were used for in silico experiments on modeling of HA CT interactions with matrix protein M1 at physiological and acidic pH levels and revealed two different areas of binding. Finally, tripeptides capable of blocking interactions between HA CT and M1 were proposed.
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Popinako А, Pometun А, Nilov D, Dibrova D, Khrustalev V, Khrustaleva T, Iurchenko T, Nikolaeva А, Švedas V, Boyko K, Tishkov V, Popov V. The role of Tyr102 residue in the functioning of bacterial NAD+-dependent formate dehydrogenase of Pseudomonas sp. 101. Biochem Biophys Res Commun 2022; 616:134-139. [DOI: 10.1016/j.bbrc.2022.05.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
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