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Abstract
A rapid-acting insulin lispro and long-acting insulin glargine are commonly used for the treatment of diabetes. Clinical cases have described the formation of injectable amyloidosis with these insulin analogues, but their amyloid core regions of fibrils were unknown. To reveal these regions, we have analysed the hydrolyzates of insulin fibrils and its analogues using high-performance liquid chromatography and mass spectrometry methods and found that insulin and its analogues have almost identical amyloid core regions that intersect with the predicted amyloidogenic regions. The obtained results can be used to create new insulin analogues with a low ability to form fibrils. Abbreviations a.a., amino acid residues; HPLC-MS, high-performance liquid chromatography/mass spectrometry; m/z, mass-to-charge ratio; TEM, transmission electron microscopy.
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Affiliation(s)
- Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Russian Federation.,State Research Center for Applied Microbiology and Biotechnology , Obolensk, Russian Federation.,The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences , Pushchino, Russian Federation
| | - Sergei Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Russian Federation
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Russian Federation.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino, Russian Federation
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Grishin SY, Dzhus UF, Glukhov AS, Selivanova OM, Surin AK, Galzitskaya OV. Identification of Amyloidogenic Regions in Pseudomonas aeruginosa Ribosomal S1 Protein. Int J Mol Sci 2021; 22:ijms22147291. [PMID: 34298910 PMCID: PMC8305250 DOI: 10.3390/ijms22147291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
Bacterial S1 protein is a functionally important ribosomal protein. It is a part of the 30S ribosomal subunit and is also able to interact with mRNA and tmRNA. An important feature of the S1 protein family is a strong tendency towards aggregation. To study the amyloidogenic properties of S1, we isolated and purified the recombinant ribosomal S1 protein of Pseudomonas aeruginosa. Using the FoldAmyloid, Waltz, Pasta 2.0, and AGGRESCAN programs, amyloidogenic regions of the protein were predicted, which play a key role in its aggregation. The method of limited proteolysis in combination with high performance liquid chromatography and mass spectrometric analysis of the products, made it possible to identify regions of the S1 protein from P. aeruginosa that are protected from the action of proteinase K, trypsin, and chymotrypsin. Sequences of theoretically predicted and experimentally identified amyloidogenic regions were used to synthesize four peptides, three of which demonstrated the ability to form amyloid-like fibrils, as shown by electron microscopy and fluorescence spectroscopy. The identified amyloidogenic sites can further serve as a basis for the development of new antibacterial peptides against the pathogenic microorganism P. aeruginosa.
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Affiliation(s)
- Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Ulyana F. Dzhus
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Anatoly S. Glukhov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Olga M. Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (U.F.D.); (A.S.G.); (O.M.S.); (A.K.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
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Grishin SY, Dzhus UF, Selivanova OM, Balobanov VA, Surin AK, Galzitskaya OV. Comparative Analysis of Aggregation of Thermus thermophilus Ribosomal Protein bS1 and Its Stable Fragment. BIOCHEMISTRY (MOSCOW) 2021; 85:344-354. [PMID: 32564739 DOI: 10.1134/s0006297920030104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Functionally important multidomain bacterial protein bS1 is the largest ribosomal protein of subunit 30S. It interacts with both mRNA and proteins and is prone to aggregation, although this process has not been studied in detail. Here, we obtained bacterial strains overproducing ribosomal bS1 protein from Thermus thermophilus and its stable fragment bS1(49) and purified these proteins. Using fluorescence spectroscopy, dynamic light scattering, and high-performance liquid chromatography combined with mass spectrometric analysis of products of protein limited proteolysis, we demonstrated that disordered regions at the N- and C-termini of bS1 can play a key role in the aggregation of this protein. The truncated fragment bS1(49) was less prone to aggregation compared to the full-size bS1. The revealed properties of the studied proteins can be used to obtain protein crystals for elucidating the structure of the bS1 stable fragment.
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Affiliation(s)
- S Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - U F Dzhus
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.,Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Hirai M, Ajito S, Sugiyama M, Iwase H, Takata SI, Shimizu N, Igarashi N, Martel A, Porcar L. Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition. Biophys J 2019; 115:313-327. [PMID: 30021107 DOI: 10.1016/j.bpj.2018.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 01/07/2023] Open
Abstract
The mechanisms of protein stabilization by uncharged solutes, such as polyols and sugars, have been intensively studied with respect to the chemical thermodynamics of molecular crowding. In particular, many experimental and theoretical studies have been conducted to explain the mechanism of the protective action on protein structures by glycerol through the relationship between hydration and glycerol solvation on protein surfaces. We used wide-angle x-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation to quantitatively characterize the hydration and/or solvation shell of myoglobin in aqueous solutions of up to 75% v/v glycerol. At glycerol concentrations below ∼40% v/v, the preservation of the hydration shell was dominant, which was reasonably explained by the preferential exclusion of glycerol from the protein surface (preferential hydration). In contrast, at concentrations above 50% v/v, the partial penetration or replacement of glycerol into or with hydration-shell water (neutral solvation by glycerol) was gradually promoted. WAXS results quantitatively demonstrated the neutral solvation, in which the replacement of hydrated water by glycerol was proportional to the volume fraction of glycerol in the solvent multiplied by an exchange rate (β ≤ 1). These phenomena were confirmed by small-angle neutron scattering measurements. The observed WAXS data covered the entire hierarchical structure of myoglobin, ranging from tertiary to secondary structures. We separately analyzed the effect of glycerol on the thermal stability of myoglobin at each hierarchical structural level. The thermal transition midpoint temperature at each hierarchical structural level was raised depending on the glycerol concentration, with enhanced transition cooperativeness between different hierarchical structural levels. The onset temperature of the helix-to-cross β-sheet transition (the initial process of amyloid formation) was evidently elevated. However, oligomerization connected to fibril formation was suppressed, even at a low glycerol concentration.
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Affiliation(s)
- Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, Maebashi, Gunma, Japan.
| | - Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, Maebashi, Gunma, Japan
| | - Masaaki Sugiyama
- Kyoto University Research Reactor Institute, Kumatori, Osaka, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, Tokai, Japan
| | | | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
| | - Noriyuki Igarashi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
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Hirai M, Ajito S, Iwase H, Takata SI, Ohta N, Igarashi N, Shimizu N. Restoration of Myoglobin Native Fold from Its Initial State of Amyloid Formation by Trehalose. J Phys Chem B 2018; 122:11962-11968. [DOI: 10.1021/acs.jpcb.8b09379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
| | - Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, Tokai 319-1106, Japan
| | - Shin-ichi Takata
- J-PARC Center, Japan Atomic Energy Agency, Tokai 319-1106, Japan
| | - Noboru Ohta
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Noriyuki Igarashi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
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