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Nakayoshi T, Kato K, Kurimoto E, Oda A. Influence of the conformations of αA-crystallin peptides on the isomerization rates of aspartic acid residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140480. [PMID: 32599296 DOI: 10.1016/j.bbapap.2020.140480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 10/24/2022]
Abstract
The isomerization rate of aspartic acid (Asp) residue is known to be affected by the three-dimensional structures of peptides and proteins. Although the isomerized Asp residues were experimentally observed, structural features which affect the isomerization cannot be elucidated sufficiently because of protein denaturation and aggregation. In this study, molecular dynamics (MD) simulations were conducted on three αA-crystallin peptides (T6, T10, and T18), each containing a single Asp residue with different isomerization rate (T18 > T6 > T10) to clarify the structural factors of Asp isomerization tendency. For MD trajectories, distances between side-chain carboxyl carbon of Asp and main-chain amide nitrogen of (n + 1) residue (Cγ-N distances), root mean square fluctuations (RMSFs), and polar surface areas for main-chain amide nitrogen of (n + 1) residues (PSAN) were calculated, because these structural features are considered to relate to the formations of cyclic imide intermediates. RMSFs and PSAN are indexes of peptide backbone flexibilities and solvent exposure of the amide nitrogen, respectively. The average Cγ-N distances of T10 was longer than those of the other two peptides. In addition, the peptide containing Asp residue with a higher isomerization rate showed higher flexibility of the peptide backbone around the Asp residue. PSAN for amide nitrogen in T18 were much larger than those of other two peptides. The computational results suggest that Asp-residue isomerization rates are affected by these factors.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Department of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan.
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan.
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Takata T, Murakami K, Toyama A, Fujii N. Identification of Isomeric Aspartate residues in βB2-crystallin from Aged Human Lens. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:767-774. [DOI: 10.1016/j.bbapap.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 12/17/2022]
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Nakayoshi T, Kato K, Fukuyoshi S, Takahashi O, Kurimoto E, Oda A. Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:759-766. [PMID: 29305913 DOI: 10.1016/j.bbapap.2017.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H2PO4-). We performed the study using B3LYP/6-31+G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H2PO4- catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0kcalmol-1, respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher stability of β-Asp residue than α-Asp residue may be caused by an entropic effect associated with the succinimide formation.
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Affiliation(s)
- Tomoki Nakayoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan; Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan
| | - Koichi Kato
- Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan; Department of Pharmacy, Kinjo Gakuin University, 463-8521 Nagoya, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan
| | - Akifumi Oda
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan; Faculty of Pharmacy, Meijo University, Nagoya 468-0077, Japan; Institute for Protein Research, Osaka University, Suita 565-0871, Japan.
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Hooi MYS, Raftery MJ, Truscott RJW. Interconversion of the peptide isoforms of aspartate: stability of isoaspartates. Mech Ageing Dev 2013; 134:103-9. [PMID: 23385093 DOI: 10.1016/j.mad.2013.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 01/04/2013] [Accepted: 01/12/2013] [Indexed: 01/10/2023]
Abstract
A common modification of human long-lived proteins is spontaneous isomerisation of aspartate residues, and its biological importance can be inferred from the ubiquitous presence of protein isoaspartate methyl transferase (PIMT), that repairs this damage. Cyclisation of L-Asp residues yields four isomers: L-Asp, L-isoAsp, D-Asp and D-isoAsp, however little is known about their rate of formation or interconversion. This is important because PIMT is inactive towards D-isoAsp. Peptides containing the four Asp isoforms corresponding to a susceptible site (Asp 151) in the chaperone, αA-crystallin, were examined for their interconversion at pH 7. D-Asp formed from L-Asp readily, whereas L-isoAsp was not detected until significantly later. D-isoAsp formed very slowly, with just 1% present after 8 days at 60°C. These findings can be used to rationalise the substrate specificity of PIMT. In addition, both the D-isoAsp and L-isoAsp peptides were found to be remarkably stable, showing little conversion to other isomers, even after weeks of incubation. Therefore L-isoAsp and D-isoAsp appear to represent "terminal" stages of L-Asp modification. If PIMT is present, L-isoAsp may be reverted to L-Asp, however there appears to be no prospect of reversing D-isoAsp formation in aged proteins. Interestingly, Asp 151 in recombinant αA crystallin isomerised more rapidly than in the L-Asp peptide.
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Affiliation(s)
- Michelle Y S Hooi
- Save Sight Institute, Sydney Eye Hospital, University of Sydney, 8 Macquarie Street, Sydney, New South Wales 2000, Australia
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Hooi MYS, Raftery MJ, Truscott RJW. Accelerated aging of Asp 58 in αA crystallin and human cataract formation. Exp Eye Res 2012; 106:34-9. [PMID: 23142040 DOI: 10.1016/j.exer.2012.10.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 01/10/2023]
Abstract
Racemisation of amino acids is one of the most abundant modifications in long-lived proteins. In this study racemisation of Asp 58 in the small heat shock protein, αA crystallin, was investigated. In normal human lenses, levels of l-isoAsp, d-isoAsp and d-Asp increased with age, such that by age 70 they accounted for approximately half of the total Asp at this site. Levels of d-isoAsp were significantly higher in all cataract lenses than age-matched normal lenses. The introduction of d-isoAsp in αA crystallin could therefore be associated with the development of cataract. Its more rapid formation in cataract lenses may represent an example of accelerated protein aging leading to a human age-related disease.
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Affiliation(s)
- Michelle Y S Hooi
- Save Sight Institute, Sydney Eye Hospital, University of Sydney, 8 Macquarie Street, Sydney, New South Wales 2000, Australia
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Sadakane Y, Fujii N, Nakagomi K. Determination of rate constants for β-linkage isomerization of three specific aspartyl residues in recombinant human αA-crystallin protein by reversed-phase HPLC. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3240-6. [DOI: 10.1016/j.jchromb.2011.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Revised: 02/20/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
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Fujii N, Kaji Y, Fujii N, Nakamura T, Motoie R, Mori Y, Kinouchi T. Collapse of Homochirality of Amino Acids in Proteins from Various Tissues during Aging. Chem Biodivers 2010; 7:1389-97. [DOI: 10.1002/cbdv.200900337] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nakamura T, Sakai M, Sadakane Y, Haga T, Goto Y, Kinouchi T, Saito T, Fujii N. Differential rate constants of racemization of aspartyl and asparaginyl residues in human alpha A-crystallin mutants. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1192-9. [PMID: 18477484 DOI: 10.1016/j.bbapap.2008.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 03/27/2008] [Accepted: 04/07/2008] [Indexed: 10/22/2022]
Abstract
Asp58 and Asp151 in alpha A-crystallin of human eye lenses become highly inverted and isomerized to d-beta-Asp residues with age. Racemization was previously shown to proceed rapidly when the residue on the carboxyl side of the Asp residue is small. Asn was also demonstrated to be more susceptible to racemization than Asp in protein. In this study, the changes of rate constants for racemization at Asp58 and Asp151 and at Asn58 and Asn151 were investigated using D58N, S59T, D151N and A152V mutants obtained through site-directed mutagenesis. The rate constant of racemization at Asn151 in D151N was found to be 1.5 times more rapid than Asp151 in the wild-type. For A152V, the rate constant at Asp151 was 1/4 that of the wild-type. There were no significant differences in the rate constants of racemization for both Asp58 and Asn58 residues. The aggregate size of D58N, S59T and D151N mutants increased or increased in polydispersity and their chaperone activities decreased. The size and chaperone activity of A152V was unchanged. These results suggest that structures close to Asp58 and Asp151 residues in the protein affect the rate constant of Asp racemization and the size and chaperone function of alpha A-crystallin.
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Affiliation(s)
- Tooru Nakamura
- Research Reactor Institute, Faculty of Science, Kyoto University, Kumatori, Sennan, Osaka, Japan
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Févotte G. In Situ Raman Spectroscopy for In-Line Control of Pharmaceutical Crystallization and Solids Elaboration Processes: A Review. Chem Eng Res Des 2007. [DOI: 10.1205/cherd06229] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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