1
|
Nakayoshi T, Kato K, Kurimoto E, Oda A. Theoretical Studies on the Effect of Isomerized Aspartic Acid Residues on the Three-Dimensional Structures of Bovine Pancreatic Ribonucleases A. Biol Pharm Bull 2021; 44:967-975. [PMID: 34193692 DOI: 10.1248/bpb.b21-00083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isomerized aspartic acid (Asp) residues have previously been identified in various aging tissues, and are suspected to contribute to age-related diseases. Asp-residue isomerization occurs nonenzymatically under physiological conditions, resulting in the formation of three types of isomerized Asp (i.e., L-isoAsp, D-Asp, and D-isoAsp) residues. Asp-residue isomerization often accelerates protein aggregation and insolubilization, making structural biology analyses difficult. Recently, Sakaue et al. reported the synthesis of a ribonuclease A (RNase A) in which Asp121 was artificially replaced with different isomerized Asp residues, and experimentally demonstrated that the enzymatic activities of these artificial mutants were completely lost. However, their structural features have not yet been elucidated. In the present study, the three-dimensional (3D) structures of these artificial-mutant RNases A were predicted using molecular dynamics (MD) simulations. The 3D structures of wild-type and artificial-mutant RNases A were converged by 3000-ns MD simulations. Our computational data show that the structures of the active site and the formation frequencies of the appropriate catalytic dyad structures in the artificial-mutant RNases A were quite different from wild-type RNase A. These computational findings may provide an explanation for the experimental data which show that artificial-mutant RNases A lack enzymatic activity. Herein, MD simulations have been used to evaluate the influences of isomerized Asp residues on the 3D structures of proteins.
Collapse
Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University.,College of Pharmacy, Kinjo Gakuin University
| | | | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University.,Institute for Protein Research, Osaka University
| |
Collapse
|
2
|
Nakayoshi T, Kato K, Fukuyoshi S, Takahashi O, Kurimoto E, Oda A. Molecular Mechanisms of Succinimide Formation from Aspartic Acid Residues Catalyzed by Two Water Molecules in the Aqueous Phase. Int J Mol Sci 2021; 22:ijms22020509. [PMID: 33419172 PMCID: PMC7825500 DOI: 10.3390/ijms22020509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
Aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. The formation of isomerized Asp residues is considered to be associated with various age-related diseases, such as cataracts and Alzheimer’s disease. In the present paper, we describe the reaction pathway of Suc residue formation from Asp residues catalyzed by two water molecules using the B3LYP/6-31+G(d,p) level of theory. Single-point energies were calculated using the MP2/6-311+G(d,p) level of theory. For these calculations, we used a model compound in which an Asp residue was capped with acetyl and methylamino groups on the N- and C-termini, respectively. In the aqueous phase, Suc residue formation from an Asp residue was roughly divided into three steps, namely, iminolization, cyclization, and dehydration, with the activation energy estimated to be 109 kJ mol−1. Some optimized geometries and reaction modes in the aqueous phase were observed that differed from those in the gas phase.
Collapse
Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Aichi, Japan; (T.N.); (K.K.); (E.K.)
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan;
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Aichi, Japan; (T.N.); (K.K.); (E.K.)
- Department of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya 463-8521, Aichi, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan;
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan;
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Aichi, Japan; (T.N.); (K.K.); (E.K.)
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Aichi, Japan; (T.N.); (K.K.); (E.K.)
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Ishikawa, Japan;
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Osaka, Japan
- Correspondence: ; Tel.: +81-52-832-1151
| |
Collapse
|
3
|
Kato K, Nakayoshi T, Kurimoto E, Oda A. Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy. Int J Mol Sci 2020; 21:ijms21197035. [PMID: 32987875 PMCID: PMC7582646 DOI: 10.3390/ijms21197035] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and hypofunction of monoclonal antibodies. Deamidation rate is known to be affected by the residue following Asn on the carboxyl side and by secondary structure. Information about main-chain conformation of Asn residues is necessary to accurately predict deamidation rate. In this study, the effect of main-chain conformation of Asn residues on deamidation rate was computationally investigated using molecular dynamics (MD) simulations and quantum chemical calculations. The results of MD simulations for γS-crystallin suggested that frequently deamidated Asn residues have common main-chain conformations on the N-terminal side. Based on the simulated structure, initial structures for the quantum chemical calculations were constructed and optimized geometries were obtained using the B3LYP density functional method. Structures that were frequently deamidated had a lower activation energy barrier than that of the little deamidated structure. We also showed that dihydrogen phosphate and bicarbonate ions are important catalysts for deamidation of Asn residues.
Collapse
Affiliation(s)
- Koichi Kato
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
- Correspondence: ; Tel.: +81-527-980-180
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
| | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|