1
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Chang C, Jin X, Bai H, Zhang F, Chen L. Molecular Dynamics Simulation for the Acidic Compounds Retention Mechanism Study on Octyl-Quaternary Ammonium Mixed-Mode Stationary Phase. J Chromatogr Sci 2024:bmae036. [PMID: 38803160 DOI: 10.1093/chromsci/bmae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 03/17/2024] [Indexed: 05/29/2024]
Abstract
With the widespread application of mixed-mode chromatography in separation analysis, it is becoming increasingly important to study its retention mechanism. The retention behavior of acidic compounds on mixed-mode octyl-quaternary ammonium (Sil-C8-QA) columns was investigated by computer simulation. Firstly, the benzoic acid homologues were used as the analytes, and the simulation model was constructed by the Materials Studio. Geometric optimization, annealing and molecular dynamics (MD) simulation of these complexes resulted in optimized conformations. The binding energy, mean square displacement (MSD) and torsion angle distribution generated by MD simulation were then analyzed. The results showed that the more negative binding energy, the greater the MSD and the narrower the torsion angle distribution, indicating that the stationary phase behaves with stronger interaction and retention. The retention behavior of five acidic drugs on the Sil-C8-QA column was then successfully explained by simulation. Acidic drugs are more retentive on the mixed-mode column due to the more substantial interaction brought by the reversed-phase/ion-exchange mixed-mode mechanism compared to other single-mode columns. This simulation method is expected to provide ideas for studying the separation mechanism and predicting the retention behavior of more complex samples.
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Affiliation(s)
- Chaoqun Chang
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Xinghua Jin
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Hui Bai
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Fan Zhang
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Lei Chen
- Pharmaceutical Analysis Department, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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2
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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.
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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
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3
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Wang X, Wang C, Chu H, Qin H, Wang D, Xu F, Ai X, Quan C, Li G, Qing G. Molecular chirality mediated amyloid formation on phospholipid surfaces. Chem Sci 2020; 11:7369-7378. [PMID: 34123018 PMCID: PMC8159450 DOI: 10.1039/d0sc02212h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
One of the neuropathological features of Alzheimer's disease (AD) is the misfolding of amyloid-β to form amyloid aggregates, a process highly associated with biological membranes. However, how molecular chirality affects the amyloid formation on phospholipid surfaces has seldom been reported. Here, l- and d-aspartic acid-modified 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (l-/d-Asp–DPPE) is synthesized to construct chiral phospholipid bilayers. We discover that the l-Asp–DPPE liposomes slightly inhibit the Aβ(1–40) nucleation process but cannot affect the oligomer elongation process. By contrast, the d-Asp–DPPE liposomes strongly inhibit both nucleation and elongation of the peptide. Notably, l- and d-Asp–DPPE liposomes not only have good biocompatibility but can also rescue Aβ(1–40)-aggregation induced cytotoxicity with significant chiral discrimination, in which the cell viability is higher in the presence of d-Asp–DPPE liposomes. Mechanism analysis and molecular dynamics simulation clearly demonstrate that differential electrostatic interactions of Lys16 in Aβ(1–40) with l- or d-Asp on the phospholipid contribute to the remarkable chiral discrimination. This study provides a deeper understanding of the crucial amyloidosis process from the perspective of the chiral interface and reveals that the convergence of d-amino acids with the liposomes might be a feasible route for AD prevention. A remarkable inhibition effect and chiral discrimination are observed when the amyloid peptide aggregates on chiral phospholipid surfaces.![]()
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology 122 Luoshi Road Wuhan 430070 P. R. China.,Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Haijuan Qin
- Research Centre of Modern Analytical Technology, Tianjin University of Science and Technology Tianjin 300457 P. R. China
| | - Dongdong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Feifei Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Xuanjun Ai
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Chunshan Quan
- College of Life Science, Dalian Minzu University Dalian 116600 P. R. China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
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4
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Li G, Delafield DG, Li L. Improved structural elucidation of peptide isomers and their receptors using advanced ion mobility-mass spectrometry. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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5
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Oda A, Nakayoshi T, Kato K, Fukuyoshi S, Kurimoto E. Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality. Sci Rep 2019; 9:11594. [PMID: 31406272 PMCID: PMC6690948 DOI: 10.1038/s41598-019-48134-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Primitive proteins are likely to have been constructed from non-enzymatically generated amino acids, due to the weak enzymatic activities of primitive biomolecules such as ribozymes. On the other hand, almost all present proteins are constructed only from L-amino acids. Therefore, there must have been a mechanism early in the origins of life that selected for one of the optical isomers of amino acids. In this study, we used molecular dynamics simulations to predict the three-dimensional structures of the putative primitive proteins constructed only from glycine, alanine, aspartic acid, and valine ([GADV]-peptides). The [GADV]-peptides were generated computationally at random from L-amino acids (L-[GADV]-peptides) and from both L- and D-amino acids (DL-[GADV]-peptides). The results indicate that the tendency of secondary structure formation for L-[GADV]-peptides was larger than that for DL-[GADV]-peptides, and L-[GADV]-peptides were more rigid than DL-[GADV]-peptides. These results suggest that the proteins with rigid structure motifs were more prone to have been generated in a primordial soup that included only L-amino acids than a the soup including racemic amino acids. The tendency of the rigid structure motif formation may have played a role in selecting for the homochirality that dominates life on Earth today.
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Affiliation(s)
- Akifumi Oda
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan. .,Osaka University, Institute for Protein Research, Suita, 565-0871, Japan. .,Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan.
| | - Tomoki Nakayoshi
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan.,Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan
| | - Koichi Kato
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan.,Kinjo Gakuin University, Faculty of Pharmacy, Nagoya, 463-8521, Japan
| | - Shuichi Fukuyoshi
- Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan
| | - Eiji Kurimoto
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan
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6
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Nakayoshi T, Kato K, Fukuyoshi S, Takahashi O, Kurimoto E, Oda A. Computational studies on the water-catalyzed stereoinversion mechanism of glutamic acid residues in peptides and proteins. Chirality 2018. [DOI: 10.1002/chir.22841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tomoki Nakayoshi
- Faculty of Pharmacy; Meijo University; Nagoya Japan
- Institute of Medical, Pharmaceutical and Health Sciences; Kanazawa University; Kanazawa Japan
| | - Koichi Kato
- Faculty of Pharmacy; Meijo University; Nagoya Japan
- Department of Pharmacy; Kinjo Gakuin University; Nagoya Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences; Kanazawa University; Kanazawa Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; Sendai Japan
| | | | - Akifumi Oda
- Faculty of Pharmacy; Meijo University; Nagoya Japan
- Institute of Medical, Pharmaceutical and Health Sciences; Kanazawa University; Kanazawa Japan
- Institute for Protein Research; Osaka University; Osaka Japan
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7
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Oda A, Nakayoshi T, Fukuyoshi S, Kurimoto E, Yamaotsu N, Hirono S, Takahashi O. Validation of molecular force field parameters for peptides including isomerized amino acids. Chirality 2018; 30:332-341. [PMID: 29393985 DOI: 10.1002/chir.22821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022]
Abstract
Recently, stereoinversions and isomerizations of amino acid residues in the proteins of living beings have been observed. Because isomerized amino acids cause structural changes and denaturation of proteins, isomerizations of amino acid residues are suspected to cause age-related diseases. In this study, AMBER molecular force field parameters were tested by using computationally generated nonapeptides and tripeptides including stereoinverted and/or isomerized amino acid residues. Energy calculations by using density functional theory were also performed for comparison. Although the force field parameters were developed by parameter fitting for l-α-amino acids, the accuracy of the computational results for d-amino acids and β-amino acids was comparable to those for l-α-amino acids. The conformational energies for tripeptides calculated by using density functional theory were reproduced more accurately than those for nonapeptides calculated by using the molecular mechanical force field. The evaluations were performed for the ff99SB, ff03, ff12SB, and the latest ff14SB force field parameters.
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Affiliation(s)
- Akifumi Oda
- Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan.,Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Nagoya, Aichi, Japan
| | | | | | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
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8
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Oda A, Nakayoshi T, Fukuyoshi S, Kurimoto E, Takahashi O. Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:783-788. [PMID: 29331333 DOI: 10.1016/j.bbapap.2018.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 01/12/2023]
Abstract
Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and peptides have been reported. Here, we performed replica exchange molecular dynamics (REMD) simulations of model peptides (exon 6, 26A-1, and 26A-2) extracted from elastin to investigate their structural features, thereby revealing the factor that influences stereoinversions. For REMD trajectories, we calculated distances between carboxyl carbon in Asp and amide nitrogen in the (n + 1) residue (CN distances). Because bond formation between carbon and nitrogen is indispensable to the formation of a succinimide intermediate the distance between them seems to play an important role in stereoinversion. Moreover, we calculated polar surface areas (PSAs) for the trajectories, finding that CN distances and PSA were different for each peptide, with the longest CN distance and smallest PSA observed for exon 6 peptide, where stereoinversion of Asp is the slowest. Although the average CN distance was shorter for exon 26A-1 peptide than for exon 26A-2 peptide, the number of conformations with CN distances <3.0 Å was greater for exon 26A-2 peptide than for exon 26A-1 peptide. Furthermore, PSA for amide nitrogen of the (n + 1) residue was larger for exon 26A-2 peptide than for exon 26A-1 peptide. These results indicated that the flexibility of Asp and (n + 1) residues and hydrophilicity of peptides, especially in the (n + 1) residue, play important roles in the stereoinversion of Asp. This article is part of a Special Issue entitled: D-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.
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Affiliation(s)
- Akifumi Oda
- Faculty 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.
| | - Tomoki Nakayoshi
- Faculty 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
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
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9
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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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10
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Nakayoshi T, Fukuyoshi S, Takahashi O, Oda A. Computational studies on non-succinimide-mediated stereoinversion mechanism of aspartic acid residues assisted by phosphate. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1414964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tomoki Nakayoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Akifumi Oda
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
- Faculty of Pharmacy, Meijo University, Nagoya, Japan
- Institute for Protein Research, Osaka University, Suita, Japan
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11
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Wang L, Jin Z, Wang X, Zeng S, Sun C, Pan Y. Pair of Stereodynamic Chiral Benzylicaldehyde Probes for Determination of Absolute Configuration of Amino Acid Residues in Peptides by Mass Spectrometry. Anal Chem 2017; 89:11902-11907. [DOI: 10.1021/acs.analchem.7b03804] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lin Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Department
of Chemistry and Chemical Engineering, Beijing University of Technology, 100124, Beijing, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Zhe Jin
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Xiayan Wang
- Department
of Chemistry and Chemical Engineering, Beijing University of Technology, 100124, Beijing, China
| | - Su Zeng
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Cuirong Sun
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuanjiang Pan
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, China
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12
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Kato K, Nakayoshi T, Fukuyoshi S, Kurimoto E, Oda A. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins. Molecules 2017; 22:molecules22101716. [PMID: 29023395 PMCID: PMC6151455 DOI: 10.3390/molecules22101716] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton’s equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10–46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10–34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.
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Affiliation(s)
- Koichi Kato
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
- Department of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan.
| | - Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Јapan.
- 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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13
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Fukuyoshi S, Nakayoshi T, Takahashi O, Oda A. Theoretical study on keto–enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional theory. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1232844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shuichi Fukuyoshi
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Japan
| | - Tomoki Nakayoshi
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University , Sendai, Japan
| | - Akifumi Oda
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Japan
- Institute for Protein Research, Osaka University , Osaka, Japan
- Faculty of Pharmacy, Meijo University , Nagoya, Japan
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14
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Oda A, Noji I, Fukuyoshi S, Takahashi O. Prediction of binding modes between protein l-isoaspartyl (d-aspartyl) O-methyltransferase and peptide substrates including isomerized aspartic acid residues using in silico analytic methods for the substrate screening. J Pharm Biomed Anal 2015; 116:116-22. [DOI: 10.1016/j.jpba.2015.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/11/2015] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
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Oda A, Fukuyoshi S. Predicting three-dimensional conformations of peptides constructed of only glycine, alanine, aspartic acid, and valine. ORIGINS LIFE EVOL B 2015; 45:183-93. [PMID: 25794830 DOI: 10.1007/s11084-015-9418-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/09/2015] [Indexed: 11/28/2022]
Abstract
The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins (Lacey et al. 1999; Ikehara 2002; Andras 2006). In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acid, and valine ([GADV]-proteins). In this study, the three-dimensional (3D) conformations of randomly generated short [GADV]-peptides were computationally investigated using replica-exchange molecular dynamics (REMD) simulations (Sugita and Okamoto 1999). Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations. The results indicate that secondary structures can be formed in several randomly generated [GADV]-peptides. A long helical structure was found in one of the hydrophobic peptides, supporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup. In addition, these results indicate that REMD simulations can be used for the structural investigation of short peptides.
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Affiliation(s)
- Akifumi Oda
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan,
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Velmurugan P, Jonnalagadda RR, Unni Nair B. Engineering D-Amino Acid Containing Collagen Like Peptide at the Cleavage Site of Clostridium histolyticum Collagenase for Its Inhibition. PLoS One 2015; 10:e0124398. [PMID: 25973613 PMCID: PMC4431724 DOI: 10.1371/journal.pone.0124398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/13/2015] [Indexed: 02/02/2023] Open
Abstract
Collagenase is an important enzyme which plays an important role in degradation of collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism of this degradation has not yet been completely understood. In the field of biomedical and protein engineering, the design and development of new peptide based materials is of main concern. In the present work an attempt has been made to study the effect of DAla in collagen like peptide (imino-poor region of type I collagen) on the structure and stability of peptide against enzyme hydrolysis. Effect of replacement of DAla in the collagen like peptide has been studied using circular dichroic spectroscopy (CD). Our findings suggest that, DAla substitution leads to conformational changes in the secondary structure and favours the formation of polyproline II conformation than its L-counterpart in the imino-poor region of collagen like peptides. Change in the chirality of alanine at the cleavage site of collagenase in the imino-poor region inhibits collagenolytic activity. This may find application in design of peptides and peptidomimics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins.
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Affiliation(s)
- Punitha Velmurugan
- Council of Scientific and Industrial Research—Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai, 600 020, India
| | - Raghava Rao Jonnalagadda
- Council of Scientific and Industrial Research—Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai, 600 020, India
- * E-mail:
| | - Balachandran Unni Nair
- Council of Scientific and Industrial Research—Central Leather Research Institute, Chemical Laboratory, Adyar, Chennai, 600 020, India
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17
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Structural Prediction of [GADV]-Proteins Using Threading and Ab initio Modeling for Investigations of the Origin of Life. JOURNAL OF COMPUTER AIDED CHEMISTRY 2013. [DOI: 10.2751/jcac.14.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Barz B, Urbanc B. Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study. PLoS One 2012; 7:e34345. [PMID: 22509291 PMCID: PMC3324527 DOI: 10.1371/journal.pone.0034345] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 02/26/2012] [Indexed: 11/18/2022] Open
Abstract
Amyloid β-protein (Aβ) is central to the pathology of Alzheimer's disease. A 5% difference in the primary structure of the two predominant alloforms, Aβ(1-40) and Aβ(1-42), results in distinct assembly pathways and toxicity properties. Discrete molecular dynamics (DMD) studies of Aβ(1-40) and Aβ(1-42) assembly resulted in alloform-specific oligomer size distributions consistent with experimental findings. Here, a large ensemble of DMD-derived Aβ(1-40) and Aβ(1-42) monomers and dimers was subjected to fully atomistic molecular dynamics (MD) simulations using the OPLS-AA force field combined with two water models, SPCE and TIP3P. The resulting all-atom conformations were slightly larger, less compact, had similar turn and lower β-strand propensities than those predicted by DMD. Fully atomistic Aβ(1-40) and Aβ(1-42) monomers populated qualitatively similar free energy landscapes. In contrast, the free energy landscape of Aβ(1-42) dimers indicated a larger conformational variability in comparison to that of Aβ(1-40) dimers. Aβ(1-42) dimers were characterized by an increased flexibility in the N-terminal region D1-R5 and a larger solvent exposure of charged amino acids relative to Aβ(1-40) dimers. Of the three positively charged amino acids, R5 was the most and K16 the least involved in salt bridge formation. This result was independent of the water model, alloform, and assembly state. Overall, salt bridge propensities increased upon dimer formation. An exception was the salt bridge propensity of K28, which decreased upon formation of Aβ(1-42) dimers and was significantly lower than in Aβ(1-40) dimers. The potential relevance of the three positively charged amino acids in mediating the Aβ oligomer toxicity is discussed in the light of available experimental data.
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Affiliation(s)
- Bogdan Barz
- Physics Department, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Brigita Urbanc
- Physics Department, Drexel University, Philadelphia, Pennsylvania, United States of America
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19
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Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 2012; 12:1111-21. [PMID: 22577012 PMCID: PMC3918884 DOI: 10.1002/pmic.201100463] [Citation(s) in RCA: 434] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 01/16/2012] [Indexed: 01/17/2023]
Abstract
Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.
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Affiliation(s)
- Claudia Escher
- Biognosys AG, Wagistrasse 25, 8952 Schlieren, Switzerland
| | - Lukas Reiter
- Biognosys AG, Wagistrasse 25, 8952 Schlieren, Switzerland
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States
| | - Reto Ossola
- Biognosys AG, Wagistrasse 25, 8952 Schlieren, Switzerland
| | - Franz Herzog
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - John Chilton
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States
| | - Oliver Rinner
- Biognosys AG, Wagistrasse 25, 8952 Schlieren, Switzerland
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