1
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Ochiai H, Elouali S, Yamamoto T, Asai H, Noguchi M, Nishiuchi Y. Chemical and Chemoenzymatic Synthesis of Peptide and Protein Therapeutics Conjugated with Human N-Glycans. ChemMedChem 2024; 19:e202300692. [PMID: 38572578 DOI: 10.1002/cmdc.202300692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Glycosylation is one of the most ubiquitous post-translational modifications. It affects the structure and function of peptides/proteins and consequently has a significant impact on various biological events. However, the structural complexity and heterogeneity of glycopeptides/proteins caused by the diversity of glycan structures and glycosylation sites complicates the detailed elucidation of glycan function and hampers their clinical applications. To address these challenges, chemical and/or enzyme-assisted synthesis methods have been developed to realize glycopeptides/proteins with well-defined glycan morphologies. In particular, N-glycans are expected to be useful for improving the solubility, in vivo half-life and aggregation of bioactive peptides/proteins that have had limited clinical applications so far due to their short duration of action in the blood and unsuitable physicochemical properties. Chemical glycosylation performed in a post-synthetic procedure can be used to facilitate the development of glycopeptide/protein analogues or mimetics that are superior to the original molecules in terms of physicochemical and pharmacokinetic properties. N-glycans are used to modify targets because they are highly biodegradable and biocompatible and have structures that already exist in the human body. On the practical side, from a quality control perspective, close attention should be paid to their structural homogeneity when they are to be applied to pharmaceuticals.
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Affiliation(s)
- Hirofumi Ochiai
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Sofia Elouali
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Takahiro Yamamoto
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Hiroaki Asai
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Masato Noguchi
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Yuji Nishiuchi
- GlyTech, Inc., 134 Chudoji Minamimachi KRP #1-2F, Shimogyo-ku, Kyoto, 600-8813, Japan
- Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
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2
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Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
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Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
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3
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Sharon I, Schmeing TM. Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation. Sci Rep 2023; 13:8314. [PMID: 37221236 PMCID: PMC10206079 DOI: 10.1038/s41598-023-34587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.
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Affiliation(s)
- Itai Sharon
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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4
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Butler KE, Dodds JN, Flick T, Campuzano IDG, Baker ES. High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening. Anal Chem 2022; 94:6191-6199. [PMID: 35421308 DOI: 10.1021/acs.analchem.1c05533] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isomeric peptide analyses are an analytical challenge of great importance to therapeutic monoclonal antibody and other biotherapeutic product development workflows. Aspartic acid (Asp, D) to isoaspartic acid (isoAsp, isoD) isomerization is a critical quality attribute (CQA) that requires careful control, monitoring, and quantitation during the drug discovery and production processes. While the formation of isoAsp has been implicated in a variety of disease states such as autoimmune diseases and several types of cancer, it is also understood that the formation of isoAsp results in a structural change impacting efficacy, potency, and immunogenic properties, all of which are undesirable. Currently, lengthy ultrahigh-performance liquid chromatography (UPLC) separations are coupled with MS for CQA analyses; however, these measurements often take over an hour and drastically limit analysis throughput. In this manuscript, drift tube ion mobility spectrometry-mass spectrometry (DTIMS-MS) and both a standard and high-resolution demultiplexing approach were utilized to study eight isomeric Asp and isoAsp peptide pairs. While the limited resolving power associated with the standard DTIMS analysis only separated three of the eight pairs, the application of HRdm distinguished seven of the eight and was only unable to separate DL and isoDL. The rapid high-throughput HRdm DTIMS-MS method was also interfaced with both flow injection and an automated solid phase extraction system to present the first application of HRdm for isoAsp and Asp assessment and demonstrate screening capabilities for isomeric peptides in complex samples, resulting in a workflow highly suitable for biopharmaceutical research needs.
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Affiliation(s)
- Karen E Butler
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Tawnya Flick
- Pivotal Attribute Sciences, Amgen Process Development, Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Discovery Attribute Sciences, Amgen Research, Thousand Oaks, California 91320, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695, United States
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5
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Irudayanathan FJ, Zarzar J, Lin J, Izadi S. Deciphering deamidation and isomerization in therapeutic proteins: Effect of neighboring residue. MAbs 2022; 14:2143006. [PMID: 36377085 PMCID: PMC9673968 DOI: 10.1080/19420862.2022.2143006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Deamidation of asparagine (Asn) and isomerization of aspartic acid (Asp) residues are among the most commonly observed spontaneous post-translational modifications (PTMs) in proteins. Understanding and predicting a protein sequence's propensity for such PTMs can help expedite protein therapeutic discovery and development. In this study, we used proton-affinity calculations with semi-empirical quantum mechanics and microsecond long equilibrium molecular dynamics simulations to investigate mechanistic roles of structural conformation and chemical environment in dictating spontaneous degradation of Asn and Asp residues in 131 clinical-stage therapeutic antibodies. Backbone secondary structure, side-chain rotamer conformation and solvent accessibility were found to be key molecular indicators of Asp isomerization and Asn deamidation. Comparative analysis of backbone dihedral angles along with N-H proton affinity calculations provides a mechanistic explanation for the strong influence of the identity of the n + 1 residue on the rate of Asn/Asp degradation. With these findings, we propose a minimalistic physics-based classification model that can be leveraged to predict deamidation and isomerization propensity of proteins.
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Affiliation(s)
| | - Jonathan Zarzar
- Pharmaceutical Development Department, Genentech Inc, South San Francisco, United States
| | - Jasper Lin
- Pharmaceutical Development Department, Genentech Inc, South San Francisco, United States
| | - Saeed Izadi
- Pharmaceutical Development Department, Genentech Inc, South San Francisco, United States,CONTACT Saeed Izadi Pharmaceutical Development Department, Genentech Inc, South San Francisco, United States
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6
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Dykstra AB, Flick TG, Lee B, Blue LE, Angell N. Chip-Based Capillary Zone Electrophoresis Mass Spectrometry for Rapid Resolution and Quantitation of Critical Quality Attributes in Protein Biotherapeutics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1952-1963. [PMID: 33730487 DOI: 10.1021/jasms.0c00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The aspiration of the multi-attribute method (MAM) is to utilize a single mass spectrometry-based method that can measure multiple attributes simultaneously, thus enabling data-driven decisions more quickly and efficiently. However, challenges associated with identifying and quantitating critical quality attributes such as asparagine deamidation and isoaspartic acid using conventional ultrahigh-pressure liquid chromatography (UHPLC) coupled to mass spectrometry have necessitated long gradients to ensure sufficient separation for quantitation. Microfluidic chip-based capillary zone electrophoresis mass spectrometry (CZE-MS) shows potential to enable rapid charge-based separation of peptide mixtures, and this approach was evaluated using multipeptide mixtures of synthetic peptides as well as digested protein therapeutics. In these experiments, repeatability, linearity, and peak-to-peak resolution of several peptide families containing asparagine deamidation and/or isoaspartic acid were demonstrated. In addition, a comparison of peptide map results acquired with both UHPLC-MS and CZE-MS for two enzymatically digested biological therapeutics showed comparable sequence coverage and quantitation results between the two approaches. As MAM becomes increasingly utilized for analysis of biological therapeutics, MS instrument demand will rapidly increase, resulting in a bottleneck. A CZE-based separation shows potential to alleviate this bottleneck by drastically increasing MAM throughput while providing results comparable to those acquired using conventional UHPLC separations.
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Affiliation(s)
- Andrew B Dykstra
- Department of Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Tawnya G Flick
- Department of Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Burton Lee
- Department of Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Laura E Blue
- Department of Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Nic Angell
- Department of Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
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7
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Quan BD, Wojtas M, Sone ED. Polyaminoacids in Biomimetic Collagen Mineralization: Roles of Isomerization and Disorder in Polyaspartic and Polyglutamic Acids. Biomacromolecules 2021; 22:2996-3004. [PMID: 34152724 DOI: 10.1021/acs.biomac.1c00402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The extracellular matrix of hard connective tissues is composed primarily of mineralized collagen fibrils. Acidic noncollagenous proteins play important roles in mediating mineralization of collagen. Polyaspartate, a homopolymer substitute for such proteins, has been used extensively in in vitro models to produce biomimetic mineralized collagen. Polyglutamate behaves differently in mineralization models, despite its chemical similarity. We show that polyaspartate is a 350 times more effective inhibitor of solution precipitation of hydroxyapatite than polyglutamate. Supersaturated CaP solutions stabilized with polyaspartic acid produce collagen with aligned intrafibrillar mineral, while solutions containing polyglutamate lead to the formation of unaligned mineral clusters on the fibril surface. Molecular analysis showed that the commercial polyaspartic acid contains substantial isomerization, unlike polyglutamic acid. Hence, the secondary structure of polyaspartic acid is more disordered than that of polyglutamic acid. The increased flexibility of the polyaspartic acid chain may explain its potency as an inhibitor of solution crystallization and a mediator of intrafibrillar collagen mineralization.
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Affiliation(s)
- Bryan D Quan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Magdalena Wojtas
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Eli D Sone
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada.,Department of Materials Science & Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada.,Faculty of Dentistry, University of Toronto, Toronto, Ontario M5G 1G6, Canada
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8
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Zhang XY, Dou PH, Lu WY, You Y, Zhao JQ, Wang ZH, Yuan WC. Benzylidene succinimides as 3C synthons for the asymmetric tandem Mannich reaction/transamidation of cyclic trifluoromethyl ketimines to obtain F 3C-containing polycyclic dihydroquinazolinones. Chem Commun (Camb) 2021; 57:2927-2930. [PMID: 33620365 DOI: 10.1039/d0cc08131k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By taking advantage of benzylidene succinimides as a new class of 3C synthons, a highly diastereo- and enantioselective tandem Mannich reaction/transamidation has been established by reacting them with cyclic trifluoromethyl N-acyl ketimines. Using a Cinchona alkaloid-derived squaramide as the catalyst, the tandem reaction proceeded smoothly under mild conditions and afforded a range of F3C-containing chiral polycyclic dihydroquinazolinones with excellent results (up to 99% yield, all cases >20 : 1 dr, up to 99% ee).
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Affiliation(s)
- Xia-Yan Zhang
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China. and National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pei-Hao Dou
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China. and National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Ya Lu
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China. and National Engineering Research Center of Chiral Drugs, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong You
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China.
| | - Jian-Qiang Zhao
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China.
| | - Zhen-Hua Wang
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China.
| | - Wei-Cheng Yuan
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China.
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9
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Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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10
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Van Orman BL, Wu HT, Julian RR. Differentiation of peptide isomers by excited-state photodissociation and ion-molecule interactions. Phys Chem Chem Phys 2020; 22:23678-23685. [PMID: 33052992 DOI: 10.1039/d0cp04111d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solvochromatic effects are most frequently associated with solution-phase phenomena. However, in the gas phase, the absence of solvent leads to intramolecular solvation that can be driven by strong forces including hydrogen bonds and ion-dipole interactions. Here we examine whether isomerization of a single residue in a peptide results in structural changes sufficient to shift the absorption of light by an appended chromophore. By carrying out the experiments inside a mass spectrometer, we can easily monitor photodissociation yield as a readout for chromophore excitation. A series of peptides of different lengths, charge states, and position and identity of the isomerized residue were examined by excitation with both 266 and 213 nm light. The results reveal that differences in intramolecular solvation do lead to solvochromatic shifts in many cases. In addition, the primary product following photoexcitation is a radical. Ion-molecule reactions with this radical and adventitious oxygen were monitored and also found to vary as a function of isomeric state. In this case, differences in intramolecular solvation alter the availability of the reactive radical. Overall, the results reveal that small changes in a single amino acid can influence the overall structural ensemble sufficient to alter the efficiency of multiple gas-phase reactions.
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Affiliation(s)
- Brielle L Van Orman
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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11
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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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12
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Dyakin VV, Wisniewski TM, Lajtha A. Chiral Interface of Amyloid Beta (Aβ): Relevance to Protein Aging, Aggregation and Neurodegeneration. Symmetry (Basel) 2020; 12. [PMID: 34327009 PMCID: PMC8317441 DOI: 10.3390/sym12040585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biochirality is the subject of distinct branches of science, including biophysics, biochemistry, the stereochemistry of protein folding, neuroscience, brain functional laterality and bioinformatics. At the protein level, biochirality is closely associated with various post-translational modifications (PTMs) accompanied by the non-equilibrium phase transitions (PhTs NE). PTMs NE support the dynamic balance of the prevalent chirality of enzymes and their substrates. The stereoselective nature of most biochemical reactions is evident in the enzymatic (Enz) and spontaneous (Sp) PTMs (PTMs Enz and PTMs Sp) of proteins. Protein chirality, which embraces biophysics and biochemistry, is a subject of this review. In this broad field, we focus attention to the amyloid-beta (Aβ) peptide, known for its essential cellular functions and associations with neuropathology. The widely discussed amyloid cascade hypothesis (ACH) of Alzheimer’s disease (AD) states that disease pathogenesis is initiated by the oligomerization and subsequent aggregation of the Aβ peptide into plaques. The racemization-induced aggregation of protein and RNA have been extensively studied in the search for the contribution of spontaneous stochastic stereo-specific mechanisms that are common for both kinds of biomolecules. The failure of numerous Aβ drug-targeting therapies requires the reconsolidation of the ACH with the concept of PTMs Sp. The progress in methods of chiral discrimination can help overcome previous limitations in the understanding of AD pathogenesis. The primary target of attention becomes the network of stereospecific PTMs that affect the aggregation of many pathogenic agents, including Aβ. Extensive recent experimental results describe the truncated, isomerized and racemized forms of Aβ and the interplay between enzymatic and PTMs Sp. Currently, accumulated data suggest that non-enzymatic PTMs Sp occur in parallel to an existing metabolic network of enzymatic pathways, meaning that the presence and activity of enzymes does not prevent non-enzymatic reactions from occurring. PTMs Sp impact the functions of many proteins and peptides, including Aβ. This is in logical agreement with the silently accepted racemization hypothesis of protein aggregation (RHPA). Therefore, the ACH of AD should be complemented by the concept of PTMs Sp and RHPA.
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Affiliation(s)
- Victor V. Dyakin
- Departmemts: Virtual Reality Perception Lab. (VV. Dyakin) and Center for Neurochemistry (A. Lajtha), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
- Correspondence:
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Departmemts: Virtual Reality Perception Lab. (VV. Dyakin) and Center for Neurochemistry (A. Lajtha), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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13
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Ballard A, Narduolo S, Ahmed HO, Keymer NI, Asaad N, Cosgrove DA, Buurma NJ, Leach AG. Racemisation in Chemistry and Biology. Chemistry 2020; 26:3661-3687. [PMID: 31709642 DOI: 10.1002/chem.201903917] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Indexed: 11/09/2022]
Abstract
The two enantiomers of a compound often have profoundly different biological properties and thus their liability to racemisation in aqueous solutions is an important piece of information. The authors reviewed the available data concerning the process of racemisation in vivo, in the presence of biological molecules (e.g., racemase enzymes, serum albumin, cofactors and derivatives) and under purely chemical but aqueous conditions (acid, base and other aqueous systems). Mechanistic studies are described critically in light of reported kinetic data. The types of experimental measurement that can be used to effectively determine rate constants of racemisation in various conditions are discussed and the data they provide is summarised. The proposed origins of enzymatic racemisation are presented and suggest ways to promote the process that are different from processes taking place in bulk water. Experimental and computational studies that provide understanding and quantitative predictions of racemisation risk are also presented.
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Affiliation(s)
- Andrew Ballard
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Stefania Narduolo
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Hiwa O Ahmed
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK.,Pharmaceutical Chemistry Department, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Nathaniel I Keymer
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Nabil Asaad
- AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | | | - Niklaas J Buurma
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Andrew G Leach
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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14
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Riggs DL, Silzel JW, Lyon YA, Kang AS, Julian RR. Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics. Anal Chem 2019; 91:13032-13038. [PMID: 31498611 PMCID: PMC8805438 DOI: 10.1021/acs.analchem.9b03127] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in a growing list of human pathologies, but the relatively minor chemical change associated with these processes has presented a long standing analytical challenge. Although the adoption of high-resolution mass spectrometry has greatly aided the identification of deamidation sites in proteomic studies, isomerization (and the isomeric products of deamidation) remain exceptionally challenging to characterize. Herein, we present a liquid chromatography/mass spectrometry-based approach for rapidly characterizing the isomeric products of Gln deamidation using diagnostic fragments that are abundantly produced and capable of unambiguously identifying both Glu and isoGlu. Importantly, the informative fragment ions are produced through orthogonal fragmentation pathways, thereby enabling the simultaneous detection of both isomeric forms while retaining compatibility with shotgun proteomics. Furthermore, the diagnostic fragments associated with isoGlu pinpoint the location of the modified residue. The utility of this technique is demonstrated by characterizing the isomeric products generated during in vitro aging of a series of glutamine-containing peptides. Sequence-dependent product profiles are obtained, and the abundance of deamidation-linked racemization is examined. Finally, comparisons are made between Gln deamidation, which is relatively poorly understood, and asparagine deamidation, which has been more thoroughly studied.
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Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jacob W. Silzel
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yana A. Lyon
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Amrik S. Kang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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15
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Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions. Amino Acids 2019; 51:1409-1431. [DOI: 10.1007/s00726-019-02787-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/07/2019] [Indexed: 12/12/2022]
Abstract
AbstractPeptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.
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16
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Gamage CL, Hageman TS, Weis DD. Rapid Prediction of Deamidation Rates of Proteins to Assess Their Long-Term Stability Using Hydrogen Exchange–Mass Spectrometry. J Pharm Sci 2019; 108:1964-1972. [DOI: 10.1016/j.xphs.2019.01.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
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17
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Nakayoshi T, Fukuyoshi S, Kato K, Kurimoto E, Oda A. Computational Studies on Water-Catalyzed Mechanisms for Stereoinversion of Glutarimide Intermediates Formed from Glutamic Acid Residues in Aqueous Phase. Int J Mol Sci 2019; 20:E2410. [PMID: 31096657 PMCID: PMC6567045 DOI: 10.3390/ijms20102410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 11/25/2022] Open
Abstract
Aspartic acid (Asp) residues are prone to non-enzymatic stereoinversion, and Asp-residue stereoinversion is believed to be mediated via a succinimide (SI) intermediate. The stereoinverted Asp residues are believed to cause several age-related diseases. However, in peptides and proteins, few studies have reported the stereoinversion of glutamic acid (Glu) residues whose structures are similar to that of Asp. We previously presumed that Glu-residue stereoinversion proceeds via a glutarimide (GI) intermediate and showed that the calculated activation barriers of SI- and GI-intermediate stereoinversion are almost equivalent in the gas phase. In this study, we investigated the stereoinversion pathways of the l-GI intermediate in the aqueous phase using B3LYP density functional methods. The calculated activation barrier of l-GI-intermediate stereoinversion in the aqueous phase was approximately 36 kcal·mol-1, which was much higher than that in the gas phase. Additionally, as this activation barrier exceeded that of Asp-residue stereoinversion, it is presumed that Glu-residue stereoinversion has a lower probability of proceeding under physiological conditions than Asp-residue stereoinversion.
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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.
| | - Shuichi Fukuyoshi
- 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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18
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Nagy G, Kedia K, Attah IK, Garimella SVB, Ibrahim YM, Petyuk VA, Smith RD. Separation of β-Amyloid Tryptic Peptide Species with Isomerized and Racemized l-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations. Anal Chem 2019; 91:4374-4380. [PMID: 30816701 PMCID: PMC6596305 DOI: 10.1021/acs.analchem.8b04696] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Accumulation of β-amyloid (Aβ) is one of the hallmarks of Alzheimer's disease. The deposition of β-amyloid plaques is likely to start years in advance of manifestation of clinical symptoms, although the exact timing is unknown. Over the years, Aβ peptides undergo both post-translational modification and stereoisomerization. Analysis of the resulting stereoisomers is particularly challenging because of their identical elemental composition and similar physicochemical properties. Herein, we have utilized our recently developed structures for lossless ion manipulations ion mobility-mass spectrometry platform (SLIM IM-MS), in conjunction with serpentine ultralong path with extended routing (SUPER), to baseline resolve four distinct sets of Aβ17-28 tryptic peptide epimers on a rapid (∼1 s) time scale. We discovered that sodium adduct ions, [M + H + Na]2+, allowed baseline SLIM SUPER IM resolution for all Aβ epimer sets assessed, while such baseline separations were unachievable for their [M + 2H]2+ doubly protonated ions.
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Affiliation(s)
- Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Komal Kedia
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Isaac K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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19
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Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study. Catalysts 2017. [DOI: 10.3390/catal7120363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Spontaneous, nonenzymatic reactions in proteins are known to have relevance to aging and age-related diseases, such as cataract and Alzheimer’s disease. Among such reactions is the racemization of Ser residues, but its mechanism in vivo remains to be clarified. The most likely intermediate is an enol. Although being nonenzymatic, the enolization would need to be catalyzed to occur at a biologically relevant rate. In the present study, we computationally found plausible reaction pathways for the enolization of a Ser residue where a dihydrogen phosphate ion, H2PO4−, acts as a catalyst. The H2PO4− ion mediates the proton transfer required for the enolization by acting simultaneously as both a general base and a general acid. Using the B3LYP density functional theory method, reaction pathways were located in the gas phase and hydration effects were evaluated by single-point calculations using the SM8 continuum model. The activation barriers calculated for the reaction pathways found were around 100 kJ mol−1, which is consistent with spontaneous reactions occurring at physiological temperature. Our results are also consistent with experimental observations that Ser residue racemization occurs more readily in flexible regions in proteins.
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20
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Munegumi T, Tanikawa N. Polycondensation of Asparagine-comprising Dipeptides in Aqueous Media-A Simulation of Polypeptide Formation in Primordial Earth Hydrosphere. ORIGINS LIFE EVOL B 2017; 47:355-369. [PMID: 28744686 DOI: 10.1007/s11084-017-9547-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 06/30/2017] [Indexed: 11/28/2022]
Abstract
Asparagine and aspartic acid might have mutually transformed in the primordial hydrosphere of the earth, if ammonia and aspartic acid had existed in equilibrium. These amino acids seem to contribute to polypeptides, while the simple amino acids glycine and alanine easily form cyclic dipeptides and do not achieve long peptide chains. Asparagine-comprising dipeptides contribute some kinds of activation forms of dipeptides because these can polymerize faster than asparagine only. The new finding of polypeptide formation suggests a pathway of sequential polypeptides to evolve a diversity of polypeptides.
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Affiliation(s)
| | - Naoya Tanikawa
- Gifu Shotoku Gakuen University, Gifu-shi, Gifu, 501-6194, Japan
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21
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Jia L, Sun Y. Protein asparagine deamidation prediction based on structures with machine learning methods. PLoS One 2017; 12:e0181347. [PMID: 28732052 PMCID: PMC5521779 DOI: 10.1371/journal.pone.0181347] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/29/2017] [Indexed: 11/19/2022] Open
Abstract
Chemical stability is a major concern in the development of protein therapeutics due to its impact on both efficacy and safety. Protein "hotspots" are amino acid residues that are subject to various chemical modifications, including deamidation, isomerization, glycosylation, oxidation etc. A more accurate prediction method for potential hotspot residues would allow their elimination or reduction as early as possible in the drug discovery process. In this work, we focus on prediction models for asparagine (Asn) deamidation. Sequence-based prediction method simply identifies the NG motif (amino acid asparagine followed by a glycine) to be liable to deamidation. It still dominates deamidation evaluation process in most pharmaceutical setup due to its convenience. However, the simple sequence-based method is less accurate and often causes over-engineering a protein. We introduce structure-based prediction models by mining available experimental and structural data of deamidated proteins. Our training set contains 194 Asn residues from 25 proteins that all have available high-resolution crystal structures. Experimentally measured deamidation half-life of Asn in penta-peptides as well as 3D structure-based properties, such as solvent exposure, crystallographic B-factors, local secondary structure and dihedral angles etc., were used to train prediction models with several machine learning algorithms. The prediction tools were cross-validated as well as tested with an external test data set. The random forest model had high enrichment in ranking deamidated residues higher than non-deamidated residues while effectively eliminated false positive predictions. It is possible that such quantitative protein structure-function relationship tools can also be applied to other protein hotspot predictions. In addition, we extensively discussed metrics being used to evaluate the performance of predicting unbalanced data sets such as the deamidation case.
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Affiliation(s)
- Lei Jia
- Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, United States of America
- * E-mail:
| | - Yaxiong Sun
- Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, United States of America
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22
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Thermal Synthesis of Polypeptides from N-Butyloxycarbonyl Oligopeptides Containing Aspartyl Residue at C-Terminus. INT J POLYM SCI 2017. [DOI: 10.1155/2017/8364710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The thermal reactions of amino acids have been investigated for pure organic synthesis, materials preparation in industry, and prebiotic chemistry. N-t-Butyloxycarbonyl aspartic acid (Boc-Asp) releases 2-butene and carbon dioxide upon heating without solvents. The resulting mixture of the free molten aspartic acid was dehydrated to give peptide bonds. This study describes the thermal reactions of N-t-butyloxycarbonyl peptides (Boc-Gly-L-Asp, Boc-L-Ala-L-Asp, Boc-L-Val-L-Asp, and Boc-Gly-Gly-L-Asp) having an aspartic residue at the carboxyl terminus. The peptides were deprotected upon heating at a constant temperature between 110 and 170°C for 1 to 24 h to afford polypeptides in which the average molecular weight reached 7800.
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23
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Takahashi O, Kirikoshi R, Manabe N. Racemization of the Succinimide Intermediate Formed in Proteins and Peptides: A Computational Study of the Mechanism Catalyzed by Dihydrogen Phosphate Ion. Int J Mol Sci 2016; 17:ijms17101698. [PMID: 27735868 PMCID: PMC5085730 DOI: 10.3390/ijms17101698] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/22/2016] [Accepted: 09/30/2016] [Indexed: 02/06/2023] Open
Abstract
In proteins and peptides, d-aspartic acid (d-Asp) and d-β-Asp residues can be spontaneously formed via racemization of the succinimide intermediate formed from l-Asp and l-asparagine (l-Asn) residues. These biologically uncommon amino acid residues are known to have relevance to aging and pathologies. Although nonenzymatic, the succinimide racemization will not occur without a catalyst at room or biological temperature. In the present study, we computationally investigated the mechanism of succinimide racemization catalyzed by dihydrogen phosphate ion, H2PO4−, by B3LYP/6-31+G(d,p) density functional theory calculations, using a model compound in which an aminosuccinyl (Asu) residue is capped with acetyl (Ace) and NCH3 (Nme) groups on the N- and C-termini, respectively (Ace–Asu–Nme). It was shown that an H2PO4− ion can catalyze the enolization of the Hα–Cα–C=O portion of the Asu residue by acting as a proton-transfer mediator. The resulting complex between the enol form and H2PO4− corresponds to a very flat intermediate region on the potential energy surface lying between the initial reactant complex and its mirror-image geometry. The calculated activation barrier (18.8 kcal·mol−1 after corrections for the zero-point energy and the Gibbs energy of hydration) for the enolization was consistent with the experimental activation energies of Asp racemization.
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Affiliation(s)
- Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Ryota Kirikoshi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
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24
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Kumar S, Prakash S, Gupta K, Dongre A, Balaram P, Balaram H. Unexpected functional implication of a stable succinimide in the structural stability of Methanocaldococcus jannaschii glutaminase. Nat Commun 2016; 7:12798. [PMID: 27677693 PMCID: PMC5052720 DOI: 10.1038/ncomms12798] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Protein ageing is often mediated by the formation of succinimide intermediates. These short-lived intermediates derive from asparaginyl deamidation and aspartyl dehydration and are rapidly converted into β-aspartyl or D-aspartyl residues. Here we report the presence of a highly stable succinimide intermediate in the glutaminase subunit of GMP synthetase from the hyperthermophile Methanocaldoccocus jannaschii. By comparing the biophysical properties of the wild-type protein and of several mutants, we show that the presence of succinimide increases the structural stability of the glutaminase subunit. The protein bearing this modification in fact remains folded at 100 °C and in 8 M guanidinium chloride. Mutation of the residue following the reactive asparagine provides insight into the factors that contribute to the hydrolytic stability of the succinimide. Our findings suggest that sequences that stabilize succinimides from hydrolysis may be evolutionarily selected to confer extreme thermal stability. Succinimide is a post-translational modification susceptible to rapid hydrolysis and generally associated with protein destabilisation. Here, the authors use mass spectroscopy to identify a stable succinimide intermediate that is responsible for the high thermostability of a thermophilic enzyme.
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Affiliation(s)
- Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kallol Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Dongre
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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25
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Abel BA, McCormick CL. “One-Pot” Aminolysis/Thiol–Maleimide End-Group Functionalization of RAFT Polymers: Identifying and Preventing Michael Addition Side Reactions. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01512] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brooks A. Abel
- Department of Polymer Science and
Engineering and ‡Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Charles L. McCormick
- Department of Polymer Science and
Engineering and ‡Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
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26
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Deuteration protects asparagine residues against racemization. Amino Acids 2016; 48:2189-96. [PMID: 27169868 DOI: 10.1007/s00726-016-2250-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 12/24/2022]
Abstract
Racemization in proteins and peptides at sites of L-asparaginyl and L-aspartyl residues contributes to their spontaneous degradation, especially in the biological aging process. Amino acid racemization involves deprotonation of the alpha carbon and replacement of the proton in the opposite stereoconfiguration; this reaction is much faster for aspartate/asparagine than for other amino acids because these residues form a succinimide ring in which resonance stabilizes the carbanion resulting from proton loss. To determine if the replacement of the hydrogen atom on the alpha carbon with a deuterium atom might decrease the rate of racemization and thus stabilize polypeptides, we synthesized a hexapeptide, VYPNGA, in which the three carbon-bound protons in the asparaginyl residue were replaced with deuterium atoms. Upon incubation of this peptide in pH 7.4 buffer at 37 °C, we found that the rate of deamidation via the succinimide intermediate was unchanged by the presence of the deuterium atoms. However, the accumulation of the D-aspartyl and D-isoaspartyl-forms resulting from racemization and hydrolysis of the succinimide was decreased more than five-fold in the deuterated peptide over a 20 day incubation at physiological temperature and pH. Additionally, we found that the succinimide intermediate arising from the degradation of the deuterated asparaginyl peptide was slightly less likely to open to the isoaspartyl configuration than was the protonated succinimide. These findings suggest that the kinetic isotope effect resulting from the presence of deuteriums in asparagine residues can limit the accumulation of at least some of the degradation products that arise as peptides and proteins age.
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27
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Takahashi O, Manabe N, Kirikoshi R. A Computational Study of the Mechanism of Succinimide Formation in the Asn-His Sequence: Intramolecular Catalysis by the His Side Chain. Molecules 2016; 21:327. [PMID: 27005609 PMCID: PMC6274526 DOI: 10.3390/molecules21030327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of the succinimide intermediate is by far the fastest when Xxx is glycine (Gly), the smallest amino acid residue, while extremely slow when Xxx is bulky such as isoleucine (Ile) and valine (Val). In this respect, it is very interesting to note that the succinimide formation is definitely accelerated when Xxx is histidine (His) despite its large size. In this paper, we computationally show that, in an Asn-His sequence, the His side-chain imidazole group (in the neutral Nε-protonated form) can specifically catalyze the formation of the tetrahedral intermediate in the succinimide formation by mediating a proton transfer. The calculations were performed for Ace-Asn-His-Nme (Ace = acetyl, Nme = methylamino) as a model compound by the density functional theory with the B3LYP functional and the 6-31+G(d,p) basis set. We also show that the tetrahedral intermediate, once protonated at the NH₂ group, easily releases an ammonia molecule to give the succinimide species.
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Affiliation(s)
- Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Ryota Kirikoshi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
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28
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Kaliman I, Nemukhin A, Varfolomeev S. Free Energy Barriers for the N-Terminal Asparagine to Succinimide Conversion: Quantum Molecular Dynamics Simulations for the Fully Solvated Model. J Chem Theory Comput 2015; 6:184-9. [PMID: 26614331 DOI: 10.1021/ct900398a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deamidation of asparagine residues represents one of the main routes for the post-translational modification of protein sequences. We computed the estimates of the free energy barriers for three stages of the deamidation process, deprotonation, cyclization, and deamination, of the conversion of asparagine to the succinimide intermediate within the fully solvated model with explicit water molecules. The Born-Oppenheimer molecular dynamics in the Gaussian and Plane Wave (GPW) approximation as implemented in the CP2K quantum chemistry package was utilized to sample the configurational space. By applying the metadynamics technique, the estimates of the free energy barriers were obtained for three separated stages of the reaction. In agreement with the experimental kinetic measurements, the estimated activation barriers do not exceed 21 kcal/mol. We demonstrate that the use of fully solvated models is the critical issue in theoretical studies of these reactions. We also conclude that more extensive sampling is necessary to obtain full free energy profiles and accurate barriers for the reaction stages.
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Affiliation(s)
- Ilya Kaliman
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - Sergei Varfolomeev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russian Federation, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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29
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Elferich J, Williamson DM, David LL, Shinde U. Determination of Histidine pKa Values in the Propeptides of Furin and Proprotein Convertase 1/3 Using Histidine Hydrogen-Deuterium Exchange Mass Spectrometry. Anal Chem 2015; 87:7909-17. [PMID: 26110992 PMCID: PMC4903077 DOI: 10.1021/acs.analchem.5b01721] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Propeptides of proprotein convertases regulate activation of their protease domains by sensing the organellar pH within the secretory pathway. Earlier experimental work highlighted the importance of a conserved histidine residue within the propeptide of a widely studied member, furin. A subsequent evolutionary analysis found an increase in histidine content within propeptides of secreted eukaryotic proteases compared with their prokaryotic orthologs. However, furin activates in the trans-golgi network at a pH of 6.5 while a paralog, proprotein convertase 1/3, activates in secretory vesicles at a pH of 5.5. It is unclear how a conserved histidine can mediate activation at two different pH values. In this manuscript, we measured the pKa values of histidines within the propeptides of furin and proprotein convertase 1/3 using a histidine hydrogen-deuterium exchange mass spectrometry approach. The high density of histidine residues combined with an abundance of basic residues provided challenges for generation of peptide ions with unique histidine residues, which were overcome by employing ETD fragmentation. During this analysis, we found slow hydrogen-deuterium exchange in residues other than histidine at basic pH. Finally, we demonstrate that the pKa of the conserved histidine in proprotein convertase 1/3 is acid-shifted compared with furin and is consistent with its lower pH of activation.
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Affiliation(s)
- Johannes Elferich
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Danielle M. Williamson
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Larry L. David
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Ujwal Shinde
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239, United States
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30
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Ince HH, Konuklar FAS, Ugur I, Ozcan ÖA, Sayadi M, Feig M, Aviyente V. Role of then+1 amino acid residue on the deamidation of asparagine in pentapeptides. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1068394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Dörr AA, Lubell WD. γ-Turn Mimicry with Benzodiazepinones and Pyrrolobenzodiazepinones Synthesized from a Common Amino Ketone Intermediate. Org Lett 2015; 17:3592-5. [DOI: 10.1021/acs.orglett.5b01679] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Aurélie A. Dörr
- Département de Chimie, Université de Montréal, C.P.6128,
Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - William D. Lubell
- Département de Chimie, Université de Montréal, C.P.6128,
Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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32
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Ugur I, Marion A, Aviyente V, Monard G. Why Does Asn71 Deamidate Faster Than Asn15 in the Enzyme Triosephosphate Isomerase? Answers from Microsecond Molecular Dynamics Simulation and QM/MM Free Energy Calculations. Biochemistry 2015; 54:1429-39. [DOI: 10.1021/bi5008047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ilke Ugur
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P.
70239, F-54506 Vandoeuvre-les-Nancy, France
- CNRS, UMR 7565
SRSMC, Boulevard des Aiguillettes
B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
- Department
of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Antoine Marion
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P.
70239, F-54506 Vandoeuvre-les-Nancy, France
- CNRS, UMR 7565
SRSMC, Boulevard des Aiguillettes
B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
| | - Viktorya Aviyente
- Department
of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P.
70239, F-54506 Vandoeuvre-les-Nancy, France
- CNRS, UMR 7565
SRSMC, Boulevard des Aiguillettes
B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
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33
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Takahashi O, Kirikoshi R, Manabe N. Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study. Int J Mol Sci 2015; 16:1613-26. [PMID: 25588215 PMCID: PMC4307323 DOI: 10.3390/ijms16011613] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/04/2015] [Indexed: 11/16/2022] Open
Abstract
Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.
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Affiliation(s)
- Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Ryota Kirikoshi
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
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34
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Kretz J, Kerwat D, Schubert V, Grätz S, Pesic A, Semsary S, Cociancich S, Royer M, Süssmuth RD. Total synthesis of albicidin: a lead structure from Xanthomonas albilineans for potent antibacterial gyrase inhibitors. Angew Chem Int Ed Engl 2014; 54:1969-73. [PMID: 25504839 DOI: 10.1002/anie.201409584] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 11/09/2022]
Abstract
The peptide antibiotic albicidin, which is synthesized by the plant pathogenic bacterium Xanthomonas albilineans, displays remarkable antibacterial activity against various Gram-positive and Gram-negative microorganisms. The low amounts of albicidin obtainable from the producing organism or through heterologous expression are limiting factors in providing sufficient material for bioactivity profiling and structure-activity studies. Therefore, we developed a convergent total synthesis route toward albicidin. The unexpectedly difficult formation of amide bonds between the aromatic amino acids was achieved through a triphosgene-mediated coupling strategy. The herein presented synthesis of albicidin confirms the previously determined chemical structure and underlines the extraordinary antibacterial activity of this compound. The synthetic protocol will provide multigram amounts of albicidin for further profiling of its drug properties.
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Affiliation(s)
- Julian Kretz
- Institut für Organische Chemie, Technische Universität Berlin, Straße des 17 Juni 124, 10623 Berlin (Germany) http://www.biochemie.tu-berlin.de
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35
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Kretz J, Kerwat D, Schubert V, Grätz S, Pesic A, Semsary S, Cociancich S, Royer M, Süssmuth RD. Totalsynthese von Albicidin - eine Leitstruktur ausXanthomonas albilineansfür potente antibakterielle Gyrase-Inhibitoren. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409584] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Wahl O, Holzgrabe U. Evaluation of enantiomeric purity of magnesium-L-aspartate dihydrate. J Pharm Biomed Anal 2014; 102:100-9. [PMID: 25262412 DOI: 10.1016/j.jpba.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Magnesium supplementation in form of organic magnesium salts is a very popular practice. We examined the enantiomeric purity of "Magnesium aspartate dihydrate" monographed in the European Pharmacopeia. A chiral capillary zone electrophoresis using (2-hydroxypropyl)-β-cyclodextrin coupled to laser induced fluorescence detection and a HPLC-fluorescence method with chiral derivatization using o-phthaldialdehyde and N-acetyl-L-cysteine as an orthogonal method were developed and validated. Two batch samples of this substance and three drug products containing the salt were analyzed by means of both methods. The concentration of the D-enantiomer of aspartic acid ranged from 0.03 to 0.12%. Simulations of the synthesis revealed that the d-aspartic acid content is elevated if the dissolution of L-aspartic acid was performed at acidic pH values.
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Affiliation(s)
- Oliver Wahl
- University of Würzburg, Institute for Pharmacy and Food Chemistry, Würzburg 97074, Germany
| | - Ulrike Holzgrabe
- University of Würzburg, Institute for Pharmacy and Food Chemistry, Würzburg 97074, Germany.
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37
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Klaene JJ, Ni W, Alfaro JF, Zhou ZS. Detection and quantitation of succinimide in intact protein via hydrazine trapping and chemical derivatization. J Pharm Sci 2014; 103:3033-42. [PMID: 25043726 DOI: 10.1002/jps.24074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/01/2014] [Accepted: 06/04/2014] [Indexed: 12/19/2022]
Abstract
The formation of aspartyl succinimide is a common post-translational modification of protein pharmaceuticals under acidic conditions. We present a method to detect and quantitate succinimide in intact protein via hydrazine trapping and chemical derivatization. Succinimide, which is labile under typical analytical conditions, is first trapped with hydrazine to form stable hydrazide and can be directly analyzed by mass spectrometry. The resulting aspartyl hydrazide can be selectively derivatized by various tags, such as fluorescent rhodamine sulfonyl chloride that absorbs strongly in the visible region (570 nm). Our tagging strategy allows the labeled protein to be analyzed by orthogonal methods, including HPLC-UV-Vis, liquid chromatography mass spectrometry (LC-MS), and SDS-PAGE coupled with fluorescence imaging. A unique advantage of our method is that variants containing succinimide, after derivatization, can be readily resolved via either affinity enrichment or chromatographic separation. This allows further investigation of individual factors in a complex protein mixture that affect succinimide formation. Some additional advantages are imparted by fluorescence labeling including the facile detection of the intact protein without proteolytic digestion to peptides; and high sensitivity, for example, without optimization, 0.41% succinimide was readily detected. As such, our method should be useful for rapid screening, optimization of formulation conditions, and related processes relevant to protein pharmaceuticals.
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Affiliation(s)
- Joshua J Klaene
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
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38
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Nadimpally KC, Paul A, Mandal B. Reversal of aggregation using β-breaker dipeptide containing peptides: Application to Aβ(1-40) self-assembly and its inhibition. ACS Chem Neurosci 2014; 5:400-8. [PMID: 24661180 DOI: 10.1021/cn500064z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Reversion of protein or peptide aggregation is a formidable task, important in various domains of research at the interface of chemistry, medicine, and nanoscience. A novel class of dipeptides, termed as β-breaker dipeptides (BBDPs), is identified, which can be incorporated into the self-recognizing sequences to generate a novel class of conformational switch which forms β-sheet at an initial stage and then converts in a controlled manner to random coil at specific conditions. Incorporation of BBDPs in a well designed amyloidogenic peptides generates a special class of β-sheet breaker peptides those undergo a chemical change at physiological condition generating a breaker element in situ. These β-breaker peptides are shown to first incorporate into the amyloid and then disrupt it. Such conformational switches may be used to study agrregation/disaggregation process and may find many biomedical applications relevant to aggregation related disorders. Such strategy for reversion of peptide aggregation using chemical tricks may find application in material chemistry as well.
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Affiliation(s)
- Krishna Chaitanya Nadimpally
- Laboratory of Peptide and
Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati, Assam-781039, India
| | - Ashim Paul
- Laboratory of Peptide and
Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati, Assam-781039, India
| | - Bhubaneswar Mandal
- Laboratory of Peptide and
Amyloid Research, Department of Chemistry, Indian Institute of Technology Guwahati, Assam-781039, India
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39
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Patananan AN, Capri J, Whitelegge JP, Clarke SG. Non-repair pathways for minimizing protein isoaspartyl damage in the yeast Saccharomyces cerevisiae. J Biol Chem 2014; 289:16936-53. [PMID: 24764295 DOI: 10.1074/jbc.m114.564385] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The spontaneous degradation of asparaginyl and aspartyl residues to isoaspartyl residues is a common type of protein damage in aging organisms. Although the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (EC 2.1.1.77) can initiate the repair of l-isoaspartyl residues to l-aspartyl residues in most organisms, no gene homolog or enzymatic activity is present in the budding yeast Saccharomyces cerevisiae. Therefore, we used biochemical approaches to elucidate how proteins containing isoaspartyl residues are metabolized in this organism. Surprisingly, the level of isoaspartyl residues in yeast proteins (50-300 pmol of isoaspartyl residues/mg of protein extract) is comparable with organisms with protein-l-isoaspartyl (d-aspartyl) O-methyltransferase, suggesting a novel regulatory pathway. Interfering with common protein quality control mechanisms by mutating and inhibiting the proteasomal and autophagic pathways in vivo did not increase isoaspartyl residue levels compared with wild type or uninhibited cells. However, the inhibition of metalloproteases in in vitro aging experiments by EDTA resulted in an ∼3-fold increase in the level of isoaspartyl-containing peptides. Characterization by mass spectrometry of these peptides identified several proteins involved in metabolism as targets of isoaspartyl damage. Further analysis of these peptides revealed that many have an N-terminal isoaspartyl site and originate from proteins with short half-lives. These results suggest that one or more metalloproteases participate in limiting isoaspartyl formation by robust proteolysis.
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Affiliation(s)
- Alexander N Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
| | - Joseph Capri
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
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40
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Synthetic and quantum chemical study on the regioselective addition of amines to methyl maleamate. J Mol Model 2013; 19:3683-94. [DOI: 10.1007/s00894-013-1905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/30/2013] [Indexed: 10/26/2022]
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41
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Brückner C, Bunz SC, Imhof D, Neusüß C, Scriba GKE. Isomerization and epimerization of the aspartyl tetrapeptide Ala-Phe-Asp-GlyOH at pH 10-A CE study. Electrophoresis 2013; 34:2666-73. [DOI: 10.1002/elps.201200685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Christin Brückner
- Department of Pharmaceutical Chemistry; School of Pharmacy; Friedrich Schiller University Jena; Jena; Germany
| | | | - Diana Imhof
- Department of Pharmaceutical Chemistry I; School of Pharmacy; University of Bonn; Bonn; Germany
| | | | - Gerhard K. E. Scriba
- Department of Pharmaceutical Chemistry; School of Pharmacy; Friedrich Schiller University Jena; Jena; Germany
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42
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Brückner C, Imhof D, Scriba GK. Capillary electrophoretic study of the degradation pathways and kinetics of the aspartyl model tetrapeptide Gly-Phe-Asp-GlyOH in alkaline solution. J Pharm Biomed Anal 2013; 76:96-103. [DOI: 10.1016/j.jpba.2012.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
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43
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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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44
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Takahashi O. Two-water-assisted racemization of the succinimide intermediate formed in proteins. A computational model study. Health (London) 2013. [DOI: 10.4236/health.2013.512273] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Selvaraj ARK, Murugan NA, Ågren H. Solvent Polarity-Induced Conformational Unlocking of Asparagine. J Phys Chem A 2012; 116:11702-8. [DOI: 10.1021/jp307715n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ananda Rama Krishnan Selvaraj
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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46
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Brückner C, Fahr A, Imhof D, Scriba GK. Degradation Kinetics of an Aspartyl-Tripeptide-Derived Diketopiperazine under Forced Conditions. J Pharm Sci 2012; 101:4178-90. [DOI: 10.1002/jps.23272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/13/2012] [Accepted: 07/02/2012] [Indexed: 12/23/2022]
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47
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CE-MS Identification of Amino Acid Sequence Inversion as a New Degradation Pathway of an Aspartyl Model Tripeptide. Chromatographia 2012. [DOI: 10.1007/s10337-012-2306-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hendy EJ, Tomiak PJ, Collins MJ, Hellstrom J, Tudhope AW, Lough JM, Penkman KE. Assessing amino acid racemization variability in coral intra-crystalline protein for geochronological applications. GEOCHIMICA ET COSMOCHIMICA ACTA 2012; 86:338-353. [PMID: 23564968 PMCID: PMC3617617 DOI: 10.1016/j.gca.2012.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 02/15/2012] [Indexed: 05/17/2023]
Abstract
Over 500 Free Amino Acid (FAA) and corresponding Total Hydrolysed Amino Acid (THAA) analyses were completed from eight independently-dated, multi-century coral cores of massive Porites sp. colonies. This dataset allows us to re-evaluate the application of amino acid racemization (AAR) for dating late Holocene coral material, 20 years after Goodfriend et al. (GCA56 (1992), 3847) first showed AAR had promise for developing chronologies in coral cores. This re-assessment incorporates recent method improvements, including measurement by RP-HPLC, new quality control approaches (e.g. sampling and sub-sampling protocols, statistically-based data screening criteria), and cleaning steps to isolate the intra-crystalline skeletal protein. We show that the removal of the extra-crystalline contaminants and matrix protein is the most critical step for reproducible results and recommend a protocol of bleaching samples in NaOCl for 48 h to maximise removal of open system proteins while minimising the induced racemization. We demonstrate that AAR follows closed system behaviour in the intra-crystalline fraction of the coral skeletal proteins. Our study is the first to assess the natural variability in intra-crystalline AAR between colonies, and we use coral cores taken from the Great Barrier Reef, Australia, and Jarvis Island in the equatorial Pacific to explore variability associated with different environmental conditions and thermal histories. Chronologies were developed from THAA Asx D/L, Ala D/L, Glx D/L and FAA Asx D/L for each core and least squares Monte Carlo modelling applied in order to quantify uncertainty of AAR age determinations and assess the level of dating resolution possible over the last 5 centuries. AAR within colonies follow consistent stratigraphic aging. However, there are systematic differences in rates between the colonies, which would preclude direct comparison from one colony to another for accurate age estimation. When AAR age models are developed from a combined dataset to include this natural inter-colony variability THAA Asx D/L, Glx D/L and Ala D/L give a 2σ age uncertainty of ±19, ±38 and ±29 year, for the 20th C respectively; in comparison 2σ age uncertainties from a single colony are ±12, ±12 and ±14 year. This is the first demonstration of FAA D/L for dating coral and following strict protocols 2σ precisions of ±24 years can be achieved across different colonies in samples from the last 150 years, and can be ±10 years within a core from a single colony. Despite these relatively large error estimates, AAR would be a valuable tool in situations where a large number of samples need to be screened rapidly and cheaply (e.g. identifying material from mixed populations in beach or uplift deposits), prior to and complementing the more time-consuming geochronological tools of U/Th or seasonal isotopic timeseries.
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Affiliation(s)
- Erica J. Hendy
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, BS8 1UG, United Kingdom
| | - Peter J. Tomiak
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, United Kingdom
| | - Matthew J. Collins
- BioArCh, Departments of Archaeology and Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - John Hellstrom
- School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Janice M. Lough
- Australian Institute of Marine Science, PMB3, Townsville M.C., QLD 4810, Australia
| | - Kirsty E.H. Penkman
- BioArCh, Departments of Archaeology and Chemistry, University of York, York, YO10 5DD, United Kingdom
- Corresponding author. Tel.: +44 (0) 1904 322574; fax: +44 (0) 1904 322516.
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Ugur I, Aviyente V, Monard G. Initiation of the reaction of deamidation in triosephosphate isomerase: investigations by means of molecular dynamics simulations. J Phys Chem B 2012; 116:6288-301. [PMID: 22574817 DOI: 10.1021/jp3013305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deamidation of asparagine is the spontaneous degradation of this residue into aspartic acid. The kinetics of this slow reaction is mainly dependent on the nature of the adjacent amino acid that follows asparagine in a peptide or protein primary sequence. In the homodimer triosephosphate isomerase (TPI), there are two main deamidation sites per subunit: Asn15-Gly16 and Asn71-Gly72 for which deamidation dynamics are known to be interrelated. In this study, we investigate the initiation of the deamidation reaction in TPI by means of molecular dynamics. Simulations based on classical AMBER force field are performed in a 60 to 90 ns time scale for six distinct samples. Conformational changes, desolvation effects, and hydrogen bond networks are analyzed to interpret the experimental findings and previous quantum mechanical (QM) results. Results that are based on desolvation analysis clarify the assignments in the literature about the different behaviors of two deamidating sites in TPI. Conformational analysis supports findings suggested by QM studies: the most favorable reaction mechanism is the one that yields to succinimide intermediate via one or two step routes. The mechanism leading to the succinimide intermediate most likely involves the formation of a tetrahedral intermediate that is formed either directly from asparagine or via a side chain tautomer intermediate. In all cases, surrounding water molecules are present to assist the reaction.
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Affiliation(s)
- Ilke Ugur
- Department of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
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Boeckx B, Maes G. The conformational behavior and H-bond structure of asparagine: A theoretical and experimental matrix-isolation FT-IR study. Biophys Chem 2012; 165-166:62-73. [DOI: 10.1016/j.bpc.2012.03.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 03/11/2012] [Accepted: 03/12/2012] [Indexed: 11/16/2022]
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