1
|
Abdulbagi M, Di B, Li B. Resolving D-Amino Acid Containing Peptides Using Ion Mobility-Mass Spectrometry: Challenges and Recent Developments. Crit Rev Anal Chem 2023:1-10. [PMID: 37975700 DOI: 10.1080/10408347.2023.2282510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Peptides and proteins having D-amino acids in their sequences are now believed to be widespread among different living organisms. Their significance is attributed to the diverse functions of these molecules, such as having a certain pathological implication or enhancing biological activity. Indeed, some peptide molecules with D-amino acids in their structure have already found their way to clinical use such as the antibacterial gramicidin and the antidiabetic nateglinide. Ion mobility mass spectrometry (IM-MS) added an additional dimension of separation as it depends on ions mobility in the space, which is dependent on their shapes, and the shape depends on the orientation of atoms. Thus, D-amino acids containing peptides (DAACPs) will have different mobility and collision cross-section values than those with L-amino acids. Eventually, this will lead to baseline separation of the two peptides. Additionally, ion mobility can precisely locate the position of D-amino acids by analyzing the difference in the arrival times of the fragment ions. The importance of DAACPs, as well as the difficulties in discovering them, were addressed in this review. Similarly, we emphasized how recent developments in IM-MS have improved their detection and analysis. Consequently, the LC-IM-MS/MS platform appears to be promising in isomeric mixture analysis.
Collapse
Affiliation(s)
- Mohamed Abdulbagi
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
| | - Bin Di
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Bo Li
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
2
|
Kandi S, Cline EN, Rivera BM, Viola KL, Zhu J, Condello C, LeDuc RD, Klein WL, Kelleher NL, Patrie SM. Amyloid β Proteoforms Elucidated by Quantitative LC/MS in the 5xFAD Mouse Model of Alzheimer's Disease. J Proteome Res 2023; 22:3475-3488. [PMID: 37847596 PMCID: PMC10840081 DOI: 10.1021/acs.jproteome.3c00353] [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] [Indexed: 10/19/2023]
Abstract
Numerous Aβ proteoforms, identified in the human brain, possess differential neurotoxic and aggregation propensities. These proteoforms contribute in unknown ways to the conformations and resultant pathogenicity of oligomers, protofibrils, and fibrils in Alzheimer's disease (AD) manifestation owing to the lack of molecular-level specificity to the exact chemical composition of underlying protein products with widespread interrogating techniques, like immunoassays. We evaluated Aβ proteoform flux using quantitative top-down mass spectrometry (TDMS) in a well-studied 5xFAD mouse model of age-dependent Aβ-amyloidosis. Though the brain-derived Aβ proteoform landscape is largely occupied by Aβ1-42, 25 different forms of Aβ with differential solubility were identified. These proteoforms fall into three natural groups defined by hierarchical clustering of expression levels in the context of mouse age and proteoform solubility, with each group sharing physiochemical properties associated with either N/C-terminal truncations or both. Overall, the TDMS workflow outlined may hold tremendous potential for investigating proteoform-level relationships between insoluble fibrils and soluble Aβ, including low-molecular-weight oligomers hypothesized to serve as the key drivers of neurotoxicity. Similarly, the workflow may also help to validate the utility of AD-relevant animal models to recapitulate amyloidosis mechanisms or possibly explain disconnects observed in therapeutic efficacy in animal models vs humans.
Collapse
Affiliation(s)
- Soumya Kandi
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Erika N Cline
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Brianna M Rivera
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, California 94158, United States
| | - Kirsten L Viola
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiuhe Zhu
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Carlo Condello
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, California 94158, United States
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, California 94158, United States
| | - Richard D LeDuc
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - William L Klein
- Department of Neurobiology, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
3
|
Ortigosa-Pascual L, Leiding T, Linse S, Pálmadóttir T. Photo-Induced Cross-Linking of Unmodified α-Synuclein Oligomers. ACS Chem Neurosci 2023; 14:3192-3205. [PMID: 37621159 PMCID: PMC10485903 DOI: 10.1021/acschemneuro.3c00326] [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: 05/12/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Photo-induced cross-linking of unmodified proteins (PICUP) has been used in the past to study size distributions of protein assemblies. PICUP may, for example, overcome the significant experimental challenges related to the transient nature, heterogeneity, and low concentration of amyloid protein oligomers relative to monomeric and fibrillar species. In the current study, a reaction chamber was designed, produced, and used for PICUP reaction optimization in terms of reaction conditions and lighting time from ms to s. These efforts make the method more reproducible and accessible and enable the use of shorter reaction times compared to previous studies. We applied the optimized method to an α-synuclein aggregation time course to monitor the relative concentration and size distribution of oligomers over time. The data are compared to the time evolution of the fibril mass concentration, as monitored by thioflavin T fluorescence. At all time points, the smaller the oligomer, the higher its concentration observed after PICUP. Moreover, the total oligomer concentration is highest at short aggregation times, and the decline over time follows the disappearance of monomers. We can therefore conclude that these oligomers form from monomers.
Collapse
Affiliation(s)
- Lei Ortigosa-Pascual
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| | - Thom Leiding
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| | - Sara Linse
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| | - Tinna Pálmadóttir
- Department of Biochemistry and Structural
Biology, Lund University, 221 00 Lund, Sweden
| |
Collapse
|
4
|
Li G, Jeon CK, Ma M, Jia Y, Zheng Z, Delafield DG, Lu G, Romanova EV, Sweedler JV, Ruotolo BT, Li L. Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chem Sci 2023; 14:5936-5944. [PMID: 37293657 PMCID: PMC10246695 DOI: 10.1039/d3sc00678f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/06/2023] [Indexed: 06/10/2023] Open
Abstract
Growing evidence supports the confident association between distinct amyloid beta (Aβ) isoforms and Alzheimer's Disease (AD) pathogenesis. As such, critical investigations seeking to uncover the translational factors contributing to Aβ toxicity represent a venture of significant value. Herein, we comprehensively assess full-length Aβ42 stereochemistry, with a specific focus on models that consider naturally-occurring isomerization of Asp and Ser residues. We customize various forms of d-isomerized Aβ as natural mimics, ranging from fragments containing a single d residue to full length Aβ42 that includes multiple isomerized residues, systematically evaluating their cytotoxicity against a neuronal cell line. Combining multidimensional ion mobility-mass spectrometry experimental data with replica exchange molecular dynamics simulations, we confirm that co-d-epimerization at Asp and Ser residues within Aβ42 in both N-terminal and core regions effectively reduces its cytotoxicity. We provide evidence that this rescuing effect is associated with the differential and domain-specific compaction and remodeling of Aβ42 secondary structure.
Collapse
Affiliation(s)
- Gongyu Li
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
- Haihe Laboratory of Sustainable Chemical Transformations Tianjin 300192 China
| | - Chae Kyung Jeon
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Min Ma
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Yifei Jia
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University Tianjin 300070 China
| | - Daniel G Delafield
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Gaoyuan Lu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Elena V Romanova
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Jonathan V Sweedler
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| |
Collapse
|
5
|
Murata T, Ito G, Utsunomiya-Tate N. Site-specific amino acid D-isomerization of Tau R2 and R3 peptides changes the fibril morphology, resulting in attenuation of Tau aggregation inhibitor potency. Biochem Biophys Res Commun 2023; 654:18-25. [PMID: 36878036 DOI: 10.1016/j.bbrc.2023.02.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023]
Abstract
Tau, a microtubule-binding protein, is a major component of neurofibrillary tangles in the brains of Alzheimer's disease patients. Tau aggregation following fibril formation induces Alzheimer's disease pathogenesis. The accumulation of D-isomerized amino acids in proteins that occurs in several tissues with aging is thought to be implicated in age-related diseases. D-isomerized Asp accumulation has also been found in Tau in neurofibrillary tangles. We previously demonstrated the effects of D-isomerization of Asp within microtubule-binding repeat peptides of Tau, Tau R2, and R3 on the rates of structural transition and fibril formation. Here, we investigated the potency of Tau aggregation inhibitors on fibril formation of wild-type Tau R2 and R3 peptides and D-isomerized Asp-containing Tau R2 and R3 peptides. D-isomerization of Asp within Tau R2 and R3 peptides attenuated the potency of inhibitors. We next investigated the fibril morphology of D-isomerized Asp-containing Tau R2 and R3 peptides by electron microscopy. D-isomerized Asp-containing Tau R2 and R3 fibrils showed significantly different fibril morphology from that of wild-type peptides. Our results indicate that D-isomerization of Asp within Tau R2 and R3 peptides affects fibril morphology, resulting in attenuation of the potency of Tau aggregation inhibitors.
Collapse
Affiliation(s)
- Takuya Murata
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
| |
Collapse
|
6
|
Yan L, Ke Y, Wang Y, Yang J, He Y, Wu L. Effect of Mini-PEGs Modification on the Enzymatic Digestion of D-Amino Acid-Containing Peptides under the Action of PROK. Chemistry 2023; 29:e202203524. [PMID: 36541269 DOI: 10.1002/chem.202203524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
It was previously reported that D-amino acid-containing peptides exhibited the ability to resist enzymatic hydrolysis. This study investigated the influence of mini-PEGs modification on enzymatic hydrolysis ability of D-amino acid-containing peptides. The results showed that PEGylation promoted enzymatic hydrolysis of the D-amino acid-containing peptide, especially, the cleavage rate of the D-amino acid-containing peptide 6-w with PEG3 modification at the N-ends was up to 17 times higher in the presence of proteinase K (PROK) compared to those without PEG3 modification. Moreover, analysis of the enzymatic cleavage sites demonstrated a similar cleavage pattern of the PEGylated D-amino acid-containing peptide to that of the unmodified peptide. The computational simulations further showed that the enhanced enzymatic hydrolysis ability can be attributed to the strong interaction between PROK and the peptide after PEG3 modification and the resulting formation of a mature catalytic triad structure.
Collapse
Affiliation(s)
- Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jingkui Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| |
Collapse
|
7
|
Ozaki M, Shimotsuma M, Kuranaga T, Kakeya H, Hirose T. Separation of amyloid β fragment peptides with racemised and isomerised aspartic acid residues using an original chiral resolution labeling reagent. Analyst 2023; 148:1209-1213. [PMID: 36779274 DOI: 10.1039/d2an01885c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
We developed a system to separate and identify racemised and isomerised aspartic acid (Asp) residues in amyloid β (Aβ) by labeling with an original chiral resolution labeling reagent, 1-fluoro-2,4-dinitrophenyl-5-D-leucine-N,N-dimethylethylenediamine-amide (D-FDLDA). The racemised and isomerised Asp residues labeled with D-FDLDA in Aβ fragments generated by digesting with trypsin and endoproteinase Glu-C were separated and identified by liquid chromatography-mass spectrometry (LC-MS) under simple gradient conditions. Furthermore, the labeled Aβ fragments did not aggregate and remained stable at least for 1 week at 4 °C.
Collapse
Affiliation(s)
- Makoto Ozaki
- Research and Development Department, Purification Section, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Motoshi Shimotsuma
- Research and Development Department, Purification Section, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Takefumi Kuranaga
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Kyoto 606-8501, Japan.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Kyoto 606-8501, Japan.
| | - Tsunehisa Hirose
- Research and Development Department, Purification Section, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| |
Collapse
|
8
|
Cai W, Wu T, Chen N. The Amyloid-Beta Clearance: From Molecular Targets to Glial and Neural Cells. Biomolecules 2023; 13:313. [PMID: 36830682 PMCID: PMC9953441 DOI: 10.3390/biom13020313] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
The deposition of amyloid-beta (Aβ) plaques in the brain is one of the primary pathological characteristics of Alzheimer's disease (AD). It can take place 20-30 years before the onset of clinical symptoms. The imbalance between the production and the clearance of Aβ is one of the major causes of AD. Enhancing Aβ clearance at an early stage is an attractive preventive and therapeutic strategy of AD. Direct inhibition of Aβ production and aggregation using small molecules, peptides, and monoclonal antibody drugs has not yielded satisfactory efficacy in clinical trials for decades. Novel approaches are required to understand and combat Aβ deposition. Neurological dysfunction is a complex process that integrates the functions of different types of cells in the brain. The role of non-neurons in AD has not been fully elucidated. An in-depth understanding of the interactions between neurons and non-neurons can contribute to the elucidation of Aβ formation and the identification of effective drug targets. AD patient-derived pluripotent stem cells (PSCs) contain complete disease background information and have the potential to differentiate into various types of neurons and non-neurons in vitro, which may bring new insight into the treatment of AD. Here, we systematically review the latest studies on Aβ clearance and clarify the roles of cell interactions among microglia, astroglia and neurons in response to Aβ plaques, which will be beneficial to explore methods for reconstructing AD disease models using inducible PSCs (iPSCs) through cell differentiation techniques and validating the applications of models in understanding the formation of Aβ plaques. This review may provide the most promising directions of finding the clues for preventing and delaying the development of AD.
Collapse
Affiliation(s)
| | | | - Ning Chen
- Tianjiu Research and Development Center for Exercise Nutrition and Foods, Hubei Key Laboratory of Exercise Training and Monitoring, College of Sports Medicine, Wuhan Sports University, Wuhan 430079, China
| |
Collapse
|
9
|
Xu X, Han L, Zheng Z, Zhao R, Li L, Shao X, Li G. Composite Multidimensional Ion Mobility-Mass Spectrometry for Improved Differentiation of Stereochemical Modifications. Anal Chem 2023; 95:2221-2228. [PMID: 36635260 DOI: 10.1021/acs.analchem.2c03522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Stereochemical modifications (SCMs), mostly present in the form of d-amino acid substitution, have been increasingly identified from a wide range of neuropeptides and disease-associated biomarker proteins. Traditional mass spectrometry-based SCM identification has been effectively enhanced with technological and strategic advancements in ion mobility spectrometry. With the additional separation provided by ion mobility, SCM-induced structural changes can be probed both in theory and in practice, although the structural resolution for low-abundance SCMs still requires further improvement to enable accurate quantification or unambiguous identification of stereoisomers. Herein, we present a multi-component-enabled multidimensional ion mobility-mass spectrometry (3M-IM-MS) analytical workflow, based upon the metal-enhanced chiral amplification strategy we proposed previously (Nat. Commun., 2019, 5038). Notably, the 3M-IM-MS strategy comprises and features the powerful mathematical tools of continuous wavelet transform and Gaussian fitting-enabled peak splitting. Consequently, the resolving capability of ion mobility spectrometry for SCM analysis has been significantly enhanced, providing mobility profiles with baseline separation and more than fivefold improvement in resolving power and overall resolution. This study represents an alternative toward ultrahigh-resolution structural interrogation of mixtures with very small differences, featuring an important and long-lasting topic in chemical measurement.
Collapse
Affiliation(s)
- Xia Xu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Li Han
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Rui Zhao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Gongyu Li
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| |
Collapse
|
10
|
Wu J, Chen Y. Signal peptide stabilizes folding and inhibits misfolding of serum amyloid A. Protein Sci 2022; 31:e4485. [PMID: 36309973 PMCID: PMC9667897 DOI: 10.1002/pro.4485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Signal peptide (SP) plays an important role in membrane targeting for insertion of secretory and membrane proteins during translocation processes in prokaryotes and eukaryotes. Beside the targeting functions, SP has also been found to affect the stability and folding of several proteins. Serum amyloid A (SAA) proteins are apolipoproteins responding to acute-phase inflammation. The fibrillization of SAA results in a protein misfolding disease named amyloid A (AA) amyloidosis. The main disease-associated isoform of human SAA, SAA1.1, is expressed as a precursor protein with an N-terminal signal peptide composed of 18 residues. The cleavage of the SP generates mature SAA1.1. To investigate whether the SP affects properties of SAA1.1, we systematically examined the structure, protein stability, and fibrillization propensity of pre-SAA1.1, which possesses the SP, and Ser-SAA1.1 without the SP but containing with an additional N-terminal serine residue. We found that the presence of the SP did not significantly affect the predominant helical structure but changed the tertiary conformation as evidenced by intrinsic fluorescence and exposed hydrophobic surfaces. Pre-SAA1.1 and Ser-SAA1.1 formed distinct oligomeric assemblies in which pre-SAA1.1 populated as tetramer and octamer, whereas Ser-SAA1.1 existed as a predominant hexamer. Pre-SAA1.1 was found significantly more stable than Ser-SAA1.1 upon thermal and chemical unfolding. Ser-SAA1.1, but not pre-SAA1.1, is capable of forming amyloid fibrils in protein misfolding study, indicating a protective role of the SP. Altogether, our results demonstrated a novel role of the SP in SAA folding and misfolding and provided a novel direction for therapeutic development of AA amyloidosis.
Collapse
Affiliation(s)
- Jin‐Lin Wu
- Ph.D. Program for Cancer Biology and Drug DiscoveryChina Medical University and Academia SinicaTaichungTaiwan
- Genomics Research Center, Academia SinicaTaipeiTaiwan
| | - Yun‐Ru Chen
- Ph.D. Program for Cancer Biology and Drug DiscoveryChina Medical University and Academia SinicaTaichungTaiwan
- Genomics Research Center, Academia SinicaTaipeiTaiwan
| |
Collapse
|
11
|
Gibson K, Cooper-Shepherd DA, Pallister E, Inman SE, Jackson SE, Lindo V. Toward Rapid Aspartic Acid Isomer Localization in Therapeutic Peptides Using Cyclic Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1204-1212. [PMID: 35609180 PMCID: PMC9264384 DOI: 10.1021/jasms.2c00053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
There is an increasing emphasis on the critical evaluation of interbatch purity and physical stability of therapeutic peptides. This is due to concerns over the impact that product- and process-related impurities may have on safety and efficacy of this class of drug. Aspartic acid isomerization to isoaspartic acid is a common isobaric impurity that can be very difficult to identify without first synthesizing isoAsp peptide standards for comparison by chromatography. As such, analytical tools that can determine if an Asp residue has isomerized, as well as the site of isomerization within the peptide sequence, are highly sought after. Ion mobility-mass spectrometry is a conformation-selective method that has developed rapidly in recent years particularly with the commercialization of traveling wave ion mobility instruments. This study employed a cyclic ion mobility (cIMS) mass spectrometry system to investigate the conformational characteristics of a therapeutic peptide and three synthetic isomeric forms, each with a single Asp residue isomerized to isoAsp. cIMS was able to not only show distinct conformational differences between each peptide but crucially, in conjunction with a simple workflow for comparing ion mobility data, it correctly located which Asp residue in each peptide had isomerized to isoAsp. This work highlights the value of cIMS as a potential screening tool in the analysis of therapeutic peptides prone to the formation of isoAsp impurities.
Collapse
Affiliation(s)
- Katherine Gibson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Analytical
Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | | | - Edward Pallister
- Analytical
Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | - Sophie E. Inman
- Analytical
Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | - Sophie E. Jackson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
| | - Viv Lindo
- Analytical
Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| |
Collapse
|
12
|
Ozaki M, Kuwayama T, Hirose T, Shimotsuma M, Hashimoto A, Kuranaga T, Kakeya H. Separation and identification of the DL-forms of short-chain peptides using a new chiral resolution labeling reagent. Anal Bioanal Chem 2022; 414:4039-4046. [PMID: 35384472 DOI: 10.1007/s00216-022-04048-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
There are several reports of D-amino acids being the causative molecules of serious diseases, resulting in the formation of, for example, prion protein and amyloid β. D-Amino acids in peptides and proteins are typically identified by sequencing each residue by Edman degradation or by hydrolysis with hydrochloric acid for amino acid analysis. However, these approaches can result in racemization of the L-form to the D-form by hydrolysis and long pre-treatment for hydrolysis. To address these problems, we aimed to identify the DL-forms of amino acids in peptides without hydrolysis. Here, we showed that the DL-forms in peptides which are difficult to separate on a chiral column can be precisely separated by labeling with 1-fluoro-2,4-dinitrophenyl-5-D-leucine-N,N-dimethylethylenediamine-amide (D-FDLDA). Additionally, the peptides could be quantitatively analyzed using the same labeling method as for amino acids. Furthermore, the detection sensitivity of a sample labeled with D-FDLDA was higher than that of the conventional reagents Nα-(5-fluoro-2,4-dinitrophenyl)-L-alaninamide (L-FDAA) and Nα-(5-fluoro-2,4-dinitrophenyl)-L-leucinamide (L-FDLA) used in Marfey's method. The proposed method for identifying DL-forms of amino acids in peptides is a powerful tool for use in organic chemistry, biochemistry, and medical science.
Collapse
Affiliation(s)
- Makoto Ozaki
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko-shi, Kyoto, 617-0004, Japan
| | - Tomomi Kuwayama
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko-shi, Kyoto, 617-0004, Japan
| | - Tsunehisa Hirose
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko-shi, Kyoto, 617-0004, Japan.
| | - Motoshi Shimotsuma
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko-shi, Kyoto, 617-0004, Japan
| | - Akira Hashimoto
- Nacalai Tesque, Inc., Ishibashi Kaide-Cho, Muko-shi, Kyoto, 617-0004, Japan
| | - Takefumi Kuranaga
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.
| |
Collapse
|
13
|
Ageeva AA, Doktorov AB, Polyakov NE, Leshina TV. Chiral Linked Systems as a Model for Understanding D-Amino Acids Influence on the Structure and Properties of Amyloid Peptides. Int J Mol Sci 2022; 23:ijms23063060. [PMID: 35328481 PMCID: PMC8955658 DOI: 10.3390/ijms23063060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/10/2022] [Indexed: 01/27/2023] Open
Abstract
In this review, we provide an illustration of the idea discussed in the literature of using model compounds to study the effect of substitution of L- for D-amino acid residues in amyloid peptides. The need for modeling is due to the inability to study highly disordered peptides by traditional methods (high-field NMR, X-ray). At the same time, the appearance of such peptides, where L-amino acids are partially replaced by D-analogs is one of the main causes of Alzheimer’s disease. The review presents examples of the use diastereomers with L-/D-tryptophan in model process—photoinduced electron transfer (ET) for studying differences in reactivity and structure of systems with L- and D-optical isomers. The combined application of spin effects, including those calculated using the original theory, fluorescence techniques and molecular modeling has demonstrated a real difference in the structure and efficiency of ET in diastereomers with L-/D-tryptophan residues. In addition, the review compared the factors governing chiral inversion in model metallopeptides and Aβ42 amyloid.
Collapse
Affiliation(s)
- Aleksandra A. Ageeva
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia; (A.A.A.); (N.E.P.); (T.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander B. Doktorov
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia; (A.A.A.); (N.E.P.); (T.V.L.)
- Correspondence: author:
| | - Nikolay E. Polyakov
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia; (A.A.A.); (N.E.P.); (T.V.L.)
| | - Tatyana V. Leshina
- Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russia; (A.A.A.); (N.E.P.); (T.V.L.)
| |
Collapse
|
14
|
Wang J, Lundström SL, Seelow S, Rodin S, Meng Z, Astorga-Wells J, Jia Q, Zubarev RA. First Immunoassay for Measuring Isoaspartate in Human Serum Albumin. Molecules 2021; 26:molecules26216709. [PMID: 34771115 PMCID: PMC8587401 DOI: 10.3390/molecules26216709] [Citation(s) in RCA: 5] [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: 09/07/2021] [Revised: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 01/01/2023] Open
Abstract
Isoaspartate (isoAsp) is a damaging amino acid residue formed in proteins mostly as a result of spontaneous deamidation of asparaginyl residues. An association has been found between isoAsp in human serum albumin (HSA) and Alzheimer’s disease (AD). Here we report on a novel monoclonal antibody (mAb) 1A3 with excellent specificity to isoAsp in the functionally important domain of HSA. Based on 1A3 mAb, an indirect enzyme-linked immunosorbent assay (ELISA) was developed, and the isoAsp occupancy in 100 healthy plasma samples was quantified for the first time, providing the average value of (0.74 ± 0.13)%. These results suggest potential of isoAsp measurements for supplementary AD diagnostics as well as for assessing the freshness of stored donor blood and its suitability for transfusion.
Collapse
Affiliation(s)
- Jijing Wang
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
| | - Susanna L. Lundström
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
| | - Sven Seelow
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
| | - Sergey Rodin
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
- Department of Surgical Sciences, Uppsala University, 752 36 Uppsala, Sweden
- Endocrinology Research Centre, 115478 Moscow, Russia
| | - Zhaowei Meng
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
| | - Juan Astorga-Wells
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
- HDXperts AB, 183 48 Danderyd, Sweden
| | - Qinyu Jia
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
- HDXperts AB, 183 48 Danderyd, Sweden
| | - Roman A. Zubarev
- Department of Medical Biophysics and Biochemistry, Karolinska Institute, 171 77 Stockholm, Sweden; (J.W.); (S.L.L.); (S.S.); (S.R.); (Z.M.); (J.A.-W.); (Q.J.)
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- The National Medical Research Center for Endocrinology, 115478 Moscow, Russia
- Correspondence:
| |
Collapse
|
15
|
Hu ZW, Cruceta L, Zhang S, Sun Y, Qiang W. Cross-Seeded Fibrillation Induced by Pyroglutamate-3 and Truncated Aβ 40 Variants Leads to Aβ 40 Structural Polymorphism Modulation and Elevated Toxicity. ACS Chem Neurosci 2021; 12:3625-3637. [PMID: 34524791 DOI: 10.1021/acschemneuro.1c00341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The pathological amyloid plaques in Alzheimer's disease (AD) patients contain not only the wild-type β-amyloid (wt-Aβ) peptide sequences but also a variety of post-translationally modified variants. The pyroglutamate-3 Aβ (pyroE3-Aβ), which is generated from its truncated precursors ΔE3-Aβ, shows the highest abundance among all modified Aβ variants. Previous works have shown that pyroE3-Aβ and/or ΔE3-Aβ, compared with the wild-type sequences, led to a more rapid fibrillation process and final fibrils with higher neuronal cytotoxicity levels. However, much less is known about how the formation of pyroE3/ΔE3-Aβ fibrils would affect the amyloid deposition of wt-Aβ peptides, which are the main pathological events in AD. We show in the present work that the pyroE3/ΔE3-Aβ40 fibrils differ significantly from the wt-Aβ40 fibrils in terms of their molecular structures. When added into monomeric wt-Aβ40 peptides, these variant fibrils can cross-seed the formation of wt-Aβ40 fibrils with fibrillation kinetics that are greater than the self-seeded fibrillation of wt-Aβ40. Furthermore, the cross-seeding process modulates the molecular structures of the yielded wt-Aβ40 fibrils, which show similar features as their variant seeds. The cross-seeded fibrillation process also induces higher cytotoxicity levels compared with the self-seeded fibrillation of wt-Aβ40. Overall, our results support the hypothesis that pyroE3 and ΔE3-Aβ40 variants may serve as triggering factors of the pathological amyloid aggregation of wt-Aβ40 and may underlie the pathological significance of pyroE3/ΔE3-Aβ40 variants on the structural polymorphism of Aβ deposits.
Collapse
Affiliation(s)
- Zhi-Wen Hu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Letticia Cruceta
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Shiyue Zhang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Yan Sun
- Small Scale Systems Integration and Package (S3IP) Center, Binghamton University, Binghamton, New York 13902, United States
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| |
Collapse
|
16
|
Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity. Molecules 2020; 25:molecules25235698. [PMID: 33287192 PMCID: PMC7730986 DOI: 10.3390/molecules25235698] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 02/08/2023] Open
Abstract
One of the molecular hallmarks of amyloidoses is ordered protein aggregation involving the initial formation of soluble protein oligomers that eventually grow into insoluble fibrils. The identification and characterization of molecular species critical for amyloid fibril formation and disease development have been the focus of intense analysis in the literature. Here, using photo-induced cross-linking of unmodified proteins (PICUP), we studied the early stages of oligomerization of human transthyretin (TTR), a plasma protein involved in amyloid diseases (ATTR amyloidosis) with multiple clinical manifestations. Upon comparison, the oligomerization processes of wild-type TTR (TTRwt) and several TTR variants (TTRV30M, TTRL55P, and TTRT119M) clearly show distinct oligomerization kinetics for the amyloidogenic variants but a similar oligomerization mechanism. The oligomerization kinetics of the TTR amyloidogenic variants under analysis showed a good correlation with their amyloidogenic potential, with the most amyloidogenic variants aggregating faster (TTRL55P > TTRV30M > TTRwt). Moreover, the early stage oligomerization mechanism for these variants involves stepwise addition of monomeric units to the growing oligomer. A completely different behavior was observed for the nonamyloidogenic TTRT119M variant, which does not form oligomers in the same acidic conditions and even for longer incubation times. Thorough characterization of the initial steps of TTR oligomerization is critical for better understanding the origin of ATTR cytotoxicity and developing novel therapeutic strategies for the treatment of ATTR amyloidosis.
Collapse
|
17
|
Gnoth K, Piechotta A, Kleinschmidt M, Konrath S, Schenk M, Taudte N, Ramsbeck D, Rieckmann V, Geissler S, Eichentopf R, Barendrecht S, Hartlage-Rübsamen M, Demuth HU, Roßner S, Cynis H, Rahfeld JU, Schilling S. Targeting isoaspartate-modified Aβ rescues behavioral deficits in transgenic mice with Alzheimer's disease-like pathology. ALZHEIMERS RESEARCH & THERAPY 2020; 12:149. [PMID: 33189132 PMCID: PMC7666770 DOI: 10.1186/s13195-020-00719-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/29/2020] [Indexed: 11/12/2022]
Abstract
Background Amyloid β (Aβ)-directed immunotherapy has shown promising results in preclinical and early clinical Alzheimer’s disease (AD) trials, but successful translation to late clinics has failed so far. Compelling evidence suggests that post-translationally modified Aβ peptides might play a decisive role in onset and progression of AD and first clinical trials targeting such Aβ variants have been initiated. Modified Aβ represents a small fraction of deposited material in plaques compared to pan-Aβ epitopes, opening up pathways for tailored approaches of immunotherapy. Here, we generated the first monoclonal antibodies that recognize l-isoaspartate-modified Aβ (isoD7-Aβ) and tested a lead antibody molecule in 5xFAD mice. Methods This work comprises a combination of chemical and biochemical techniques as well as behavioral analyses. Aβ peptides, containing l-isoaspartate at position 7, were chemically synthesized and used for immunization of mice and antibody screening methods. Biochemical methods included anti-isoD7-Aβ monoclonal antibody characterization by surface plasmon resonance, immunohistochemical staining of human and transgenic mouse brain, and the development and application of isoD7-Aβ ELISA as well as different non-modified Aβ ELISA. For antibody treatment studies, 12 mg/kg anti-isoD7-Aβ antibody K11_IgG2a was applied intraperitoneally to 5xFAD mice for 38 weeks. Treatment controls implemented were IgG2a isotype as negative and 3D6_IgG2a, the parent molecule of bapineuzumab, as positive control antibodies. Behavioral studies included elevated plus maze, pole test, and Morris water maze. Results Our advanced antibody K11 showed a KD in the low nM range and > 400fold selectivity for isoD7-Aβ compared to other Aβ variants. By using this antibody, we demonstrated that formation of isoD7-Aβ may occur after formation of aggregates; hence, the presence of the isoD7-modification differentiates aged Aβ from newly formed peptides. Importantly, we also show that the Tottori mutation responsible for early-onset AD in a Japanese pedigree is characterized by massively accelerated formation of isoD7-Aβ in cell culture. The presence of isoD7-Aβ was verified by K11 in post mortem human cortex and 5xFAD mouse brain tissue. Passive immunization of 5xFAD mice resulted in a significant reduction of isoD7-Aβ and total Aβ in brain. Amelioration of cognitive impairment was demonstrated by Morris water maze, elevated plus maze, pole, and contextual fear conditioning tests. Interestingly, despite the lower abundance of the isoD7-Aβ epitope, the application of anti-isoD7-Aβ antibodies showed comparable treatment efficacy in terms of reduction of brain amyloid and spatial learning but did not result in an increase of plasma Aβ concentration as observed with 3D6 treatment. Conclusions The present study demonstrates, for the first time, that the antibody-mediated targeting of isoD7-modified Aβ peptides leads to attenuation of AD-like amyloid pathology. In conjunction with previously published data on antibodies directed against pGlu-modified Aβ, the results highlight the crucial role of modified Aβ peptides in AD pathophysiology. Hence, the results also underscore the therapeutic potential of targeting modified amyloid species for defining tailored approaches in AD therapy. Supplementary information The online version contains supplementary material available at 10.1186/s13195-020-00719-x.
Collapse
Affiliation(s)
- Kathrin Gnoth
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Anke Piechotta
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Martin Kleinschmidt
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Sandra Konrath
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.,Present address: Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mathias Schenk
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Nadine Taudte
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.,Present address: PerioTrap Pharmaceuticals GmbH, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Vera Rieckmann
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Stefanie Geissler
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Rico Eichentopf
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.,Present address: Fraunhofer Center for Chemical-Biotechnological Processes CBP, Leuna, Germany
| | - Susan Barendrecht
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | | | - Hans-Ulrich Demuth
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Steffen Roßner
- Paul Flechsig Institute of Brain Research, Leipzig University, Leipzig, Germany
| | - Holger Cynis
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| | - Jens-Ulrich Rahfeld
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany.
| | - Stephan Schilling
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Germany
| |
Collapse
|
18
|
Yan L, Ke Y, Kan Y, Lin D, Yang J, He Y, Wu L. New insight into enzymatic hydrolysis of peptides with site-specific amino acid d-isomerization. Bioorg Chem 2020; 105:104389. [PMID: 33120320 DOI: 10.1016/j.bioorg.2020.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 10/11/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
The isomerization of l-amino acids in peptides and proteins into d-configuration under physiological conditions would affect the physiological dysfunction and caused protein conformational diseases. The presence of d-amino acids might change the higher-order structure of proteins and triggered abnormal aggregation. In order to better understand this phenomenon and promote degradation, we systematically studied the enzymatic hydrolysis of a series of peptides obtained by replacing l-amino acids in different positions of template peptide KYNETWRSED with d-amino acids under the action of Protease K. The results showed that, compared with normal peptide, isomerization of different amino acids had different effects on the anti-enzymatic hydrolysis of the peptides, especially d-tryptophan at position 6, which significantly inhibited enzymatic hydrolysis. The analysis of the peptide cleavage site revealed that the efficiency of enzymatic hydrolysis mainly depended on the isomerization of the amino acids at a specific site of the peptide cleavage. Further studies showed that the enzymatic hydrolysis of substrates could be facilitated by optimized reaction conditions such as temperature, pH, addition of metal ions, and change of buffer. In this way the accumulation of disease-associated d-amino acid containing polypeptides/proteins could be prevented.
Collapse
Affiliation(s)
- Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dao Lin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingkui Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| |
Collapse
|
19
|
Wang X, Wang C, Chu H, Qin H, Wang D, Xu F, Ai X, Quan C, Li G, Qing G. Molecular chirality mediated amyloid formation on phospholipid surfaces. Chem Sci 2020; 11:7369-7378. [PMID: 34123018 PMCID: PMC8159450 DOI: 10.1039/d0sc02212h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
One of the neuropathological features of Alzheimer's disease (AD) is the misfolding of amyloid-β to form amyloid aggregates, a process highly associated with biological membranes. However, how molecular chirality affects the amyloid formation on phospholipid surfaces has seldom been reported. Here, l- and d-aspartic acid-modified 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (l-/d-Asp–DPPE) is synthesized to construct chiral phospholipid bilayers. We discover that the l-Asp–DPPE liposomes slightly inhibit the Aβ(1–40) nucleation process but cannot affect the oligomer elongation process. By contrast, the d-Asp–DPPE liposomes strongly inhibit both nucleation and elongation of the peptide. Notably, l- and d-Asp–DPPE liposomes not only have good biocompatibility but can also rescue Aβ(1–40)-aggregation induced cytotoxicity with significant chiral discrimination, in which the cell viability is higher in the presence of d-Asp–DPPE liposomes. Mechanism analysis and molecular dynamics simulation clearly demonstrate that differential electrostatic interactions of Lys16 in Aβ(1–40) with l- or d-Asp on the phospholipid contribute to the remarkable chiral discrimination. This study provides a deeper understanding of the crucial amyloidosis process from the perspective of the chiral interface and reveals that the convergence of d-amino acids with the liposomes might be a feasible route for AD prevention. A remarkable inhibition effect and chiral discrimination are observed when the amyloid peptide aggregates on chiral phospholipid surfaces.![]()
Collapse
Affiliation(s)
- Xue Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology 122 Luoshi Road Wuhan 430070 P. R. China.,Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Haijuan Qin
- Research Centre of Modern Analytical Technology, Tianjin University of Science and Technology Tianjin 300457 P. R. China
| | - Dongdong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Feifei Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Xuanjun Ai
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Chunshan Quan
- College of Life Science, Dalian Minzu University Dalian 116600 P. R. China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 P. R. China
| |
Collapse
|
20
|
Chatterjee T, Das G, Chatterjee BK, Dhar J, Ghosh S, Chakrabarti P. The role of isoaspartate in fibrillation and its prevention by Protein-L-isoaspartyl methyltransferase. Biochim Biophys Acta Gen Subj 2019; 1864:129500. [PMID: 31785325 DOI: 10.1016/j.bbagen.2019.129500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
BACKGROUND Isomerization of aspartate to isoaspartate (isoAsp) on aging causes protein damage and malfunction. Protein-L-isoaspartyl methyltransferase (PIMT) performs a neuroprotective role by repairing such residues. A hexapeptide, Val-Tyr-Pro-(isoAsp)-His-Ala (VA6), a substrate of PIMT, is shown to form fibrils, while the normal Asp-containing peptide does not. Considering the role of PIMT against epileptic seizure, the combined effect of PIMT and two antiepileptic drugs (AEDs) (valproic acid and stiripentol) was investigated for anti-fibrillation activity. METHODS Structural/functional modulations due to the binding of AEDs to PIMT were investigated using biophysical techniques. Thioflavin T (ThT) fluorescence assay and microscopic methods were employed to study fibril formation by VA6. In vitro experiments with PC12 cells were carried out with PIMT/AEDs. RESULTS ThT assay indicated reduction of fibrillation of VA6 by PIMT. AEDs stabilize PIMT, bind close to the cofactor binding site, possibly exerting allosteric effect, increase the enzymatic activity, and anti-fibrillation efficacy. Furthermore, Aβ42, implicated in Alzheimer's disease, undergoes β-sheet to α-helix transition in presence of PIMT. Studies with PC12 derived neurons showed that PIMT and PIMT/AEDs exerted neuroprotective effect against anti-NGF induced neurotoxicity. This was further validated against neurotoxicity induced by Aβ42 in primary rat cortical neurons. CONCLUSIONS The study provides a new perspective to the role isoAsp in protein fibrillation, PIMT in its prevention and AEDs in enhancing the activity of the enzyme. GENERAL SIGNIFICANCE IsoAsp, with an additional C atom in the main-chain of polypeptide chain, may make it more susceptible to fibrillation. PIMT alone, or in association with AEDs prevents this.
Collapse
Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
| | - Gaurav Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Barun K Chatterjee
- Department of Physics, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Jesmita Dhar
- Bioinformatics Center, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India; Bioinformatics Center, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
| |
Collapse
|
21
|
Molecular basis for chirality-regulated Aβ self-assembly and receptor recognition revealed by ion mobility-mass spectrometry. Nat Commun 2019; 10:5038. [PMID: 31695027 PMCID: PMC6834639 DOI: 10.1038/s41467-019-12346-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 09/02/2019] [Indexed: 12/22/2022] Open
Abstract
Despite extensive efforts on probing the mechanism of Alzheimer’s disease (AD) and enormous investments into AD drug development, the lack of effective disease-modifying therapeutics and the complexity of the AD pathogenesis process suggest a great need for further insights into alternative AD drug targets. Herein, we focus on the chiral effects of truncated amyloid beta (Aβ) and offer further structural and molecular evidence for epitope region-specific, chirality-regulated Aβ fragment self-assembly and its potential impact on receptor-recognition. A multidimensional ion mobility-mass spectrometry (IM-MS) analytical platform and in-solution kinetics analysis reveal the comprehensive structural and molecular basis for differential Aβ fragment chiral chemistry, including the differential and cooperative roles of chiral Aβ N-terminal and C-terminal fragments in receptor recognition. Our method is applicable to many other systems and the results may shed light on the potential development of novel AD therapeutic strategies based on targeting the D-isomerized Aβ, rather than natural L-Aβ. Chiral inversion of amino acids is thought to modulate the structure and function of amyloid beta (Aβ) but these processes are poorly understood. Here, the authors develop an ion mobility-mass spectrometry based approach to study chirality-regulated structural features of Aβ fragments and their influence on receptor recognition.
Collapse
|
22
|
Cline EN, Bicca MA, Viola KL, Klein WL. The Amyloid-β Oligomer Hypothesis: Beginning of the Third Decade. J Alzheimers Dis 2019; 64:S567-S610. [PMID: 29843241 PMCID: PMC6004937 DOI: 10.3233/jad-179941] [Citation(s) in RCA: 535] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The amyloid-β oligomer (AβO) hypothesis was introduced in 1998. It proposed that the brain damage leading to Alzheimer’s disease (AD) was instigated by soluble, ligand-like AβOs. This hypothesis was based on the discovery that fibril-free synthetic preparations of AβOs were potent CNS neurotoxins that rapidly inhibited long-term potentiation and, with time, caused selective nerve cell death (Lambert et al., 1998). The mechanism was attributed to disrupted signaling involving the tyrosine-protein kinase Fyn, mediated by an unknown toxin receptor. Over 4,000 articles concerning AβOs have been published since then, including more than 400 reviews. AβOs have been shown to accumulate in an AD-dependent manner in human and animal model brain tissue and, experimentally, to impair learning and memory and instigate major facets of AD neuropathology, including tau pathology, synapse deterioration and loss, inflammation, and oxidative damage. As reviewed by Hayden and Teplow in 2013, the AβO hypothesis “has all but supplanted the amyloid cascade.” Despite the emerging understanding of the role played by AβOs in AD pathogenesis, AβOs have not yet received the clinical attention given to amyloid plaques, which have been at the core of major attempts at therapeutics and diagnostics but are no longer regarded as the most pathogenic form of Aβ. However, if the momentum of AβO research continues, particularly efforts to elucidate key aspects of structure, a clear path to a successful disease modifying therapy can be envisioned. Ensuring that lessons learned from recent, late-stage clinical failures are applied appropriately throughout therapeutic development will further enable the likelihood of a successful therapy in the near-term.
Collapse
Affiliation(s)
- Erika N Cline
- Department of Neurobiology, Cognitive Neurology and Alzheimer's Disease Center, International Institute for Nanotechnology, and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Maíra Assunção Bicca
- Department of Neurobiology, Cognitive Neurology and Alzheimer's Disease Center, International Institute for Nanotechnology, and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Kirsten L Viola
- Department of Neurobiology, Cognitive Neurology and Alzheimer's Disease Center, International Institute for Nanotechnology, and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - William L Klein
- Department of Neurobiology, Cognitive Neurology and Alzheimer's Disease Center, International Institute for Nanotechnology, and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| |
Collapse
|
23
|
Effect of site-specific amino acid D-isomerization on β-sheet transition and fibril formation profiles of Tau microtubule-binding repeat peptides. Biochem Biophys Res Commun 2019; 508:184-190. [PMID: 30471859 DOI: 10.1016/j.bbrc.2018.11.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 11/23/2022]
Abstract
d-amino acid-containing proteins have been found in several human tissues, and the spontaneous accumulation of d-amino acids in proteins is thought to be involved in age-dependent diseases including dementia. Tau, a microtubule-associated protein, is a major component of neurofibrillary tangles in Alzheimer's disease. Site-specific amino acid D-isomerization in Tau has been observed in the brains of patients with Alzheimer's disease. Here, we conducted amino acid D-isomerization at specific sites in microtubule-binding repeat peptides of Tau (Tau R2 and R3) and examined the effects on Tau structure and fibril formation. Our results demonstrate that amino acid D-isomerization in Tau R2 peptides decreased the rates of β-sheet transition and fibril formation compared with those of the wild-type peptide composed of all l-amino acids. In contrast, Tau R3 peptides that had undergone amino acid D-isomerization at either Asp314, Ser316, or Ser324 showed increased rates of β-sheet transition and fibril formation compared with those of the wild-type Tau R3 peptide.
Collapse
|
24
|
Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins. Sci Rep 2017; 7:12433. [PMID: 28970487 PMCID: PMC5624888 DOI: 10.1038/s41598-017-10525-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered protein (IDP) conformers occupy large regions of conformational space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively folded proteins, have folding trajectories that frequently involve movements up shallow energy gradients prior to the “downhill” folding leading to fibril formation. We suggest that structural perturbations caused by chiral inversions of amino acid side-chains may be especially valuable in elucidating these pathways of IDP folding. Chiral inversions are subtle in that they do not change side-chain size, flexibility, hydropathy, charge, or polarizability. They allow focus to be placed solely on the question of how changes in amino acid side-chain orientation, and the resultant alterations in peptide backbone structure, affect a peptide’s conformational landscape (Ramachandran space). If specific inversions affect folding and assembly, then the sites involved likely are important in mediating these processes. We suggest here a “focused chiral mutant library” approach for the unbiased study of amyloid-forming IDPs.
Collapse
|
25
|
Zheng X, Deng L, Baker ES, Ibrahim YM, Petyuk VA, Smith RD. Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry. Chem Commun (Camb) 2017; 53:7913-7916. [PMID: 28654112 PMCID: PMC5555368 DOI: 10.1039/c7cc03321d] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While α-linked amino acids in the l-form are exclusively utilized in mammalian protein building, β-linked and d-form amino acids also have important biological roles. Unfortunately, the structural elucidation and separation of these different amino acid types in peptides has been analytically challenging to date due to the numerous isomers present, limiting our knowledge about their existence and biological roles. Here, we utilized an ultrahigh resolution ion mobility spectrometry platform coupled with mass spectrometry (IMS-MS) to separate amyloid β (Aβ) peptides containing l-aspartic acid, d-aspartic acid, l-isoaspartic acid, and d-isoaspartic acid residues which span α- and β-linked amino acids in both d- and l-forms. The results illustrate how IMS-MS could be used to better understand age-related diseases or protein folding disorders resulting from amino acid modifications.
Collapse
Affiliation(s)
- Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Liulin Deng
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| |
Collapse
|
26
|
Sakaue H, Kinouchi T, Fujii N, Takata T, Fujii N. Isomeric Replacement of a Single Aspartic Acid Induces a Marked Change in Protein Function: The Example of Ribonuclease A. ACS OMEGA 2017; 2:260-267. [PMID: 31457226 PMCID: PMC6641078 DOI: 10.1021/acsomega.6b00346] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/16/2017] [Indexed: 05/11/2023]
Abstract
lα-Aspartic acid (Asp) residues in proteins are nonenzymatically isomerized to abnormal lβ-, dα-, and dβ-Asp isomers under physiological conditions. Such an isomerization of Asp residues is considered to be a trigger of protein denaturation because it either elongates the main chain or induces a different orientation of the side chain within the protein structure or both. However, previous studies have found no direct evidence of the effects of Asp isomers on protein function. Therefore, the production of Asp-isomer-containing proteins is required to verify the effects of Asp isomerization. Here, we describe the production of an Asp-isomer-containing protein using the expressed protein ligation. As a model protein, bovine pancreatic ribonuclease A (RNase A, EC 3.1.27.5), which catalyzes the cleavage of phosphodiester bonds in RNA, was used. In this study, lα-Asp at position 121 in RNase A was replaced by lβ-, dα-, and dβ-Asp. The objective aspartic acid at position 121 is located near the active site and related to RNA cleavage. The RNase A with lα-Asp at position 121 showed a normal activity. By contrast, the catalytic activity of lβ-, dα-, and dβ-Asp-containing RNase A was markedly decreased. This study represents the first synthesis and analysis of a protein containing four different Asp isomers.
Collapse
Affiliation(s)
- Hiroaki Sakaue
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tadatoshi Kinouchi
- Research
Reactor Institute, Kyoto University, Sennan-gun, Kumatori-cho, Osaka 590-0494, Japan
| | - Norihiko Fujii
- Radioisotope
Research Center, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Takumi Takata
- Research
Reactor Institute, Kyoto University, Sennan-gun, Kumatori-cho, Osaka 590-0494, Japan
| | - Noriko Fujii
- Research
Reactor Institute, Kyoto University, Sennan-gun, Kumatori-cho, Osaka 590-0494, Japan
- E-mail:
| |
Collapse
|
27
|
Suprun EV, Khmeleva SA, Radko SP, Archakov AI, Shumyantseva VV. Electrochemical Analysis of Amyloid-β Domain 1-16 Isoforms and Their Complexes with Zn(II) Ions. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2015.11.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
28
|
Radko SP, Khmeleva SA, Suprun EV, Kozin SA, Bodoev NV, Makarov AA, Archakov AI, Shumyantseva VV. [Physico-chemical methods for studing β-amyloid aggregation]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:203-18. [PMID: 25978387 DOI: 10.18097/pbmc20156102203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Alzheimer's disease is the most prevalent neurodegenerative pathology. According to the amyloid cascade hypothesis, a key event of the Alzheimer's disease pathogenesis is a transition of the β-amyloid peptide (Аβ) from the monomeric form to the aggregated state. The mechanism of Аβ aggregation is intensively studied in vitro, by means of synthetic peptides and various physico-chemical methods allowing evaluation of size, molecular structure, and morphology of the formed aggregates. The paper reviews both the well-known and recently introduced physico-chemical methods for analysis of Аβ aggregation, including microscopу, optical and fluorescent methods, method of electron paramagnetic resonance, electrochemical and electrophoretic methods, gel-filtration, and mass spectrometric methods. Merits and drawbacks of the methods are discussed. The unique possibility to simultaneously observe Аβ monomers as well oligomers and large aggregates by means of atomic force microscopy or fluorescence correlation spectroscopy is emphasized. The high detection sensitivity of the latter method, monitoring the aggregation process in Аβ solutions at low peptide concentrations is underlined. Among mass spectrometric methods, the ion mobility mass spectrometry is marked out as a method enabling to obtain information about both the spectrum of Аβ oligomers and their structure. It is pointed out that the use of several methods giving the complementary data about Аβ aggregates is the best experimental approach to studying the process of b-amyloid peptide aggregation in vitro.
Collapse
Affiliation(s)
- S P Radko
- Institute of Biomedical Chemistry, Moscow, Russia; Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - S A Khmeleva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E V Suprun
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S A Kozin
- Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - N V Bodoev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Makarov
- Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | |
Collapse
|
29
|
Radko SP, Khmeleva SA, Suprun EV, Kozin SA, Bodoev NV, Makarov AA, Archakov AI, Shumyantseva VV. Physico-chemical methods for studying amyloid-β aggregation. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s1990750815030075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
30
|
Yamin G, Huynh TPV, Teplow DB. Design and Characterization of Chemically Stabilized Aβ42 Oligomers. Biochemistry 2015; 54:5315-21. [PMID: 26241378 DOI: 10.1021/acs.biochem.5b00318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A popular working hypothesis of Alzheimer's disease causation is amyloid β-protein oligomers are the key neuropathogenetic agents. Rigorously elucidating the role of oligomers requires the production of stable oligomers of each size. We previously used zero-length photochemical cross-linking to allow stabilization, isolation, and determination of structure-activity relationships of pure populations of Aβ40 dimers, trimers, and tetramers. We also attempted to study Aβ42 but found that Aβ42 oligomers subjected to the same procedures were not completely stable. On the basis of the fact that Tyr is a critical residue in cross-linking chemistry, we reasoned that the chemical accessibility of Tyr10 in Aβ42 must differ from that in Aβ40. We thus chemically synthesized four singly substituted Tyr variants that placed the Tyr in different positions across the Aβ42 sequence. We then studied the stability of the resulting cross-linked oligomers as well as procedures for fractionating the oligomers to obtain pure populations of different sizes. We found that [Phe(10),Tyr(42)]Aβ42 produced stable oligomers yielding highly pure populations of dimers through heptamers. This provides the means to establish formal structure-activity relationships of these important Aβ42 assemblies. In addition, we were able to analyze the dissociation patterns of non-cross-linked oligomers to produce a model for oligomer formation. This work is relevant to the determination of structure-activity relationships that have the potential to provide mechanistic insights into disease pathogenesis.
Collapse
Affiliation(s)
- Ghiam Yamin
- Department of Radiology, School of Medicine, University of California , San Diego, California 92093, United States.,Department of Neurology, David Geffen School of Medicine at UCLA , Los Angeles, California 90095, United States
| | - Tien-Phat Vuong Huynh
- Department of Neurology, School of Medicine, Washington University at St. Louis , St. Louis, Missouri 63110, United States
| | - David B Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA , Los Angeles, California 90095, United States
| |
Collapse
|