1
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Lewkowicz E, Nakamura MN, Rynkiewicz MJ, Gursky O. Molecular modeling of apoE in complexes with Alzheimer's amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids. Cell Mol Life Sci 2023; 80:376. [PMID: 38010414 PMCID: PMC11061799 DOI: 10.1007/s00018-023-05026-w] [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: 08/04/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-β (Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40 and Aβ1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aβ aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβ aggregation.
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Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA
| | - Mari N Nakamura
- Undergraduate program, Department of Chemistry and Biochemistry, Middlebury College, 14 Old Chapel Rd, Middlebury, VT, 05753, USA
| | - Michael J Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA.
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2
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Tiwari D, Srivastava G, Indari O, Tripathi V, Siddiqi MI, Jha HC. An in-silico insight into the predictive interaction of Apolipoprotein-E with Epstein-Barr virus proteins and their probable role in mediating Alzheimer's disease. J Biomol Struct Dyn 2023; 41:8918-8926. [PMID: 36307908 DOI: 10.1080/07391102.2022.2138978] [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: 08/03/2022] [Accepted: 10/16/2022] [Indexed: 10/31/2022]
Abstract
Recent reports suggest that persistent Epstein-Barr virus (EBV) infection and its recurrent reactivation could instigate the formation of proteinaceous plaques in the brain: a hallmark of Alzheimer's disease (AD). Interestingly, a major genetic risk factor of AD, the apolipoprotein E (ApoE), could also influence the outcome of EBV infection in an individual. The ApoE is believed to influence the proteinaceous plaque clearance from the brain, and its defective functioning could result in the aggregate deposition. The persistent presence of EBV infection in a genetically predisposed individual could create a perfect recipe for severe neurodegenerative consequences. Therefore, in the present study, we investigated the possible interactions between ApoE and various EBV proteins using computational tools. Our results showed possibly stable de-novo interactions between the C-terminal domain of ApoE3 and EBV proteins: EBV nuclear antigen-1 (EBNA1) and BamHI Z fragment leftward open reading frame-1 (BZLF1). The EBNA1 protein of EBV plays a crucial role in establishing latency and replication of the virus. Whereas BZLF1 is involved in the lytic replication cycle. The proposed interaction of EBV proteins at the ligand-binding site of ApoE3 on CTD could interfere with- its capability to sequester amyloid fragments and, hence their clearance from the brain giving rise to AD pathology. This study provides a new outlook on EBV's underexplored role in AD development and paves the way for novel avenues of investigation which could further our understanding of AD pathogenesis.Communicated by Ramaswamy H. Sarma[Figure: see text].
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Affiliation(s)
- Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Gaurava Srivastava
- Division of Biochemistry and Structural Biology, CSIR-CDRI, Lucknow, India
| | - Omkar Indari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | | | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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3
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Lewkowicz E, Nakamura MN, Rynkiewicz MJ, Gursky O. Molecular modeling of apoE in complexes with Alzheimer's amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.551703. [PMID: 37577501 PMCID: PMC10418262 DOI: 10.1101/2023.08.04.551703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-β (Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40 and Aβ1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aβ aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβ aggregation.
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Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Mari N. Nakamura
- Undergraduate program, Department of Chemistry, Middlebury College, 14 Old Chapel Rd, Middlebury, VT 05753VT United States
| | - Michael J. Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
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4
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Zhang L, Xia Y, Gui Y. Neuronal ApoE4 in Alzheimer's disease and potential therapeutic targets. Front Aging Neurosci 2023; 15:1199434. [PMID: 37333457 PMCID: PMC10272394 DOI: 10.3389/fnagi.2023.1199434] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
The most prevalent genetic risk factor for Alzheimer's disease (AD) is Apolipoprotein E (ApoE), a gene located on chromosome 19 that encodes three alleles (e2, e3, and e4) that give rise to the ApoE subtypes E2, E3, and E4, respectively. E2 and E4 have been linked to increased plasma triglyceride concentrations and are known to play a critical role in lipoprotein metabolism. The prominent pathological features of AD mainly include senile plaques formed by amyloid β (Aβ42) aggregation and neuronal fibrous tangles (NFTs), and the deposited plaques are mainly composed of Aβ hyperphosphorylation and truncated head. In the central nervous system, the ApoE protein is primarily derived from astrocytes, but ApoE is also produced when neurons are stressed or affected by certain stress, injury, and aging conditions. ApoE4 in neurons induces Aβ and tau protein pathologies, leading to neuroinflammation and neuronal damage, impairing learning and memory functions. However, how neuronal ApoE4 mediates AD pathology remains unclear. Recent studies have shown that neuronal ApoE4 may lead to greater neurotoxicity, which increases the risk of AD development. This review focuses on the pathophysiology of neuronal ApoE4 and explains how neuronal ApoE4 mediates Aβ deposition, pathological mechanisms of tau protein hyperphosphorylation, and potential therapeutic targets.
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Lennol MP, Sánchez-Domínguez I, Cuchillo-Ibañez I, Camporesi E, Brinkmalm G, Alcolea D, Fortea J, Lleó A, Soria G, Aguado F, Zetterberg H, Blennow K, Sáez-Valero J. Apolipoprotein E imbalance in the cerebrospinal fluid of Alzheimer's disease patients. Alzheimers Res Ther 2022; 14:161. [PMID: 36324176 PMCID: PMC9628034 DOI: 10.1186/s13195-022-01108-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The purpose of this study was to examine the levels of cerebrospinal fluid (CSF) apolipoprotein E (apoE) species in Alzheimer's disease (AD) patients. METHODS We analyzed two CSF cohorts of AD and control individuals expressing different APOE genotypes. Moreover, CSF samples from the TgF344-AD rat model were included. Samples were run in native- and SDS-PAGE under reducing or non-reducing conditions (with or without β-mercaptoethanol). Immunoprecipitation combined with mass spectrometry or western blotting analyses served to assess the identity of apoE complexes. RESULTS In TgF344-AD rats expressing a unique apoE variant resembling human apoE4, a ~35-kDa apoE monomer was identified, increasing at 16.5 months compared with wild-types. In humans, apoE isoforms form disulfide-linked dimers in CSF, except apoE4, which lacks a cysteine residue. Thus, controls showed a decrease in the apoE dimer/monomer quotient in the APOE ε3/ε4 group compared with ε3/ε3 by native electrophoresis. A major contribution of dimers was found in APOE ε3/ε4 AD cases, and, unexpectedly, dimers were also found in ε4/ε4 AD cases. Under reducing conditions, two apoE monomeric glycoforms at 36 kDa and at 34 kDa were found in all human samples. In AD patients, the amount of the 34-kDa species increased, while the 36-kDa/34-kDa quotient was lower compared with controls. Interestingly, under reducing conditions, a ~100-kDa apoE complex, the identity of which was confirmed by mass spectrometry, also appeared in human AD individuals across all APOE genotypes, suggesting the occurrence of aberrantly resistant apoE aggregates. A second independent cohort of CSF samples validated these results. CONCLUSION These results indicate that despite the increase in total apoE content the apoE protein is altered in AD CSF, suggesting that function may be compromised.
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Affiliation(s)
- Matthew Paul Lennol
- grid.466805.90000 0004 1759 6875Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, Av. Ramón y Cajal s/n, E-03550 Sant Joan d’Alacant, Spain ,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d’Alacant, Spain
| | - Irene Sánchez-Domínguez
- grid.5841.80000 0004 1937 0247Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Institute of Neurosciences, University of Barcelona, Barcelona, Spain
| | - Inmaculada Cuchillo-Ibañez
- grid.466805.90000 0004 1759 6875Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, Av. Ramón y Cajal s/n, E-03550 Sant Joan d’Alacant, Spain ,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d’Alacant, Spain ,grid.513062.30000 0004 8516 8274Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Elena Camporesi
- grid.8761.80000 0000 9919 9582Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Gunnar Brinkmalm
- grid.8761.80000 0000 9919 9582Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Daniel Alcolea
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d’Alacant, Spain ,grid.7080.f0000 0001 2296 0625Sant Pau Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Fortea
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d’Alacant, Spain ,grid.7080.f0000 0001 2296 0625Sant Pau Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain ,Barcelona Down Medical Center, Fundació Catalana Síndrome de Down, Barcelona, Spain
| | - Alberto Lleó
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d’Alacant, Spain ,grid.7080.f0000 0001 2296 0625Sant Pau Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Guadalupe Soria
- grid.5841.80000 0004 1937 0247Institute of Neurosciences, University of Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Laboratory of Surgical Neuroanatomy, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Fernando Aguado
- grid.5841.80000 0004 1937 0247Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Institute of Neurosciences, University of Barcelona, Barcelona, Spain
| | - Henrik Zetterberg
- grid.8761.80000 0000 9919 9582Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden ,grid.1649.a000000009445082XClinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden ,grid.83440.3b0000000121901201Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, UK ,grid.83440.3b0000000121901201UK Dementia Research Institute at UCL, London, UK ,grid.24515.370000 0004 1937 1450Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Kaj Blennow
- grid.8761.80000 0000 9919 9582Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden ,grid.1649.a000000009445082XClinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Javier Sáez-Valero
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, Av. Ramón y Cajal s/n, E-03550, Sant Joan d'Alacant, Spain. .,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d'Alacant, Spain. .,Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.
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6
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Zhang W, Gong P, Shan Y, Zhao L, Hu H, Wei Q, Liang Z, Liu C, Zhang L, Zhang Y. SpotLink enables sensitive and precise identification of site nonspecific cross-links at the proteome scale. Brief Bioinform 2022; 23:6652569. [PMID: 36093786 DOI: 10.1093/bib/bbac316] [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: 04/22/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
Nonspecific cross-linker can provide distance restraints between surface residues of any type, which could be used to investigate protein structure construction and protein-protein interaction (PPI). However, the vast number of potential combinations of cross-linked residues or sites obtained with such a cross-linker makes the data challenging to analyze, especially for the proteome-wide applications. Here, we developed SpotLink software for identifying site nonspecific cross-links at the proteome scale. Contributed by the dual pointer dynamic pruning algorithm and the quality control of cross-linking sites, SpotLink identified > 3000 cross-links from human cell samples within a short period of days. We demonstrated that SpotLink outperformed other approaches in terms of sensitivity and precision on the datasets of the simulated succinimidyl 4,4'-azipentanoate dataset and the condensin complexes with known structures. In addition, some valuable PPI were discovered in the datasets of the condensin complexes and the HeLa dataset, indicating the unique identification advantages of site nonspecific cross-linking. These findings reinforce the importance of SpotLink as a fundamental characteristic of site nonspecific cross-linking technologies.
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Affiliation(s)
- Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Pengyun Gong
- School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hongke Hu
- School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Qiushi Wei
- School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Chao Liu
- School of Engineering Medicine & School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
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7
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Chai AB, Lam HHJ, Kockx M, Gelissen IC. Apolipoprotein E isoform-dependent effects on the processing of Alzheimer's amyloid-β. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158980. [PMID: 34044125 DOI: 10.1016/j.bbalip.2021.158980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 12/28/2022]
Abstract
Since the identification of the apolipoprotein E (apoE) *ε4 allele as a major genetic risk factor for late-onset Alzheimer's disease, significant efforts have been aimed at elucidating how apoE4 expression confers greater brain amyloid-β (Aβ) burden, earlier disease onset and worse clinical outcomes compared to apoE2 and apoE3. ApoE primarily functions as a lipid carrier to regulate cholesterol metabolism in circulation as well as in the brain. However, it has also been suggested to interact with hydrophobic Aβ peptides to influence their processing in an isoform-dependent manner. Here, we review evidence from in vitro and in vivo studies extricating the effects of the three apoE isoforms, on different stages of the Aβ processing pathway including synthesis, aggregation, deposition, clearance and degradation. ApoE4 consistently correlates with impaired Aβ clearance, however data regarding Aβ synthesis and aggregation are conflicting and likely reflect inconsistencies in experimental approaches across studies. We further discuss the physical and chemical properties of apoE that may explain the inherent differences in activity between the isoforms. The lipidation status and lipid transport function of apoE are intrinsically linked with its ability to interact with Aβ. Traditionally, apoE-oriented therapeutic strategies for Alzheimer's disease have been proposed to non-specifically enhance or inhibit apoE activity. However, given the wide-ranging physiological functions of apoE in the brain and periphery, a more viable approach may be to specifically target and neutralise the pathological apoE4 isoform.
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Affiliation(s)
- Amanda B Chai
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Hin Hei Julian Lam
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Maaike Kockx
- ANZAC Research Institute, Concord Repatriation General Hospital, University of Sydney, Concord, NSW 2139, Australia
| | - Ingrid C Gelissen
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
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8
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Dashnaw CM, Koone JC, Abdolvahabi A, Shaw BF. Measuring how two proteins affect each other's net charge in a crowded environment. Protein Sci 2021; 30:1594-1605. [PMID: 33928693 DOI: 10.1002/pro.4092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester-Staudinger pairs) can be used to mimic crowding by linking two non-interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine-acyl "protein charge ladders" and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Zmonomer = -0.43 ± 0.01) and α-lactalbumin (Zmonomer = -4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = -0.04 ± 0.09 upon crowding by this pair (Zdimer = -5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.
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Affiliation(s)
- Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Alireza Abdolvahabi
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
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9
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Wang Y, Xue Y, Wang S, Huang J, Yang X. Real-Time Analysis of Specific Binding between Apolipoprotein E Isoforms and Amyloid β-Peptide by Dual Polarization Interferometry. Anal Chem 2021; 93:1472-1479. [PMID: 33342209 DOI: 10.1021/acs.analchem.0c03542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
One of the pathogenesis hypotheses of Alzheimer's disease (AD) is amyloid depositions and neurofibrillary tangles. Apolipoprotein E (Apo E) acts a vital part in the development of AD by affecting the aggregation and clearance of amyloid-β (Aβ). In this paper, a dual polarization interferometry (DPI) technique was employed for a real-time investigation toward the binding events of Apo E isoforms, for instance, Apo E2, Apo E3, and Apo E4, with Aβ1-40. By evaluation of detailed binding information provided by DPI, the affinities between Apo E isoforms and Aβ1-40 follow the order of E4 > E3 > E2, and the dissociation constants (KD) of Aβ1-40 with Apo E2, Apo E3, and Apo E4 were determined to be 251 ± 37, 40 ± 0.65, and 24.6 ± 2.42 nM, respectively. Our findings reveal the isoform-specific binding behaviors from a kinetics perspective, which can help us understand that Apo E4 has a higher risk of causing AD because of its promoting effect on Aβ aggregation and fibrillation and inefficient clearance of Aβ. Remarkably, this work provides a promising method for exploring the dynamics of interactions between biomolecules and expectantly contributes to the development of AD drugs and therapies targeting Apo E and Aβ.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yu Xue
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
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10
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Bruni AC, Bernardi L, Gabelli C. From beta amyloid to altered proteostasis in Alzheimer's disease. Ageing Res Rev 2020; 64:101126. [PMID: 32683041 DOI: 10.1016/j.arr.2020.101126] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is an age related neurodegenerative disorder causing severe disability and important socio-economic burden, but with no cure available to date. To disentangle this puzzling disease genetic studies represented an important way for the comprehension of pathogenic mechanisms. Abnormal processing and accumulation of amyloid-β peptide (Aβ) has been considered the main cause and trigger factor of the disease. The amyloid cascade theory has fallen into crisis because the failure of several anti-amyloid drugs trials and because of the simple equation AD = abnormal Aβ deposition is not always the case. We now know that multiple neurodegenerative diseases share common pathogenic mechanisms leading to accumulation of misfolded protein species. Genome Wide Association studies (GWAS) led to the identification of large numbers of DNA common variants (SNPs) distributed on different chromosomes and modulating the Alzheimer's risk. GWAS genes fall into several common pathways such as immune system and neuroinflammation, lipid metabolism, synaptic dysfunction and endocytosis, all of them addressing to novel routes for different pathogenic mechanisms. Other hints could be derived from epidemiological and experimental studies showing some lifestyles may have a major role in the pathogenesis of many age-associated diseases by modifying cell metabolism, proteostasis and microglia mediated neuroinflammation.
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Affiliation(s)
- Amalia C Bruni
- Regional Neurogenetic Centre, ASP Catanzaro, Lamezia Terme (CZ), Italy.
| | - Livia Bernardi
- Regional Neurogenetic Centre, ASP Catanzaro, Lamezia Terme (CZ), Italy
| | - Carlo Gabelli
- Regional Brain Aging Centre, Azienda Ospedale Università Di Padova, Padova Italy
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11
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Inexpensive, non-invasive biomarkers predict Alzheimer transition using machine learning analysis of the Alzheimer's Disease Neuroimaging (ADNI) database. PLoS One 2020; 15:e0235663. [PMID: 32716914 PMCID: PMC7384664 DOI: 10.1371/journal.pone.0235663] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 06/21/2020] [Indexed: 11/22/2022] Open
Abstract
The Alzheimer’s Disease Neuroimaging (ADNI) database is an expansive undertaking by government, academia, and industry to pool resources and data on subjects at various stage of symptomatic severity due to Alzheimer’s disease. As expected, magnetic resonance imaging is a major component of the project. Full brain images are obtained at every 6-month visit. A range of cognitive tests studying executive function and memory are employed less frequently. Two blood draws (baseline, 6 months) provide samples to measure concentrations of approximately 145 plasma biomarkers. In addition, other diagnostic measurements are performed including PET imaging, cerebral spinal fluid measurements of amyloid-beta and tau peptides, as well as genetic tests, demographics, and vital signs. ADNI data is available upon review of an application. There have been numerous reports of how various processes evolve during AD progression, including alterations in metabolic and neuroendocrine activity, cell survival, and cognitive behavior. Lacking an analytic model at the onset, we leveraged recent advances in machine learning, which allow us to deal with large, non-linear systems with many variables. Of particular note was examining how well binary predictions of future disease states could be learned from simple, non-invasive measurements like those dependent on blood samples. Such measurements make relatively little demands on the time and effort of medical staff or patient. We report findings with recall/precision/area under the receiver operator curve after application of CART, Random Forest, Gradient Boosting, and Support Vector Machines, Our results show (i) Random Forests and Gradient Boosting work very well with such data, (ii) Prediction quality when applied to relatively easily obtained measurements (Cognitive scores, Genetic Risk and plasma biomarkers) achieve results that are competitive with magnetic resonance techniques. This is by no means an exhaustive study, but instead an exploration of the plausibility of defining a series of relatively inexpensive, broad population based tests.
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12
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Hoshi M. Multi-angle development of therapeutic methods for Alzheimer's disease. Br J Pharmacol 2020; 178:770-783. [PMID: 32592177 DOI: 10.1111/bph.15174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023] Open
Abstract
Recent clinical trial results support the idea that treatment based on the so-called amyloid hypothesis is a promising approach in Alzheimer's disease (AD), but actually, developing effective treatments for AD remains highly challenging. The discovery that neuron-specific sodium pump activity is impaired in AD and other neurodegenerative diseases such as Parkinson's disease has suggested a role for the sodium pump in the pathogenesis of these diseases. This opens up new possibilities for intervention, such as inhibiting the aberrant interaction of the sodium pump with the disease-specific ligand(s) or activating the sodium pump itself or its downstream signalling. In this review article, I would like to discuss possible anti-amyloid therapies, focusing especially on our own research. LINKED ARTICLES: This article is part of a themed issue on Neurochemistry in Japan. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.4/issuetoc.
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Affiliation(s)
- Minako Hoshi
- Department for Brain and Neurodegenerative Disease Research, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
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13
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Wisniewski T, Drummond E. APOE-amyloid interaction: Therapeutic targets. Neurobiol Dis 2020; 138:104784. [PMID: 32027932 PMCID: PMC7118587 DOI: 10.1016/j.nbd.2020.104784] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/22/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder that is growing in prevalence globally. It is the only major cause of death without any effective pharmacological means to treat or slow progression. Inheritance of the ε4 allele of the Apolipoprotein (APO) E gene is the strongest genetic risk factor for late-onset AD. The interaction between APOE and amyloid β (Aβ) plays a key role in AD pathogenesis. The APOE-Aβ interaction regulates Aβ aggregation and clearance and therefore directly influences the development of amyloid plaques, congophilic amyloid angiopathy and subsequent tau related pathology. Relatively few AD therapeutic approaches have directly targeted the APOE-Aβ interaction thus far. Here we review the critical role of APOE in the pathogenesis of AD and some of the most promising therapeutic approaches that focus on the APOE-Aβ interaction.
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Affiliation(s)
- Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, Science Building, Rm 1017, 435 East 30(th) Street, New York, NY 10016, USA.
| | - Eleanor Drummond
- Brain & Mind Centre and Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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14
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Lima D, Hacke ACM, Inaba J, Pessôa CA, Kerman K. Electrochemical detection of specific interactions between apolipoprotein E isoforms and DNA sequences related to Alzheimer's disease. Bioelectrochemistry 2019; 133:107447. [PMID: 32006858 DOI: 10.1016/j.bioelechem.2019.107447] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/14/2019] [Accepted: 12/15/2019] [Indexed: 12/26/2022]
Abstract
Apolipoprotein E4 (ApoE4) has a key role on the onset and progression of Alzheimer's disease (AD), since it favours the deposition of toxic amyloid-beta (Aβ) aggregates in the brain. These effects might result from the interaction between ApoE4 and specific DNA promoters related to cellular autophagy pathways and to the expression of neuroprotective proteins, like sirtuin-1. Herein, we modified gold electrodes with mixed self-assembled monolayers of 6-mercapto-1-hexanol and thiolated DNA oligonucleotides related to CLEAR (associated with autophagic processes that enable the clearance of toxic species, such as Aβ) and SirT1 (related to the expression of sirtuin-1) promoter sequences. The interactions of the immobilized DNA sequences with isoforms of ApoE (ApoE4/ApoE3/ApoE2) were investigated by differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) measurements. By monitoring current and charge transfer resistance (Rct) variations, CLEAR showed to interact specifically with ApoE4, whereas SirT1 showed a higher affinity to ApoE4 compared to ApoE3 and ApoE2. To the best of our knowledge, this is the first report about the application of electrochemical techniques to investigate the sequence-specific interaction between ApoE isoforms and CLEAR and SirT1 oligonucleotides.
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Affiliation(s)
- Dhésmon Lima
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Ana Carolina M Hacke
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Juliana Inaba
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Christiana A Pessôa
- Department of Chemistry, Universidade Estadual de Ponta Grossa, Av. General Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, PR, Brazil
| | - Kagan Kerman
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, M1C 1A4 Toronto, ON, Canada.
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15
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Ghosh S, Sil TB, Dolai S, Garai K. High‐affinity multivalent interactions between apolipoprotein E and the oligomers of amyloid‐β. FEBS J 2019; 286:4737-4753. [DOI: 10.1111/febs.14988] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/06/2019] [Accepted: 07/06/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shamasree Ghosh
- Tata Institute of Fundamental Research Hyderabad Hyderabad India
| | - Timir Baran Sil
- Tata Institute of Fundamental Research Hyderabad Hyderabad India
| | | | - Kanchan Garai
- Tata Institute of Fundamental Research Hyderabad Hyderabad India
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16
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Drummond E, Goñi F, Liu S, Prelli F, Scholtzova H, Wisniewski T. Potential Novel Approaches to Understand the Pathogenesis and Treat Alzheimer's Disease. J Alzheimers Dis 2019; 64:S299-S312. [PMID: 29562516 DOI: 10.3233/jad-179909] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is growing genetic and proteomic data highlighting the complexity of Alzheimer's disease (AD) pathogenesis. Greater use of unbiased "omics" approaches is being increasingly recognized as essential for the future development of effective AD research, that need to better reflect the multiple distinct pathway abnormalities that can drive AD pathology. The track record of success in AD clinical trials thus far has been very poor. In part, this high failure rate has been related to the premature translation of highly successful results in animal models that mirror only limited aspects of AD pathology to humans. We highlight our recent efforts to increase use of human tissue to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity. These therapeutic approaches include the blocking of the Aβ/apoE interaction, stimulation of innate immunity, and the simultaneous blocking of Aβ/tau oligomer toxicity. We believe that future successful therapeutic approaches will need to be combined to better reflect the complexity of the abnormal pathways triggered in AD pathogenesis.
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Affiliation(s)
- Eleanor Drummond
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Fernando Goñi
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Shan Liu
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Frances Prelli
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Henrieta Scholtzova
- Department of Neurology, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, USA
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17
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Spasov AA, Brel AK, Litvinov RA, Lisina SV, Kucheryavenko AF, Budaeva YN, Salaznikova OA, Rashchenko AI, Shamshina DD, Batrakov VV, Ivanov AV. Evaluation of N-Hydroxy-, N-Metoxy-, and N-Acetoxybenzoyl-Substituted Derivatives of Thymine and Uracil as New Substances for Prevention and Treatment of Long-Term Complications of Diabetes Mellitus. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Wisniewski T, Drummond E. Future horizons in Alzheimer's disease research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:223-241. [PMID: 31699317 DOI: 10.1016/bs.pmbts.2019.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There are growing genetic, transcriptomic and proteomic data pointing to the complexity of Alzheimer's disease (AD) pathogenesis. Unbiased "omics" approaches are essential for the future development of effective AD research, which will need to be combined and personalized, given that multiple distinct pathways can drive AD pathology. It is essential to gain a better understanding of the AD pathogenesis subtype variety and to develop several distinct therapeutic approaches tailored to address this diversity, as well as the common presence of mixed pathologies. These nonmutually exclusive therapeutic approaches include the targeting of multiple toxic oligomeric species concurrently, targeting the apolipoprotein E/amyloid β interaction and the modulation of innate immunity, as well as more "out of the box" ideas such as targeting infectious agents that may play a role in AD.
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Affiliation(s)
- Thomas Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, NYU School of Medicine, New York, NY, United States.
| | - Eleanor Drummond
- Central Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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19
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Su H, Jin Y, Noroozifar M, Kerman K. Electrochemical Detection of Isoform‐Specific Interaction between Apolipoprotein E and Amyloid‐β. ChemElectroChem 2018. [DOI: 10.1002/celc.201800985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Han Su
- Department of Physical and Environmental SciencesUniversity of Toronto Scarborough Toronto Ontario M1 C 1 A4 Canada
| | - Yiyun Jin
- Department of Physical and Environmental SciencesUniversity of Toronto Scarborough Toronto Ontario M1 C 1 A4 Canada
| | - Meissam Noroozifar
- Department of ChemistryUniversity of Sistan and Baluchestan Zahedan Iran
| | - Kagan Kerman
- Department of Physical and Environmental SciencesUniversity of Toronto Scarborough Toronto Ontario M1 C 1 A4 Canada
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20
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Dafnis I, Argyri L, Chroni A. Amyloid-peptide β 42 Enhances the Oligomerization and Neurotoxicity of apoE4: The C-terminal Residues Leu279, Lys282 and Gln284 Modulate the Structural and Functional Properties of apoE4. Neuroscience 2018; 394:144-155. [PMID: 30367942 DOI: 10.1016/j.neuroscience.2018.10.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 11/25/2022]
Abstract
Apolipoprotein E4 (apoE4), one of the three apoE isoforms, is the strongest factor for raising the risk for late-onset Alzheimer's disease (AD) and has been proposed to play a major role in AD pathogenesis. Amyloid-peptide β 42 (Aβ42) has also been proposed to affect neuronal degeneration and AD pathogenesis, possibly by interacting with apoE. Previous studies have shown that the functions of apoE forms can be dictated by their structural and biophysical properties. Here we show that apoE4 can form SDS-stable oligomers, possibly reflecting aggregated forms, which increase following incubation of apoE4 with Aβ42. In addition, extracellular apoE4 is cytotoxic for human neuroblastoma SK-N-SH cells, while Aβ42 enhances the cytotoxicity of apoE4. Carboxyl-terminal point mutations L279Q, K282A or Q284A reduced the capacity of apoE4 to form SDS-stable oligomers, as well as its cytotoxicity, both in the absence and presence of Aβ42. Structural and thermodynamic analyses showed that all three apoE4 mutants have significantly increased α-helical and decreased β-sheet content, have reduced portion of hydrophobic surfaces exposed to the solvent and have a reduced conformational stability during chemical denaturation. Overall, our data highlight a pathogenic role of apoE4 that could be linked to the capacity of the protein to form oligomeric species especially in the presence of Aβ42 and to induce cytotoxicity. Carboxyl-terminal residues L279, K282 or Q284 appear to be involved in the conformation of apoE4 that may underlie the protein's functional properties related to neurotoxicity.
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Affiliation(s)
- Ioannis Dafnis
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Agia Paraskevi, Athens 15341, Greece
| | - Letta Argyri
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Agia Paraskevi, Athens 15341, Greece
| | - Angeliki Chroni
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Agia Paraskevi, Athens 15341, Greece.
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21
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Henry N, Krammer EM, Stengel F, Adams Q, Van Liefferinge F, Hubin E, Chaves R, Efremov R, Aebersold R, Vandenbussche G, Prévost M, Raussens V, Deroo S. Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach. PLoS Comput Biol 2018; 14:e1006165. [PMID: 29933361 PMCID: PMC6033463 DOI: 10.1371/journal.pcbi.1006165] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 07/05/2018] [Accepted: 04/30/2018] [Indexed: 11/18/2022] Open
Abstract
Apolipoprotein E (apoE) is a forefront actor in the transport of lipids and the maintenance of cholesterol homeostasis, and is also strongly implicated in Alzheimer’s disease. Upon lipid-binding apoE adopts a conformational state that mediates the receptor-induced internalization of lipoproteins. Due to its inherent structural dynamics and the presence of lipids, the structure of the biologically active apoE remains so far poorly described. To address this issue, we developed an innovative hybrid method combining experimental data with molecular modeling and dynamics to generate comprehensive models of the lipidated apoE4 isoform. Chemical cross-linking combined with mass spectrometry provided distance restraints, characterizing the three-dimensional organization of apoE4 molecules at the surface of lipidic nanoparticles. The ensemble of spatial restraints was then rationalized in an original molecular modeling approach to generate monomeric models of apoE4 that advocated the existence of two alternative conformations. These two models point towards an activation mechanism of apoE4 relying on a regulation of the accessibility of its receptor binding region. Further, molecular dynamics simulations of the dimerized and lipidated apoE4 monomeric conformations revealed an elongation of the apoE N-terminal domain, whereby helix 4 is rearranged, together with Arg172, into a proper orientation essential for lipoprotein receptor association. Overall, our results show how apoE4 adapts its conformation for the recognition of the low density lipoprotein receptor and we propose a novel mechanism of activation for apoE4 that is based on accessibility and remodeling of the receptor binding region. Among the proteins involved in the transport of lipids and their distribution to the cells, apolipoprotein E (apoE) mediates the internalization of cholesterol rich lipoproteins by acting as a ligand for cell-surface receptors. In the central nervous system, while apoE is the major cholesterol transport protein, a dysfunction of apoE in the transport and metabolism of lipids is associated with Alzheimer’s disease. A molecular understanding of the mechanisms underlying the receptor binding abilities of apoE is crucial to address its biological functions, but is so far hindered by the dynamic and complex nature of these assemblies. We have designed an original hybrid approach combining experimental data and bioinformatics tools to generate high resolution models of lipidated apoE. Based on these models, we can propose how apoE adapts its conformation at the surface of lipid nanoparticles. Further, we propose a novel mechanism of regulation of the activation and receptor recognition of apoE that could prove valuable to interpret its role in Alzheimer and apoE-related cardiovascular diseases.
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Affiliation(s)
- Nicolas Henry
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Eva-Maria Krammer
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Quentin Adams
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - François Van Liefferinge
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ellen Hubin
- Structural Biology Research Center, VIB, Brussels, Belgium
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Rui Chaves
- Structural Biology Research Center, VIB, Brussels, Belgium
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rouslan Efremov
- Structural Biology Research Center, VIB, Brussels, Belgium
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Guy Vandenbussche
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martine Prévost
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Vincent Raussens
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
- * E-mail: (SD); (VT)
| | - Stéphanie Deroo
- Center for Structural Biology and Bioinformatics, Structure and Function of Biological Membranes, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
- * E-mail: (SD); (VT)
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22
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Hosp F, Mann M. A Primer on Concepts and Applications of Proteomics in Neuroscience. Neuron 2017; 96:558-571. [DOI: 10.1016/j.neuron.2017.09.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023]
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23
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Liu S, Park S, Allington G, Prelli F, Sun Y, Martá-Ariza M, Scholtzova H, Biswas G, Brown B, Verghese PB, Mehta PD, Kwon YU, Wisniewski T. Targeting Apolipoprotein E/Amyloid β Binding by Peptoid CPO_Aβ17-21 P Ameliorates Alzheimer's Disease Related Pathology and Cognitive Decline. Sci Rep 2017; 7:8009. [PMID: 28808293 PMCID: PMC5556019 DOI: 10.1038/s41598-017-08604-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/12/2017] [Indexed: 02/01/2023] Open
Abstract
Inheritance of the apolipoprotein E4 (apoE4) genotype has been identified as the major genetic risk factor for late onset Alzheimer's disease (AD). Studies have shown that apoE, apoE4 in particular, binds to amyloid-β (Aβ) peptides at residues 12-28 of Aβ and this binding modulates Aβ accumulation and disease progression. We have previously shown in several AD transgenic mice lines that blocking the apoE/Aβ interaction with Aβ12-28 P reduced Aβ and tau-related pathology, leading to cognitive improvements in treated AD mice. Recently, we have designed a small peptoid library derived from the Aβ12-28 P sequence to screen for new apoE/Aβ binding inhibitors with higher efficacy and safety. Peptoids are better drug candidates than peptides due to their inherently more favorable pharmacokinetic properties. One of the lead peptoid compounds, CPO_Aβ17-21 P, diminished the apoE/Aβ interaction and attenuated the apoE4 pro-fibrillogenic effects on Aβ aggregation in vitro as well as apoE4 potentiation of Aβ cytotoxicity. CPO_Aβ17-21 P reduced Aβ-related pathology coupled with cognitive improvements in an AD APP/PS1 transgenic mouse model. Our study suggests the non-toxic, non-fibrillogenic peptoid CPO_Aβ17-21 P has significant promise as a new AD therapeutic agent which targets the Aβ related apoE pathway, with improved efficacy and pharmacokinetic properties.
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Affiliation(s)
- Shan Liu
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, USA
| | - Shinae Park
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Korea
| | | | - Frances Prelli
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, USA
| | - Yanjie Sun
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, USA
| | - Mitchell Martá-Ariza
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, USA
| | - Henrieta Scholtzova
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, USA
| | - Goutam Biswas
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Korea
| | - Bernard Brown
- Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, USA
| | - Philip B Verghese
- C2N Diagnostics, Center for Emerging Technologies, 4041 Forest Park Avenue, St. Louis, MO, 63108, USA
| | - Pankaj D Mehta
- Department of Immunology, New York State Institute for Basic Research in Developmental Disabilities, New York, USA
| | - Yong-Uk Kwon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Korea.
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Departments of Neurology, Psychiatry and Pathology, Neuroscience Institute, New York University School of Medicine, New York, USA.
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24
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Huebbe P, Rimbach G. Evolution of human apolipoprotein E (APOE) isoforms: Gene structure, protein function and interaction with dietary factors. Ageing Res Rev 2017. [PMID: 28647612 DOI: 10.1016/j.arr.2017.06.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Apolipoprotein E (APOE) is a member of the vertebrate protein family of exchangeable apolipoproteins that is characterized by amphipathic α-helices encoded by multiple nucleotide tandem repeats. Its equivalent in flying insects - apolipophorin-III - shares structural and functional commonalities with APOE, suggesting the possibility of an evolutionary relationship between the proteins. In contrast to all other known species, human APOE is functionally polymorphic and possesses three major allelic variants (ε4, ε3 and ε2). The present review examines the current knowledge on APOE gene structure, phylogeny and APOE protein topology as well as its human isoforms. The ε4 allele is associated with an increased age-related disease risk but is also the ancestral form. Despite increased mortality in the elderly, ε4 has not become extinct and is the second-most common allele worldwide after ε3. APOE ε4, moreover, shows a non-random geographical distribution, and similarly, the ε2 allele is not homogenously distributed among ethnic populations. This likely suggests the existence of selective forces that are driving the evolution of human APOE isoforms, which may include differential interactions with dietary factors. To that effect, micronutrients such as vitamin D and carotenoids or dietary macronutrient composition are elucidated with respect to APOE evolution.
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Affiliation(s)
- Patricia Huebbe
- Institute of Human Nutrition and Food Science, University of Kiel, H. Rodewald Str. 6, 24118 Kiel, Germany.
| | - Gerald Rimbach
- Institute of Human Nutrition and Food Science, University of Kiel, H. Rodewald Str. 6, 24118 Kiel, Germany.
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25
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Rostgaard N, Roos P, Budtz-Jørgensen E, Johannsen P, Waldemar G, Nørremølle A, Lindquist SG, Gydesen S, Brown JM, Collinge J, Isaacs AM, Nielsen TT, Nielsen JE. TMEM106B and ApoE polymorphisms in CHMP2B-mediated frontotemporal dementia (FTD-3). Neurobiol Aging 2017; 59:221.e1-221.e7. [PMID: 28888721 DOI: 10.1016/j.neurobiolaging.2017.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 06/24/2017] [Accepted: 06/30/2017] [Indexed: 12/12/2022]
Abstract
Single-nucleotide polymorphisms in the TMEM106B gene have been identified as a risk factor in frontotemporal dementia (FTD). The major allele of SNP rs3173615 is a risk factor in sporadic FTD, whereas the minor allele seems protective in GRN- and C9orf72-mediated FTD. The role of apolipoprotein E (ApoE) in FTD is uncertain, though an established risk factor in Alzheimer's disease. In a unique Danish family, inherited FTD is caused by a mutation in the CHMP2B gene located on chromosome 3 (FTD-3). In this family, both risk factors TMEM106B and ApoE were analyzed and correlated to age at onset (AAO) and progression in terms of age at institutionalization (AAI) and age at death (AAD). Although TMEM106B and CHMP2B share cellular function in that both localize to endolysosomes, TMEM106B genotypes appeared to have no influence on the clinical disease course. ApoE ε4 was found to be a protective factor with later AAO and AAI, whereas ε2 seemed to aggravate the disease with earlier AAO and AAD. These results indicate ApoE ε2 as a risk factor in FTD-3 and suggest a protective role of ε4.
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Affiliation(s)
- Nina Rostgaard
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark
| | - Peter Roos
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark.
| | | | - Peter Johannsen
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark
| | - Gunhild Waldemar
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark
| | - Anne Nørremølle
- Section of Neurogenetics, Institute of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen N, Denmark
| | - Suzanne G Lindquist
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark; Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Section 4062, Copenhagen, Denmark
| | - Susanne Gydesen
- Department of Psychiatry, Community Mental Health Services in Region Zealand, Nykøbing Sjælland, Denmark
| | - Jeremy M Brown
- Department of Neurology, Addenbrooke's Hospital, Cambridge, UK
| | - John Collinge
- MRC Prion Unit, Institute of Neurology, London, UK; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
| | | | - Troels T Nielsen
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark
| | - Jørgen E Nielsen
- Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Section 6911, Copenhagen, Denmark; Section of Neurogenetics, Institute of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Copenhagen N, Denmark
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26
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Lu C, Tian S, Zhai G, Yuan Z, Li Y, He X, Zhang Y, Zhang K. Probing the Binding Interfaces of Histone-Aptamer by Photo Cross-Linking Mass Spectrometry. ACS Chem Biol 2017; 12:57-62. [PMID: 27936569 DOI: 10.1021/acschembio.6b00797] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Histone proteins, which could interact with DNA, play important roles in the regulation of chromatin structures, transcription, and other DNA-based biological processes. Here, we developed a novel aptamer-based probe for the analysis of histone H4-aptamer interfaces. This probe contains a DNA sequence for specific recognition of histone H4, a biotin tag for affinity enrichment, an aryl azide photoactive group for cross-linking and a cleavable disulfide group to dissociate aptamer from labeled histones. We successfully achieved specific enrichment of histone H4 and further developed a new analysis strategy for histone-aptamer interaction by photo cross-linking mass spectrometry. The binding area of histone H4 to aptamer was investigated and discussed for the first time. This strategy exhibits great potential and might further contribute to the understanding of histone-DNA interaction patterns.
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Affiliation(s)
- Congcong Lu
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Shanshan Tian
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Guijin Zhai
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Zuofei Yuan
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yijun Li
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Xiwen He
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Yukui Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Kai Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
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27
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Pate KM, Murphy RM. Cerebrospinal Fluid Proteins as Regulators of Beta-amyloid Aggregation and Toxicity. Isr J Chem 2017; 57:602-612. [PMID: 29129937 DOI: 10.1002/ijch.201600078] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Amyloid disorders, such as Alzheimer's, are almost invariably late-onset diseases. One defining diagnostic feature of Alzheimer's disease is the deposition of beta-amyloid as extracellular plaques, primarily in the hippocampus. This raises the question: are there natural protective agents that prevent beta-amyloid from depositing, and is it loss of this protection that leads to onset of disease? Proteins in cerebrospinal fluid (CSF) have been suggested to act as just such natural protective agents. Here, we describe some of the early evidence that led to this suggestion, and we discuss, in greater detail, two CSF proteins that have garnered the bulk of the attention.
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Affiliation(s)
- Kayla M Pate
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison WI 53706 (USA)
| | - Regina M Murphy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison WI 53706 (USA)
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28
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Singh S, Dubinsky-Davidchik IS, Kluger R. Strain-promoted azide–alkyne cycloaddition for protein–protein coupling in the formation of a bis-hemoglobin as a copper-free oxygen carrier. Org Biomol Chem 2016; 14:10011-10017. [DOI: 10.1039/c6ob01817c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Conventional chemical approaches to protein–protein coupling present challenges due to the intrinsic competition between the desired interactions of reagents with groups of the protein as well as reactions with water.
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Affiliation(s)
- Serena Singh
- Davenport Chemical Laboratories
- Department of Chemistry
- University of Toronto
- Toronto
- Canada M5S 3H6
| | | | - Ronald Kluger
- Davenport Chemical Laboratories
- Department of Chemistry
- University of Toronto
- Toronto
- Canada M5S 3H6
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29
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Abstract
Neurodegeneration correlates with Alzheimer's disease (AD) symptoms, but the molecular identities of pathogenic amyloid β-protein (Aβ) oligomers and their targets, leading to neurodegeneration, remain unclear. Amylospheroids (ASPD) are AD patient-derived 10- to 15-nm spherical Aβ oligomers that cause selective degeneration of mature neurons. Here, we show that the ASPD target is neuron-specific Na(+)/K(+)-ATPase α3 subunit (NAKα3). ASPD-binding to NAKα3 impaired NAKα3-specific activity, activated N-type voltage-gated calcium channels, and caused mitochondrial calcium dyshomeostasis, tau abnormalities, and neurodegeneration. NMR and molecular modeling studies suggested that spherical ASPD contain N-terminal-Aβ-derived "thorns" responsible for target binding, which are distinct from low molecular-weight oligomers and dodecamers. The fourth extracellular loop (Ex4) region of NAKα3 encompassing Asn(879) and Trp(880) is essential for ASPD-NAKα3 interaction, because tetrapeptides mimicking this Ex4 region bound to the ASPD surface and blocked ASPD neurotoxicity. Our findings open up new possibilities for knowledge-based design of peptidomimetics that inhibit neurodegeneration in AD by blocking aberrant ASPD-NAKα3 interaction.
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30
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Tran BQ, Goodlett DR, Goo YA. Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:123-9. [PMID: 26025770 DOI: 10.1016/j.bbapap.2015.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 01/12/2023]
Abstract
For the analysis of protein-protein interactions and protein conformations, cross-linking coupled with mass spectrometry (CXMS) has become an essential tool in recent years. A variety of cross-linking reagents are used to covalently link interacting amino acids to identify protein-binding partners. The spatial proximity of cross-linked amino acid residues is used to elucidate structural models of protein complexes. The main challenges for mapping protein-protein interaction are low stoichiometry and low frequency of cross-linked peptides relative to unmodified linear peptides as well as accurate and efficient matches to corresponding peptide sequences with low false discovery rates for identifying the site of cross-link. We evaluate the current state of chemical cross-linking and mass spectrometry applications with the special emphasis on the recent development of informatics data processing and analysis tools that help complexity of interpreting CXMS data. This article is part of a Special Issue entitled:Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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