51
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Rana M, Sharma AK. Cu and Zn interactions with Aβ peptides: consequence of coordination on aggregation and formation of neurotoxic soluble Aβ oligomers. Metallomics 2019; 11:64-84. [DOI: 10.1039/c8mt00203g] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The coordination chemistry of transition metal ions (Fe, Cu, Zn) with the amyloid-β (Aβ) peptides has attracted a lot of attention in recent years due to its repercussions in Alzheimer's disease (AD).
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Affiliation(s)
- Monika Rana
- Department of Chemistry
- Central University of Rajasthan
- Ajmer 305817
- India
| | - Anuj Kumar Sharma
- Department of Chemistry
- Central University of Rajasthan
- Ajmer 305817
- India
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52
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Fernández-Castaño Romera M, Lou X, Schill J, Ter Huurne G, Fransen PPKH, Voets IK, Storm C, Sijbesma RP. Strain-Stiffening in Dynamic Supramolecular Fiber Networks. J Am Chem Soc 2018; 140:17547-17555. [PMID: 30465604 PMCID: PMC6302312 DOI: 10.1021/jacs.8b09289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The cytoskeleton is a highly adaptive network of filamentous proteins capable of stiffening under stress even as it dynamically assembles and disassembles with time constants of minutes. Synthetic materials that combine reversibility and strain-stiffening properties remain elusive. Here, strain-stiffening hydrogels that have dynamic fibrous polymers as their main structural components are reported. The fibers form via self-assembly of bolaamphiphiles (BA) in water and have a well-defined cross-section of 9 to 10 molecules. Fiber length recovery after sonication, H/D exchange experiments, and rheology confirm the dynamic nature of the fibers. Cross-linking of the fibers yields strain-stiffening, self-healing hydrogels that closely mimic the mechanics of biological networks, with mechanical properties that can be modulated by chemical modification of the components. Comparison of the supramolecular networks with covalently fixated networks shows that the noncovalent nature of the fibers limits the maximum stress that fibers can bear and, hence, limits the range of stiffening.
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53
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Murcia Rios A, Vahidi S, Dunn SD, Konermann L. Evidence for a Partially Stalled γ Rotor in F 1-ATPase from Hydrogen-Deuterium Exchange Experiments and Molecular Dynamics Simulations. J Am Chem Soc 2018; 140:14860-14869. [PMID: 30339028 DOI: 10.1021/jacs.8b08692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
F1-ATPase uses ATP hydrolysis to drive rotation of the γ subunit. The γ C-terminal helix constitutes the rotor tip that is seated in an apical bearing formed by α3β3. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we interrogated E. coli F1-ATPase by hydrogen-deuterium exchange (HDX) mass spectrometry. Rotation of γ caused greatly enhanced deuteration in the γ C-terminal helix. The HDX kinetics implied that most F1 complexes operate with an intact rotor at any given time, but that the rotor tip is prone to occasional unfolding. A molecular dynamics (MD) strategy was developed to model the off-axis forces acting on γ. MD runs showed stalling of the rotor tip and unfolding of the γ C-terminal helix. MD-predicted H-bond opening events coincided with experimental HDX patterns. Our data suggest that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get "stuck" (and unfold) sporadically while the remainder of γ continues to rotate. This scenario contrasts the traditional "greasy bearing" model that envisions smooth rotation of the γ C-terminal helix. The fragility of the apical rotor tip in F1-ATPase is attributed to the absence of a c10 ring that stabilizes the rotation axis in intact FoF1. Overall, the MD/HDX strategy introduced here appears well suited for interrogating the inner workings of molecular motors.
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Affiliation(s)
- Angela Murcia Rios
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Siavash Vahidi
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Stanley D Dunn
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry , The University of Western Ontario , London , Ontario N6A 5B7 , Canada
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54
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Zheng Y, Xu L, Yang J, Peng X, Wang H, Yu N, Hua Y, Zhao J, He J, Hong T. The effects of fluorescent labels on Aβ42
aggregation detected by fluorescence correlation spectroscopy. Biopolymers 2018; 109:e23237. [DOI: 10.1002/bip.23237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/02/2018] [Accepted: 09/13/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Yanpeng Zheng
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Lingwan Xu
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Jingfa Yang
- Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Xianglei Peng
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - He Wang
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Na Yu
- School of Sciences; Beijing Jiaotong University; Beijing China
- Shandong Xinchuang Biological Technology Co., Ltd.; Jinan China
| | - Ying Hua
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Jiang Zhao
- Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Jinsheng He
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Tao Hong
- School of Sciences; Beijing Jiaotong University; Beijing China
- Institute for Viral Disease Control and Prevention; Chinese Centre for Disease Control and Prevention; Beijing China
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55
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Przygońska K, Poznański J, Mistarz UH, Rand KD, Dadlez M. Side-chain moieties from the N-terminal region of Aβ are Involved in an oligomer-stabilizing network of interactions. PLoS One 2018; 13:e0201761. [PMID: 30080867 PMCID: PMC6078298 DOI: 10.1371/journal.pone.0201761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/20/2018] [Indexed: 12/31/2022] Open
Abstract
Oligomeric forms of the Aβ peptide represent the most probable neurotoxic agent in Alzheimer’s disease. The dynamic and heterogeneous character of these oligomers makes their structural characterization by classic methods difficult. Native mass spectrometry, when supported by additional gas phase techniques, like ion mobility separation and hydrogen-deuterium exchange (IM-HDX-MS), enable analysis of different oligomers coexisting in the sample and may provide species-specific structural information for each oligomeric form populated in the gas phase. Here, we have combined these three techniques to obtain insight into the structural properties of oligomers of Aβ1–40 and two variants with scrambled sequences. Gas-phase HDX-MS revealed a sequence-specific engagement of the side-chains of residues located at the N-terminal part of the peptide in a network of oligomer-stabilizing interactions. Oligomer-specific interactions were no longer observed in the case of the fully scrambled sequence. Also, the ability to form alternative structures, observed for WT Aβ peptide, was lost upon scrambling. Our data underscore a role for the N-terminal residues in shaping the equilibria of oligomeric forms. Although the peptide lacking the N-terminal 1–16 residues (p3 peptide) is thought to be benign, the role of the N-terminus has not been sufficiently characterized yet. We speculate that the interaction networks revealed here may be crucial for enabling structural transitions necessary to obtain mature parallel cross-β structures from smaller antiparallel oligomers. We provide a hypothetical molecular model of the trajectory that allows a gradual conversion from antiparallel to parallel oligomers without decomposition of oligomers. Oligomer-defining interactions involving the Aβ peptide N-terminus may be important in production of the neurotoxic forms and thus should not be neglected.
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Affiliation(s)
- Kaja Przygońska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ulrik H. Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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56
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Illes-Toth E, Rempel DL, Gross ML. Pulsed Hydrogen-Deuterium Exchange Illuminates the Aggregation Kinetics of α-Synuclein, the Causative Agent for Parkinson's Disease. ACS Chem Neurosci 2018; 9:1469-1476. [PMID: 29601177 DOI: 10.1021/acschemneuro.8b00052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
α-Synuclein (aS) forms toxic intermediates ranging from small oligomers and protofibrils to large amyloid fibrils. Understanding the time course of aS fibril formation and the role played by its regions is critical for therapeutic intervention. Here, we used pulsed hydrogen-deuterium exchange and mass spectrometry (HDX-MS) for the first time to probe kinetic intermediates of the full aS aggregation in vitro, achieving kinetic snapshots containing spatially resolved protein information about critical stages. Monitoring the resultant mass shifts shows distinct binomial abundances for two main exchange profiles: one that represents a fast-exchanging, solvent-accessible species and another with a more protected nature. We show using a series of proteolytic peptides from the full protein that self-association is most pronounced in the non-amyloid-β-component region and less so for either terminus. The N-terminus, however, shows a minor protected population at mid- and late times, whereas the C-terminus shows predominantly unimodal HDX, indicating that these regions are devoid of any large conformational rearrangements. Focusing on the hydrophobic core, we confirmed and modeled the different isotopic distributions and calculated their relative fractions to discern their individual contributions. The data fitting reports respective t1/2 values, which are nearly identical and do not depend on location. We followed the aggregation by complementary transmission electron microscopy to observe the morphology of aggregates and circular dichroism to assess changes in secondary structure. Our results provide a detailed picture of aS aggregation in vitro and demonstrate that HDX-MS offers unique spatially resolved, coexisting kinetic intermediates in solution. This new platform is suitable for testing promising inhibitors of aS aggregation.
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Affiliation(s)
- Eva Illes-Toth
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Don L. Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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57
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Liu H, Zhou X, Shen Q, Xing D. Paper-based electrochemiluminescence sensor for highly sensitive detection of amyloid-β oligomerization: Toward potential diagnosis of Alzheimer's disease. Theranostics 2018; 8:2289-2299. [PMID: 29721080 PMCID: PMC5928890 DOI: 10.7150/thno.23483] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/04/2018] [Indexed: 02/06/2023] Open
Abstract
Development of a rapid and sensitive method for Aβ(1-42) aggregation detection is of great importance to overcome the limitations of conventional techniques. In this study, we developed a label-free paper-based electrochemiluminescence sensor for amyloid-β aggregation detection toward potential diagnosis of Alzheimer's disease (AD). The paper-based chip used in the system serves as a low-cost and disposable detection method. In this detection platform, the bonding of [Ru(phen)2dppz]2+ to Aβ(1-42) aggregates results in enhanced electrochemiluminescence due to the change in the polarity of the microenvironment when [Ru(phen)2dppz]2+ intercalated into the β-sheets during oligomerization. The oligomerization process of Aβ(1-42) can be monitored in real time by the novel method, and as low as 100 pM equivalent monomer concentration of Aβ(1-42) could be detected simultaneously. In addition, the cerebrospinal fluid of transgenic AD model mice was tested by this method, which is highly consistent with genetic identification. In addition, we demonstrated that this detection platform could be a potential new method for the screening of Aβ(1-42) aggregation inhibitors, highlighting the practical application capacity of this platform. The platform is label free, low cost and sensitive. Therefore, the proposed platform holds great promise for the diagnosis of AD.
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Affiliation(s)
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | | | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
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58
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Zhao W, Ai H. Effect of pH on Aβ 42 Monomer and Fibril-like Oligomers-Decoding in Silico of the Roles of pK Values of Charged Residues. Chemphyschem 2018; 19:1103-1116. [PMID: 29380494 DOI: 10.1002/cphc.201701384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 01/10/2023]
Abstract
Amyloid beta-peptide (Aβ) is the key to developing Alzheimer's disease. Experiments have confirmed that different acidity influences directly not only the structural morphology and population of Aβ oligomers, but also the toxicity. The atomic-level association between the pH, charged residues, and Aβ properties remains obscure. Herein, conformational changes of Aβ42 monomer, fibril-like trimer, and pentamer in the medium pH range of 4.0-7.5 are studied. The results reveal that, as the pH changes from 7.5 to the isoelectric pH, His6, His13, and His14 are protonated in turn, successively approach the center of mass of folded Aβ monomer, trigger ionic interactions and changes of neighboring turns (Asp7-Ser8, His14-Lys16) and even a distant one (Leu34-Met35), as well as concomitant changes of secondary structure, and promote the conformation transition from unfolded to folded. This observation discloses that protonation can convert these charged residues from originally hydrophilic to "hydrophobic-like". For fibril-like oligomers, the pH susceptibility essentially stems from the pK values of charged residues in the context of the Aβ fibril, and in turn one can predict the dynamic behavior of these residues in the processes of dissociation or stabilization of a fibril by comparing the pK values of residues involved in salt bridges in the normal state with those in the current context. This idea is justified by two fibril models and appears to be applicable to other peptides and their fibril systems.
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Affiliation(s)
- Wei Zhao
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory, of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, P. R. China
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59
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Rana M, Cho HJ, Roy TK, Mirica LM, Sharma AK. Azo-dyes based small bifunctional molecules for metal chelation and controlling amyloid formation. Inorganica Chim Acta 2018; 471:419-429. [PMID: 30344337 PMCID: PMC6191838 DOI: 10.1016/j.ica.2017.11.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical tools are needed to discover new effective drugs for tackling multifaceted complex neurodegenerative diseases like Alzheimer's disease (AD). Multifunctional nature of two compounds, 5-((4-nitro-phenyl)diazenyl)quinolin-8-ol (HL1) and 4-((4-nitrophenyl)diazenyl)benzene-1,3-diol (HL2) is reported w.r.t. their ability to bind Cu2+ ions and amyloid aggregates related to AD. HL1 and HL2 have half congo-red type azo-stilbene structural framework incorporated with metal chelating groups, designed to chelate metal ions from metal-amyloid species. Metal binding studies of HL1 and HL2 are established by the methods of Job's Plot, UV-vis spectra with metal ions and stability constant determination. In addition, their metal complexes are isolated, purity checked by elemental analysis, spectroscopically characterized and their structural analyses were obtained from DFT based calculations including binding energy determination. Chicken egg white Lysozyme (CEWL) was used as a model peptide for fibrillation studies. HL1 is found as an excellent colorimetric sensor for amyloid fibrils. Inhibitory effect of HL1 and HL2 and their isolated metal complexes L1-Cu and L2-Cu on CEWL fibrillation was studied using ThT and ANS fluorescence assay along with TEM imaging. In addition, the cell toxicity studies on these compounds suggest that although azo dyes may be non-toxic but having a nitro-substitution lead to significant cell toxicity. Overall, these results suggest that this new class of multifunctional small molecules can interact with amyloids as well as metal ions and could be potential anti-aggregation metal chelating agents.
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Affiliation(s)
- Monika Rana
- Department of Chemistry, Central University of Rajasthan, NH-8,
Bandarsindri, Ajmer, Rajasthan 305817, India
| | - Hong-Jun Cho
- Department of Chemistry, Washington University, One Brookings Drive,
St. Louis, MO 63130-4899, United States
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of
Jammu, Jammu 180011, India
| | - Liviu M. Mirica
- Department of Chemistry, Washington University, One Brookings Drive,
St. Louis, MO 63130-4899, United States
| | - Anuj K. Sharma
- Department of Chemistry, Central University of Rajasthan, NH-8,
Bandarsindri, Ajmer, Rajasthan 305817, India
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60
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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61
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Sharma AK, Schultz JW, Prior JT, Rath NP, Mirica LM. Coordination Chemistry of Bifunctional Chemical Agents Designed for Applications in 64Cu PET Imaging for Alzheimer's Disease. Inorg Chem 2017; 56:13801-13814. [PMID: 29112419 PMCID: PMC5698879 DOI: 10.1021/acs.inorgchem.7b01883] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Positron emission
tomography (PET) is emerging as one of the most important diagnostic
tools for brain imaging, yet the most commonly used radioisotopes
in PET imaging, 11C and 18F, have short half-lives,
and their usage is thus somewhat limited. By comparison, the 64Cu radionuclide has a half-life of 12.7 h, which is ideal
for administering and imaging purposes. In spite of appreciable research
efforts, high-affinity copper chelators suitable for brain imaging
applications are still lacking. Herein, we present the synthesis and
characterization of a series of bifunctional compounds (BFCs) based
on macrocyclic 1,4,7-triazacyclononane and 2,11-diaza[3.3](2,6)pyridinophane
ligand frameworks that exhibit a high affinity for Cu2+ ions. In addition, these BFCs contain a 2-phenylbenzothiazole fragment
that is known to interact tightly with amyloid β fibrillar aggregates.
Determination of the protonation constants (pKa values) and stability constants (log β values) of these
BFCs, as well as characterization of the isolated copper complexes
using X-ray crystallography, electron paramagnetic resonance spectroscopy,
and electrochemical studies, suggests that these BFCs exhibit desirable
properties for the development of novel 64Cu PET imaging
agents for Alzheimer’s disease. Novel bifunctional chelators
(BFCs) containing 1,4,7-triazacyclononane or pyridinophane macrocycles
and amyloid-binding 2-phenylbenzothiazole fragments have been synthesized,
and their copper coordination properties have been characterized in
detail. These BFCs are attractive candidates for the development of
novel 64Cu-labeled PET imaging agents for Alzheimer’s
disease.
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Affiliation(s)
- Anuj K Sharma
- Department of Chemistry, Washington University , One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Jason W Schultz
- Department of Chemistry, Washington University , One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - John T Prior
- Department of Chemistry, Washington University , One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Nigam P Rath
- Department of Chemistry and Biochemistry, University of Missouri St. Louis , One University Boulevard, St. Louis, Missouri 63121-4400, United States
| | - Liviu M Mirica
- Department of Chemistry, Washington University , One Brookings Drive, St. Louis, Missouri 63130-4899, United States
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62
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Cao Y, Jiang X, Han W. Self-Assembly Pathways of β-Sheet-Rich Amyloid-β(1-40) Dimers: Markov State Model Analysis on Millisecond Hybrid-Resolution Simulations. J Chem Theory Comput 2017; 13:5731-5744. [PMID: 29019683 DOI: 10.1021/acs.jctc.7b00803] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Early oligomerization during amyloid-β (Aβ) aggregation is essential for Aβ neurotoxicity. Understanding how unstructured Aβs assemble into oligomers, especially those rich in β-sheets, is essential but remains challenging as the assembly process is too transient for experimental characterization and too slow for molecular dynamics simulations. So far, atomic simulations are limited only to studies of either oligomer structures or assembly pathways for short Aβ segments. To overcome the computational challenge, we combine in this study a hybrid-resolution model and adaptive sampling techniques to perform over 2.7 ms of simulations of formation of full-length Aβ40 dimers that are the earliest toxic oligomeric species. The Markov state model is further employed to characterize the transition pathways and associated kinetics. Our results show that for two major forms of β-sheet-rich structures reported experimentally, the corresponding assembly mechanisms are markedly different. Hairpin-containing structures are formed by direct binding of soluble Aβ in β-hairpin-like conformations. Formation of parallel, in-register structures resembling fibrils occurs ∼100-fold more slowly and involves a rapid encounter of Aβ in arbitrary conformations followed by a slow structural conversion. The structural conversion proceeds via diverse pathways but always requires transient unfolding of encounter complexes. We find that the transition kinetics could be affected differently by intra-/intermolecular interactions involving individual residues in a conformation-dependent manner. In particular, the interactions involving Aβ's N-terminal part promote the assembly into hairpin-containing structures but delay the formation of fibril-like structures, thus explaining puzzling observations reported previously regarding the roles of this region in the early assembly process.
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Affiliation(s)
- Yang Cao
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Xuehan Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Wei Han
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
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63
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Wang H, Shu Q, Rempel DL, Frieden C, Gross ML. Understanding Curli Amyloid-Protein Aggregation by Hydrogen-Deuterium Exchange and Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:16-23. [PMID: 29056864 PMCID: PMC5644351 DOI: 10.1016/j.ijms.2016.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Bacteria within Curli biofilms are protected from environmental pressures (e.g., disinfectants, antibiotics), and this is responsible for intractable infections. Understanding aggregation of the major protein component of Curli, CsgA, may uncover disease-associated amyloidogenesis mechanisms. Here, we report the application of pulsed hydrogen-deuterium exchange and mass spectrometry (HDX-MS) to study CsgA aggregation, thereby obtaining region-specific information. By following time-dependent peptide signal depletion, presumably a result of insoluble fibril formation, we acquired sigmoidal profiles that are specific for regions (region-specific) of the protein. These signal-depletion profiles not only provide an alternative aggregation measurement, but also give insight on soluble species in the aggregation. The HDX data present as bimodal isotopic distributions, one representing a highly disordered species whereas the other a well-structured one. Although the extents of deuterium uptake of the two species remain the same with time, the relative abundance of the lower mass, less-exchanged species increases in a region-specific manner. The same region-specific aggregation properties also pertain to different aggregation conditions. Although CsgA is an intrinsically disordered protein, within the fibril it is thought to consist of five imperfect β-strand repeating units (labeled R1-R5). We found that the exterior repeating units R1 and R5 have higher aggregation propensities than do the interior units R2, R3, and R4. We also employed TEM to obtain complementary information of the well-structured species. The results provide insight on aggregation and a new approach for further application of HDX-MS to unravel aggregation mechanisms of amyloid proteins.
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Affiliation(s)
- Hanliu Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
| | - Qin Shu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Don L Rempel
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
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64
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Dong M, Zhao W, Hu D, Ai H, Kang B. N-Terminus Binding Preference for Either Tanshinone or Analogue in Both Inhibition of Amyloid Aggregation and Disaggregation of Preformed Amyloid Fibrils-Toward Introducing a Kind of Novel Anti-Alzheimer Compounds. ACS Chem Neurosci 2017; 8:1577-1588. [PMID: 28406293 DOI: 10.1021/acschemneuro.7b00080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Amyloid-β (Aβ40/Aβ42) peptide with a length of 40 or 42 residues is naturally secreted as cleavage product of the amyloid precursor protein, and formation of Aβ aggregates in a patient's brain is a hallmark of Alzheimer's disease (AD). Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. The disaggregation/inhibition effect of the inhibitors applies generally to both Aβ40 and Aβ42 aggregations. Here we capture the atomic-level details of the interaction between Aβ40/Aβ42 and either natural tanshinone compound TS1 or its derivative TS0, and observe novel results by using molecular dynamics simulations. We observe that the natural TS1 indeed inhibits the monomolecular Aβ42 (mAβ42) aggregation and disaggregates Aβ42 amyloid fibrils, being in good agreement with the experimental results. TS1 is favorable to stabilize mAβ40 and even Aβ40 fibril, playing an opposite role to that in the Aβ42 counterpart, however. TS0 can inhibit the misfolding of either mAβ40 or mAβ42 and disaggregate Aβ42 fibril but stabilize the Aβ40 fibril. Using a combination of secondary structural analysis, MM-PBSA binding energy calculations, and radial distribution functions computations, we find that both TS0 and TS1, especially the former, prefer to bind at the charged residues within disordered N-terminus with a scarce positive binding energy and disappear the characteristic C-terminal bend region of Aβ42 fibril, as well as twist the Aβ42 fibril seriously. It turns out to destabilize the Aβ42 fibril and enable the conversion of U-shaped Aβ42 fibril from the onefold to the twofold morphologies. The N-terminal binding preference helps us to identify N-terminal region as the specific epitope for specific inhibitors/drugs (such as TS0 and analogues), heralding unusual inhibition/disaggregation or stabilization mechanisms, and offering an alternative direction in engineering new inhibitors to treat AD.
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Affiliation(s)
- Mingyan Dong
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Wei Zhao
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Dingkun Hu
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Hongqi Ai
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Baotao Kang
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
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65
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Lou X, Lafleur RPM, Leenders CMA, Schoenmakers SMC, Matsumoto NM, Baker MB, van Dongen JLJ, Palmans ARA, Meijer EW. Dynamic diversity of synthetic supramolecular polymers in water as revealed by hydrogen/deuterium exchange. Nat Commun 2017; 8:15420. [PMID: 28504253 PMCID: PMC5440672 DOI: 10.1038/ncomms15420] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/29/2017] [Indexed: 02/02/2023] Open
Abstract
Numerous self-assembling molecules have been synthesized aiming at mimicking both the structural and dynamic properties found in living systems. Here we show the application of hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to unravel the nanoscale organization and the structural dynamics of synthetic supramolecular polymers in water. We select benzene-1,3,5-tricarboxamide (BTA) derivatives that self-assemble in H2O to illustrate the strength of this technique for supramolecular polymers. The BTA structure has six exchangeable hydrogen atoms and we follow their exchange as a function of time after diluting the H2O solution with a 100-fold excess of D2O. The kinetic H/D exchange profiles reveal that these supramolecular polymers in water are dynamically diverse; a notion that has previously not been observed using other techniques. In addition, we report that small changes in the molecular structure can be used to control the dynamics of synthetic supramolecular polymers in water.
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Affiliation(s)
- Xianwen Lou
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - René P M Lafleur
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - Christianus M A Leenders
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - Sandra M C Schoenmakers
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - Nicholas M Matsumoto
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - Matthew B Baker
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - Joost L J van Dongen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - Anja R A Palmans
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, Eindhoven 5600 MB, The Netherlands
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66
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Mandacaru SC, do Vale LHF, Vahidi S, Xiao Y, Skinner OS, Ricart CAO, Kelleher NL, de Sousa MV, Konermann L. Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools. Biochemistry 2017; 56:1645-1655. [PMID: 28252287 DOI: 10.1021/acs.biochem.7b00020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Royal jelly (RJ) triggers the development of female honeybee larvae into queens. This effect has been attributed to the presence of major royal jelly protein 1 (MRJP1) in RJ. MRJP1 isolated from royal jelly is tightly associated with apisimin, a 54-residue α-helical peptide that promotes the noncovalent assembly of MRJP1 into multimers. No high-resolution structural data are available for these complexes, and their binding stoichiometry remains uncertain. We examined MRJP1/apisimin using a range of biophysical techniques. We also investigated the behavior of deglycosylated samples, as well as samples with reduced apisimin content. Our mass spectrometry (MS) data demonstrate that the native complexes predominantly exist in a (MRJP14 apisimin4) stoichiometry. Hydrogen/deuterium exchange MS reveals that MRJP1 within these complexes is extensively disordered in the range of residues 20-265. Marginally stable secondary structure (likely antiparallel β-sheet) exists around residues 266-432. These weakly structured regions interchange with conformers that are extensively unfolded, giving rise to bimodal (EX1) isotope distributions. We propose that the native complexes have a "dimer of dimers" quaternary structure in which MRJP1 chains are bridged by apisimin. Specifically, our data suggest that apisimin acts as a linker that forms hydrophobic contacts involving the MRJP1 segment 316VLFFGLV322. Deglycosylation produces large soluble aggregates, highlighting the role of glycans as aggregation inhibitors. Samples with reduced apisimin content form dimeric complexes with a (MRJP12 apisimin1) stoichiometry. The information uncovered in this work will help pave the way toward a better understanding of the unique physiological role played by MRJP1 during queen differentiation.
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Affiliation(s)
- Samuel C Mandacaru
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7.,Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Luis H F do Vale
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil.,Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Siavash Vahidi
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| | - Yiming Xiao
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
| | - Owen S Skinner
- Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Carlos A O Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Neil L Kelleher
- Proteomics Center of Excellence, Departments of Chemistry and Molecular Biosciences, Northwestern University , Evanston, Illinois 60611, United States
| | - Marcelo Valle de Sousa
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, University of Brasilia , Brasilia, Brazil
| | - Lars Konermann
- Department of Chemistry, Western University , London, Ontario, Canada N6A 5B7
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67
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Li KS, Rempel DL, Gross ML. Conformational-Sensitive Fast Photochemical Oxidation of Proteins and Mass Spectrometry Characterize Amyloid Beta 1-42 Aggregation. J Am Chem Soc 2016; 138:12090-8. [PMID: 27568528 PMCID: PMC5221481 DOI: 10.1021/jacs.6b07543] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Preventing and treating Alzheimer's disease require understanding the aggregation of amyloid beta 1-42 (Aβ1-42) to give oligomers, protofibrils, and fibrils. Here we describe footprinting of Aβ1-42 by hydroxyl radical-based fast photochemical oxidation of proteins (FPOP) and mass spectrometry (MS) to monitor the time-course of Aβ1-42 aggregation. We resolved five distinct stages characterized by two sigmoidal behaviors, showing the time-dependent transitions of monomers-paranuclei-protofibrils-fibrillar aggregates. Kinetic modeling allows deciphering the amounts and interconversion of the dominant Aβ1-42 species. Moreover, the irreversible footprinting probe provides insights into the kinetics of oligomerization and subsequent fibrillar growth by allowing the conformational changes of Aβ1-42 at subregional and even amino-acid-residue levels to be revealed. The middle domain of Aβ1-42 plays a major role in aggregation, whereas the N-terminus retains most of its solvent-accessibility during aggregation, and the hydrophobic C-terminus is involved to an intermediate extent. This approach affords an in situ, real-time monitoring of the solvent accessibility of Aβ1-42 at various stages of oligomerization, and provides new insights on site-specific aggregation of Aβ1-42 for a sample state beyond the capabilities of most other biophysical methods.
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Affiliation(s)
- Ke Sherry Li
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Don L. Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
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68
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Probing the dynamic regulation of peripheral membrane proteins using hydrogen deuterium exchange-MS (HDX-MS). Biochem Soc Trans 2016; 43:773-86. [PMID: 26517882 DOI: 10.1042/bst20150065] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many cellular signalling events are controlled by the selective recruitment of protein complexes to membranes. Determining the molecular basis for how lipid signalling complexes are recruited, assembled and regulated on specific membrane compartments has remained challenging due to the difficulty of working in conditions mimicking native biological membrane environments. Enzyme recruitment to membranes is controlled by a variety of regulatory mechanisms, including binding to specific lipid species, protein-protein interactions, membrane curvature, as well as post-translational modifications. A powerful tool to study the regulation of membrane signalling enzymes and complexes is hydrogen deuterium exchange-MS (HDX-MS), a technique that allows for the interrogation of protein dynamics upon membrane binding and recruitment. This review will highlight the theory and development of HDX-MS and its application to examine the molecular basis of lipid signalling enzymes, specifically the regulation and activation of phosphoinositide 3-kinases (PI3Ks).
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69
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Surin AK, Grigorashvili EI, Suvorina MY, Selivanova OM, Galzitskaya OV. Determination of regions involved in amyloid fibril formation for Aβ(1-40) peptide. BIOCHEMISTRY (MOSCOW) 2016; 81:762-769. [DOI: 10.1134/s0006297916070130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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70
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Zhang Y, Cui W, Wecksler AT, Zhang H, Molina P, Deperalta G, Gross ML. Native MS and ECD Characterization of a Fab-Antigen Complex May Facilitate Crystallization for X-ray Diffraction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1139-42. [PMID: 27103115 PMCID: PMC4899112 DOI: 10.1007/s13361-016-1398-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 05/11/2023]
Abstract
Native mass spectrometry (MS) and top-down electron-capture dissociation (ECD) combine as a powerful approach for characterizing large proteins and protein assemblies. Here, we report their use to study an antibody Fab (Fab-1)-VEGF complex in its near-native state. Native ESI with analysis by FTICR mass spectrometry confirms that VEGF is a dimer in solution and that its complex with Fab-1 has a binding stoichiometry of 2:2. Applying combinations of collisionally activated dissociation (CAD), ECD, and infrared multiphoton dissociation (IRMPD) allows identification of flexible regions of the complex, potentially serving as a guide for crystallization and X-ray diffraction analysis. Graphical Abstract ᅟ.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Analytical Research and Development, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Patricia Molina
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
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71
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One of the possible mechanisms of amyloid fibrils formation based on the sizes of primary and secondary folding nuclei of Aβ40 and Aβ42. J Struct Biol 2016; 194:404-14. [PMID: 27016282 DOI: 10.1016/j.jsb.2016.03.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022]
Abstract
In the presented paper, theoretical as well as electron microscopy and X-ray diffraction experimental approaches were employed for studding the process of Aβ amyloid formation. Using quantitative estimates of a number of monomers which form the nuclei of amyloid fibrils the sizes of folding nuclei of amyloid fibrils for Aβ40 and 42 have been determined for the first time. We have shown that the size of the primary nucleus of Aβ42 peptide fibrils corresponds to 3 monomers, the size of the secondary nucleus for this peptide is 2 monomers. Applying the same analysis to Aβ40 we conclude that the size of the primary nucleus is 2 monomers, and the size of the secondary nucleus is one monomer. Summation of our theoretical and experimental results has allowed us to propose a new model of the structural organization of amyloid fibrils. Our model suggests that the generation of fibrils takes place along the following simplified pathway: a monomer→a ring oligomer→a mature fibril consisting of ring oligomers. These data shed more light upon our understanding of what sizes of the oligomers could represent main targets for future therapies (tetramers for Aβ42 and trimers for Aβ40), and aid in the development of inhibitors of Aβ40 and 42 oligomer formation.
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72
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Maity S, Lyubchenko YL. Probing of Amyloid Aβ (14-23) Trimers by Single-Molecule Force Spectroscopy. JACOBS JOURNAL OF MOLECULAR AND TRANSLATIONAL MEDICINE 2016; 1:004. [PMID: 28239686 PMCID: PMC5321571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Self-assembly and aggregation of amyloid peptides, such as Aβ(1-40) and Aβ(1-42), lead to the development of Alzheimer disease and similar neurodegenerative disorders associated with protein aggregation. The structures of large aggregates, specifically fibrils, are well characterized. However, our understanding about the structure of oligomeric forms of amyloids is incomplete and needs to be expanded, particularly given the finding that oligomeric rather than fibrillar amyloid morphologies are neurotoxic. This lack of knowledge is primarily due to the existence of transient oligomeric forms that require the use of non-traditional approaches capable of probing transiently existing amyloid forms. We have recently developed the Single-Molecule Force Spectroscopy (SMFS) approach enabling us to probe dimeric forms of amyloids. These studies suggest that the assembly of amyloid proteins into dimers leads to extremely stabilized amyloids in non-native, misfolded states [1]. Herein, we applied the SMFS approach to probe amyloid trimers. We used the Aβ(14-23) segment of Aβ42 protein that is responsible for full-size protein aggregation. The dimerization of this peptide was recently characterized [2]. The dimeric form of Aβ (14-23) was assembled by the use of a tandem Aβ(14-23)-YNGK-Aβ(14-23), in which the YNGK motif between the two Aβ(14-23) monomers makes a β turn to form a hairpin loop with an antiparallel arrangement of Aβ(14-23) monomers[3]. The Aβ(14-23) monomer was tethered to the AFM tip, and trimers were formed by approaching the tip to the mica surface on which the Aβ(14-23)-YNGK-Aβ(14-23) dimer was immobilized via a polyethylene glycol tether. We identified trimers by rupture forces that were considerably larger than those for dimers. Models for the trimer assembly process are discussed.
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Affiliation(s)
| | - Yuri L. Lyubchenko
- Corresponding author: Dr. Yuri L. Lyubchenko, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198, United States, Tel: (402) 559-1971, (402) 559-1973; Fax: (402) 559-9543;
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73
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Doussineau T, Mathevon C, Altamura L, Vendrely C, Dugourd P, Forge V, Antoine R. Mass Determination of Entire Amyloid Fibrils by Using Mass Spectrometry. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tristan Doussineau
- Institut Lumière Matière; UMR5306 Université Lyon 1-CNRS; Université de Lyon; 5 rue de la Doua 69622 Villeurbanne France
| | - Carole Mathevon
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux; UMR5249 CEA-CNRS-UJF; CEA Grenoble; 17 rue des Martyrs 38054 Grenoble France
| | - Lucie Altamura
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux; UMR5249 CEA-CNRS-UJF; CEA Grenoble; 17 rue des Martyrs 38054 Grenoble France
| | - Charlotte Vendrely
- ERRMECe, I-MAT FD4122; Université de Cergy-Pontoise; France
- LMGP, CNRS UMR 5628; Grenoble France
| | - Philippe Dugourd
- Institut Lumière Matière; UMR5306 Université Lyon 1-CNRS; Université de Lyon; 5 rue de la Doua 69622 Villeurbanne France
| | - Vincent Forge
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux; UMR5249 CEA-CNRS-UJF; CEA Grenoble; 17 rue des Martyrs 38054 Grenoble France
| | - Rodolphe Antoine
- Institut Lumière Matière; UMR5306 Université Lyon 1-CNRS; Université de Lyon; 5 rue de la Doua 69622 Villeurbanne France
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74
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Doussineau T, Mathevon C, Altamura L, Vendrely C, Dugourd P, Forge V, Antoine R. Mass Determination of Entire Amyloid Fibrils by Using Mass Spectrometry. Angew Chem Int Ed Engl 2015; 55:2340-4. [DOI: 10.1002/anie.201508995] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/12/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Tristan Doussineau
- Institut Lumière Matière; UMR5306 Université Lyon 1-CNRS; Université de Lyon; 5 rue de la Doua 69622 Villeurbanne France
| | - Carole Mathevon
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux; UMR5249 CEA-CNRS-UJF; CEA Grenoble; 17 rue des Martyrs 38054 Grenoble France
| | - Lucie Altamura
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux; UMR5249 CEA-CNRS-UJF; CEA Grenoble; 17 rue des Martyrs 38054 Grenoble France
| | - Charlotte Vendrely
- ERRMECe, I-MAT FD4122; Université de Cergy-Pontoise; France
- LMGP, CNRS UMR 5628; Grenoble France
| | - Philippe Dugourd
- Institut Lumière Matière; UMR5306 Université Lyon 1-CNRS; Université de Lyon; 5 rue de la Doua 69622 Villeurbanne France
| | - Vincent Forge
- CEA, DSV, iRTSV, Laboratoire de Chimie et Biologie des Métaux; UMR5249 CEA-CNRS-UJF; CEA Grenoble; 17 rue des Martyrs 38054 Grenoble France
| | - Rodolphe Antoine
- Institut Lumière Matière; UMR5306 Université Lyon 1-CNRS; Université de Lyon; 5 rue de la Doua 69622 Villeurbanne France
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75
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Moorthy BS, Ghomi HT, Lill MA, Topp EM. Structural transitions and interactions in the early stages of human glucagon amyloid fibrillation. Biophys J 2015; 108:937-948. [PMID: 25692598 DOI: 10.1016/j.bpj.2015.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/07/2014] [Accepted: 01/08/2015] [Indexed: 01/08/2023] Open
Abstract
A mechanistic understanding of the intermolecular interactions and structural changes during fibrillation is crucial for the design of safe and efficacious glucagon formulations. Amide hydrogen/deuterium exchange with mass spectrometric analysis was used to identify the interactions and amino acids involved in the initial stages of glucagon fibril formation at acidic pH. Kinetic measurements from intrinsic and thioflavin T fluorescence showed sigmoidal behavior. Secondary structural measurement of fibrillating glucagon using far-UV circular dichroism spectroscopy showed changes in structure from random coil → α-helix → β-sheet, with increase in α-helix content during the lag phase followed by increase in β-sheet content during the growth phase. Hydrogen/deuterium exchange with mass spectrometric analysis of fibrillating glucagon suggested that C-terminal residues 22-29 are involved in interactions during the lag phase, during which N-terminal residues 1-6 showed no changes. Molecular dynamics simulations of glucagon fragments showed C-terminal to C-terminal interactions with greater α-helix content for the 20-29 fragment, with hydrophobic and aromatic residues (Phe-22, Trp-25, Val-23, and Met-27) predominantly involved. Overall, the study shows that glucagon interactions during the early phase of fibrillation are mediated through C-terminal residues, which facilitate the formation of α-helix-rich oligomers, which further undergo structural rearrangement and elongation to form β-sheet-rich mature fibrils.
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Affiliation(s)
- Balakrishnan S Moorthy
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana
| | - Hamed Tabatabaei Ghomi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Markus A Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana.
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76
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Wang H, Shu Q, Rempel DL, Frieden C, Gross ML. Continuous and pulsed hydrogen-deuterium exchange and mass spectrometry characterize CsgE oligomerization. Biochemistry 2015; 54:6475-81. [PMID: 26418947 DOI: 10.1021/acs.biochem.5b00871] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the use of hydrogen-deuterium amide exchange coupled to mass spectrometry (HDX-MS) to study the interfaces of and conformational changes accompanying CsgE oligomerization. This protein plays an important role in enteric bacteria biofilm formation. Biofilms provide protection for enteric bacteria from environmental extremes and raise concerns about controlling bacteria and infectious disease. Their proteinaceous components, called curli, are extracellular functional amyloids that initiate surface contact and biofilm formation. The highly regulated curli biogenesis involves a major subunit, CsgA, a minor subunit CsgB, and a series of other accessory proteins. CsgE, possibly functioning as oligomer, is a chaperonin-like protein that delivers CsgA to an outer-membrane bound oligomeric CsgG complex. No higher-order structure, or interfaces and dynamics of its oligomerization, however, are known. In this work, we determined regions involved in CsgE self-association by continuous HDX, and, on the basis of that, prepared a double mutant W48A/F79A, derived from interface alanine scan, and verified that it exists as monomer. Using pulsed HDX and MS, we suggest there is a structural rearrangement occurring during the oligomerization of CsgE.
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Affiliation(s)
- Hanliu Wang
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
| | - Qin Shu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Don L Rempel
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Michael L Gross
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
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77
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Sengupta K, Chatterjee S, Pramanik D, Dey SG, Dey A. Self-assembly of stable oligomeric and fibrillar aggregates of Aβ peptides relevant to Alzheimer's disease: morphology dependent Cu/heme toxicity and inhibition of PROS generation. Dalton Trans 2015; 43:13377-83. [PMID: 25076262 DOI: 10.1039/c4dt01991a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Large and small aggregates of Aβ peptides, resembling the morphology and dimensions of fibrillar and oligomeric forms of Aβ respectively, relevant to Alzheimer's disease, are stabilized on electrodes using self-assembly. Both of these forms were found to bind redox active Cu and heme, resulting in active sites having distinctive biophysical properties. The reduced metal bound Aβ active sites of both the oligomeric and fibrillar forms of Aβ produce detrimental partially reduced oxygen species (PROS). While the larger aggregates of heme-Aβ produce more PROS in situ, the smaller aggregates of Cu-Aβ produce more PROS. 8-Hydroxy quinoline and methylene blue are inhibitors of Cu and heme bound Aβ respectively, and are shown to efficiently reduce PROS formation in the oligomeric forms. However, these inhibitors are ineffective in reducing the toxicities of the Cu and heme bound Aβ peptides in the fibrils, making them significantly more lethal than the smaller Aβ aggregates.
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Affiliation(s)
- Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India.
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78
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Soulby AJ, Heal JW, Barrow MP, Roemer RA, O'Connor PB. Does deamidation cause protein unfolding? A top-down tandem mass spectrometry study. Protein Sci 2015; 24:850-60. [PMID: 25653127 DOI: 10.1002/pro.2659] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 01/25/2023]
Abstract
Deamidation is a nonenzymatic post-translational modification of asparagine to aspartic acid or glutamine to glutamic acid, converting an uncharged amino acid to a negatively charged residue. It is plausible that deamidation of asparagine and glutamine residues would result in disruption of a proteins' hydrogen bonding network and thus lead to protein unfolding. To test this hypothesis Calmodulin and B2M were deamidated and analyzed using tandem mass spectrometry on a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). The gas phase hydrogen bonding networks of deamidated and nondeamidated protein isoforms were probed by varying the infra-red multi-photon dissociation laser power in a linear fashion and plotting the resulting electron capture dissociation fragment intensities as a melting curve at each amino acid residue. Analysis of the unfolding maps highlighted increased fragmentation at lower laser powers localized around heavily deamidated regions of the proteins. In addition fragment intensities were decreased across the rest of the proteins which we propose is because of the formation of salt-bridges strengthening the intramolecular interactions of the central regions. These results were supported by a computational flexibility analysis of the mutant and unmodified proteins, which would suggest that deamidation can affect the global structure of a protein via modification of the hydrogen bonding network near the deamidation site and that top down FTICR-MS is an appropriate technique for studying protein folding.
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Affiliation(s)
- Andrew J Soulby
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
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79
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 478] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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80
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Zhang Y, Rempel DL, Zhang H, Gross ML. An improved fast photochemical oxidation of proteins (FPOP) platform for protein therapeutics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:526-9. [PMID: 25519854 PMCID: PMC5993200 DOI: 10.1007/s13361-014-1055-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 05/16/2023]
Abstract
Unlike small-molecule drugs, the size and dynamics of protein therapeutics challenge existing methods for assessing their high order structures (HOS). To extend fast photochemical oxidation of proteins (FPOP) to protein therapeutics, we modified its platform by introducing a mixing step prior to laser irradiation to minimize unwanted H(2)O(2)-induced oxidation. This improvement plus standardizing each step yield better reproducibility as determined by a fitting process whereby we used a non-FPOP spectrum as a template to report the unmodified level. We also tested different buffer systems for this modified FPOP platform with cytochrome c. The outcome is a standard oxidation profile that can be compared between different laboratories and regulatory agencies that wish to adopt FPOP for quality control purposes.
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81
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Proteomics beyond large-scale protein expression analysis. Curr Opin Biotechnol 2015; 34:162-70. [PMID: 25636126 DOI: 10.1016/j.copbio.2015.01.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 11/21/2022]
Abstract
Proteomics is commonly referred to as the application of high-throughput approaches to protein expression analysis. Typical results of proteomics studies are inventories of the protein content of a sample or lists of differentially expressed proteins across multiple conditions. Recently, however, an explosion of novel proteomics workflows has significantly expanded proteomics beyond the analysis of protein expression. Targeted proteomics methods, for example, enable the analysis of the fine dynamics of protein systems, such as a specific pathway or a network of interacting proteins, and the determination of protein complex stoichiometries. Structural proteomics tools allow extraction of restraints for structural modeling and identification of structurally altered proteins on a proteome-wide scale. Other variations of the proteomic workflow can be applied to the large-scale analysis of protein activity, location, degradation and turnover. These exciting developments provide new tools for multi-level 'omics' analysis and for the modeling of biological networks in the context of systems biology studies.
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82
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Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
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83
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Klinger AL, Kiselar J, Ilchenko S, Komatsu H, Chance MR, Axelsen PH. A synchrotron-based hydroxyl radical footprinting analysis of amyloid fibrils and prefibrillar intermediates with residue-specific resolution. Biochemistry 2014; 53:7724-34. [PMID: 25382225 PMCID: PMC4270378 DOI: 10.1021/bi5010409] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Structural models of the fibrils
formed by the 40-residue amyloid-β
(Aβ40) peptide in Alzheimer’s disease typically consist
of linear polypeptide segments, oriented approximately perpendicular
to the long axis of the fibril, and joined together as parallel in-register
β-sheets to form filaments. However, various models differ in
the number of filaments that run the length of a fibril, and in the
topological arrangement of these filaments. In addition to questions
about the structure of Aβ40 monomers in fibrils, there are important
unanswered questions about their structure in prefibrillar intermediates,
which are of interest because they may represent the most neurotoxic
form of Aβ40. To assess different models of fibril structure
and to gain insight into the structure of prefibrillar intermediates,
the relative solvent accessibility of amino acid residue side chains
in fibrillar and prefibrillar Aβ40 preparations was characterized
in solution by hydroxyl radical footprinting and structural mass spectrometry.
A key to the application of this technology was the development of
hydroxyl radical reactivity measures for individual side chains of
Aβ40. Combined with mass-per-length measurements performed by
dark-field electron microscopy, the results of this study are consistent
with the core filament structure represented by two- and three-filament
solid state nuclear magnetic resonance-based models of the Aβ40
fibril (such as 2LMN, 2LMO, 2LMP, and 2LMQ), with minor refinements,
but they are inconsistent with the more recently proposed 2M4J model. The results
also demonstrate that individual Aβ40 fibrils exhibit structural
heterogeneity or polymorphism, where regions of two-filament structure
alternate with regions of three-filament structure. The footprinting
approach utilized in this study will be valuable for characterizing
various fibrillar and nonfibrillar forms of the Aβ peptide.
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Affiliation(s)
- Alexandra L Klinger
- Department of Pharmacology, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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84
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Serra-Vidal B, Pujadas L, Rossi D, Soriano E, Madurga S, Carulla N. Hydrogen/deuterium exchange-protected oligomers populated during Aβ fibril formation correlate with neuronal cell death. ACS Chem Biol 2014; 9:2678-85. [PMID: 25265274 DOI: 10.1021/cb500621x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The aggregation of the amyloid-β peptide (Aβ) to form fibrils and plaques is strongly associated with Alzheimer's disease (AD). Although it is well established that this process generates neurotoxicity, it is also heterogeneous with a variety of species being formed during the conversion process. This heterogeneity makes it difficult to detect and characterize each of the aggregates formed, which precludes establishing the specific features responsible for the neurotoxicity observed. Here we use pulse-labeling hydrogen-deuterium exchange experiments analyzed by electrospray ionization mass spectrometry (PL-HDX-ESI-MS) to distinguish three ensembles populated during the aggregation of the 40 and 42 residue forms of the Aβ peptide, Aβ40 and Aβ42, on the basis of differences in their persistent structure. Noticeably, two of them are more abundant at the beginning and at the end of the lag phase and are therefore not detectable by conventional assays such as Thioflavin T (ThT). The ensembles populated at different stages of the aggregation process have a surprisingly consistent average degree of exchange, indicating that there are definite structural transitions between the different stages of aggregation. To determine whether an ensemble of species with a given hydrogen exchange pattern correlates with neurotoxicity, we combined PL-HDX-ESI-MS experiments with parallel measurements of the neurotoxicity of the samples under study. The results of this dual approach show that the maximum toxicity correlates with the ensemble comprising HDX protected oligomers, indicating that development of persistent structure within Aβ oligomers is a determinant of neurotoxicity.
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Affiliation(s)
- Bernat Serra-Vidal
- Institute for
Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Lluís Pujadas
- Department
of Cell Biology, University of Barcelona and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Diagonal
647, Barcelona 08028, Spain
| | - Daniela Rossi
- Department
of Cell Biology, University of Barcelona and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Diagonal
647, Barcelona 08028, Spain
| | - Eduardo Soriano
- Department
of Cell Biology, University of Barcelona and Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Diagonal
647, Barcelona 08028, Spain
- CIEN Foundation, Madrid 28031, Spain
| | - Sergio Madurga
- Department
of Physical Chemistry and Research Institute of Theoretical and Computational
Chemistry (IQTCUB), University of Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for
Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
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85
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Sharma AK, Kim J, Prior JT, Hawco NJ, Rath NP, Kim J, Mirica LM. Small bifunctional chelators that do not disaggregate amyloid β fibrils exhibit reduced cellular toxicity. Inorg Chem 2014; 53:11367-76. [PMID: 25333939 PMCID: PMC4220862 DOI: 10.1021/ic500926c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 01/22/2023]
Abstract
Multifunctional metal chelators that can modulate the amyloid β (Aβ) peptide aggregation and its interaction with metal ions such as copper and zinc hold considerable promise as therapeutic agents for Alzheimer's disease (AD). However, specific rather than systemic metal chelation by these compounds is needed in order to limit any side effects. Reported herein are two novel small bifunctional chelators, 2-[2-hydroxy-4-(diethylamino)phenyl]benzothiazole (L1) and 2-(2-hydroxy-3-methoxyphenyl)benzothiazole (L2), in which the metal-binding donor atoms are integrated within a molecular framework derived from the amyloid-binding fluorescent dye thioflavin T (ThT). The metal-binding properties of L1 and L2 were probed by pH spectrophotometric titrations to determine their pKa values and the corresponding metal complex stability constants, and the isolated metal complexes were structurally characterized. The amyloid-fibril-binding properties of L1 and L2 were investigated by fluorescence titrations and ThT competition assays. Interestingly, L1 and L2 do not lead to the formation of neurotoxic Aβ42 oligomers in the presence or absence of metal ions, as observed by native gel electrophoresis, Western blotting, and transmission electron microscopy. In addition, L1 and L2 were able to reduce the cell toxicity of preformed Aβ42 oligomers and of the copper-stabilized Aβ42 oligomers. Given their ability to reduce the toxicity of soluble Aβ42 and Cu-Aβ42 species, L1 and L2 are promising lead compounds for the development of chemical agents that can control the neurotoxicity of soluble Aβ42 species in AD.
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Affiliation(s)
- Anuj K. Sharma
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Jaekwang Kim
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63108, United States
| | - John T. Prior
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Nicholas J. Hawco
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
| | - Nigam P. Rath
- Department
of Chemistry and Biochemistry, University
of Missouri—St. Louis, One University Boulevard, St. Louis, Missouri 63121-4400, United States
| | - Jungsu Kim
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63108, United States
| | - Liviu M. Mirica
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130-4899, United States
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86
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Brody DL, Gross ML. The remarkable properties of amyloid-β derived from human Alzheimer’s disease brain: swinging the streetlight. Brain 2014; 137:2874-5. [DOI: 10.1093/brain/awu261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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87
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Li J, Rodnin MV, Ladokhin AS, Gross ML. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain. Biochemistry 2014; 53:6849-56. [PMID: 25290210 PMCID: PMC4222528 DOI: 10.1021/bi500893y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.
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Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
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88
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Hyung SJ, Feng X, Che Y, Stroh JG, Shapiro M. Detection of conformation types of cyclosporin retaining intramolecular hydrogen bonds by mass spectrometry. Anal Bioanal Chem 2014; 406:5785-94. [DOI: 10.1007/s00216-014-8023-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/02/2014] [Accepted: 07/07/2014] [Indexed: 11/24/2022]
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89
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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90
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Hubin E, van Nuland NAJ, Broersen K, Pauwels K. Transient dynamics of Aβ contribute to toxicity in Alzheimer's disease. Cell Mol Life Sci 2014; 71:3507-21. [PMID: 24803005 PMCID: PMC4143600 DOI: 10.1007/s00018-014-1634-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/15/2014] [Accepted: 04/22/2014] [Indexed: 12/20/2022]
Abstract
The aggregation and deposition of the amyloid-β peptide (Aβ) in the brain has been linked with neuronal death, which progresses in the diagnostic and pathological signs of Alzheimer’s disease (AD). The transition of an unstructured monomeric peptide into self-assembled and more structured aggregates is the crucial conversion from what appears to be a harmless polypeptide into a malignant form that causes synaptotoxicity and neuronal cell death. Despite efforts to identify the toxic form of Aβ, the development of effective treatments for AD is still limited by the highly transient and dynamic nature of interconverting forms of Aβ. The variability within the in vivo “pool” of different Aβ peptides is another complicating factor. Here we review the dynamical interplay between various components that influence the heterogeneous Aβ system, from intramolecular Aβ flexibility to intermolecular dynamics between various Aβ alloforms and external factors. The complex dynamics of Aβ contributes to the causative role of Aβ in the pathogenesis of AD.
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Affiliation(s)
- E Hubin
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, University of Twente, 7500 AE, Enschede, The Netherlands
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91
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Zhang T, Xu W, Mu Y, Derreumaux P. Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity. ACS Chem Neurosci 2014; 5:148-59. [PMID: 24246047 DOI: 10.1021/cn400197x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12-28 and 17-42, none of these studies were conducted on the full-length Aβ1-42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1-42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1-42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1-42 dimer against AD.
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Affiliation(s)
- Tong Zhang
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- State Key Laboratory of Precision Spectroscopy, Department
of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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92
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Nguyen PH, Tarus B, Derreumaux P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer. J Phys Chem B 2014; 118:501-10. [DOI: 10.1021/jp4115404] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Bogdan Tarus
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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Konermann L, Vahidi S, Sowole MA. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal Chem 2013; 86:213-32. [DOI: 10.1021/ac4039306] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
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94
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Zhang H, Cui W, Gross ML. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett 2013; 588:308-17. [PMID: 24291257 DOI: 10.1016/j.febslet.2013.11.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/16/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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