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Mitchell J, Balem F, Tirupula K, Man D, Dhiman HK, Yanamala N, Ollesch J, Planas-Iglesias J, Jennings BJ, Gerwert K, Iannaccone A, Klein-Seetharaman J. Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin. PLoS One 2019; 14:e0214639. [PMID: 31100078 PMCID: PMC6524802 DOI: 10.1371/journal.pone.0214639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
Mutations in the RHO gene encoding for the visual pigment protein, rhodopsin, are among the most common cause of autosomal dominant retinitis pigmentosa (ADRP). Previous studies of ADRP mutations in different domains of rhodopsin have indicated that changes that lead to more instability in rhodopsin structure are responsible for more severe disease in patients. Here, we further test this hypothesis by comparing side-by-side and therefore quantitatively two RHO mutations, N15S and P23H, both located in the N-terminal intradiscal domain. The in vitro biochemical properties of these two rhodopsin proteins, expressed in stably transfected tetracycline-inducible HEK293S cells, their UV-visible absorption, their Fourier transform infrared, circular dichroism and Metarhodopsin II fluorescence spectroscopy properties were characterized. As compared to the severely impaired P23H molecular function, N15S is only slightly defective in structure and stability. We propose that the molecular basis for these structural differences lies in the greater distance of the N15 residue as compared to P23 with respect to the predicted rhodopsin folding core. As described previously for WT rhodopsin, addition of the cytoplasmic allosteric modulator chlorin e6 stabilizes especially the P23H protein, suggesting that chlorin e6 may be generally beneficial in the rescue of those ADRP rhodopsin proteins whose stability is affected by amino acid replacement.
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Affiliation(s)
- James Mitchell
- Division of Biomedical Sciences, Medical School, University of Warwick, Coventry, United Kingdom
| | - Fernanda Balem
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kalyan Tirupula
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - David Man
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Harpreet Kaur Dhiman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Julian Ollesch
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Joan Planas-Iglesias
- Division of Biomedical Sciences, Medical School, University of Warwick, Coventry, United Kingdom
| | - Barbara J Jennings
- Retinal Degeneration & Ophthalmic Genetics Service & Lions Visual Function Diagnostic Lab, Hamilton Eye Institute, Dept. Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Alessandro Iannaccone
- Retinal Degeneration & Ophthalmic Genetics Service & Lions Visual Function Diagnostic Lab, Hamilton Eye Institute, Dept. Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Judith Klein-Seetharaman
- Division of Biomedical Sciences, Medical School, University of Warwick, Coventry, United Kingdom
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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Nabers A, Ollesch J, Schartner J, Kötting C, Genius J, Haußmann U, Klafki H, Wiltfang J, Gerwert K. An infrared sensor analysing label-free the secondary structure of the Abeta peptide in presence of complex fluids. JOURNAL OF BIOPHOTONICS 2016; 9:224-234. [PMID: 25808829 DOI: 10.1002/jbio.201400145] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/19/2015] [Accepted: 03/01/2015] [Indexed: 06/04/2023]
Abstract
The secondary structure change of the Abeta peptide to beta-sheet was proposed as an early event in Alzheimer's disease. The transition may be used for diagnostics of this disease in an early state. We present an Attenuated Total Reflection (ATR) sensor modified with a specific antibody to extract minute amounts of Abeta peptide out of a complex fluid. Thereby, the Abeta peptide secondary structure was determined in its physiological aqueous environment by FTIR-difference-spectroscopy. The presented results open the door for label-free Alzheimer diagnostics in cerebrospinal fluid or blood. It can be extended to further neurodegenerative diseases. An immunologic ATR-FTIR sensor for Abeta peptide secondary structure analysis in complex fluids is presented.
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Affiliation(s)
- Andreas Nabers
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Julian Ollesch
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jonas Schartner
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Carsten Kötting
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Just Genius
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Ute Haußmann
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Hans Klafki
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Jens Wiltfang
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
- University Medical Center, Department of Psychiatry and Psychotherapy, Georg-August-University, 37073, Göttingen, Germany
| | - Klaus Gerwert
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany.
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3
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Nabers A, Ollesch J, Schartner J, Kötting C, Genius J, Hafermann H, Klafki H, Gerwert K, Wiltfang J. Amyloid-β-Secondary Structure Distribution in Cerebrospinal Fluid and Blood Measured by an Immuno-Infrared-Sensor: A Biomarker Candidate for Alzheimer's Disease. Anal Chem 2016; 88:2755-62. [PMID: 26828829 DOI: 10.1021/acs.analchem.5b04286] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The misfolding of the Amyloid-beta (Aβ) peptide into β-sheet enriched conformations was proposed as an early event in Alzheimer's Disease (AD). Here, the Aβ peptide secondary structure distribution in cerebrospinal fluid (CSF) and blood plasma of 141 patients was measured with an immuno-infrared-sensor. The sensor detected the amide I band, which reflects the overall secondary structure distribution of all Aβ peptides extracted from the body fluid. We observed a significant downshift of the amide I band frequency of Aβ peptides in Dementia Alzheimer type (DAT) patients, which indicated an overall shift to β-sheet. The secondary structure distribution of all Aβ peptides provides a better marker for DAT detection than a single Aβ misfold or the concentration of a specific oligomer. The discrimination between DAT and disease control patients according to the amide I frequency was in excellent agreement with the clinical diagnosis (accuracy 90% for CSF and 84% for blood). The amide I band maximum above or below the decisive marker frequency appears as a novel spectral biomarker candidate of AD. Additionally, a preliminary proof-of-concept study indicated an amide I band shift below the marker band already in patients with mild cognitive impairment due to AD. The presented immuno-IR-sensor method represents a promising, simple, robust, and label-free diagnostic tool for CSF and blood analysis.
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Affiliation(s)
- Andreas Nabers
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Julian Ollesch
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Jonas Schartner
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Just Genius
- Clinics for Psychiatry and Psychotherapy, LVR-Clinical Center Essen , 45147 Essen, Germany
| | - Henning Hafermann
- Clinics for Psychiatry and Psychotherapy, LVR-Clinical Center Essen , 45147 Essen, Germany
| | - Hans Klafki
- Department of Psychiatry and Psychotherapy, Georg-August-University Göttingen, University Medical Center , 37099 Göttingen, Germany
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Jens Wiltfang
- Clinics for Psychiatry and Psychotherapy, LVR-Clinical Center Essen , 45147 Essen, Germany.,Department of Psychiatry and Psychotherapy, Georg-August-University Göttingen, University Medical Center , 37099 Göttingen, Germany.,German Center for Neurodegenerative Diseases (DZNE) , 37099 Göttingen, Germany
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4
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Kumar ST, Meinhardt J, Fuchs AK, Aumüller T, Leppert J, Büchele B, Knüpfer U, Ramachandran R, Yadav JK, Prell E, Morgado I, Ohlenschläger O, Horn U, Simmet T, Görlach M, Fändrich M. Structure and biomedical applications of amyloid oligomer nanoparticles. ACS NANO 2014; 8:11042-11052. [PMID: 25337989 DOI: 10.1021/nn503960h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid oligomers are nonfibrillar polypeptide aggregates linked to diseases, such as Alzheimer's and Parkinson's. Here we show that these aggregates possess a compact, quasi-crystalline architecture that presents significant nanoscale regularity. The amyloid oligomers are dynamic assemblies and are able to release their individual subunits. The small oligomeric size and spheroid shape confer diffusible characteristics, electrophoretic mobility, and the ability to enter hydrated gel matrices or cells. We finally showed that the amyloid oligomers can be labeled with both fluorescence agents and iron oxide nanoparticles and can target macrophage cells. Oligomer amyloids may provide a new biological nanomaterial for improved targeting, drug release, and medical imaging.
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Affiliation(s)
- Senthil T Kumar
- Institute for Pharmaceutical Biotechnology, Ulm University , 89081 Ulm, Germany
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Li C, Kumar S, Montigny C, le Maire M, Barth A. Quality assessment of recombinant proteins by infrared spectroscopy. Characterisation of a protein aggregation related band of the Ca2+-ATPase. Analyst 2014; 139:4231-40. [DOI: 10.1039/c4an00483c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FTIR spectroscopy detects aggregates of recombinantly produced protein and can therefore be used for quality control.
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Affiliation(s)
- Chenge Li
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- SE-106 91 Stockholm, Sweden
| | - Saroj Kumar
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- SE-106 91 Stockholm, Sweden
| | | | | | - Andreas Barth
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- SE-106 91 Stockholm, Sweden
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Ollesch J, Drees SL, Heise HM, Behrens T, Brüning T, Gerwert K. FTIR spectroscopy of biofluids revisited: an automated approach to spectral biomarker identification. Analyst 2013; 138:4092-102. [PMID: 23712384 DOI: 10.1039/c3an00337j] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The extraction of disease specific information from Fourier transform infrared (FTIR) spectra of human body fluids demands the highest standards of accuracy and reproducibility of measurements because the expected spectral differences between healthy and diseased subjects are very small in relation to a large background absorbance of the whole sample. Here, we demonstrate that with the increased sensitivity of modern FTIR spectrometers, automatisation of sample preparation and modern bioinformatics, it is possible to identify and validate spectral biomarker candidates for distinguishing between urinary bladder cancer (UBC) and inflammation in suspected bladder cancer patients. The current dataset contains spectra of blood serum and plasma samples of 135 patients. All patients underwent cytology and pathological biopsy characterization to distinguish between patients without UBC (46) and confirmed UBC cases (89). A minimally invasive blood test could spare control patients a repeated cystoscopy including a transurethral biopsy, and three-day stationary hospitalisation. Blood serum, EDTA and citrate plasma were collected from each patient and processed following predefined strict standard operating procedures. Highly reproducible dry films were obtained by spotting sub-nanoliter biofluid droplets in defined patterns, which were compared and optimized. Particular attention was paid to the automatisation of sample preparation and spectral preprocessing to exclude errors by manual handling. Spectral biomarker candidates were identified from absorbance spectra and their 1(st) and 2(nd) derivative spectra using an advanced Random Forest (RF) approach. It turned out that the 2(nd) derivative spectra were most useful for classification. Repeat validation on 21% of the dataset not included in predictor training with Linear Discriminant Analysis (LDA) classifiers and Random Forests (RFs) yielded a sensitivity of 93 ± 10% and a specificity of 46 ± 18% for bladder cancer. The low specificity can be most likely attributed to the unbalanced and small number of control samples. Using this approach, spectral biomarker candidates in blood-derived biofluids were identified, which allow us to distinguish between cancer and inflammation, but the observed differences were tiny. Obviously, a much larger sample number has to be investigated to reliably validate such candidates.
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Affiliation(s)
- Julian Ollesch
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstrasse 150, 44780 Bochum, Germany.
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7
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Naeem A, Amani S. Deciphering structural intermediates and genotoxic fibrillar aggregates of albumins: a molecular mechanism underlying for degenerative diseases. PLoS One 2013; 8:e54061. [PMID: 23342075 PMCID: PMC3544675 DOI: 10.1371/journal.pone.0054061] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/05/2012] [Indexed: 11/23/2022] Open
Abstract
The misfolding and aggregation of proteins is involved in some of the most prevalent neurodegenerative disorders. The importance of human serum albumin (HSA) stems from the fact that it is involved in bio-regulatory and transport phenomena. Here the effect of acetonitrile (ACN) on the conformational stability of HSA and by comparison, ovalbumin (OVA) has been evaluated in the presence and absence of NaCl. The results show the presence of significant amount of secondary structure in HSA at 70% ACN and in OVA at 50% ACN, as evident from far-UV Circular Dichroism (CD) and Attenuated Total Reflection Fourier transformed infra red spectroscopy (ATR-FTIR). Tryptophan and 8-Anilino-1-Naphthalene-Sulphonic acid (ANS) fluorescence indicate altered tryptophan environment and high ANS binding suggesting a compact “molten globule”-like conformation with enhanced exposure of hydrophobic surface area. However, in presence of NaCl no intermediate state was observed. Detection of aggregates in HSA and OVA was possible at 90% ACN. Aggregates possess extensive β-sheet structure as revealed by far-UV CD and ATR-FTIR. These aggregates exhibit increase Thioflavin T (Th T) fluorescence with a red shift of Congo red (CR) absorption spectrum. X-ray diffraction (XRD) and Scanning Electron Microscopy (SEM) analysis confirmed the presence of fibrillar aggregates. Single cell gel electrophoresis (SCGE) assay of these fibrillar aggregates showed the DNA damage resulting in cell necrosis confirming their genotoxic nature. Some proteins not related to any human disease form fibrils in vitro. In the present study ACN gives access to a model system to study the process of aggregation.
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Affiliation(s)
- Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
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Li H, Ye S, Wei F, Ma S, Luo Y. In situ molecular-level insights into the interfacial structure changes of membrane-associated prion protein fragment [118-135] investigated by sum frequency generation vibrational spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:16979-16988. [PMID: 23116165 DOI: 10.1021/la302655p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein aggregation is associated with many "protein deposition diseases". A precise molecular detail of the conformational transitions of such a membrane-associated protein structure is critical to understand the disease mechanism and develop effective treatments. One potential model peptide for studying the mechanism of protein deposition diseases is prion protein fragment [118-135] (PrP118-135), which shares homology with the C-terminal domain of the Alzheimer's β-amyloid peptide. In this study, sum frequency generation vibrational spectroscopy (SFG-VS) has been applied to characterize interactions between PrP118-135 and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayer in situ. The conformation change and orientation of PrP118-135 in lipid bilayers have been determined using SFG spectra with different polarization combinations. It is found that low-concentration PrP118-135 predominantly adopts α-helical structure but with tiny β-sheet structure. With the PrP118-135 concentration increasing, the molecular number ratio of parallel β-sheet structure increases and reaches about 44% at a concentration of 0.10 mg/mL, indicating the formation of abnormally folded scrapie isoforms. The α-helical structure inserts into the lipid bilayer with a tilt angle of ~32° versus the surface normal, while the β-sheet structure lies down on the lipid bilayer with the tilt and twist angle both of 90°. The 3300 cm(-1) N-H stretching signal in psp spectra arises from α-helical structure at low PrP concentration and from the β-sheet structure at high PrP concentration. Results from this study will provide an in-depth insight into the early events in the aggregation of PrP in cell membrane.
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Affiliation(s)
- Hongchun Li
- Hefei National Laboratory for Physical Sciences at Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, People's Republic of China 230026
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Qi X, Moore RA, McGuirl MA. Dissociation of recombinant prion protein fibrils into short protofilaments: implications for the endocytic pathway and involvement of the N-terminal domain. Biochemistry 2012; 51:4600-8. [PMID: 22591453 DOI: 10.1021/bi300201e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fibril dissociation is necessary for efficient conversion of normal prion protein to its misfolded state and continued propagation into amyloid. Recent studies have revealed that conversion occurs along the endocytic pathway. To improve our understanding of the dissociation process, we have investigated the effect of low pH on the stability of recombinant prion fibrils. We show that under conditions that mimic the endocytic environment, amyloid fibrils made from full-length prion protein dissociate both laterally and axially to form protofilaments. Approximately 5% of the protofilaments are short enough to be considered soluble and contain ~100-300 monomers per structure; these also retain the biophysical characteristics of the filaments. We propose that protonation of His residues and charge repulsion in the N-terminal domain trigger fibril dissociation. Our data suggest that lysosomes and late endosomes are competent milieus for propagating the misfolded state not only by destabilizing the normal prion protein but also by accelerating the dissociation of fibrils into smaller structures that may act as seeds.
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Affiliation(s)
- Xu Qi
- Center for Biomolecular Structure and Dynamics and Division of Biological Sciences, 204 CHCB, The University of Montana, Missoula, Montana 59812, United States
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Cao Z, Liu L, Wu P, Wang J. Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution. Acta Biochim Biophys Sin (Shanghai) 2011; 43:172-80. [PMID: 21289072 DOI: 10.1093/abbs/gmr002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The structural and thermodynamics characters of α-syn12 (residues 1-12 of the human α-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational α-helix and an irregular structure, respectively. Each replica was run for 300 ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded β-hairpin structure, and favorite conformations. The results showed that the isolated α-syn12 peptide in water adopted four different conformational states: the first state was a β-hairpin ensemble with Turn(9-6) and four hydrogen bonds, the second state was a β-hairpin ensemble with two turns (Turn(9-6) and Turn(5-2)) and three hydrogen bonds, the third state was a disordered structure with both Turn(8-5) and Turn(5-2), and the last state was a π-helix ensemble. Meanwhile, we studied the free energy change of α-syn12 peptide from the unfolded state to the β-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition. The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated α-syn12 peptide in water by T-REMD.
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Affiliation(s)
- Zanxia Cao
- Key Lab of Biophysics in Universities of Shandong, Dezhou, China
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Changing the solvent accessibility of the prion protein disulfide bond markedly influences its trafficking and effect on cell function. Biochem J 2010; 428:169-82. [PMID: 20337594 DOI: 10.1042/bj20091635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prion diseases are fatal transmissible neurodegenerative diseases that result from structural conversion of the prion protein into a disease-associated isoform. The prion protein contains a single disulfide bond. Our analysis of all NMR structures of the prion protein (total of 440 structures over nine species) containing an explicit disulfide bond reveals that the bond exists predominantly in a stable low-energy state, but can also adopt a high-energy configuration. The side chains of two tyrosine residues and one phenylalanine residue control access of solvent to the disulfide bond. Notably, the side chains rotate away from the disulfide bond in the high-energy state, exposing the disulfide bond to solvent. The importance of these aromatic residues for protein function was analysed by mutating them to alanine residues and analysing the properties of the mutant proteins using biophysical and cell biological approaches. Whereas the mutant protein behaved similarly to wild-type prion protein in recombinant systems, the mutants were retained in the endoplasmic reticulum of mammalian cells and degraded by the proteasomal system. The cellular behaviour of the aromatic residue mutants was similar to the cellular behaviour of a disulfide bond mutant prion protein in which the cysteine residues were replaced with alanine, a result which is consistent with an unstable disulfide bond in the aromatic residue mutants. These observations suggest that the conformation of the prion protein disulfide bond may have implications for correct maturation and function of this protein.
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Morris AM, Watzky MA, Finke RG. Protein aggregation kinetics, mechanism, and curve-fitting: A review of the literature. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:375-97. [DOI: 10.1016/j.bbapap.2008.10.016] [Citation(s) in RCA: 507] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 10/17/2008] [Accepted: 10/27/2008] [Indexed: 11/25/2022]
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13
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Güldenhaupt J, Adigüzel Y, Kuhlmann J, Waldmann H, Kötting C, Gerwert K. Secondary structure of lipidated Ras bound to a lipid bilayer. FEBS J 2009; 275:5910-8. [PMID: 19021766 DOI: 10.1111/j.1742-4658.2008.06720.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ras proteins are small guanine nucleotide binding proteins that regulate many cellular processes, including growth control. They undergo distinct post-translational lipid modifications that are required for appropriate targeting to membranes. This, in turn, is critical for Ras biological function. However, most in vitro studies have been conducted on nonlipidated truncated forms of Ras proteins. Here, for the first time, attenuated total reflectance-FTIR studies of lipid-modified membrane-bound N-Ras are performed, and compared with nonlipidated truncated Ras in solution. For these studies, lipidated N-Ras was prepared by linking a farnesylated and hexadecylated N-Ras lipopeptide to a truncated N-Ras protein (residues 1-181). It was then bound to a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer tethered on an attenuated total reflectance crystal. The structurally sensitive amide I absorbance band in the IR was detected and analysed to determine the secondary structure of the protein. The NMR three-dimensional structure of truncated Ras was used to calibrate the contributions of the different secondary structural elements to the amide I absorbance band of truncated Ras. Using this novel approach, the correct decomposition was selected from several possible solutions. The same parameter set was then used for the membrane-bound lipidated Ras, and provided a reliable decomposition for the membrane-bound form in comparison with truncated Ras. This comparison indicates that the secondary structure of membrane-bound Ras is similar to that determined for the nonlipidated truncated Ras protein for the highly conserved G-domain. This result validates the multitude of investigations of truncated Ras without anchor in vitro. The novel attenuated total reflectance approach opens the way for detailed studies of the interaction network of the membrane-bound Ras protein.
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Frost B, Ollesch J, Wille H, Diamond MI. Conformational diversity of wild-type Tau fibrils specified by templated conformation change. J Biol Chem 2008; 284:3546-51. [PMID: 19010781 DOI: 10.1074/jbc.m805627200] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tauopathies are sporadic and genetic neurodegenerative diseases characterized by aggregation of the microtubule-associated protein Tau. Tau pathology occurs in over 20 phenotypically distinct neurodegenerative diseases, including Alzheimer disease and frontotemporal dementia. The molecular basis of this diversity among sporadic tauopathies is unknown, but distinct fibrillar wild-type (WT) Tau conformations could play a role. Using Fourier transform infrared spectroscopy, circular dichroism, and electron microscopy, we show that WT Tau fibrils and P301L/V337M Tau fibrils have distinct secondary structures, fragilities, and morphologies. Furthermore, P301L/V337M fibrillar seeds induce WT Tau monomer to form a novel fibrillar conformation, termed WT*, that is maintained over multiple seeding reactions. WT* has secondary structure, fragility, and morphology that are similar to P301L/V337M fibrils and distinct from WT fibrils. WT Tau is thus capable of conformational diversity that arises via templated conformation change, as has been described for amyloid beta, beta2-microglobulin, and prion proteins.
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Affiliation(s)
- Bess Frost
- Department of Neurology, University of California, San Francisco, California 94158, USA
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15
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Natalello A, Prokorov VV, Tagliavini F, Morbin M, Forloni G, Beeg M, Manzoni C, Colombo L, Gobbi M, Salmona M, Doglia SM. Conformational Plasticity of the Gerstmann–Sträussler–Scheinker Disease Peptide as Indicated by Its Multiple Aggregation Pathways. J Mol Biol 2008; 381:1349-61. [DOI: 10.1016/j.jmb.2008.06.063] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/17/2008] [Accepted: 06/21/2008] [Indexed: 10/21/2022]
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Abstract
Misfolding and subsequent aggregation of endogenous proteins constitute essential steps in many human disorders, including Alzheimer and prion diseases. In most prion protein-folding studies, the posttranslational modifications, the lipid anchor in particular, were lacking. Here, we studied a fully posttranslationally modified cellular prion protein, carrying two N-glycosylations and the natural GPI anchor. We used time-resolved FTIR to study the prion protein secondary structure changes when binding to a raft-like lipid membrane via its GPI anchor. We observed that membrane anchoring above a threshold concentration induced refolding of the prion protein to intermolecular beta-sheets. Such transition is not observed in solution and is membrane specific. Excessive membrane anchoring, analyzed with molecular sensitivity, is thought to be a crucial event in the development of prion diseases.
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17
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Kretlow A, Wang Q, Beekes M, Naumann D, Miller LM. Changes in protein structure and distribution observed at pre-clinical stages of scrapie pathogenesis. Biochim Biophys Acta Mol Basis Dis 2008; 1782:559-65. [PMID: 18625306 DOI: 10.1016/j.bbadis.2008.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 06/02/2008] [Accepted: 06/03/2008] [Indexed: 01/19/2023]
Abstract
Scrapie is a neurodegenerative disorder that involves the misfolding, aggregation and accumulation of the prion protein (PrP). The normal cellular PrP (PrP(C)) is rich in alpha-helical secondary structure, whereas the disease-associated pathogenic form of the protein (PrP(Sc)) has an anomalously high beta-sheet content. In this study, protein structural changes were examined in situ in the dorsal root ganglia from perorally 263K scrapie-infected and mock-infected hamsters using synchrotron Fourier Transform InfraRed Microspectroscopy (FTIRM) at four time points over the course of the disease (pre-clinical, 100 and 130 days post-infection (dpi); first clinical signs ( approximately 145 dpi); and terminal ( approximately 170 dpi)). Results showed clear changes in the total protein content, structure, and distribution as the disease progressed. At pre-clinical time points, the scrapie-infected animals exhibited a significant increase in protein expression, but the beta-sheet protein content was significantly lower than controls. Based on these findings, we suggest that the pre-clinical stages of scrapie are characterized by an overexpression of proteins low in beta-sheet content. As the disease progressed, the beta-sheet content increased significantly. Immunostaining with a PrP-specific antibody, 3F4, confirmed that this increase was partly - but not solely - due to the formation of PrP(Sc) in the tissue and indicated that other proteins high in beta-sheet were produced, either by overexpression or misfolding. Elevated beta-sheet was observed near the cell membrane at pre-clinical time points and also in the cytoplasm of infected neurons at later stages of infection. At the terminal stage of the disease, the protein expression declined significantly, likely due to degeneration and death of neurons. These dramatic changes in protein content and structure, especially at pre-clinical time points, emphasize the possibility for identifying other proteins involved in early pathogenesis, which are important for a further understanding of the disease.
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Affiliation(s)
- Ariane Kretlow
- P25, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
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18
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Secondary structure and distribution of fusogenic LV-peptides in lipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:435-45. [DOI: 10.1007/s00249-007-0233-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 10/11/2007] [Accepted: 10/28/2007] [Indexed: 11/26/2022]
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