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Article ; Online: Ratiometric Single-Molecule FRET Measurements to Probe Conformational Subpopulations of Intrinsically Disordered Proteins.

Nasir, Irem / Bentley, Emily P / Deniz, Ashok A

Current protocols in chemical biology

2020 Volume 12, Issue 1, Page(s) e80

Abstract: Over the past few decades, numerous examples have demonstrated that intrinsic disorder in proteins lies at the heart of many vital processes, including transcriptional regulation, stress response, cellular signaling, and most recently protein liquid- ... ...

Abstract	Over the past few decades, numerous examples have demonstrated that intrinsic disorder in proteins lies at the heart of many vital processes, including transcriptional regulation, stress response, cellular signaling, and most recently protein liquid-liquid phase separation. The so-called intrinsically disordered proteins (IDPs) involved in these processes have presented a challenge to the classic protein "structure-function paradigm," as their functions do not necessarily involve well-defined structures. Understanding the mechanisms of IDP function is likewise challenging because traditional structure determination methods often fail with such proteins or provide little information about the diverse array of structures that can be related to different functions of a single IDP. Single-molecule fluorescence methods can overcome this ensemble-average masking, allowing the resolution of subpopulations and dynamics and thus providing invaluable insights into IDPs and their function. In this protocol, we describe a ratiometric single-molecule Förster resonance energy transfer (smFRET) routine that permits the investigation of IDP conformational subpopulations and dynamics. We note that this is a basic protocol, and we provide brief information and references for more complex analysis schemes available for in-depth characterization. This protocol covers optical setup preparation and protein handling and provides insights into experimental design and outcomes, together with background information about theory and a brief discussion of troubleshooting. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Ratiometric smFRET detection and analysis of IDPs Support Protocol 1: Fluorophore labeling of a protein through maleimide chemistry Support Protocol 2: Sample chamber preparation Support Protocol 3: Determination of direct excitation of acceptor by donor excitation and leakage of donor emission to acceptor emission channel.
MeSH term(s)	Fluorescence Resonance Energy Transfer/methods ; Fluorescent Dyes/analysis ; Intrinsically Disordered Proteins/analysis ; Intrinsically Disordered Proteins/chemistry ; Protein Conformation ; Single Molecule Imaging/methods
Chemical Substances	Fluorescent Dyes ; Intrinsically Disordered Proteins
Language	English
Publishing date	2020-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2160-4762
ISSN (online)	2160-4762
DOI	10.1002/cpch.80
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Article ; Online: Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions.

Martinez-Yamout, Maria A / Nasir, Irem / Shnitkind, Sergey / Ellis, Jamie P / Berlow, Rebecca B / Kroon, Gerard / Deniz, Ashok A / Dyson, H Jane / Wright, Peter E

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 47, Page(s) e2313835120

Abstract: The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three ...

Abstract	The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREB
MeSH term(s)	Glutamine/metabolism ; Transcriptional Activation ; Cyclic AMP Response Element-Binding Protein/genetics ; Cyclic AMP Response Element-Binding Protein/metabolism ; Gene Expression Regulation ; Binding Sites ; Protein Binding/physiology
Chemical Substances	Glutamine (0RH81L854J) ; Cyclic AMP Response Element-Binding Protein
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2313835120
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Article ; Online: Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation.

Nasir, Irem / Onuchic, Paulo L / Labra, Sergio R / Deniz, Ashok A

Biochimica et biophysica acta. Proteins and proteomics

2019 Volume 1867, Issue 10, Page(s) 980–987

Abstract: Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases ... ...

Abstract	Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions.
MeSH term(s)	Animals ; Cell Nucleolus/chemistry ; Cell Nucleolus/metabolism ; Cytoplasmic Granules/chemistry ; Cytoplasmic Granules/metabolism ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Molecular Imaging ; Neurodegenerative Diseases/metabolism ; Protein Aggregates
Chemical Substances	Intrinsically Disordered Proteins ; Protein Aggregates
Language	English
Publishing date	2019-05-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2019.04.007
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Article: Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation

Nasir, Irem / Onuchic, Paulo L / Labra, Sergio R / Deniz, Ashok A

Biochimica et biophysica acta. 2019 Oct., v. 1867, no. 10

2019

Abstract	Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions.
Keywords	cell nucleolus ; cytoplasmic granules ; fluorescence ; liquids ; motivation ; neoplasms ; neurodegenerative diseases ; organelles ; proteins ; proteome ; separation
Language	English
Dates of publication	2019-10
Size	p. 980-987.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2019.04.007
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Article ; Online: Size and surface chemistry of nanoparticles lead to a variant behavior in the unfolding dynamics of human carbonic anhydrase.

Nasir, Irem / Lundqvist, Martin / Cabaleiro-Lago, Celia

Nanoscale

2015 Volume 7, Issue 41, Page(s) 17504–17515

Abstract: The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and ...

Abstract	The adsorption induced conformational changes of human carbonic anhydrase I (HCAi) and pseudo wild type human carbonic anhydrase II truncated at the 17th residue at the N-terminus (trHCAii) were studied in presence of nanoparticles of different sizes and polarities. Isothermal titration calorimetry (ITC) studies showed that the binding to apolar surfaces is affected by the nanoparticle size in combination with the inherent protein stability. 8-Anilino-1-naphthalenesulfonic acid (ANS) fluorescence revealed that HCAs adsorb to both hydrophilic and hydrophobic surfaces, however the dynamics of the unfolding at the nanoparticle surfaces drastically vary with the polarity. The size of the nanoparticles has opposite effects depending on the polarity of the nanoparticle surface. The apolar nanoparticles induce seconds timescale structural rearrangements whereas polar nanoparticles induce hours timescale structural rearrangements on the same charged HCA variant. Here, a simple model is proposed where the difference in the timescales of adsorption is correlated with the energy barriers for initial docking and structural rearrangements which are firmly regulated by the surface polarity. Near-UV circular dichorism (CD) further supports that both protein variants undergo structural rearrangements at the nanoparticle surfaces regardless of being "hard" or "soft". However, the conformational changes induced by the apolar surfaces differ for each HCA isoform and diverge from the previously reported effect of silica nanoparticles.
MeSH term(s)	Calorimetry ; Carbonic Anhydrase I/chemistry ; Circular Dichroism ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Nanoparticles/chemistry ; Protein Unfolding
Chemical Substances	Carbonic Anhydrase I (EC 4.2.1.-)
Language	English
Publishing date	2015-11-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/c5nr05360a
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Article ; Online: Fluorescent filter-trap assay for amyloid fibril formation kinetics in complex solutions.

Nasir, Irem / Linse, Sara / Cabaleiro-Lago, Celia

ACS chemical neuroscience

2015 Volume 6, Issue 8, Page(s) 1436–1444

Abstract: Amyloid fibrils are the most distinct components of the plaques associated with various neurodegenerative diseases. Kinetic studies of amyloid fibril formation shed light on the microscopic mechanisms that underlie this process as well as the ... ...

Abstract	Amyloid fibrils are the most distinct components of the plaques associated with various neurodegenerative diseases. Kinetic studies of amyloid fibril formation shed light on the microscopic mechanisms that underlie this process as well as the contributions of internal and external factors to the interplay between different mechanistic steps. Thioflavin T is a widely used noncovalent fluorescent probe for monitoring amyloid fibril formation; however, it may suffer from limitations due to the unspecific interactions between the dye and the additives. Here, we present the results of a filter-trap assay combined with the detection of fluorescently labeled amyloid β (Aβ) peptide. The filter-trap assay separates formed aggregates based on size, and the fluorescent label attached to Aβ allows for their detection. The times of half completion of the process (t1/2) obtained by the filter-trap assay are comparable to values from the ThT assay. High concentrations of human serum albumin (HSA) and carboxyl-modified polystyrene nanoparticles lead to an elevated ThT signal, masking a possible fibril formation event. The filter-trap assay allows fibril formation to be studied in the presence of those substances and shows that Aβ fibril formation is kinetically inhibited by HSA and that the amount of fibrils formed are reduced. In contrast, nanoparticles exhibit a dual-behavior governed by their concentration.
MeSH term(s)	Amyloid/chemistry ; Amyloid beta-Peptides/chemistry ; Benzothiazoles ; Chemistry Techniques, Analytical/methods ; Escherichia coli ; Fluorescent Dyes ; Humans ; Kinetics ; Microscopy, Electron, Transmission ; Nanoparticles ; Peptide Fragments/chemistry ; Polystyrenes ; Protein Multimerization ; Serum Albumin/chemistry ; Solutions ; Thiazoles
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Benzothiazoles ; Fluorescent Dyes ; Peptide Fragments ; Polystyrenes ; Serum Albumin ; Solutions ; Thiazoles ; amyloid beta-protein (1-42) ; thioflavin T (2390-54-7)
Language	English
Publishing date	2015-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.5b00104
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Article ; Online: Colchicine and high-intensity rosuvastatin in the treatment of non-critically ill patients hospitalised with COVID-19: a randomised clinical trial.

BMJ open

2023 Volume 13, Issue 2, Page(s) e067910

Abstract: Objective: To evaluate the effect of colchicine and high-intensity rosuvastatin in addition to standard of care on the progression of COVID-19 disease in hospitalised patients.: Design: A pragmatic, open-label, multicentre, randomised controlled ... ...

Abstract	Objective: To evaluate the effect of colchicine and high-intensity rosuvastatin in addition to standard of care on the progression of COVID-19 disease in hospitalised patients. Design: A pragmatic, open-label, multicentre, randomised controlled trial conducted from October 2020 to September 2021. Follow-up was conducted at 30 and 60 days. The electronic medical record was used at all stages of the trial including screening, enrolment, randomisation, event ascertainment and follow-up. Setting: Four centres in the Yale New Haven Health System. Participants: Non-critically ill hospitalised patients with COVID-19. Interventions: Patients were randomised 1:1 to either colchicine plus high-intensity rosuvastatin in addition to standard of care versus standard of care alone. Assigned treatment was continued for the duration of index hospitalisation or 30 days, whichever was shorter. Primary and secondary outcome measures: The prespecified primary endpoint was progression to severe COVID-19 disease (new high-flow or non-invasive ventilation, mechanical ventilation, need for vasopressors, renal replacement therapy or extracorporeal membrane oxygenation, or death) or arterial/venous thromboembolic events (ischaemic stroke, myocardial infarction, deep venous thrombosis or pulmonary embolism) evaluated at 30 days. Results: Among the 250 patients randomised in this trial (125 to each arm), the median age was 61 years, 44% were women, 15% were Black and 26% were Hispanic/Latino. As part of the standard of care, patients received remdesivir (87%), dexamethasone (92%), tocilizumab (18%), baricitinib (2%), prophylactic/therapeutic anticoagulation (98%) and aspirin (91%). The trial was terminated early by the data and safety monitoring board for futility. No patients were lost to follow-up due to electronic medical record follow-up. There was no significant difference in the primary endpoint at 30 days between the active arm and standard of care arm (15.2% vs 8.8%, respectively, p=0.17). Conclusions: In this small, open-label, randomised trial of non-critically ill hospitalised patients with COVID-19, the combination of colchicine and rosuvastatin in addition to standard of care did not appear to reduce the risk of progression of COVID-19 disease or thromboembolic events, although the trial was underpowered due to a lower-than-expected event rate. The trial leveraged the power of electronic medical records for efficiency and improved follow-up and demonstrates the utility of incorporating electronic medical records into future trials. Trial registration: NCT04472611.
MeSH term(s)	Female ; Humans ; Middle Aged ; Male ; COVID-19 ; Rosuvastatin Calcium ; SARS-CoV-2 ; Colchicine ; Brain Ischemia ; Stroke ; Treatment Outcome
Chemical Substances	Rosuvastatin Calcium (83MVU38M7Q) ; Colchicine (SML2Y3J35T)
Language	English
Publishing date	2023-02-24
Publishing country	England
Document type	Randomized Controlled Trial ; Multicenter Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2022-067910
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Article ; Online: The syndemic burden of HIV/AIDS in Africa amidst the COVID-19 pandemic.

Uwishema, Olivier / Taylor, Charles / Lawal, Lukman / Hamiidah, Nakyanzi / Robert, Isoke / Nasir, Abdulrasheed / Chalhoub, Elie / Sun, Jeffrey / Akin, Burak T / Adanur, Irem / Mwazighe, Rehema M / Onyeaka, Helen

Immunity, inflammation and disease

2021 Volume 10, Issue 1, Page(s) 26–32

Abstract: Introduction: The human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) has long affected millions of individuals across the globe. Historically, the prevalence of this disease is particularly noted within the African continent. ... ...

Abstract	Introduction: The human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) has long affected millions of individuals across the globe. Historically, the prevalence of this disease is particularly noted within the African continent. Before the coronavirus disease 2019 (COVID-19) pandemic, many African countries struggled to effectively manage the increasing burden associated with HIV/AIDS. There is now a need to reassess this in a COVID-19 pandemic context so that the impact of COVID-19 on HIV/AIDS healthcare within Africa can be adequately evaluated. Methods: Data collection was performed on the PubMed, Ovid MEDLINE and Embase bibliographical databases with a predefined search strategy. Searches were performed in blind duplicate and all articles considering COVID-19 and HIV/AIDS within African healthcare were considered. Results: The COVID-19 pandemic has severely exacerbated the many issues surrounding HIV/AIDS care within many African countries. These impacts are noticeable in medical, psychological, and socio-political contexts. Conclusions: Before efforts are made to improve the provision of HIV/AIDS and COVID-19 care within Africa, it is important that this issue is brought to the attention of the scientific and clinical community so that the continent can receive the necessary support and aid.
MeSH term(s)	Acquired Immunodeficiency Syndrome/epidemiology ; Africa/epidemiology ; COVID-19 ; HIV Infections/epidemiology ; Humans ; Pandemics ; SARS-CoV-2 ; Syndemic
Language	English
Publishing date	2021-10-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2740382-8
ISSN	2050-4527 ; 2050-4527
ISSN (online)	2050-4527
ISSN	2050-4527
DOI	10.1002/iid3.544
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Article ; Online: A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli

Kalyani Sanagavarapu / Elisabeth Nüske / Irem Nasir / Georg Meisl / Jasper N. Immink / Pietro Sormanni / Michele Vendruscolo / Tuomas P. J. Knowles / Anders Malmendal / Celia Cabaleiro-Lago / Sara Linse

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 14

Abstract: Abstract Overexpression of recombinant proteins in bacteria may lead to their aggregation and deposition in inclusion bodies. Since the conformational properties of proteins in inclusion bodies exhibit many of the characteristics typical of amyloid ... ...

Abstract	Abstract Overexpression of recombinant proteins in bacteria may lead to their aggregation and deposition in inclusion bodies. Since the conformational properties of proteins in inclusion bodies exhibit many of the characteristics typical of amyloid fibrils. Based on these findings, we hypothesize that the rate at which proteins form amyloid fibrils may be predicted from their propensity to form inclusion bodies. To establish a method based on this concept, we first measured by SDS-PAGE and confocal microscopy the level of inclusion bodies in E. coli cells overexpressing the 40-residue amyloid-beta peptide, Aβ40, wild-type and 24 charge mutants. We then compared these results with a number of existing computational aggregation propensity predictors as well as the rates of aggregation measured in vitro for selected mutants. Our results show a strong correlation between the level of inclusion body formation and aggregation propensity, thus demonstrating the power of this approach and its value in identifying factors modulating aggregation kinetics.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
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Article ; Online: A method of predicting the in vitro fibril formation propensity of Aβ40 mutants based on their inclusion body levels in E. coli.

Sanagavarapu, Kalyani / Nüske, Elisabeth / Nasir, Irem / Meisl, Georg / Immink, Jasper N / Sormanni, Pietro / Vendruscolo, Michele / Knowles, Tuomas P J / Malmendal, Anders / Cabaleiro-Lago, Celia / Linse, Sara

Scientific reports

2019 Volume 9, Issue 1, Page(s) 3680

Abstract: Overexpression of recombinant proteins in bacteria may lead to their aggregation and deposition in inclusion bodies. Since the conformational properties of proteins in inclusion bodies exhibit many of the characteristics typical of amyloid fibrils. Based ...

Abstract	Overexpression of recombinant proteins in bacteria may lead to their aggregation and deposition in inclusion bodies. Since the conformational properties of proteins in inclusion bodies exhibit many of the characteristics typical of amyloid fibrils. Based on these findings, we hypothesize that the rate at which proteins form amyloid fibrils may be predicted from their propensity to form inclusion bodies. To establish a method based on this concept, we first measured by SDS-PAGE and confocal microscopy the level of inclusion bodies in E. coli cells overexpressing the 40-residue amyloid-beta peptide, Aβ40, wild-type and 24 charge mutants. We then compared these results with a number of existing computational aggregation propensity predictors as well as the rates of aggregation measured in vitro for selected mutants. Our results show a strong correlation between the level of inclusion body formation and aggregation propensity, thus demonstrating the power of this approach and its value in identifying factors modulating aggregation kinetics.
MeSH term(s)	Alzheimer Disease/metabolism ; Amyloid/genetics ; Amyloid/metabolism ; Amyloid beta-Peptides/genetics ; Amyloid beta-Peptides/metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/cytology ; Escherichia coli/genetics ; Humans ; Inclusion Bodies/metabolism ; Kinetics ; Microscopy, Confocal ; Mutation ; Peptide Fragments/genetics ; Peptide Fragments/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Peptide Fragments ; Recombinant Proteins ; amyloid beta-protein (1-40)
Language	English
Publishing date	2019-03-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-39216-z
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