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  1. Book: Computational approaches for understanding dynamical systems

    Strodel, Birgit

    protein folding and assembly

    (Progress in molecular biology and translational science ; volume 170)

    2020  

    Author's details edited by Birgit Strodel, Bogdan Barz
    Series title Progress in molecular biology and translational science ; volume 170
    Collection
    Language English
    Size xv, 535 Seiten, Illustrationen
    Edition First edition
    Publisher Elsevier Academic Press
    Publishing place Cambridge, MA
    Publishing country United States
    Document type Book
    HBZ-ID HT020480170
    ISBN 978-0-12-821135-9 ; 0-12-821135-0
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Uc I Zs 357 -170- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins.

    Strodel, Birgit

    Journal of molecular biology

    2021  Volume 433, Issue 20, Page(s) 167182

    Abstract: The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it ... ...

    Abstract The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it only treats about half of the human proteome, as the remaining proteins are intrinsically disordered or contain disordered regions. By definition these proteins differ from natively folded proteins and do not adopt a properly folded structure in solution. However these intrinsically disordered proteins (IDPs) also systematically differ in amino acid composition and uniquely often become folded upon binding to an interaction partner. These factors preclude solving IDP structures by current machine-learning methods like AlphaFold, which also cannot solve the protein aggregation problem, since this meta-folding process can give rise to different aggregate sizes and structures. An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. These energy landscapes are very different from those of 'simple' protein folding, where one energy funnel leads to a unique protein structure. Instead, the energy landscapes of IDP conformational switching and protein aggregation feature a number of minima for different competing low-energy structures. In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes.
    MeSH term(s) Amyloid/chemistry ; Animals ; Humans ; Intrinsically Disordered Proteins/chemistry ; Models, Molecular ; Protein Aggregates ; Protein Conformation ; Protein Folding ; Thermodynamics
    Chemical Substances Amyloid ; Intrinsically Disordered Proteins ; Protein Aggregates
    Language English
    Publishing date 2021-08-03
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167182
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
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  3. Article ; Online: Amyloid aggregation simulations: challenges, advances and perspectives.

    Strodel, Birgit

    Current opinion in structural biology

    2020  Volume 67, Page(s) 145–152

    Abstract: In amyloid aggregation diseases soluble proteins coalesce into a wide array of undesirable structures, ranging through oligomers and prefibrillar assemblies to highly ordered amyloid fibrils and plaques. Explicit-solvent all-atom molecular dynamics (MD) ... ...

    Abstract In amyloid aggregation diseases soluble proteins coalesce into a wide array of undesirable structures, ranging through oligomers and prefibrillar assemblies to highly ordered amyloid fibrils and plaques. Explicit-solvent all-atom molecular dynamics (MD) simulations of amyloid aggregation have been performed for almost 20 years, revealing valuable information about this phenomenon. However, these simulations are challenged by three main problems. Firstly, current force fields modeling amyloid aggregation are insufficiently accurate. Secondly, the protein concentrations in MD simulations are usually orders of magnitude higher than those used in vitro or found in vivo, which has direct consequences on the aggregates that form. Finally, the third problem is the well-known time-scale limit of MD simulations. In this review I highlight recent approaches to overcome these three limitations.
    MeSH term(s) Amyloid ; Amyloid beta-Peptides ; Amyloidogenic Proteins ; Molecular Dynamics Simulation ; Solvents
    Chemical Substances Amyloid ; Amyloid beta-Peptides ; Amyloidogenic Proteins ; Solvents
    Language English
    Publishing date 2020-12-03
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2020.10.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3206: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  4. Article: Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins

    Strodel, Birgit

    Journal of molecular biology. 2021 Oct. 01, v. 433, no. 20

    2021  

    Abstract: The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it ... ...

    Abstract The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it only treats about half of the human proteome, as the remaining proteins are intrinsically disordered or contain disordered regions. By definition these proteins differ from natively folded proteins and do not adopt a properly folded structure in solution. However these intrinsically disordered proteins (IDPs) also systematically differ in amino acid composition and uniquely often become folded upon binding to an interaction partner. These factors preclude solving IDP structures by current machine-learning methods like AlphaFold, which also cannot solve the protein aggregation problem, since this meta-folding process can give rise to different aggregate sizes and structures. An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. These energy landscapes are very different from those of ‘simple’ protein folding, where one energy funnel leads to a unique protein structure. Instead, the energy landscapes of IDP conformational switching and protein aggregation feature a number of minima for different competing low-energy structures. In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes.
    Keywords amino acid composition ; artificial intelligence ; energy ; humans ; molecular biology ; molecular dynamics ; prediction ; proteome
    Language English
    Dates of publication 2021-1001
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167182
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  5. Article ; Online: Does the inclusion of electronic polarisability lead to a better modelling of peptide aggregation?

    Kav, Batuhan / Strodel, Birgit

    RSC advances

    2022  Volume 12, Issue 32, Page(s) 20829–20837

    Abstract: Simulating the process of amyloid aggregation with atomic detail is a challenging task for various reasons. One of them is that it is difficult to parametrise a force field such that all protein states ranging from the folded through the unfolded to the ... ...

    Abstract Simulating the process of amyloid aggregation with atomic detail is a challenging task for various reasons. One of them is that it is difficult to parametrise a force field such that all protein states ranging from the folded through the unfolded to the aggregated state are represented with the same level of accuracy. Here, we test whether the consideration of electronic polarisability improves the description of the different states of Aβ
    Language English
    Publishing date 2022-07-21
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d2ra01478e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Does the inclusion of electronic polarisability lead to a better modelling of peptide aggregation?

    Kav, Batuhan / Strodel, Birgit

    RSC advances. 2022 July 21, v. 12, no. 32

    2022  

    Abstract: Simulating the process of amyloid aggregation with atomic detail is a challenging task for various reasons. One of them is that it is difficult to parametrise a force field such that all protein states ranging from the folded through the unfolded to the ... ...

    Abstract Simulating the process of amyloid aggregation with atomic detail is a challenging task for various reasons. One of them is that it is difficult to parametrise a force field such that all protein states ranging from the folded through the unfolded to the aggregated state are represented with the same level of accuracy. Here, we test whether the consideration of electronic polarisability improves the description of the different states of Aβ₁₆–₂₂. Surprisingly, the CHARMM Drude polarisable force field is found to perform worse than its unpolarisable counterpart CHARMM36m. Sources for this failure of the Drude model are discussed.
    Keywords amyloid ; models ; peptides
    Language English
    Dates of publication 2022-0721
    Size p. 20829-20837.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ISSN 2046-2069
    DOI 10.1039/d2ra01478e
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers.

    Khaled, Mohammed / Strodel, Birgit / Sayyed-Ahmad, Abdallah

    Frontiers in molecular biosciences

    2023  Volume 10, Page(s) 1143353

    Abstract: Polyglutamine expansion at the N-terminus of the huntingtin protein exon 1 (Htt-ex1) is closely associated with a number of neurodegenerative diseases, which result from the aggregation of the increased polyQ repeat. However, the underlying structures ... ...

    Abstract Polyglutamine expansion at the N-terminus of the huntingtin protein exon 1 (Htt-ex1) is closely associated with a number of neurodegenerative diseases, which result from the aggregation of the increased polyQ repeat. However, the underlying structures and aggregation mechanism are still poorly understood. We performed microsecond-long all-atom molecular dynamics simulations to study the folding and dimerization of Htt-ex1 (about 100 residues) with non-pathogenic and pathogenic polyQ lengths, and uncovered substantial differences. The non-pathogenic monomer adopts a long
    Language English
    Publishing date 2023-04-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2023.1143353
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Effects of ion type and concentration on the structure and aggregation of the amyloid peptide A

    Smorodina, Eva / Kav, Batuhan / Fatafta, Hebah / Strodel, Birgit

    Proteins

    2023  

    Abstract: Among the various factors controlling the amyloid aggregation process, the influences of ions on the aggregation rate and the resulting structures are important aspects to consider, which can be studied by molecular simulations. There is a wide variety ... ...

    Abstract Among the various factors controlling the amyloid aggregation process, the influences of ions on the aggregation rate and the resulting structures are important aspects to consider, which can be studied by molecular simulations. There is a wide variety of protein force fields and ion models, raising the question of which model to use in such studies. To address this question, we perform molecular dynamics simulations of Aβ
    Language English
    Publishing date 2023-11-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.26635
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2291: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  9. Article ; Online: Transition Networks Unveil Disorder-to-Order Transformations in A

    Schäffler, Moritz / Samantray, Suman / Strodel, Birgit

    International journal of molecular sciences

    2023  Volume 24, Issue 14

    Abstract: The aggregation of amyloid-β (Aβ) peptides, particularly of Aβ1-42, has been linked to the pathogenesis of Alzheimer's disease. In this study, we focus on the conformational change of Aβ1-42 in the presence of glycosaminoglycans (GAGs) and 1-palmitoyl-2- ... ...

    Abstract The aggregation of amyloid-β (Aβ) peptides, particularly of Aβ1-42, has been linked to the pathogenesis of Alzheimer's disease. In this study, we focus on the conformational change of Aβ1-42 in the presence of glycosaminoglycans (GAGs) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids using molecular dynamics simulations. We analyze the conformational changes that occur in Aβ by extracting the key structural features that are then used to generate transition networks. Using the same three features per network highlights the transitions from intrinsically disordered states ubiquitous in Aβ1-42 in solution to more compact states arising from stable β-hairpin formation when Aβ1-42 is in the vicinity of a GAG molecule, and even more compact states characterized by a α-helix or β-sheet structures when Aβ1-42 interacts with a POPC lipid cluster. We show that the molecular mechanisms underlying these transitions from disorder to order are different for the Aβ1-42/GAG and Aβ1-42/POPC systems. While in the latter the hydrophobicity provided by the lipid tails facilitates the folding of Aβ1-42, in the case of GAG there are hardly any intermolecular Aβ1-42-GAG interactions. Instead, GAG removes sodium ions from the peptide, allowing stronger electrostatic interactions within the peptide that stabilize a β-hairpin. Our results contribute to the growing knowledge of the role of GAGs and lipids in the conformational preferences of the Aβ peptide, which in turn influences its aggregation into toxic oligomers and amyloid fibrils.
    MeSH term(s) Humans ; Glycosaminoglycans ; Amyloid beta-Peptides/chemistry ; Alzheimer Disease ; Molecular Dynamics Simulation ; Amyloid/chemistry ; Peptide Fragments/chemistry
    Chemical Substances Glycosaminoglycans ; Amyloid beta-Peptides ; Amyloid ; Peptide Fragments
    Language English
    Publishing date 2023-07-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms241411238
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The Effects of Different Glycosaminoglycans on the Structure and Aggregation of the Amyloid-β (16-22) Peptide.

    Samantray, Suman / Strodel, Birgit

    The journal of physical chemistry. B

    2021  Volume 125, Issue 21, Page(s) 5511–5525

    Abstract: Aggregates of the amyloid-β (Aβ) peptide are implicated as a causative substance in Alzheimer's disease. Molecular dynamics simulations provide valuable contributions for elucidating the conformational transitions of monomeric and aggregated forms of Aβ ... ...

    Abstract Aggregates of the amyloid-β (Aβ) peptide are implicated as a causative substance in Alzheimer's disease. Molecular dynamics simulations provide valuable contributions for elucidating the conformational transitions of monomeric and aggregated forms of Aβ be it in solution or in the presence of other molecules. Here, we study the effects of four different glycosaminoglycans (GAGs), three sulfated ones and a nonsulfated one, on the aggregation of Aβ
    MeSH term(s) Amyloid ; Amyloid beta-Peptides ; Glycosaminoglycans ; Peptide Fragments ; Protein Conformation, beta-Strand
    Chemical Substances Amyloid ; Amyloid beta-Peptides ; Glycosaminoglycans ; Peptide Fragments
    Language English
    Publishing date 2021-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c00868
    Database MEDical Literature Analysis and Retrieval System OnLINE

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