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  1. Article: Corrigendum to "Atomistic level characterisation of ssDNA translocation through the

    Rattu, Punam / Glencross, Flo / Mader, Sophie L / Skylaris, Chris-Kriton / Matthews, Stephen J / Rouse, Sarah L / Khalid, Syma

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 1027

    Abstract: This corrects the article DOI: 10.1016/j.csbj.2021.11.014.]. ...

    Abstract [This corrects the article DOI: 10.1016/j.csbj.2021.11.014.].
    Language English
    Publishing date 2022-02-15
    Publishing country Netherlands
    Document type Published Erratum
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.02.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  2. Article: Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing

    Rattu, Punam / Glencross, Flo / Mader, Sophie L. / Skylaris, Chris-Kriton / Matthews, Stephen J. / Rouse, Sarah L. / Khalid, Syma

    Computational and Structural Biotechnology Journal. 2021, v. 19

    2021  

    Abstract: Two proteins of the Escherichia coli membrane protein complex, CsgG and CsgF, are studied as proteinaceous nanopores for DNA sequencing. It is highly desirable to control the DNA as it moves through the pores, this requires characterisation of DNA ... ...

    Abstract Two proteins of the Escherichia coli membrane protein complex, CsgG and CsgF, are studied as proteinaceous nanopores for DNA sequencing. It is highly desirable to control the DNA as it moves through the pores, this requires characterisation of DNA translocation and subsequent optimization of the pores. In order to inform protein engineering to improve the pores, we have conducted a series of molecular dynamics simulations to characterise the mechanical strength and conformational dynamics of CsgG and the CsgG-CsgF complex and how these impact ssDNA, water and ion movement. We find that the barrel of CsgG is more susceptible to damage from external electric fields compared to the protein vestibule. Furthermore, the presence of CsgF within the CsgG-CsgF complex enables the complex to withstand higher electric fields. We find that the eyelet loops of CsgG play a key role in both slowing the translocation rate of DNA and modulating the conductance of the pore. CsgF also impacts the DNA translocation rate, but to a lesser degree than CsgG.
    Keywords Escherichia coli ; biotechnology ; membrane proteins ; molecular dynamics ; nanopores ; strength (mechanics)
    Language English
    Size p. 6417-6430.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.11.014
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Atomistic level characterisation of ssDNA translocation through the

    Rattu, Punam / Glencross, Flo / Mader, Sophie L / Skylaris, Chris-Kriton / Matthews, Stephen J / Rouse, Sarah L / Khalid, Syma

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 6417–6430

    Abstract: Two proteins of ... ...

    Abstract Two proteins of the
    Language English
    Publishing date 2021-11-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.11.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Optical control of ultrafast structural dynamics in a fluorescent protein.

    Hutchison, Christopher D M / Baxter, James M / Fitzpatrick, Ann / Dorlhiac, Gabriel / Fadini, Alisia / Perrett, Samuel / Maghlaoui, Karim / Lefèvre, Salomé Bodet / Cordon-Preciado, Violeta / Ferreira, Josie L / Chukhutsina, Volha U / Garratt, Douglas / Barnard, Jonathan / Galinis, Gediminas / Glencross, Flo / Morgan, Rhodri M / Stockton, Sian / Taylor, Ben / Yuan, Letong /
    Romei, Matthew G / Lin, Chi-Yun / Marangos, Jon P / Schmidt, Marius / Chatrchyan, Viktoria / Buckup, Tiago / Morozov, Dmitry / Park, Jaehyun / Park, Sehan / Eom, Intae / Kim, Minseok / Jang, Dogeun / Choi, Hyeongi / Hyun, HyoJung / Park, Gisu / Nango, Eriko / Tanaka, Rie / Owada, Shigeki / Tono, Kensuke / DePonte, Daniel P / Carbajo, Sergio / Seaberg, Matt / Aquila, Andrew / Boutet, Sebastien / Barty, Anton / Iwata, So / Boxer, Steven G / Groenhof, Gerrit / van Thor, Jasper J

    Nature chemistry

    2023  Volume 15, Issue 11, Page(s) 1607–1615

    Abstract: The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction ...

    Abstract The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
    MeSH term(s) Motion ; Vibration ; Rhodopsin ; Hydrogen Bonding
    Chemical Substances Rhodopsin (9009-81-8)
    Language English
    Publishing date 2023-08-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2464596-5
    ISSN 1755-4349 ; 1755-4330
    ISSN (online) 1755-4349
    ISSN 1755-4330
    DOI 10.1038/s41557-023-01275-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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