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  1. Article ; Online: Quantifying the thermodynamics of protein unfolding using 2D NMR spectroscopy

    Rita Puglisi / Oliver Brylski / Caterina Alfano / Stephen R. Martin / Annalisa Pastore / Piero A. Temussi

    Communications Chemistry, Vol 3, Iss 1, Pp 1-

    2020  Volume 7

    Abstract: Multidimensional NMR spectroscopy can provide insight into the unfolding of proteins in cells, but may be sensitive to the choice of residue used as a reference. Here 2D 1H-15N NMR is used to obtain thermodynamic parameters of unfolding of Yfh1, relying ... ...

    Abstract Multidimensional NMR spectroscopy can provide insight into the unfolding of proteins in cells, but may be sensitive to the choice of residue used as a reference. Here 2D 1H-15N NMR is used to obtain thermodynamic parameters of unfolding of Yfh1, relying on an internal standard to normalise peak volumes.
    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Generalized View of Protein Folding: In Medio Stat Virtus

    Pastore, Annalisa / Stephen R. Martin / Piero Andrea Temussi

    Journal of the American Chemical Society. 2018 Dec. 19, v. 141, no. 6

    2018  

    Abstract: Proteins are often described in textbooks as being only “marginally stable” but many proteins, specifically those with a high free energy of unfolding are, in fact, so stable that they exist only in the fully folded state except under harsh denaturing ... ...

    Abstract Proteins are often described in textbooks as being only “marginally stable” but many proteins, specifically those with a high free energy of unfolding are, in fact, so stable that they exist only in the fully folded state except under harsh denaturing conditions. Proteins that are truly only marginally stable, those with a low free energy of unfolding, exist as an equilibrium mixture of folded and unfolded forms under “normal” conditions. To some extent such proteins have some features in common with “intrinsically disordered” proteins. We analyzed the relationship between these marginally stable proteins and intrinsically disordered proteins in order to fully understand the twilight zone that distinguishes the two ensembles in the hope of clarifying the fuzzy borders of the current classification that divides the protein world into folded and intrinsically disordered ones. Our analysis suggests that the division may be too drastic and misleading, because it puts within the same category proteins with very different behaviors. We propose a restricted, albeit operational, definition of “marginally stable proteins”, referring by this term only to proteins whose free energy difference between the folded and unfolded states falls in the interval 0–3 kcal/mol. These proteins have special features because they normally exist as equilibrium mixtures of folded and unfolded species or as molten globule states. This coexistence makes marginally stable proteins ideal tools to study even small environmental changes to which they may behave as natural sensors.
    Keywords Gibbs free energy ; protein folding ; proteins
    Language English
    Dates of publication 2018-1219
    Size p. 2194-2200.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.8b10779
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Evolution of the SARS-CoV-2 spike protein in the human host

    Antoni G. Wrobel / Donald J. Benton / Chloë Roustan / Annabel Borg / Saira Hussain / Stephen R. Martin / Peter B. Rosenthal / John J. Skehel / Steven J. Gamblin

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 7

    Abstract: The SARS-CoV-2 spike has been evolving in the human population. The variants of concern alpha and beta evolved to optimise spike openness and so ability to bind its receptor ACE2, the affinity towards the receptor, and stability upon receptor binding. ...

    Abstract The SARS-CoV-2 spike has been evolving in the human population. The variants of concern alpha and beta evolved to optimise spike openness and so ability to bind its receptor ACE2, the affinity towards the receptor, and stability upon receptor binding.
    Keywords Science ; Q
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2

    Antoni G. Wrobel / Donald J. Benton / Pengqi Xu / Lesley J. Calder / Annabel Borg / Chloë Roustan / Stephen R. Martin / Peter B. Rosenthal / John J. Skehel / Steven J. Gamblin

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 6

    Abstract: It has been suggested that pangolin coronaviruses may be the origin of SARS-CoV-2. Here the authors show that the Pangolin-CoV spike is structurally closely related to the closed form of SARS-CoV-2 spike and exhibits similar binding properties to human ... ...

    Abstract It has been suggested that pangolin coronaviruses may be the origin of SARS-CoV-2. Here the authors show that the Pangolin-CoV spike is structurally closely related to the closed form of SARS-CoV-2 spike and exhibits similar binding properties to human and pangolin ACE2; although neither spike binds bat ACE2.
    Keywords Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient

    Lena Jaki / Sebastian Weigang / Lisa Kern / Stefanie Kramme / Antoni G. Wrobel / Andrea B. Grawitz / Philipp Nawrath / Stephen R. Martin / Theo Dähne / Julius Beer / Miriam Disch / Philipp Kolb / Lisa Gutbrod / Sandra Reuter / Klaus Warnatz / Martin Schwemmle / Steven J. Gamblin / Elke Neumann-Haefelin / Daniel Schnepf /
    Thomas Welte / Georg Kochs / Daniela Huzly / Marcus Panning / Jonas Fuchs

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: Abstract Monoclonal antibodies (mAbs) directed against the spike of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective therapeutic options to combat infections in high-risk patients. Here, we report the adaptation of SARS-CoV-2 to ...

    Abstract Abstract Monoclonal antibodies (mAbs) directed against the spike of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective therapeutic options to combat infections in high-risk patients. Here, we report the adaptation of SARS-CoV-2 to the mAb cocktail REGN-COV in a kidney transplant patient with hypogammaglobulinemia. Following mAb treatment, the patient did not clear the infection. During viral persistence, SARS-CoV-2 acquired three novel spike mutations. Neutralization and mouse protection analyses demonstrate a complete viral escape from REGN-COV at the expense of ACE-2 binding. Final clearance of the virus occurred upon reduction of the immunosuppressive regimen and total IgG substitution. Serology suggests that the development of highly neutralizing IgM rather than IgG substitution aids clearance. Our findings emphasise that selection pressure by mAbs on SARS-CoV-2 can lead to development of escape variants in immunocompromised patients. Thus, modification of immunosuppressive therapy, if possible, might be preferable to control and clearance of the viral infection.
    Keywords Science ; Q
    Subject code 616
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: An optimized strategy to measure protein stability highlights differences between cold and hot unfolded states

    Caterina Alfano / Domenico Sanfelice / Stephen R. Martin / Annalisa Pastore / Piero Andrea Temussi

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 9

    Abstract: Crowding effects—important when considering cellular environments—greatly influence protein stability. Here the authors study the impact of macromolecular crowders on high and low temperature protein unfolding, and show that volume exclusion effects are ... ...

    Abstract Crowding effects—important when considering cellular environments—greatly influence protein stability. Here the authors study the impact of macromolecular crowders on high and low temperature protein unfolding, and show that volume exclusion effects are larger when the protein and crowder volumes are similar.
    Keywords Science ; Q
    Language English
    Publishing date 2017-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Characterisation of a cyclic peptide that binds to the RAS binding domain of phosphoinositide 3-kinase p110α

    Mohamed Ismail / Stephen R. Martin / Roger George / Francesca Houghton / Geoff Kelly / Raphaël A. G. Chaleil / Panayiotis Anastasiou / Xinyue Wang / Nicola O’Reilly / Stefania Federico / Dhira Joshi / Hemavathi Nagaraj / Rachel Cooley / Ning Sze Hui / Miriam Molina-Arcas / David C. Hancock / Ali Tavassoli / Julian Downward

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    2023  Volume 12

    Abstract: Abstract P110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream of RAS. RAS proteins contribute to the activation of p110α by interacting directly with its RAS binding domain (RBD), resulting in the promotion of ...

    Abstract Abstract P110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream of RAS. RAS proteins contribute to the activation of p110α by interacting directly with its RAS binding domain (RBD), resulting in the promotion of many cellular functions such as cell growth, proliferation and survival. Previous work from our lab has highlighted the importance of the p110α/RAS interaction in tumour initiation and growth. Here we report the discovery and characterisation of a cyclic peptide inhibitor (cyclo-CRVLIR) that interacts with the p110α-RBD and blocks its interaction with KRAS. cyclo-CRVLIR was discovered by screening a “split-intein cyclisation of peptides and proteins” (SICLOPPS) cyclic peptide library. The primary cyclic peptide hit from the screen initially showed a weak affinity for the p110α-RBD (Kd about 360 µM). However, two rounds of amino acid substitution led to cyclo-CRVLIR, with an improved affinity for p110α-RBD in the low µM (Kd 3 µM). We show that cyclo-CRVLIR binds selectively to the p110α-RBD but not to KRAS or the structurally-related RAF-RBD. Further, using biophysical, biochemical and cellular assays, we show that cyclo-CRVLIR effectively blocks the p110α/KRAS interaction in a dose dependent manner and reduces phospho-AKT levels in several oncogenic KRAS cell lines.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein

    Antoni G. Wrobel / Donald J. Benton / Saira Hussain / Ruth Harvey / Stephen R. Martin / Chloë Roustan / Peter B. Rosenthal / John J. Skehel / Steven J. Gamblin

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 5

    Abstract: Here, the authors characterise the binding and neutralisation properties of CR3022, a neutralising Ab isolated from a convalescent SARS patient, against SARS-CoV-2 spike trimers and show using Cryo-EM the disruption of SARS-CoV-2 spike by CR3022 Fab. ...

    Abstract Here, the authors characterise the binding and neutralisation properties of CR3022, a neutralising Ab isolated from a convalescent SARS patient, against SARS-CoV-2 spike trimers and show using Cryo-EM the disruption of SARS-CoV-2 spike by CR3022 Fab.
    Keywords Science ; Q
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein

    Antoni G. Wrobel / Donald J. Benton / Saira Hussain / Ruth Harvey / Stephen R. Martin / Chloë Roustan / Peter B. Rosenthal / John J. Skehel / Steven J. Gamblin

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 5

    Abstract: Here, the authors characterise the binding and neutralisation properties of CR3022, a neutralising Ab isolated from a convalescent SARS patient, against SARS-CoV-2 spike trimers and show using Cryo-EM the disruption of SARS-CoV-2 spike by CR3022 Fab. ...

    Abstract Here, the authors characterise the binding and neutralisation properties of CR3022, a neutralising Ab isolated from a convalescent SARS patient, against SARS-CoV-2 spike trimers and show using Cryo-EM the disruption of SARS-CoV-2 spike by CR3022 Fab.
    Keywords Science ; Q
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Mechanism of β-actin mRNA Recognition by ZBP1

    Giuseppe Nicastro / Adela M. Candel / Michael Uhl / Alain Oregioni / David Hollingworth / Rolf Backofen / Stephen R. Martin / Andres Ramos

    Cell Reports, Vol 18, Iss 5, Pp 1187-

    2017  Volume 1199

    Abstract: Zipcode binding protein 1 (ZBP1) is an oncofetal RNA-binding protein that mediates the transport and local translation of β-actin mRNA by the KH3-KH4 di-domain, which is essential for neuronal development. The high-resolution structures of KH3-KH4 with ... ...

    Abstract Zipcode binding protein 1 (ZBP1) is an oncofetal RNA-binding protein that mediates the transport and local translation of β-actin mRNA by the KH3-KH4 di-domain, which is essential for neuronal development. The high-resolution structures of KH3-KH4 with their respective target sequences show that KH4 recognizes a non-canonical GGA sequence via an enlarged and dynamic hydrophobic groove, whereas KH3 binding to a core CA sequence occurs with low specificity. A data-informed kinetic simulation of the two-step binding reaction reveals that the overall reaction is driven by the second binding event and that the moderate affinities of the individual interactions favor RNA looping. Furthermore, the concentration of ZBP1, but not of the target RNA, modulates the interaction, which explains the functional significance of enhanced ZBP1 expression during embryonic development.
    Keywords protein-RNA interactions ; NMR ; binding mechanism ; neuronal mRNA granules ; neuronal development ; mRNA local translation ; ZBP1 ; IMP1 ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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