5
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Local frustration determines loop opening during the catalytic cycle of an oxidoreductase

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Local structural frustration, the existence of mutually exclusive competing interactions, may explain why some proteins are dynamic while others are rigid. Frustration is thought to underpin biomolecular recognition and the flexibility of protein-binding sites. Here, we show how a small chemical modification, the oxidation of two cysteine thiols to a disulfide bond, during the catalytic cycle of the N-terminal domain of the key bacterial oxidoreductase DsbD (nDsbD), introduces frustration ultimately influencing protein function. In oxidized nDsbD, local frustration disrupts the packing of the protective cap-loop region against the active site allowing loop opening. By contrast, in reduced nDsbD the cap loop is rigid, always protecting the active-site thiols from the oxidizing environment of the periplasm. Our results point toward an intricate coupling between the dynamics of the active-site cysteines and of the cap loop which modulates the association reactions of nDsbD with its partners resulting in optimized protein function.

          Related collections

          Most cited references57

          • Record: found
          • Abstract: not found
          • Article: not found

          Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity

            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.

            A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (ϕ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ(1) rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Mechanism of coupled folding and binding of an intrinsically disordered protein.

              Protein folding and binding are analogous processes, in which the protein 'searches' for favourable intramolecular or intermolecular interactions on a funnelled energy landscape. Many eukaryotic proteins are disordered under physiological conditions, and fold into ordered structures only on binding to their cellular targets. The mechanism by which folding is coupled to binding is poorly understood, but it has been hypothesized on theoretical grounds that the binding kinetics may be enhanced by a 'fly-casting' effect, where the disordered protein binds weakly and non-specifically to its target and folds as it approaches the cognate binding site. Here we show, using NMR titrations and (15)N relaxation dispersion, that the phosphorylated kinase inducible activation domain (pKID) of the transcription factor CREB forms an ensemble of transient encounter complexes on binding to the KIX domain of the CREB binding protein. The encounter complexes are stabilized primarily by non-specific hydrophobic contacts, and evolve by way of an intermediate to the fully bound state without dissociation from KIX. The carboxy-terminal helix of pKID is only partially folded in the intermediate, and becomes stabilized by intermolecular interactions formed in the final bound state. Future applications of our method will provide new understanding of the molecular mechanisms by which intrinsically disordered proteins perform their diverse biological functions.
                Bookmark

                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                22 June 2020
                2020
                : 9
                : e54661
                Affiliations
                [1 ]Department of Biochemistry, University of Oxford OxfordUnited Kingdom
                [2 ]Department of Molecular Biosciences, University of Texas at Austin AustinUnited States
                [3 ]Institute of Nanoscience and Nanotechnology, NCSR Demokritos AthensGreece
                [4 ]Laboratoire de Microbiologie, Institut de Biologie, Université de Neuchâtel NeuchâtelSwitzerland
                [5 ]Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford OxfordUnited Kingdom
                University of Toronto Canada
                University of California, Berkeley United States
                University of Toronto Canada
                University of Toronto Canada
                Dartmouth
                Author notes
                [†]

                Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.

                Author information
                https://orcid.org/0000-0002-5348-0277
                https://orcid.org/0000-0002-7449-1151
                http://orcid.org/0000-0001-7579-8844
                https://orcid.org/0000-0001-6360-7959
                https://orcid.org/0000-0001-7297-7708
                Article
                54661
                10.7554/eLife.54661
                7347389
                32568066
                a5edca91-a6f1-4f3a-b898-6b5fb3626e5b
                © 2020, Stelzl et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 21 December 2019
                : 21 June 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/F01709X/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/R00126X/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome;
                Award ID: 208361/Z/17/Z
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome;
                Award ID: 079440
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome;
                Award ID: 092532/Z/10/Z
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: P300PA_167703
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: PZ00P3_180142
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Computational and Systems Biology
                Structural Biology and Molecular Biophysics
                Custom metadata
                The cysteine pair oxidation state in nDsbD acts as a ‘switch’ controlling the presence or absence of frustration in the active-site and determining the dynamic behavior of the cap loop.

                Life sciences
                local frustration,nmr,molecular dynamics,protein dynamics,oxidoreductase,e. coli
                Life sciences
                local frustration, nmr, molecular dynamics, protein dynamics, oxidoreductase, e. coli

                Comments

                Comment on this article