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      Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin

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          Abstract

          The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to not only their large size but also the unusually high cooperativity of ligand binding. However, the cooperative oxygen binding mechanisms are still mostly unknown. Here we report the cryo-electron microscopy structure of Lumbricus terrestris Hb in its native, oxygenated state at 9.1 Å resolution, showing remarkable differences from the carbon monoxide-binding X-ray structure. Our structural analysis first indicates that the cooperative ligand binding of L. terrestris Hb requires tertiary and quaternary transitions in the heme pocket and a global subunit movement facilitated by intra-ring and inter-ring contacts. Moreover, the additional sinusoidal bracelet provides the confirmation for the long-standing debate about the additional electron densities absent in the X-ray crystal structure.

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          Most cited references31

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          Protein structure fitting and refinement guided by cryo-EM density.

          For many macromolecular assemblies, both a cryo-electron microscopy map and atomic structures of its component proteins are available. Here we describe a method for fitting and refining a component structure within its map at intermediate resolution (<15 A). The atomic positions are optimized with respect to a scoring function that includes the crosscorrelation coefficient between the structure and the map as well as stereochemical and nonbonded interaction terms. A heuristic optimization that relies on a Monte Carlo search, a conjugate-gradients minimization, and simulated annealing molecular dynamics is applied to a series of subdivisions of the structure into progressively smaller rigid bodies. The method was tested on 15 proteins of known structure with 13 simulated maps and 3 experimentally determined maps. At approximately 10 A resolution, Calpha rmsd between the initial and final structures was reduced on average by approximately 53%. The method is automated and can refine both experimental and predicted atomic structures.
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            Stereochemistry of cooperative effects in haemoglobin.

            M. PERUTZ (1970)
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              Mechanisms regulating the reactions of human hemoglobin with oxygen and carbon monoxide.

              M F Perutz (1989)
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                21 April 2015
                2015
                : 5
                : 9494
                Affiliations
                [1 ]Department of Physics, National Taiwan University , Taipei 10617, Taiwan
                [2 ]Graduate Institute of Applied Physics, National Taiwan University , Taipei 10617, Taiwan
                [3 ]Biomedical & Molecular Imaging Center, National Taiwan University College of Medicine , Taipei 10051, Taiwan
                [4 ]Division of Neurology, National Taiwan University Hospital , Taipei 10002, Taiwan
                Author notes
                Article
                srep09494
                10.1038/srep09494
                5383013
                25897633
                ead6961a-f32f-4dd4-9880-b7cf3d5062aa
                Copyright © 2015, Macmillan Publishers Limited. All rights reserved

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 28 July 2014
                : 04 March 2015
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