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MD simulations of plant hemoglobins: the hexa- to penta-coordinate structural transition

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Abstract

Hemoglobins are ubiquitous proteins found in bacteria, plants, and animals with diverse functions other than the classical transport/storage of oxygen. Different functions are expected to correspond to substantially different structures, such as the hexa- and penta-coordination of the iron atom. It is now widely believed that pentacoordinate hemoglobins evolved from the hexacoordinate ones, both in plants and in animals. Since plant hemoglobins evolved more recently than in animals, they represent a simpler and thus useful system to investigate protein sequence/structure features that specifically supported, guided by molecular evolution, the capacity for oxygen transport. In the present work, we selected a fully hexacoordinate globin, AHb2 from Arabidopsis thaliana and the pentacoordinate oxygen-transporting LegHb from yellow lupin, that share a high degree of sequence identity. Our aim is to identify the structural determinants for oxygen transport by analyzing the structural/dynamical differences of a hexacoordinate and a pentacoordinate globin using all-atom molecular dynamics simulations. Using comparative MD simulations, we were able to go beyond the simple sequence alignment, pointing out important differences between these two hemoglobins especially at the level of the CD region, whose dynamics was found, in turn, to be strongly correlated with that of the distal region.

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Acknowledgments

We acknowledge the CYBERSAR and CINECA award, the latter under the ISCRA initiative for the availability of high-performance computing resources and support. CW thanks the ERASMUS program for supporting her visit to Department of Physics, University of Cagliari.

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Authors and Affiliations

  1. Dipartimento di Scienze Chimiche, University of Cagliari, Monserrato, Italy

    Mariano Andrea Scorciapino

  2. Istituto Officina del Materiali, SLACS, CNR, Monserrato, Italy

    Mariano Andrea Scorciapino & Matteo Ceccarelli

  3. Dipartimento di Fisica, University of Cagliari, Monserrato, Italy

    Claire Wallon & Matteo Ceccarelli

Authors
  1. Mariano Andrea Scorciapino
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  2. Claire Wallon
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  3. Matteo Ceccarelli
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Corresponding author

Correspondence to Matteo Ceccarelli.

Additional information

Dedicated to Professor Akira Imamura on the occasion of his 77th birthday and published as part of the Imamura Festschrift Issue.

Electronic supplementary material

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214_2011_1041_MOESM1_ESM.tiff

Figure S1 Secondary structure analysis of the AHb2’s D region. The black horizontal lines represent the structures where the corresponding residue has been found to be involved in a helical conformation. Supplementary material 1 (TIFF 15752 kb)

214_2011_1041_MOESM2_ESM.tiff

Figure S2 Residues RMSF calculated from Ca coordinates. Residue numbers correspond to AHb2 amino acids sequence, while LegHb has been aligned with respect to the latter on the basis of Fig. 1. RMSF have been calculated for the second half of the MD simulation in order to eliminate AHb2 relaxation contribution. The two data sets have been normalized. Supplementary material 2 (TIFF 15344 kb)

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Scorciapino, M.A., Wallon, C. & Ceccarelli, M. MD simulations of plant hemoglobins: the hexa- to penta-coordinate structural transition. Theor Chem Acc 130, 1105–1114 (2011). https://doi.org/10.1007/s00214-011-1041-6

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