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Dynamics of heme complexed with human serum albumin: a theoretical approach

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Abstract

Human serum albumin (HSA) is the most abundant protein in the blood serum. It binds several ligands and has an especially strong affinity for heme, hence becoming a natural candidate for oxygen transport. In order to analyze the interaction of HSA-heme, molecular dynamics simulations of HSA with bound heme were performed. Based on the results of X-ray diffraction, the binding site of the heme, localized in subdomain IB, was considered. We analyzed the fluctuations and their correlations along trajectories to detect collective motions. The role of H bonds and salt bridges in the stabilization of heme in its pocket was also investigated. Complementarily, the localization of water molecules in the hydrophobic pocket and the interaction with heme were discussed.

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Notes

  1. The overlap between the subspaces spanned by orthonormal eigenvectors \(\{{\bf u}_{1}, \ldots, {\bf u}_{N}\}\; \hbox{ and }\; \{{\bf v}_{1}, \ldots, {\bf v}_{N}\}\) is defined as \({{\mathcal O} = \frac{1}{N} \sum\nolimits_{i,j=1}^{N} ({\bf u}_{i} .{\bf v}_{j})^{2}}\).

  2. Porcupine plots were obtained using the Dynatrj tool of the Dynamite web server (http://s12-ap550.bioch.ox.ac.uk:8078/dynamite_html/index.html).

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Acknowledgments

We acknowledge the Brazilian agencies Faperj (Foundation for Research Support, State of Rio de Janeiro) and CNPq (National Council for Scientific and Technological Development) for partial financial support. We are grateful to Pedro G. Pascutti for his useful advice about molecular modeling. We also acknowledge the developers of the free Linux software.

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Authors and Affiliations

  1. Departamento de Física, PUC-Rio, Rio de Janeiro, Brazil

    T. R. Cuya Guizado, S. R. W. Louro & C. Anteneodo

  2. National Institute of Science and Technology for Complex Systems, Rio de Janeiro, Brazil

    C. Anteneodo

Authors
  1. T. R. Cuya Guizado
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  2. S. R. W. Louro
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  3. C. Anteneodo
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Correspondence to T. R. Cuya Guizado.

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Guizado, T.R.C., Louro, S.R.W. & Anteneodo, C. Dynamics of heme complexed with human serum albumin: a theoretical approach. Eur Biophys J 41, 1033–1042 (2012). https://doi.org/10.1007/s00249-012-0860-2

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  • DOI: https://doi.org/10.1007/s00249-012-0860-2

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