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Molecular bases for heme:ligand recognition in sperm whale (Physeter Catodon) andAplysia limacine myoglobin

Basi molecolari del riconoscimento eme:leganti nella mioglobina di capodoglio (Physeter catodon) e diAplysia limacine

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Abstract

The crystal structure of sperm whale myoglobin (Mb):azide complex has been determined and refined at 1.8 Å resolution. The ligand is coordinated to the heme iron, and deeply buried in the inner part of the distal site. The structural organization of this complex differs substantially from that observed inA. limacina Mb: azide complex, in which the iron coordinated ligand is directed towards the outer solvent region of the protein. In the case of sperm whale Mb the bound ligand is stabilized by a hydrogen bond to residue HisE7; in the case ofA. limacina Mb the ligand is directly hydrogen bonded to ArgE10. The structures of the complexes described underline different mechanisms of ligand recognition and stabilization in the two Mb’s, and allow a rational interpretation of the different kinetic and thermodynamic properties observed in globins lacking a polar residue at the distal E7 site.

Riassunto

La struttura cristallina del complesso formato dalla mioglobina (Mb) di capodoglio e dall’azide è stata determinata a 1.8 Å di risoluzione. Il legante risulta coordinate al ferro eminico, e profondamente sepolto nella parte più interna del sito distale. L’organizzazione strutturale di questo complesso differisce da quella dell’analogo addotto formato dalla Mb diA. limacina e dall’azide in cui il legante è orientato verso l’esterno del sito distale della proteina. Nel caso della Mb di capodoglio il legante è stabilizzato da un legame idrogeno con il residuo HisE7; nel caso della Mb di Alimacina, il legante forma un legame idrogeno con il residuo ArgE10. Le strutture dei complessi molecolari descritti indicano l’esistenza di due diversi meccanismi di riconoscimento e stabilizzazione del legante nelle due Mb, e permettono di interpretare le diverse proprietà termodinamiche e cinetiche osservate nelle globine prive di un residuo polare al sito distale E7.

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Authors and Affiliations

  1. Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Via P. Giuria, 9, 10125, Torino

    Paolo Ascenzi

  2. Gruppo Biostrutture - IST, Università degli Studi di Genova, Via Benedetto XV, 10, 16126, Genova

    Martino Bolognesi

  3. Dipartimento di Scienze Biochimiche «A. Rossi Fanelli», Université degli Studi di Roma «La Sapienza», Piazzale A. Moro, 5, 00185, Roma

    Maurizio Brunori

  4. Dipartimento di Genetica e Microbiologia, Université degli Studi di Pavia, Via Abbiategrasso, 207, 27100, Pavia

    Menico Rizzi & Alessandro Coda

Authors
  1. Menico Rizzi
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  2. Paolo Ascenzi
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  3. Alessandro Coda
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  4. Maurizio Brunori
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  5. Martino Bolognesi
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Additional information

Nella seduta del 9 maggio 1992.

Residues of sperm whale andA. limacina Mb have been identified by their topological positions as defined by Perutz [1, 3]. The eight helices in the globin fold are identified by letters A,B,...H. The symbols AB, BC, ..., GH, indicate the nonhelical regions connecting helices A and B, B and C, ..., G and H. Numbering and nomenclature of the heme group are those adopted by Takano [5]. Water molecules (W) have been numbered sequentially, starting from 150. Abbreviations used: myoglobin, Mb; monomeric hemoglobin, Hb; monomeric erythrocruorin, Ery.

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Rizzi, M., Ascenzi, P., Coda, A. et al. Molecular bases for heme:ligand recognition in sperm whale (Physeter Catodon) andAplysia limacine myoglobin. Rend. Fis. Acc. Lincei 4, 65–73 (1993). https://doi.org/10.1007/BF03001186

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