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Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR

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Abstract

HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or Cα-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T1/T2values is described. For most proteins, the value of the atomic element radius ranges between 2.8 Å and 3.8 Å with a distribution centered at 3.3 Å. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures.

If the average structure is correct, deviations between experimental T1/T2values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.

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Authors and Affiliations

  1. Departament de Química Orgànica, Universitat de Barcelona, Martí Franquès, 1-11, 08028, Barcelona, Spain

    Pau Bernadó & Miquel Pons

  2. Departmento de Química Física, Facultad de Química, Universidad de Murcia, 30071, Murcia, Spain

    José García de la Torre

  3. Laboratori de RMN de BiomolŠcules, Parc Científíc de Barcelona, Josep Samitier 1-5, 08028, Barcelona, Spain

    Miquel Pons

Authors
  1. Pau Bernadó
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  2. José García de la Torre
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  3. Miquel Pons
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Correspondence to Miquel Pons.

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Bernadó, P., de la Torre, J.G. & Pons, M. Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. J Biomol NMR 23, 139–150 (2002). https://doi.org/10.1023/A:1016359412284

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