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Comparison of the backbone dynamics of a natural and a consensus designed 3-TPR domain

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Abstract

The tetratricopeptide repeat (TPR) is a 34-amino acid helix-turn-helix motif that occurs in tandem arrays in numerous proteins. Here we compare the backbone dynamics of a natural 3-repeat TPR domain, from the protein UBP, with the behavior of a designed protein CTPR3, which consists of three identical consensus TPR units. Although the three tandem TPR repeats in both CTPR3 and UBP behave as a single unit, with no evidence of independent repeat motions, the data indicate that certain positions in UBP are significantly more flexible than are the corresponding positions in CTPR3. Most of the dynamical changes occur at or adjacent to positions that are involved in intra-repeat packing interactions. These observations lead us to suggest that the three-TPR domain of UBP does not incorporate optimized packing, compared to that seen in the idealized CTPR. The natural TPR domain is not only less stable overall than CTPR3, but also presents increased local flexibility at the positions where the sequences differs from the conserved consensus.

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Abbreviations

ηxy :

Cross-relaxation rate constant

HSQC:

Heteronuclear single quantum coherence

MSA:

Multiple sequence alignment

NMR:

Nuclear magnetic resonance

NOE:

Nuclear Overhauser effect

R 1 :

Longitudinal relaxation rate constant

R 2 :

Transverse relaxation rate constant

R ex :

Conformational exchange rate

S 2 :

Order parameter

τe :

Internal correlation time

τm :

Rotational correlation time

UBP:

Vpu-binding protein

TPR:

Tetratricopeptide repeat

CTPR:

Consensus TPR

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Acknowledgements

We thank the reviewers and editor for helpful suggestions. We thank Drs. Douglas E. Brown and John W. Tomaszewski (Indiana University NMR Facility) for discussions and Drs. Lewis Kay (University of Toronto) and Mark Rance (University of Cincinnati) for providing pulse programs. This work was supported in part by a grant awarded to M. J. S. from the National Science Foundation (MCB-0212746), and by Human Frontier Science Program grant RGP0044 to LR and also by a sub-contract to LR from NIH grant number GM080515.

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Authors and Affiliations

  1. Department of Chemistry and Interdisciplinary Biochemistry Program, Indiana University, Bloomington, IN, 47405-0001, USA

    Virginia A. Jarymowycz

  2. Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, 266 Whitney Avenue, New Haven, CT, 06520-8114, USA

    Aitziber L. Cortajarena & Lynne Regan

  3. Department of Chemistry, Yale University, P.O. Box 208114, 266 Whitney Avenue, New Haven, CT, 06520-8114, USA

    Lynne Regan

  4. Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia

    Martin J. Stone

Authors
  1. Virginia A. Jarymowycz
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  2. Aitziber L. Cortajarena
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  3. Lynne Regan
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  4. Martin J. Stone
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Corresponding author

Correspondence to Martin J. Stone.

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Jarymowycz, V.A., Cortajarena, A.L., Regan, L. et al. Comparison of the backbone dynamics of a natural and a consensus designed 3-TPR domain. J Biomol NMR 41, 169–178 (2008). https://doi.org/10.1007/s10858-008-9250-6

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  • DOI: https://doi.org/10.1007/s10858-008-9250-6

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