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Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation

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Abstract

Proteins or regions of proteins that do not form compact globular structures are classified as intrinsically unstructured proteins (IUPs). IUPs are common in nature and have essential molecular functions, but even a limited understanding of the evolution of their dynamic behavior is lacking. The primary objective of this work was to test the evolutionary conservation of dynamic behavior for a particular class of IUPs that form intrinsically unstructured linker domains (IULD) that tether flanking folded domains. This objective was accomplished by measuring the backbone flexibility of several IULD homologues using nuclear magnetic resonance (NMR) spectroscopy. The backbone flexibility of five IULDs, representing three kingdoms, was measured and analyzed. Two IULDs from animals, one IULD from fungi, and two IULDs from plants showed similar levels of backbone flexibility that were consistent with the absence of a compact globular structure. In contrast, the amino acid sequences of the IULDs from these three taxa showed no significant similarity. To investigate how the dynamic behavior of the IULDs could be conserved in the absence of detectable sequence conservation, evolutionary rate studies were performed on a set of nine mammalian IULDs. The results of this analysis showed that many sites in the IULD are evolving neutrally, suggesting that dynamic behavior can be maintained in the absence of natural selection. This work represents the first experimental test of the evolutionary conservation of dynamic behavior and demonstrates that amino acid sequence conservation is not required for the conservation of dynamic behavior and presumably molecular function.

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Acknowledgments

The authors gratefully acknowledge Dr. Holly Wichman, Dr. Jack Sullivan, and Dr. David Lowry for helpful discussions during the preparation of the manuscript. GWD and CJB are funded by NIH Grant P20 RR 16448 from the COBRE program of the National Center for Research Resources (NCRR). C.J.B is also funded by NIH Grant P20 RR 16454-02 from the INBRE program at NCRR. The NMR data presented in this publication were collected at the University of Idaho Structural Biology Core Facility. This facility is funded by NIH Grant P20 RR 16448 from the COBRE Program and P20 RR 16454-02 from the INBRE program. The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official views of NIH.

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  1. Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID, 83844-3052, USA

    Gary W. Daughdrill, Pranesh Narayanaswami, Sara H. Gilmore & Agniezka Belczyk

  2. Department of Biological Sciences, University of Idaho, Moscow, ID, 83844-3051, USA

    Celeste J. Brown

  3. Life Science South Rm. 140, Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, ID, 83844-3052, USA

    Gary W. Daughdrill

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  1. Gary W. Daughdrill
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  2. Pranesh Narayanaswami
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Correspondence to Gary W. Daughdrill.

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Daughdrill, G.W., Narayanaswami, P., Gilmore, S.H. et al. Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation. J Mol Evol 65, 277–288 (2007). https://doi.org/10.1007/s00239-007-9011-2

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