Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

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Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?


Abstract Many proteins have modular design with multiple globular domains connected via flexible linkers. As a simple model of such system, we study a tandem construct consisting of two identical SH3 domains and a variable-length Gly/Ser linker. When the linker is short, this construct represents a dumbbell-shaped molecule with limited amount of domainâ??domain mobility. Due to its elongated shape, this molecule efficiently aligns in steric alignment media. As the length of the linker increases, the two domains become effectively uncoupled and begin to behave as independent entities. Consequently, their degree of alignment drops, approaching that found in the (near-spherical) isolated SH3 domains. To model the dependence of alignment parameters on the length of the interdomain linker, we have generated in silico a series of conformational ensembles representing SH3 tandems with different linker length. These ensembles were subsequently used as input for alignment prediction software PALES. The predicted alignment tensors were compared with the results of experimental measurements using a series of tandem-SH3 samples in PEG/hexanol alignment media. This comparison broadly confirmed the expected trends. At the same time, it has been found that the isolated SH3 domain aligns much stronger than expected. This finding can be attributed to complex morphology of the PEG/hexanol media and/or to weak site-specific interactions between the protein and the media. In the latter case, there are strong indications that electrostatic interactions may play a role. The fact that PEG/hexanol does not behave as a simple steric media should serve as a caution for studies that use PALES as a quantitative prediction tool (especially for disordered proteins). Further progress in this area depends on our ability to accurately model the anisotropic media and its site-specific interactions with protein molecules. Once this ability is improved, it should be possible to use the alignment parameters as a measure of domainâ??domain cooperativity, thus identifying the situations where two domains transiently interact with each other or become coupled through a partially structured linker.

• Content Type Journal Article
• Category Article
• Pages 131-150
• DOI 10.1007/s10858-011-9548-7
• Authors
  • Tairan Yuwen, Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
  • Carol Beth Post, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
  • Nikolai R. Skrynnikov, Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738
  • Journal Volume Volume 51
  • Journal Issue Volume 51, Numbers 1-2

Source: Journal of Biomolecular NMR