caa a22 4500 445325607 CHVBK 20180317142719.0 cr unu---uuuuu 170323e20110901xx s 000 0 eng 10.1007/s10858-011-9548-7 doi (NATIONALLICENCE)springer-10.1007/s10858-011-9548-7 Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media? [Elektronische Daten] [Tairan Yuwen, Carol Post, Nikolai Skrynnikov] 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 domain-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 domain-domain cooperativity, thus identifying the situations where two domains transiently interact with each other or become coupled through a partially structured linker. Springer Science+Business Media B.V., 2011 Multidomain proteins nationallicence Residual dipolar couplings nationallicence Alignment tensor nationallicence Generalized degree of order nationallicence Domain-domain motion nationallicence Flexible linker nationallicence Conformational ensemble nationallicence Conformational disorder nationallicence Tandem SH3 construct nationallicence PALES software nationallicence Steric alignment nationallicence Electrostatic alignment nationallicence PEG/hexanol alignment media nationallicence Yuwen Tairan Department of Chemistry, Purdue University, 47907, West Lafayette, IN, USA aut Post Carol Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 47907, West Lafayette, IN, USA aut Skrynnikov Nikolai Department of Chemistry, Purdue University, 47907, West Lafayette, IN, USA aut Journal of Biomolecular NMR Springer Netherlands 51/1-2(2011-09-01), 131-150 0925-2738 51:1-2<131 2011 51 10858 https://doi.org/10.1007/s10858-011-9548-7 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10858-011-9548-7 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Yuwen Tairan Department of Chemistry, Purdue University, 47907, West Lafayette, IN, USA aut NATIONALLICENCE 700 1- Post Carol Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 47907, West Lafayette, IN, USA aut NATIONALLICENCE 700 1- Skrynnikov Nikolai Department of Chemistry, Purdue University, 47907, West Lafayette, IN, USA aut NATIONALLICENCE 773 0- Journal of Biomolecular NMR Springer Netherlands 51/1-2(2011-09-01), 131-150 0925-2738 51:1-2<131 2011 51 10858 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer