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Instruments / Technical Area	Publication Details	Published	Actions
B21-High Throughput SAXS	Dynamic ion pair behavior stabilizes single α-helices in proteins Matthew Batchelor , Marcin Wolny , Emily G. Baker , Emanuele Paci , Arnout P. Kalverda , Michelle Peckham Journal Of Biological Chemistry 294, 3219 - 3234 DOI: 10.1074/jbc.RA118.006752 Diamond Proposal Number(s): [15454] Show Abstract ▼ Abstract: Ion pairs are key stabilizing interactions between oppositely charged amino acid side chains in proteins. They are often depicted as single conformer salt bridges (hydrogen-bonded ion pairs) in crystal structures, but it is unclear how dynamic they are in solution. Ion pairs are thought to be particularly important in stabilizing single α-helix (SAH) domains in solution. These highly stable domains are rich in charged residues (such as Arg, Lys, and Glu) with potential ion pairs across adjacent turns of the helix. They provide a good model system to investigate how ion pairs can contribute to protein stability. Using NMR spectroscopy, small-angle X-ray light scattering (SAXS), and molecular dynamics simulations, we provide here experimental evidence that ion pairs exist in a SAH in murine myosin 7a (residues 858–935), but that they are not fixed or long lasting. In silico modeling revealed that the ion pairs within this α-helix exhibit dynamic behavior, rapidly forming and breaking and alternating between different partner residues. The low-energy helical state was compatible with a great variety of ion pair combinations. Flexible ion pair formation utilizing a subset of those available at any one time avoided the entropic penalty of fixing side chain conformations, which likely contributed to helix stability overall. These results indicate the dynamic nature of ion pairs in SAHs. More broadly, thermodynamic stability in other proteins is likely to benefit from the dynamic behavior of multi-option solvent-exposed ion pairs.	Mar 2019
NONE-No attached Diamond beamline	Nanomechanical detection of antibiotic mucopeptide binding in a model for superbug drug resistance Joseph Wafula Ndieyira , Moyu Watari , Dejian Zhou , Manuel Vögtli , Matthew Batchelor , Matthew A. Cooper , Rachel A. Mckendry , Torsten Strunz , Mike A. Horton , Chris Abell , Trevor Rayment , Gabriel Aeppli Nature Nanotechnology 3 (11), 691 - 696 DOI: 10.1038/nnano.2008.275 PMID: 18989336 Show Abstract ▼ Abstract: The alarming growth of the antibiotic-resistant superbugs methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is driving the development of new technologies to investigate antibiotics and their modes of action. We report the label-free detection of vancomycin binding to bacterial cell wall precursor analogues (mucopeptides) on cantilever arrays, with 10 nM sensitivity and at clinically relevant concentrations in blood serum. Differential measurements have quantified binding constants for vancomycin-sensitive and vancomycin-resistant mucopeptide analogues. Moreover, by systematically modifying the mucopeptide density we gain new insights into the origin of surface stress. We propose that stress is a product of a local chemical binding factor and a geometrical factor describing the mechanical connectivity of regions activated by local binding in terms of a percolation process. Our findings place BioMEMS devices in a new class of percolative systems. The percolation concept will underpin the design of devices and coatings to significantly lower the drug detection limit and may also have an impact on our understanding of antibiotic drug action in bacteria.	Oct 2008

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