Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling
The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K[superscript +]-bound KcsA and Na[superscript +]-bound Kc...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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American Chemical Society (ACS)
2015
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| Online Access: | http://hdl.handle.net/1721.1/97497 https://orcid.org/0000-0002-6616-0328 |
| _version_ | 1811077699581509632 |
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| author | Stevenson, Paul Baiz, Carlos R. Akerboom, Jasper Tokmakoff, Andrei Vaziri, Alipasha Gotz, Christoph |
| author2 | Massachusetts Institute of Technology. Department of Chemistry |
| author_facet | Massachusetts Institute of Technology. Department of Chemistry Stevenson, Paul Baiz, Carlos R. Akerboom, Jasper Tokmakoff, Andrei Vaziri, Alipasha Gotz, Christoph |
| author_sort | Stevenson, Paul |
| collection | MIT |
| description | The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K[superscript +]-bound KcsA and Na[superscript +]-bound KcsA are in good qualitative agreement with spectra modeled from structural ensembles generated from molecular dynamics simulations. The molecular origins of the vibrational modes contributing to differences in these spectra are determined not only from structural differences in the selectivity filter but also from the pore helices surrounding this region. Furthermore, the coordination of K[superscript +] or Na[superscript +] to carbonyls in the selectivity filter effectively decouples the vibrations of those carbonyls from the rest of the protein, creating local probes of the electrostatic environment. The results suggest that it is necessary to include the influence of the surrounding helices in discussing selectivity and transport in KcsA and, on a more general level, that IR spectroscopy offers a nonperturbative route to studying the structure and dynamics of ion channels. |
| first_indexed | 2024-09-23T10:47:10Z |
| format | Article |
| id | mit-1721.1/97497 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:47:10Z |
| publishDate | 2015 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/974972022-09-27T14:57:44Z Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling Stevenson, Paul Baiz, Carlos R. Akerboom, Jasper Tokmakoff, Andrei Vaziri, Alipasha Gotz, Christoph Massachusetts Institute of Technology. Department of Chemistry Stevenson, Paul The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K[superscript +]-bound KcsA and Na[superscript +]-bound KcsA are in good qualitative agreement with spectra modeled from structural ensembles generated from molecular dynamics simulations. The molecular origins of the vibrational modes contributing to differences in these spectra are determined not only from structural differences in the selectivity filter but also from the pore helices surrounding this region. Furthermore, the coordination of K[superscript +] or Na[superscript +] to carbonyls in the selectivity filter effectively decouples the vibrations of those carbonyls from the rest of the protein, creating local probes of the electrostatic environment. The results suggest that it is necessary to include the influence of the surrounding helices in discussing selectivity and transport in KcsA and, on a more general level, that IR spectroscopy offers a nonperturbative route to studying the structure and dynamics of ion channels. Vienna Science and Technology Fund (Project VRG10-11) University of Vienna (Research Platform Quantum Phenomena and Nanoscale Biological System) 2015-06-22T15:25:09Z 2015-06-22T15:25:09Z 2015-04 2015-04 Article http://purl.org/eprint/type/JournalArticle 1520-6106 1520-5207 http://hdl.handle.net/1721.1/97497 Stevenson, Paul, Christoph Gotz, Carlos R. Baiz, Jasper Akerboom, Andrei Tokmakoff, and Alipasha Vaziri. “Visualizing KcsA Conformational Changes Upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling.” The Journal of Physical Chemistry B 119, no. 18 (May 7, 2015): 5824–5831. © 2015 American Chemical Society https://orcid.org/0000-0002-6616-0328 en_US http://dx.doi.org/10.1021/acs.jpcb.5b02223 The Journal of Physical Chemistry B Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Chemical Society (ACS) American Chemical Society |
| spellingShingle | Stevenson, Paul Baiz, Carlos R. Akerboom, Jasper Tokmakoff, Andrei Vaziri, Alipasha Gotz, Christoph Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling |
| title | Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling |
| title_full | Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling |
| title_fullStr | Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling |
| title_full_unstemmed | Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling |
| title_short | Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling |
| title_sort | visualizing kcsa conformational changes upon ion binding by infrared spectroscopy and atomistic modeling |
| url | http://hdl.handle.net/1721.1/97497 https://orcid.org/0000-0002-6616-0328 |
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