dorsal/arxiv
View SchemaRole of fluctuations in a snug-fit mechanism of KcsA channel selectivity
| Authors | D. Asthagiri, Lawrence R. Pratt, Michael E. Paulaitis |
|---|---|
| Categories | |
| ArXiv ID | physics/0511152 |
| URL | https://arxiv.org/abs/physics/0511152 |
| DOI | 10.1063/1.2205853 |
Abstract
The KcsA potassium channel belongs to a class of K+ channels that is selective for K+ over Na+ at rates of K+ transport approaching the diffusion limit. This selectivity is explained thermodynamically in terms of favorable partitioning of K+ relative to Na+ in a narrow selectivity filter in the channel. One mechanism for selectivity based on the atomic structure of the KcsA channel invokes the size difference between K+ and Na+, and the molecular complementarity of the selectivity filter with the larger K+ ion. An alternative view holds that size-based selectivity is precluded because atomic structural fluctuations are greater than the size difference between these two ions. We examine these hypotheses by calculating the distribution of binding energies for Na+ and K+ in a simplified model of the selectivity filter of the KcsA channel. We find that Na+ binds strongly to the selectivity filter with a mean binding energy substantially lower than that for K+. The difference is comparable to the difference in hydration free energies of Na+ and K+ in bulk aqueous solution. Thus, the average filter binding energies do not discriminate Na+ from K+ when measured from the baseline of the difference in bulk hydration free energies. Instead, Na+/K+ discrimination can be attributed to scarcity of good binding configurations for Na+ compared to K+. That relative scarcity is quantified as enhanced binding energy fluctuations, and is consistent with predicted relative constriction of the filter by Na+.
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"abstract": "The KcsA potassium channel belongs to a class of K+ channels that is\nselective for K+ over Na+ at rates of K+ transport approaching the diffusion\nlimit. This selectivity is explained thermodynamically in terms of favorable\npartitioning of K+ relative to Na+ in a narrow selectivity filter in the\nchannel. One mechanism for selectivity based on the atomic structure of the\nKcsA channel invokes the size difference between K+ and Na+, and the molecular\ncomplementarity of the selectivity filter with the larger K+ ion. An\nalternative view holds that size-based selectivity is precluded because atomic\nstructural fluctuations are greater than the size difference between these two\nions. We examine these hypotheses by calculating the distribution of binding\nenergies for Na+ and K+ in a simplified model of the selectivity filter of the\nKcsA channel. We find that Na+ binds strongly to the selectivity filter with a\nmean binding energy substantially lower than that for K+. The difference is\ncomparable to the difference in hydration free energies of Na+ and K+ in bulk\naqueous solution. Thus, the average filter binding energies do not discriminate\nNa+ from K+ when measured from the baseline of the difference in bulk hydration\nfree energies. Instead, Na+/K+ discrimination can be attributed to scarcity of\ngood binding configurations for Na+ compared to K+. That relative scarcity is\nquantified as enhanced binding energy fluctuations, and is consistent with\npredicted relative constriction of the filter by Na+.",
"arxiv_id": "physics/0511152",
"authors": [
"D. Asthagiri",
"Lawrence R. Pratt",
"Michael E. Paulaitis"
],
"categories": [
"physics.bio-ph"
],
"doi": "10.1063/1.2205853",
"title": "Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity",
"url": "https://arxiv.org/abs/physics/0511152"
},
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