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Lindahl, Viveca
Publications (2 of 2) Show all publications
Lindahl, V., Gourdon, P., Andersson, M. & Hess, B. (2018). Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function. Scientific Reports, 8, Article ID 2995.
Open this publication in new window or tab >>Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 2995Article in journal (Refereed) Published
Abstract [en]

Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-223791 (URN)10.1038/s41598-018-21357-2 (DOI)000424985800033 ()29445244 (PubMedID)2-s2.0-85042110483 (Scopus ID)
Funder
EU, European Research Council, 258980Swedish Research Council, 2014-4505Swedish e‐Science Research Center
Note

QC 20180307

Available from: 2018-03-07 Created: 2018-03-07 Last updated: 2018-03-07Bibliographically approved
Lindahl, V., Lidmar, J. & Hess, B. (2015). Sampling rare biomolecular events with adaptive pulling simulations. Paper presented at 10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY. European Biophysics Journal, 44, S144-S144
Open this publication in new window or tab >>Sampling rare biomolecular events with adaptive pulling simulations
2015 (English)In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S144-S144Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
SPRINGER, 2015
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-243669 (URN)000380001400390 ()
Conference
10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY
Note

QC 20190304

Available from: 2019-03-04 Created: 2019-03-04 Last updated: 2019-05-20Bibliographically approved
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