Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State

NMR structures of membrane proteins are often hampered by poor chemical shift dispersion and internal dynamics which limit resolved distance restraints. However, the ordering and topology of these systems can be defined with site-specific water or lipid proximity. Membrane protein water accessibilit...

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Autores principales:	Reza Amani, Charles D. Schwieters, Collin G. Borcik, Isaac R. Eason, Ruixian Han, Benjamin D. Harding, Benjamin J. Wylie
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	solid state NMR membrane protein xplor-NIH water-edited spectroscopy structure refinement potassium channel Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0cd462d8a20e445fb8fb91ca6aa22335
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spelling	oai:doaj.org-article:0cd462d8a20e445fb8fb91ca6aa223352021-12-01T18:26:37ZWater Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State2296-889X10.3389/fmolb.2021.772855https://doaj.org/article/0cd462d8a20e445fb8fb91ca6aa223352021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.772855/fullhttps://doaj.org/toc/2296-889XNMR structures of membrane proteins are often hampered by poor chemical shift dispersion and internal dynamics which limit resolved distance restraints. However, the ordering and topology of these systems can be defined with site-specific water or lipid proximity. Membrane protein water accessibility surface area is often investigated as a topological function via solid-state NMR. Here we leverage water-edited solid-state NMR measurements in simulated annealing calculations to refine a membrane protein structure. This is demonstrated on the inward rectifier K+ channel KirBac1.1 found in Burkholderia pseudomallei. KirBac1.1 is homologous to human Kir channels, sharing a nearly identical fold. Like many existing Kir channel crystal structures, the 1p7b crystal structure is incomplete, missing 85 out of 333 residues, including the N-terminus and C-terminus. We measure solid-state NMR water proximity information and use this for refinement of KirBac1.1 using the Xplor-NIH structure determination program. Along with predicted dihedral angles and sparse intra- and inter-subunit distances, we refined the residues 1–300 to atomic resolution. All structural quality metrics indicate these restraints are a powerful way forward to solve high quality structures of membrane proteins using NMR.Reza AmaniCharles D. SchwietersCollin G. BorcikIsaac R. EasonRuixian HanBenjamin D. HardingBenjamin D. HardingBenjamin J. WylieFrontiers Media S.A.articlesolid state NMRmembrane proteinxplor-NIHwater-edited spectroscopystructure refinementpotassium channelBiology (General)QH301-705.5ENFrontiers in Molecular Biosciences, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	solid state NMR membrane protein xplor-NIH water-edited spectroscopy structure refinement potassium channel Biology (General) QH301-705.5
spellingShingle	solid state NMR membrane protein xplor-NIH water-edited spectroscopy structure refinement potassium channel Biology (General) QH301-705.5 Reza Amani Charles D. Schwieters Collin G. Borcik Isaac R. Eason Ruixian Han Benjamin D. Harding Benjamin D. Harding Benjamin J. Wylie Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State
description	NMR structures of membrane proteins are often hampered by poor chemical shift dispersion and internal dynamics which limit resolved distance restraints. However, the ordering and topology of these systems can be defined with site-specific water or lipid proximity. Membrane protein water accessibility surface area is often investigated as a topological function via solid-state NMR. Here we leverage water-edited solid-state NMR measurements in simulated annealing calculations to refine a membrane protein structure. This is demonstrated on the inward rectifier K+ channel KirBac1.1 found in Burkholderia pseudomallei. KirBac1.1 is homologous to human Kir channels, sharing a nearly identical fold. Like many existing Kir channel crystal structures, the 1p7b crystal structure is incomplete, missing 85 out of 333 residues, including the N-terminus and C-terminus. We measure solid-state NMR water proximity information and use this for refinement of KirBac1.1 using the Xplor-NIH structure determination program. Along with predicted dihedral angles and sparse intra- and inter-subunit distances, we refined the residues 1–300 to atomic resolution. All structural quality metrics indicate these restraints are a powerful way forward to solve high quality structures of membrane proteins using NMR.
format	article
author	Reza Amani Charles D. Schwieters Collin G. Borcik Isaac R. Eason Ruixian Han Benjamin D. Harding Benjamin D. Harding Benjamin J. Wylie
author_facet	Reza Amani Charles D. Schwieters Collin G. Borcik Isaac R. Eason Ruixian Han Benjamin D. Harding Benjamin D. Harding Benjamin J. Wylie
author_sort	Reza Amani
title	Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State
title_short	Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State
title_full	Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State
title_fullStr	Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State
title_full_unstemmed	Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State
title_sort	water accessibility refinement of the extended structure of kirbac1.1 in the closed state
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/0cd462d8a20e445fb8fb91ca6aa22335
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Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State

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