Analysis of the quality of crystallographic data and the limitations of structural models.

The Journal of General Physiology
Valentina ArkhipovaDirk-Jan Slotboom

Abstract

Crystal structures provide visual models of biological macromolecules, which are widely used to interpret data from functional studies and generate new mechanistic hypotheses. Because the quality of the collected x-ray diffraction data directly affects the reliability of the structural model, it is essential that the limitations of the models are carefully taken into account when making interpretations. Here we use the available crystal structures of members of the glutamate transporter family to illustrate the importance of inspecting the data that underlie the structural models. Crystal structures of glutamate transporters in multiple different conformations have been solved, but most structures were determined at relatively low resolution, with deposited models based on crystallographic data of moderate quality. We use these examples to demonstrate the extent to which mechanistic interpretations can be made safely.

References

Oct 17, 1996·Nature·N Zerangue, M P Kavanaugh
Jan 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·Y ZhangB I Kanner
Mar 14, 1998·Molecular Pharmacology·K ShimamotoT Nakajima
Jun 5, 1999·Microbiology and Molecular Biology Reviews : MMBR·D J SlotboomJ S Lolkema
Mar 14, 2000·Acta Crystallographica. Section D, Biological Crystallography·G J Kleywegt
Sep 9, 2000·The Journal of Biological Chemistry·A BendahanB I Kanner
Apr 27, 2002·Acta Crystallographica. Section D, Biological Crystallography·D M Blow
Jul 1, 1963·Journal of Molecular Biology·G N RAMACHANDRANV SASISEKHARAN
Jul 22, 2004·The Journal of Biological Chemistry·Sandra GendreauChristoph Fahlke
Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Kevin Cowtan
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Thomas C TerwilligerPaul D Adams
Jun 3, 2008·Biophysical Journal·Zhijian Huang, Emad Tajkhorshid
Nov 4, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David C Holley, Michael P Kavanaugh
Feb 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Yan GuIvet Bahar
Apr 22, 2009·The Journal of Biological Chemistry·Renae M RyanJoseph A Mindell
Dec 8, 2009·Acta Crystallographica. Section D, Biological Crystallography·Alexandre UrzhumtsevPaul D Adams
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Mar 31, 2010·Biochemistry·Maarten Groeneveld, Dirk-Jan Slotboom
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Emma L R ComptonJoseph A Mindell
Jul 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·H Peter LarssonSergei Y Noskov
Feb 22, 2012·Nature Structural & Molecular Biology·Grégory Verdon, Olga Boudker
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Pavel V AfoninePaul D Adams
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Swanand GoreGerard J Kleywegt
Jan 22, 2013·Nature Structural & Molecular Biology·Elka R GeorgievaOlga Boudker
Jan 22, 2013·Nature Structural & Molecular Biology·Inga HäneltDirk Jan Slotboom
Apr 9, 2013·Nature Structural & Molecular Biology·Nicolas ReyesOlga Boudker
Jun 25, 2013·Nature·Nurunisa AkyuzOlga Boudker
Sep 10, 2013·Nature Structural & Molecular Biology·Sonja JensenDirk Jan Slotboom
Oct 19, 2013·Physiological Reviews·Robert J Vandenberg, Renae M Ryan
Nov 19, 2013·Pflügers Archiv : European journal of physiology·Christof GrewerThomas Rauen
Mar 20, 2014·PloS One·Germano Heinzelmann, Serdar Kuyucak
May 9, 2014·The Journal of Biological Chemistry·Amanda J ScopellitiRobert J Vandenberg
Feb 6, 2015·Nature·Nurunisa AkyuzScott C Blanchard

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Citations

Feb 23, 2020·Nature Communications·Valentina ArkhipovaDirk J Slotboom
May 6, 2020·Biochemical Society Transactions·Alisa A Garaeva, Dirk J Slotboom
Jun 7, 2018·Nature Structural & Molecular Biology·Alisa A GaraevaDirk J Slotboom
Aug 7, 2019·Biochemical Society Transactions·Ana PavićAdrian Goldman
May 21, 2021·Cell Chemical Biology·Cristina C SantarossaTarun M Kapoor
May 16, 2021·Neuropharmacology·Ada G Rodríguez-Campuzano, Arturo Ortega
Mar 16, 2019·Journal of Chemical Information and Modeling·Helena W Qi, Heather J Kulik

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Methods Mentioned

BETA
x-ray diffraction
electron paramagnetic resonance
x-ray
atomic force microscopy
x-ray scattering

Software Mentioned

Glt Tk

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