SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR
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SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR Lucio Ferella • Claudio Luchinat • Enrico Ravera Antonio Rosato
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Received: 7 September 2013 / Accepted: 11 November 2013 / Published online: 17 November 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity—obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device—into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment. Keywords Ultracentrifuge Sedimentation Solid state NMR Biological macromolecules Aggregates
Recent advances in theory (Laage et al. 2008; Bertini et al. 2011b; Hu et al. 2011; Loening et al. 2012; Bjerring et al. 2012; Nielsen et al. 2012; Westfeld et al. 2012; Lamley and Lewandowski, 2012; Giffard et al. 2012) and in sample preparation techniques (Lewandowski et al. 2011a; Akbey et al. 2012) have pushed the limits of solid state NMR
L. Ferella C. Luchinat (&) E. Ravera A. Rosato Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy e-mail: [email protected]; [email protected] C. Luchinat Fondazione Farmacogenomica FiorGen Onlus, Via L. Sacconi 6, 50019 Sesto Fiorentino, FI, Italy C. Luchinat E. Ravera A. Rosato Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy
(SSNMR) close to that of state-of-the-art solution NMR for the determination of structure (Bertini et al. 2010a; Knight et al. 2011; Luchinat et al. 2012; Huber et al. 2012; Knight et al. 2013; Bhaumik et al. 2013) and dynamics (Lewandowski et al. 2010; Lewandowski et al. 2011b; Knight et al. 2012; Lewandowski 2013; Haller and Schanda, 2013; Schanda et al. 2010; Zinkevich et al. 2013) for micro- to nanocrystalline systems, and even in the case of systems lacking long-range order like fibrils (Petkova et al. 2002; Tycko and Ishii 2003; Debelouchina et al. 2010; Bertini et al. 2011c; Lewandowski et al. 2011a; Bayro et al. 2011; Parthasarathy et al. 2011; Habenstein et al. 2011; Habenstein et al. 2012; Lopez del Amo et al. 2012; Qiang et al. 2012; Lv et al. 2012), large aggregates (Sun et al. 2009; Loquet et al. 2010; Loquet et al. 2012; Byeon et al. 2012; Yan et al. 2013; Loquet et al. 2013), membrane proteins(Ader et al. 2009; Lange et al. 2010; Weingarth and Baldus, 2013; Cady et al. 2010; Hong et al. 2011; Hong 2006; Hong and Schmidt-Rohr 2013; Petkova et al. 2003; Harbison et al. 1985; Marassi and Opella 2000; Opella and Marassi 2004; Marassi et al. 2011; Ding et al. 2013; Opella 2013; Murray et a
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