Conformational Ensembles from Experimental Data and Computer Simulations

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Conformational Ensembles from Experimental Data
and Computer Simulations Poster Abstracts
121
84-POS Board 4
Inferential Determination of the Dimeric Structures of TMD0 of TAPL from DEER and
PRE Data
Katrin Reichel1,2, Benesh Joseph 3, Christoph Bock4, Lukas S. Stelzl1, Jürgen Köfinger1, Lars V.
Schäfer2 , Rupert Abele4, Thomas Prisner3, Gerhard Hummer1.
1Max Planck Institute of Biophysics, Frankfurt, Germany, 2Ruhr-University Bochum, Bochum,
Germany, 3Goethe-University, Center for Biomolecular Magnetic Resonance, Frankfurt,
Germany, 4Goethe-University, Institute of Biochemisty, Frankfurt, Germany.
One of the largest membrane protein families is the ATP-binding cassette (ABC) transporter
family. Besides their core domain, which performs nucleotide binding and the actual
translocation process, some of the ABC transporter have an additional N-terminal
transmembrane domain, called TMD0. To elucidate its homodimeric configurations, TMD0 was
expressed separately from the core domain and investigated by spectroscopic techniques. In our
study, we combine spin-label distance measurements from NMR paramagnetic relaxation
enhancement (PRE) and double electron-electron resonance (DEER) experiments with ensemble
refinement. These experimental observables seem particularly valuable to detect even sparsely
populated configurations. To avoid artifacts, we explicitly model spin-label conformations and
the ensemble of structures is directly refined against the nuclear relaxation rates from the PRE
measurements and the DEER signals. To perform ensemble refinement, we generate an ensemble
of dimeric structures, and subsequently refine the ensemble by reweighting all structures using
EROS[1], a maximum-entropy method with Bayesian interpretation [2]. By exploring various
numerical approaches to solve the underlying high-dimensional optimization problem, we
identify configurations of the TMD0 that are consistent with experiments and our prior
expectations.
[1] B. Różycki , Y. C. Kim, and G. Hummer. SAXS ensemble refinement of ESCRT-III
CHMP3 conformational transitions. Structure, 19(1):109-116, 2011.
[2] G. Hummer and J. Köfinger. Bayesian ensemble refinement by replica simulations and
reweighting. J. Chem. Phys., 143(24):1-15, 2015.