Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

84-POS Board 4 Inferential Determination of the Dimeric Structures of TMD0 of TAPL from DEER and PRE Data Katrin Reichel 1,2 , Benesh Joseph 3 , Christoph Bock 4 , Lukas S. Stelzl 1 , Jürgen Köfinger 1 , Lars V. Schäfer 2 , Rupert Abele 4 , Thomas Prisner 3 , Gerhard Hummer 1 . 1 Max Planck Institute of Biophysics, Frankfurt, Germany, 2 Ruhr-University Bochum, Bochum, Germany, 3 Goethe-University, Center for Biomolecular Magnetic Resonance, Frankfurt, Germany, 4 Goethe-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.

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