caa a22 4500 445325097 CHVBK 20180317142717.0 cr unu---uuuuu 170323e20110201xx s 000 0 eng 10.1007/s10858-010-9462-4 doi (NATIONALLICENCE)springer-10.1007/s10858-010-9462-4 Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm [Elektronische Daten] [Frederik Hefke, Anurag Bagaria, Sina Reckel, Sandra Ullrich, Volker Dötsch, Clemens Glaubitz, Peter Güntert] We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273-6279 (1982)), types of amino acids are labeled with 13C or/and 15N such that cross peaks between 13CO(i - 1) and 15NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with 13C and the second with 15N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. Our computer algorithm UPLABEL for optimal unique pair labeling, implemented in the program CYANA and in a standalone program, and also available through a web portal, uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns. The method is illustrated for the assignment of the human G-protein coupled receptor bradykinin B2 (B2R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin. Springer Science+Business Media B.V., 2010 Sequence-specific assignment nationallicence Isotope labeling nationallicence Unique amino acid pairs nationallicence Combinatorial optimization nationallicence Hefke Frederik Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Bagaria Anurag Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Reckel Sina Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Ullrich Sandra Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Dötsch Volker Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Glaubitz Clemens Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Güntert Peter Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut Journal of Biomolecular NMR Springer Netherlands 49/2(2011-02-01), 75-84 0925-2738 49:2<75 2011 49 10858 https://doi.org/10.1007/s10858-010-9462-4 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10858-010-9462-4 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Hefke Frederik Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 700 1- Bagaria Anurag Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 700 1- Reckel Sina Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 700 1- Ullrich Sandra Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 700 1- Dötsch Volker Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 700 1- Glaubitz Clemens Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 700 1- Güntert Peter Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany aut NATIONALLICENCE 773 0- Journal of Biomolecular NMR Springer Netherlands 49/2(2011-02-01), 75-84 0925-2738 49:2<75 2011 49 10858 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer