ArticleJournal of biomolecular NMR2011
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.
Article in Journal of biomolecular NMR, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 45 citations in OpenAlex.
- Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra.Journal of biomolecular NMR · 2020Article
- CombLabel: rational design of optimized sequence-specific combinatorial labeling schemes. Application to backbone assignment of membrane proteins with low stability.Journal of biomolecular NMR · 2019Article
- Stable isotope labeling strategy based on coding theory.Journal of biomolecular NMR · 2015Article
- An extended combinatorial 15N, 13Cα, and 13C' labeling approach to protein backbone resonance assignment.Journal of biomolecular NMR · 2015Article
- Dipolar Assisted Assignment Protocol (DAAP) for MAS solid-state NMR of rotationally aligned membrane proteins in phospholipid bilayers.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Article
- SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR.Journal of biomolecular NMR · 2013Article
- Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins.Journal of biomolecular NMR · 2013Article
- Advances in NMR structures of integral membrane proteins.Current opinion in structural biology · 2013Review
- Prediction of peak overlap in NMR spectra.Journal of biomolecular NMR · 2013Article
- Cell-free expressed bacteriorhodopsin in different soluble membrane mimetics: biophysical properties and NMR accessibility.Structure (London, England : 1993) · 2013Article
- Rapid prediction of multi-dimensional NMR data sets.Journal of biomolecular NMR · 2012Article
- Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment.Journal of biomolecular NMR · 2012Article
- Solution NMR structure of proteorhodopsin.Angewandte Chemie (International ed. in English) · 2011Article
- A rapid and robust method for selective isotope labeling of proteins.Methods (San Diego, Calif.) · 2011Article
- A software framework for analysing solid-state MAS NMR data.Journal of biomolecular NMR · 2011Article
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7 authors at 3 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
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 (13)C or/and (15)N such that cross peaks between (13)CO(i - 1) and (15)NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with (13)C and the second with (15)N. 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 (B(2)R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin.
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