Multiply labeling proteins for studies of folding and stability

Orevi, 2014, Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics, Methods Mol Biol, 1076, 113, 10.1007/978-1-62703-649-8_7 Lakowicz, 2006 Los, 2008, HaloTag: a novel protein labeling technology for cell imaging and protein analysis, ACS Chem Biol, 3, 373, 10.1021/cb800025k Keppler, 2004, Labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase with small molecules in vivo and in vitro, Methods, 32, 437, 10.1016/j.ymeth.2003.10.007 Gautier, 2008, An engineered protein tag for multiprotein labeling in living cells, Chem Biol, 15, 128, 10.1016/j.chembiol.2008.01.007 Gallagher, 2009, An in vivo covalent TMP-tag based on proximity-induced reactivity, ACS Cheml Biol, 4, 547, 10.1021/cb900062k Carlson, 2009, Genetically encoded FRET-based biosensors for multiparameter fluorescence imaging, Curr Opin Biotechnol, 20, 19, 10.1016/j.copbio.2009.01.003 Piston, 2007, Fluorescent protein FRET: the good, the bad and the ugly, Trends Biochem Sci, 32, 407, 10.1016/j.tibs.2007.08.003 Speight, 2014, Minimalist approaches to protein labelling: getting the most fluorescent bang for your steric buck, Aust J Chem, 67, 686, 10.1071/CH13554 Griffin, 1998, Specific covalent labeling of recombinant protein molecules inside live cells, Science, 281, 269, 10.1126/science.281.5374.269 Scheck, 2011, Surveying protein structure and function using bis-arsenical small molecules, Acc Chem Res, 44, 654, 10.1021/ar2001028 Rashidian, 2013, Enzymatic labeling of proteins: techniques and approaches, Bioconj Chem, 24, 1277, 10.1021/bc400102w Boutureira, 2015, Advances in chemical protein modification, Chem Rev, 115, 2174, 10.1021/cr500399p Stephanopoulos, 2011, Choosing an effective protein bioconjugation strategy, Nat Chem Biol, 7, 876, 10.1038/nchembio.720 Spicer, 2014, Selective chemical protein modification, Nat Commun, 5, 10.1038/ncomms5740 Lang, 2014, Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins, Chem Rev, 114, 4764, 10.1021/cr400355w Dumas, 2015, Designing logical codon reassignment—expanding the chemistry in biology, Chem Sci, 6, 50, 10.1039/C4SC01534G Summerer, 2006, A genetically encoded fluorescent amino acid, Proc Natl Acad Sci U S A, 103, 9785, 10.1073/pnas.0603965103 Lee, 2009, Genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in Saccharomyces cerevisiae, J Am Chem Soc, 131, 12921, 10.1021/ja904896s Chatterjee, 2013, A genetically encoded fluorescent probe in mammalian cells, J Am Chem Soc, 135, 12540, 10.1021/ja4059553 Speight, 2013, Efficient synthesis and in vivo incorporation of acridon-2-ylalanine, a fluorescent amino acid for lifetime and Förster resonance energy transfer/luminescence resonance energy transfer studies, J Am Chem Soc, 135, 18806, 10.1021/ja403247j Tsao, 2006, The genetic incorporation of a distance probe into proteins in Escherichia coli, J Am Chem Soc, 128, 4572, 10.1021/ja058262u Brustad, 2008, A general and efficient method for the site-specific dual-labeling of proteins for single molecule fluorescence resonance energy transfer, J Am Chem Soc, 130, 17664, 10.1021/ja807430h Nguyen, 2011, genetically encoded 1,2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation, J Am Chem Soc, 133, 11418, 10.1021/ja203111c Milles, 2012, Click strategies for single-molecule protein fluorescence, J Am Chem Soc, 134, 5187, 10.1021/ja210587q Tyagi, 2013, Genetically encoded click chemistry for single-molecule FRET of proteins, vol 113, 169 Muralidharan, 2006, Protein ligation: an enabling technology for the biophysical analysis of proteins, Nat Methods, 3, 429, 10.1038/nmeth886 Kent, 2009, Total chemical synthesis of proteins, Chem Soc Rev, 38, 338, 10.1039/B700141J Wang, 2015, Semi-synthesis of thioamide containing proteins, Org Biomol Chem, 13, 5074, 10.1039/C5OB00224A Goldberg, 2013, Thioamide quenching of fluorescent probes through photoinduced electron transfer: mechanistic studies and applications, J Am Chem Soc, 135, 18651, 10.1021/ja409709x Goldberg, 2010, Thioamides as fluorescence quenching probes: minimalist chromophores to monitor protein dynamics, J Am Chem Soc, 132, 14718, 10.1021/ja1044924 Batjargal, 2012, Native chemical ligation of thioamide-containing peptides: development and application to the synthesis of labeled α-synuclein for misfolding studies, J Am Chem Soc, 134, 9172, 10.1021/ja2113245 Wissner, 2013, Labeling proteins with fluorophore/thioamide förster resonant energy transfer pairs by combining unnatural amino acid mutagenesis and native chemical ligation, J Am Chem Soc, 135, 6529, 10.1021/ja4005943 Wissner, 2013, Efficient, traceless semi-synthesis of α-synuclein labeled with a fluoro-phore/thioamide FRET pair, Synlett, 24, 2454, 10.1055/s-0033-1339853 Kajihara, 2006, FRET analysis of protein conformational change through position-specific incorporation of fluorescent amino acids, Nat Methods, 3, 923, 10.1038/nmeth945 Chen, 2013, Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids, J Am Chem Soc, 135, 12924, 10.1021/ja403007r Wu, 2012, Catalyst-free and site-specific one-pot dual-labeling of a protein directed by two genetically incorporated noncanonical amino acids, ChemBioChem, 13, 1405, 10.1002/cbic.201200281 Kim, 2013, Simple and efficient strategy for site-specific dual labeling of proteins for single-molecule fluorescence resonance energy transfer analysis, Anal Chem, 85, 1468, 10.1021/ac303089v Mukai, 2010, Codon reassignment in the Escherichia coli genetic code, Nucleic Acids Res, 38, 8188, 10.1093/nar/gkq707 Aerni, 2015, Revealing the amino acid composition of proteins within an expanded genetic code, Nucleic Acids Res, 43, e8, 10.1093/nar/gku1087 Lajoie, 2013, Genomically recoded organisms expand biological functions, Science, 342, 357, 10.1126/science.1241459 Johnson, 2011, RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites, Nat Chem Biol, 7, 779, 10.1038/nchembio.657 Wang, 2007, Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion, Nat Biotechnol, 25, 770, 10.1038/nbt1314 Neumann, 2010, Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome, Nature, 464, 441, 10.1038/nature08817 Wang, 2014, Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double labelling and FRET, Nat Chem, 6, 393, 10.1038/nchem.1919 Schmied, 2014, Efficient multisite unnatural amino acid incorporation in mammalian cells via optimized pyrrolysyl tRNA synthetase/tRNA expression and engineered eRF1, J Am Chem Soc, 136, 15577, 10.1021/ja5069728 Kalinin, 2012, A toolkit and benchmark study for FRET-restrained high-precision structural modeling, Nat Methods, 9, 1218, 10.1038/nmeth.2222 Vöpel, 2014, Triphosphate induced dimerization of human guanylate binding protein 1 involves association of the C-terminal helices: a joint double electron–electron resonance and FRET study, Biochemistry, 53, 4590, 10.1021/bi500524u Ratzke, 2014, Four-colour FRET reveals directionality in the Hsp90 multicomponent machinery, Nat Commun, 5, 10.1038/ncomms5192 Huang, 2009, Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer, Proc Natl Acad Sci U S A, 106, 20758, 10.1073/pnas.0909644106 Nath, 2012, The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulations, Biophys J, 103, 1940, 10.1016/j.bpj.2012.09.032 Elbaum-Garfinkle, 2012, Identification of an aggregation-prone structure of tau, J Am Chem Soc, 134, 16607, 10.1021/ja305206m Woolhead, 2004, Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins, Cell, 116, 725, 10.1016/S0092-8674(04)00169-2 Shen, 2012, Activated GTPase movement on an RNA scaffold drives co-translational protein targeting, Nature, 492, 271, 10.1038/nature11726 Saraogi, 2014, Regulation of cargo recognition, commitment, and unloading drives cotranslational protein targeting, J Cell Biol, 205, 693, 10.1083/jcb.201311028 Akopian, 2013, SecYEG activates GTPases to drive the completion of cotranslational protein targeting, J Cell Biol, 200, 397, 10.1083/jcb.201208045 Saraogi, 2014, Co-translational protein targeting to the bacterial membrane, Biochim Biophys Acta Mol Cell Res, 1843, 1433, 10.1016/j.bbamcr.2013.10.013 Kalstrup, 2013, Dynamics of internal pore opening in KV channels probed by a fluorescent unnatural amino acid, Proc Natl Acad Sci U S A, 110, 8272, 10.1073/pnas.1220398110 Dolino, 2015, Structural dynamics of the glycine-binding domain of the N-methyl-d-aspartate receptor, J Biol Chem, 290, 797, 10.1074/jbc.M114.605436