Coherence transfer in proteins Perttu Permi a, * , Arto Annila b a NMR Laboratory, Institute of Biotechnology, Structural Biology and Biophysics Program, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland b Department of Physics, FIN-00014 University of Helsinki, P.O. Box 64, Helsinki, Finland Received 16 October 2003 Contents 1. Introduction ............................................................................. 97 2. Strategies for the assignment of nuclei in the polypeptide main chain ................................... 99 2.1. Small and medium sized proteins ......................................................... 99 2.1.1. Traditional approach using HNCA/HN(CO)CA experiment pair ............................. 99 2.1.2. A new means used to alleviate resonance overlap: intraresidual HNCA ....................... 102 2.1.3. Sequential linking via carbonyl carbons in HN(CA)CO and HNCO pair ....................... 106 2.1.4. Going straight through: (HA)CANH and (HA)CA(CO)NH ................................ 107 2.1.5. Straight through version of the HN(CA)CO: (HACA)CO(CA)NH ........................... 110 2.1.6. Correlation of sequential amide protons and nitrogens in HN(· · ·)NH type experiments ............ 110 2.1.7. HCACO experiment for assisting sequential assignment .................................. 112 2.2. Large proteins ....................................................................... 114 2.2.1. Special considerations for improving coherence transfer efficiency in large proteins .............. 114 2.2.2. Carbonyl carbon: a bad choice at high field............................................ 116 2.2.3. Relay through alpha carbon, a remedy? .............................................. 117 2.2.4. The HNCA-TROSY scheme outperforms HN(CO)CA-TROSY at the high field ................. 117 2.2.5. Sequential assignment using 4D HNCOCA, HNCACO and HNCO i21 CA TROSY experiments...... 118 2.2.6. Spin-state-selective editing for distinguishing between intraresidual and sequential pathways ....... 119 2.2.7. Sequential connectivities acquired through HN(CO)CANH-TROSY.......................... 121 2.2.8. Sequential HNCA-TROSY ........................................................ 124 2.2.9. Doing it in an unorthodox way: iHNCA-TROSY ....................................... 126 2.2.10. Intraresidual alpha carbon connectivities through iHNCA(CO)-TROSY ....................... 129 2.2.11. Sequential correlations via DQ-HNCA-TROSY......................................... 131 3. Conclusions ............................................................................. 133 References ................................................................................ 135 Keywords: Coherence transfer; Protein NMR; TROSY 1. Introduction Modern NMR spectroscopy stands unique among many methods in its power to deliver distinct signals practically from every atom of a protein. Each signal carries a wealth of information about structure and dynamics that serves to uncover molecular mechanisms of life. Successful transfer of coherence in the polypeptide chain is a prerequisite in order to acquire multidimensional heteronuclear correlation NMR spectra. Intensive development and optimization of coherence transfer methods over the past twenty years has resulted in a bewildering myriad of NMR experiments [1–4]. Today on the brink of the protein structural genomics era, NMR spectroscopy has matured in to a technique used primarily by those interested in structural biology but often uninitiated to the intricacy of NMR [5–8]. Here we hope to 0079-6565/$ - see front matter q 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.pnmrs.2003.12.001 Progress in Nuclear Magnetic Resonance Spectroscopy 44 (2004) 97–137 www.elsevier.com/locate/pnmrs * Corresponding author. Tel.: þ 358-9-19158940; fax: þ 358-9- 19159541. E-mail address: perttu.permi@helsinki.fi (P. Permi).