Journal
PROTEIN SCIENCE
Volume 19, Issue 12, Pages 2462-2474Publisher
WILEY
DOI: 10.1002/pro.528
Keywords
NMR structure determination; NOE upper bounds; (3)J-coupling constants; GCN4p trigger site; molecular dynamics; GROMOS; time averaging; local-elevation biasing
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Funding
- Swiss National Science Foundation (SNSF) [200020 121913]
- European Research Council (ERC) [228076]
- Slovenian Research Agency (ARRS) [Z1 9576]
- National Centre of Competence in Research (NCCR) in Structural Biology
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Trigger sequences are indispensable elements for coiled-coil formation The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated recently using several solution NMR observables including nuclear Overhauser enhancement (NOE) intensities and (3)J(H-N H-C alpha)-coupling constants, and a set of 20 model structures was proposed Constrained to satisfy the NOE-derived distance bounds, the NMR model structures do not appear to reproduce all the measured (3)J(H-N-H-C alpha)-coupling constant values, indicating that the a-helical propensity is not uniform along the GCN4 trigger sequence A recent methodological study of unrestrained and restrained molecular dynamics (MD) simulations of the GCN4 trigger sequence in solution showed that only MD simulations incorporating time-averaged NOE distance restraints and instantaneous or local-elevation (3)J-coupling restraints could satisfy the entire set of the experimental data In this report, we assess by means of cluster analyses the model structures characteristic of the two simulations that are compatible with the measured data and compare them with the proposed 20 NMR model structures Striking characteristics of the MD model structures are the variability of the simulated configurations and the indication of entropic stability mediated by the aromatic N-terminal residues 17Tyr and 18His, which are absent in the set of NMR model structures
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