Structural Disorder of Folded Proteins: Isotope-Edited 2D IR Spectroscopy and Markov State Modeling

Carlos R. Baiz, Andrei Tokmakoff
2015 Biophysical Journal  
The conformational heterogeneity of the N-terminal domain of the ribosomal protein L9 (NTL9 1-39 ) in its folded state is investigated using isotope-edited two-dimensional infrared spectroscopy. Backbone carbonyls are isotope-labeled ( 13 C¼ 18 O) at five selected positions (V3, V9, V9G13, G16, and G24) to provide a set of localized spectroscopic probes of the structure and solvent exposure at these positions. Structural interpretation of the amide I line shapes is enabled by spectral
more » ... s carried out on structures extracted from a recent Markov state model. The V3 label spectrum indicates that the b-sheet contacts between strands I and II are well folded with minimal disorder. The V9 and V9G13 label spectra, which directly probe the hydrogen-bond contacts across the b-turn, show significant disorder, indicating that molecular dynamics simulations tend to overstabilize ideally folded b-turn structures in NTL9 1-39 . In addition, G24-label spectra provide evidence for a partially disordered a-helix backbone that participates in hydrogen bonding with the surrounding water.
doi:10.1016/j.bpj.2014.12.061 pmid:25863066 pmcid:PMC4390782 fatcat:x3mixndwkjfyjplx2vmcpkntjy