Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

TY - JOUR

T1 - Sequence correction of random coil chemical shifts

T2 - correlation between neighbor correction factors and changes in the Ramachandran distribution

AU - Kjærgaard, Magnus

AU - Poulsen, Flemming Martin

PY - 2011/6

Y1 - 2011/6

N2 - Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.

AB - Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.

KW - Amino Acid Sequence

KW - Amino Acids

KW - Nuclear Magnetic Resonance, Biomolecular

KW - Peptides

KW - Protein Conformation

U2 - 10.1007/s10858-011-9508-2

DO - 10.1007/s10858-011-9508-2

M3 - Journal article

C2 - 21604143

SN - 0925-2738

VL - 50

SP - 157

EP - 165

JO - Journal of Biomolecular N M R

JF - Journal of Biomolecular N M R

IS - 2

ER -