Untitled

Abstract

Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best.

Mechanism of allosteric propagation across a β‐sheet structure investigated by molecular dynamics simulations

“…Values of RMSF derived from crystallographic B factors of the low affinity state structure were calculated using the formula RMSF ${}_i^{\text{exp}}=\sqrt{\frac{3}{8{\pi }^2}{B}_i}$, where B i is the B factor of C α of residue i . Chemical shifts measured for the high affinity state35 and deposited in the BMRB database60 were used to derive RMSF values by utilizing the Random Coil Index server 61, 62. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.…”

Effect of pH, urea, peptide length, and neighboring amino acids on alanine α‐proton random coil chemical shifts

“…(In previous model systems this was also accounted for by capping the N and C-termini. 19,22 ) The current model system incorporates two buffering amino acids on either side of the alanine. That the terminal amino acids effectively absorb the protonation/deprotonation pH effects is evidenced by the fact that the -proton chemical shift of alanine did not significantly change for any of the peptides over the pH range studied ( 0.02 ppm).…”

“…Nonetheless, the tryptophan double substitution (14) does exhibit the largest upfield shift for the series (0.19 ppm), and tryptophan in either position is very important to note for -proton chemical shifts and CSI. In fact, the large aromatic amino acid tryptophan appears to dominate over the other smaller aromatic amino acids when two dissimilar aromatic amino acids are adjacent to alanine (22)(23)(24)(25). Whether in the N or C-terminal position, the chemical shift effect seen can be approximated by a single tryptophan residue.…”

“…(The shift effects listed are calculated using GGGAGG as the control peptide.) Schwarzinger et al 22 investigated both the N-terminal and C-terminal neighboring effects of each of the common amino acids on glycine (GGX aa GG, pH 2.3, 8M urea). Upfield shifts of ca 0.10 ppm were observed for both N and C-terminal phenylalanine and tyrosine residues, and no positional effect was observed for the sterically simple glycine.…”

“…Several studies have been done to measure the -proton random coil chemical shift value for each of the 20 common amino acids, and while there is general agreement among the studies, there are some notable discrepancies. 6,[18][19][20][21][22][23][24][25] For instance, in four separate studies the histidine random coil chemical shift value has been determined to be 4.630 ppm (pH 7, no urea, 358C, GGX aa A), 18 4.73 ppm (pH 5, 1M urea, 258C, GGX aa AGG, termini protected), 19 4.77 ppm (pH 5, no urea, 48C, GGX aa GG), 20 and 4.79 ppm (pH 2.3, 8M urea, 208C, GGX aa GG, termini protected). 22 Variations in the model systems (peptide length, free vs. capped termini) and the solution environment (pH, urea and temperature) are possible explanations for the different values observed.…”