Circular dichroism eigenspectra of polyproline II and β‐strand conformers of trialanine in water: Singular value decomposition analysis

Abstract

Despite that a number of experimental and theoretical investigations have been carried out to determine the structure of trialanine in water, the reported populations of polyproline II (PPII) and β-strand conformers vary and were found to be dependent on which spectroscopic method was used. Such discrepancies are due to limitations of different spectroscopic methods used. Here, the temperature- and pH-dependent circular dichroism (CD) and NMR experiments have been carried out to develop a self-consistent singular value decomposition procedure. The temperature-dependent CD spectra indicate the presence of two conformers, but due to the two peptide bonds in a trialanine, one should take into consideration of four different conformers to fully interpret the NMR results. From the pH-dependent NMR coupling constant measurements, the conformation of zwitterionic trialanine is little different from that of cationic one. The strong pH dependency of CD spectrum is likely due to charge transfer transitions between carboxylate and nearby peptide groups or internal field effects not to pH-dependent conformational change. To simultaneously analyze the temperature-dependent CD and NMR data, a self-consistent procedure was used to newly determine the reference NMR coupling constants required to estimate one of the peptide dihedral angles. From the estimated enthalpy and entropy changes associated with the transition from enthalpically favorable PPII conformer to entropically favorable β-strand conformer, the relative populations of the four possible conformers of trialanine were determined and compared with the previous experimental findings. We anticipate that the present experimental results and interpretation procedure would be of use in determining the solution structures of small oligopeptides in the future.

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

“…Cho and co-workers showed that the average ppII population over two peptide bonds in (Ala) 3 changes from 88% to 65% by simply changing the reference structure ensembles from Gromos 43A1 to AMBER ff03 but using the same experimental J -coupling constants and Karplus equations. 31 Such dependence on force fields demonstrates the need for accurate MD simulations and validation.…”

“…30 Cho and coworkers developed a self-consistent singular value decomposition based method to fit CD spectra and NMR J-coupling constant simultaneously, and determined the ppII population of the central residue in (Ala) 3 is 66%. 31 …”

Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

“…Thus, the fact that the 3 J HNa coupling constants of the dipeptides are distributed in the range from 5.5 to 9.6 Hz indicates that the backbone conformations of dipeptides are mixtures of PP II and b-strand structures consistent with the experimental finding by Avbelj et al (2006) who showed that the fractional populations of PP II and b-strand conformations are dominant in 19 blocked amino-acids (N-acetyl-X-N 0 -methylamide) except for Gly. In our previous work, we also showed that the CD spectra of the blocked dipeptides can be described as a linear combination of the CD eigenspectra of the PP II and bstrand conformations (Oh et al 2010(Oh et al , 2012 and further examined the validity of a two-state approximation by comparing our results with previous works done by other groups (Hagarman et al , 2011. However, it should also be emphasized that the fitting analysis method using reference values of two representative conformations such as PP II and b-strand is intrinsically approximate in nature.…”

“…However, over the last decade, it has been shown that the backbone conformations of such oligopeptides are not random but adopt PP II , b-strand, and some turn structures that are in dynamic equilibria. (Avbelj et al 2004(Avbelj et al , 2006Cho et al 2010;Pappu and Rose 2002;Schweitzer-Stenner et al 2002Schweitzer-Stenner and Measey 2007;Shi et al 2002a, b) Thus, the notion that the conformation of small peptide in aqueous solution is a random coil has been proven to be incorrect. Although the scalar coupling constants of short peptides have been widely used to quantitatively determine the backbone conformational distribution, the NMR chemical shifts of short peptide H N and H a have not been fully explored to elucidate the relationship between the backbone conformational distribution of unfolded proteins and that of short peptides.…”

“…This PP II hypothesis has been examined by numerous workers for a variety of oligopeptides and remains controversial (Avbelj et al 2006;Dukor and Keiderling 1991;Eker et al 2002;Hahn et al 2004;Lee et al 2006Lee et al , 2007Makowska et al 2007;Oh et al 2006Oh et al , 2010SchweitzerStenner and Measey 2007;Shi et al 2002a;Shortle and Ackerman 2001;Wright et al 1988;Zagrovic et al 2005;Zanni et al 2001). There is experimental evidence suggesting that unfolded proteins are fairly compact and often contain residual secondary structure elements.…”