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

The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs

In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.

An Improved Turn Structure for Inducing β-Hairpin Formation in Peptides

Although β-hairpins are widespread in proteins, there is no tool to coax any small peptide to adopt a β-hairpin conformation, regardless of sequence. Here, we report that δ-linked γ(R)-methyl-ornithine (^δ MeOrn) provides an improved β-turn template for inducing a β-hairpin conformation in peptides. We developed a synthesis of protected ^δ MeOrn as a building block suitable for use in Fmoc-based solid-phase peptide synthesis. The synthesis begins with l-leucine and affords gram quantities of the N^α -Boc-N^δ -Fmoc-γ(R)-methyl-ornithine building block. X-ray crystallography confirms that the ^δ MeOrn turn unit adopts a folded structure in a macrocyclic β-hairpin peptide. CD and NMR spectroscopy allow comparison of the ^δ MeOrn turn template to the δ-linked ornithine (^δ Orn) turn template that we previously introduced and to the popular d-Pro-Gly turn template. These studies show that the folding of the ^δ MeOrn turn template is substantially better than that of ^δ Orn and is comparable to d-Pro-Gly.

Interplay between Structure and Charge as a Key to Allosteric Modulation of Human 20S Proteasome by the Basic Fragment of HIV-1 Tat Protein

The proteasome is a giant protease responsible for degradation of the majority of cytosolic proteins. Competitive inhibitors of the proteasome are used against aggressive blood cancers. However, broadening the use of proteasome-targeting drugs requires new mechanistic approaches to the enzyme's inhibition. In our previous studies we described Tat1 peptide, an allosteric inhibitor of the proteasome derived from a fragment of the basic domain of HIV-Tat1 protein. Here, we attempted to dissect the structural determinants of the proteasome inhibition by Tat1. Single- and multiple- alanine walking scans were performed. Tat1 analogs with stabilized beta-turn conformation at positions 4-5 and 8-9, pointed out by the molecular dynamics modeling and the alanine scan, were synthesized. Structure of Tat1 analogs were analyzed by circular dichroism, Fourier transform infrared and nuclear magnetic resonance spectroscopy studies, supplemented by molecular dynamics simulations. Biological activity tests and structural studies revealed that high flexibility and exposed positive charge are hallmarks of Tat1 peptide. Interestingly, stabilization of a beta-turn at the 8-9 position was necessary to significantly improve the inhibitory potency.

Neighboring residue effects in terminally blocked dipeptides: implications for residual secondary structures in intrinsically unfolded/disordered proteins

For nuclear magnetic resonance (NMR)-based protein structure determinations, the random coil chemical shifts are very important because the secondary and tertiary protein structure predictions become possible by examining deviations of measured chemical shifts from those reference chemical shift values. In addition, neighboring residue effects on chemical shifts and J-coupling constants are crucial in understanding the nature of conformational propensities exhibited by unfolded or intrinsically disordered proteins. We recently reported the 1D NMR results for a complete set of terminally blocked dipeptides (Oh KI, Jung YS, Hwang GS, Cho M. J Biomol NMR 2012;53:25-41), but the NMR resonance assignments were not possible so that the average chemical shifts and J-coupling constants were only considered. In the present work, to thoroughly investigate the neighboring residue effects and random coil chemical shifts we extend the previous studies with 2D NMR, and measured all the (3) J(HNHα) values and H(α) and H(N) chemical shifts of the same set of terminally blocked dipeptides that are free from structural effects like secondary structure, hydrogen-bond, long-range backbone, and side-chain interactions. In particular, the preceding and following residue effects on amino-acid backbone conformational propensities are revealed and directly compared with previous works on either short peptides or empirical chemical shift database.