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Infrared multiphoton dissociation (IRMPD) of N-terminal sulfonated peptides improves de novo sequencing capabilities in a quadrupole ion trap mass spectrometer. Not only does IRMPD promote highly efficient dissociation of the N-terminal sulfonated peptides but also the entire series of y ions down to the [y.sub.1] fragment may be detected due to alleviation of the low-mass cutoff problem associated with conventional collisional activated dissociation (CAD) methods in a quadrupole ion trap. Commercial de novo sequencing software was applied for the interpretation of CAD and IRMPD MS/MS spectra collected for seven unmodified peptides and the corresponding N-terminal sulfonated species. In most cases, the additional information obtained by N-terminal sulfonation in combination with IRMPD provided significant improvements in sequence identification. The software sequence tag results were combined with a commercial database searching algorithm to interpret sequence information of a tryptic digest on [alpha]-casein s1. Energy-variable CAD studies confirmed a 30-40% reduction in the critical energies of the N-terminal sulfonated peptides relative to unmodified peptides. This reduction in dissociation energy facilitates IRMPD in a quadrupole ion trap.

Ab initio-derived bond polarizability tensor was used to extend the standard exciton-based model to account for mixing of the n[pi*] and [pi][pi*] transitions with transitions in the deep UV which is significant for the poly(Pro)II ([P.sub.II]) conformation to calculate the contributions of the high-energy transitions. The extended model was able to obtain improved results for [alpha]-helical polypeptides, leading to increased amplitude for the 205-nm band and decreased amplitude for a negative band predicted near 180 nm.

The 1.15 [Angstrom] X-ray crystal structure of a short [alpha]-helix in which the N-terminal i and i + 4 main chain hydrogen bond is replaced with a carbon-carbon bond is reported. The structure indicates that the hydrogen-bond surrogate (HBS) derived [alpha]-helix resembles the structure of canonical [alpha]-helices and provides support for helix nucleation strategy.

A combination of UV-pump-IR-probe spectroscopy is used to study the photoisomerization dynamics of the protected tetrathioxopeptide Boc-Ala-Gly(=S)-Ala-Aib-OMe. The findings from the study provide insight into isomerization of the thioamide bond after excitation to the [pi]-[pi]* ([S.sub.2]) electronic excited state which phototriggers the breaking of the hydrogen bond.

The isolation, characterization and removal of two structural elements responsible for avian pancreatic polypeptide (aPP) dimerization and installation of a new proline switch that single-handedly repacks aPP's signature fold are presented. The results are found to be monomeric and well-folded miniature proteins that can serve as a starting point for the in vitro and in vivo applications of these molecules.

The two-dimensional infrared (2D- IR) spectra of [C.sub.alpha]-alkylated model octapeptides Z-[(Aib).sub.8]-OtBu, Z-[(Aib).sub.5]-L-Leu-[(Aib).sub.2]-OMe and Z-[[L-([alpha]MeVal)].sub.8]-OtBu in the amide I region is evaluated to determine the 2D spectral signatures features of [3.sub.10-] and [alpha]-helical conformations. The sensitivity of cross-peak trends to various helical conformations and the dependence of chain lengths of the special characteristics for short [3.sub.10-] and alpha-helices are described.

A study presents a method of simulating two-dimensional infrared spectra accounting for nonadiabatic effects in amide I modes of a dipeptide. Results reveal that population transfer between the amide 1 site vibrations affects the anisotropy at longer mixing times.

Electronic circular dichroism (CD) spectra and transition from ground to excited states of a helical peptide incorporating Z-dehydrophenylalanine residues was studied using semiempirical orbital computation combined with time-dependent method. The results of the studies were essentially supported from CD simulation of a shorter helical analogue at ab inito or density functional time-dependent method.