Correlation of TrpGly and GlyTrp Rotamer Structure with W7 and W10 UV Resonance Raman Modes and Fluorescence Emission Shifts

Tryptophyl glycine (TrpGly) and glycyl tryptophan (GlyTrp) dipeptides at pH 5.5 and pH 9.3 show a pattern of fluorescence emission shifts with the TrpGly zwitterion emission solely blue shifted. This pattern is matched by shifts in the UV resonance Raman (UVRR) W10 band position and the W7 Fermi doublet band ratio. Ab initio calculations show that the 1340？cm？1 band of the W7 doublet is composed of three modes, two of which determine the W7 band ratios for the dipeptides. Molecular dynamics simulations show that the dipeptides take on two conformations: one with the peptide backbone extended; one with the backbone curled over the indole. The dihedral angle critical to these conformations is and takes on three discrete values. Only the TrpGly zwitterion spends an appreciable amount of time in the extended backbone conformation as this is stabilized by two hydrogen bonds with the terminal amine cation. According to a Stark effect model, a positive charge near the pyrrole keeps the 1 transition at high energy, limiting fluorescence emission red shift, as observed for the TrpGly zwitterion. The hydrogen bond stabilized backbone provides a rationale for the - - W10 symmetric stretch that is unique to the TrpGly zwitterion. 1. Introduction Tryptophan fluorescence emission is a convenient, intrinsic probe of protein environment. Thus, it is used in a wide variety of studies ranging from protein folding [1–4], structure [5, 6], and stability [2, 7, 8] to protein dynamics [5, 9] and ligand binding [10, 11]. The tryptophan emission maximum displays wide variability, anywhere from 355？nm for solvent-exposed tryptophan to 303.5？nm, for the “buried” Trp in the M97V mutant of Rhodospirillum rubrum dI transhydrogenase [12]. This association of solvent exposure with fluorescence emission maximum provides for a broad, qualitative assessment of tryptophan environment. However, a detailed molecular level understanding is lacking. Earlier work focused on classifying emission shift based on tryptophan exposure to water [13, 14]. More recently, electrostatic contributions to tryptophan emission shifts were calculated for both the protein matrix and water [15–17]. In this internal Stark effect model, the widely used but simplistic association of red-shifted fluorescence emission with water exposure was not found. Moreover, the protein matrix plays a critical role in organizing water molecules, and so there is a subtle interplay between solvent and protein. The resultant single data point, the fluorescence emission maximum, does not suggest this complexity. We apply