Experimental and Theoretical Spectroscopic Study of 3₁₀-Helical Peptides Using Isotopic Labeling to Evaluate Vibrational Coupling

Abstract

Coupling between the amide linkages in a peptide or protein is the key physical property that gives vibrational spectra and circular dichroism sensitivity to secondary structures. By use of (13)C isotopic labeling on individual and pairs of amide C═O groups, the amide I band for selected residues was effectively isolated in designed hexa- and octapeptides having dominant 3(10)-helical conformations. The resultant frequency and intensity responses were measured with IR absorption, vibrational circular dichroism (VCD), and Raman spectroscopies and simulated with density functional theory (DFT) based computations. Band fitting the spectral components and correlating the results to the computed coupling between selected labeled positions were used to determine coupling constant signs and to estimate their magnitudes for specific sequences. The observed frequency and intensity patterns, and their variation between IR and VCD with label position in the sequence, follow the theoretical predictions to a large degree, but are complicated by end effects that alter the local force field (FF) for some residues in these short peptides. These FF variations were overestimated in the theoretical models which may be evidence of structural variations not included in the model. By analyzing the simulations with different coupling models, the coupling constants were determined to lie in a range (positive) +3-5 cm(-1) for sequential residues (i,i+1) and with (negative) -3 cm(-1) as an upper bound for alternate ones (i,i+2). The sequential amide coupling for 3(10)-helices is weaker than for α-helices but has the same sign and is larger than and oppositely signed as compared to 3(1)-, or poly-(Pro)(n) type-II, helices.

Exploiting the interplay of quantum interference and backbone rigidity on electronic transport in peptides: a step towards bio-inspired quantum interferometers

“…S8), indicative of a 3 10 -helical structure. 21 Molecular modeling was used to further define the backbone geometries of peptides 5-8 ( Fig. 2d and S9).…”

Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment

“…[60] The corresponding IR spectra were recorded on the same samples using a Vertex 80 FTIR (Bruker) spectrometer. [60] The corresponding IR spectra were recorded on the same samples using a Vertex 80 FTIR (Bruker) spectrometer.…”

Parallel β-Sheet Vibrational Couplings Revealed by 2D IR Spectroscopy of an Isotopically Labeled Macrocycle: Quantitative Benchmark for the Interpretation of Amyloid and Protein Infrared Spectra

“…27,30,31 Isotope labeling has been used to study the coupling in 30-10 helices. 32 Frequency shifts associated with environments have been characterized in soluble and membrane bound α-helices, including surface bound monomers and α-helical bundles with and without water pores. 33-37 Many of the coupling constants for β-turns and anti parallel β-sheets have been measured with isotope labeling and 2D IR spectroscopy.…”