In Silico Interpretation of cw-ESR at 9 and 95 GHz of Mono- and bis- TOAC-Labeled Aib-Homopeptides in Fluid and Frozen Acetonitrile

Abstract

In this paper, we address the interpretation of molecular properties of selected singly and doubly spin-labeled peptides from continuous-wave electron spin resonance (cw-ESR) spectroscopy. This study is performed by means of an integrated computational approach that merges a stochastic treatment of long-term dynamics to ad hoc methodologies for the calculation of structural properties. In particular, our method is based on (i) the determination of geometric and local magnetic parameters of the peptides by quantum mechanical density functional calculations by taking into account solvent contribution; (ii) the hydrodynamic evaluation of dissipative properties; and (iii) molecular dynamics including equilibrium distribution of molecular conformations. The system is then described by a stochastic Liouville equation in which the spin Hamiltonian for the two electron spins, interacting with each other and coupled to two (14)N nuclear spins, is coupled to the diffusive operator describing the time evolution of slow coordinates. cw-ESR spectra are simulated for selected peptides built from the non-natural α-aminoacids α-aminoisobutyric acid (Aib) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, we study the -Aib-TOAC-Aib- singly labeled tripeptide and the -Aib-TOAC-(Aib)(7)- singly labeled and -Aib-TOAC-(Aib)(5)-TOAC-Aib- doubly labeled nonapeptides. We show that good agreement is obtained with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling is a powerful approach to the investigation of both molecular dynamics and 3D-structural properties.

Conformation and EPR characterization of rigid, 310‐helical peptides with TOAC spin labels: Models for short distances

“…Peptides NONA, NONA 2 (labeled as NONA 9 in Ref. ), NONA 2,8 , and HEPTA 3,6 have already been described.…”

“…Peptides NONA, NONA 2 (labeled as NONA 9 in Ref. ), NONA 2,8 , and HEPTA 3,6 have already been described. The difficult syntheses of the other very highly constrained TOAC/Aib peptides mentioned in this paper have been performed in solution either via step‐by‐step by using the 1‐(3‐dimetylamino)propyl‐3‐ethyl‐carbodiimide/7‐aza‐1‐hydroxy‐1,2,3‐benzotriazole method (HEXA 1,5 and OCTA 2,7 ) or via the segment condensation procedure by using the isolated, but uncharacterized, intermediate 5(4 H )‐oxazolones from Z‐(Aib) 3 ‐OH and Z‐(Aib) 5 ‐OH for HEPTA 6 and OCTA 7 , respectively.…”

“…More specifically, we analyze a series of peptides consisting of stretches of the non‐coded, host α‐amino acid α‐aminoisobutyric acid (Aib), combined with one or two 4‐amino‐1‐oxyl‐2,2,6,6‐tetramethylpiperidine‐4‐carboxylic acid (TOAC) guest residues. Both TOAC and Aib are known to strongly stabilize regular 3 10 ‐helices . The backbone and side‐chain conformations of TOAC are remarkably constrained, providing well‐defined distances between the stable nitroxide free radicals of two TOAC residues.…”

CW-EPR Spectral Simulations

“…For the SLE case, generalizing the spin system model to include more than two nuclei or more than one electron (Carlotto et al, 2011;Zerbetto et al, 2007) will significantly broaden the applicability of the method. Extensions of the diffusion models are also possible: for example, large-scale motions within assemblies or internal domain motions could be modeled by a finite elements formulation (Stillman, Zientara, & Freed, 1979;Zientara, Nagy, & Freed, 1980.…”

Computational tools for the interpretation of electron spin resonance spectra in solution

“…Systems are described by a stochastic Liouville equation in which the spin Hamiltonian for two electron spins, interacting with each other and coupled to two 14 N nuclear spins, is coupled to the diffusive operator describing the time evolution of slow re-orientation. We use ICA to interpret the cw-ESR spectra in acetonitrile (MeCN) at 293 K of the doubly spin-labelled peptide Fmoc-Aib-TOAC-(Aib) 5 -TOAC-Aib-OMe (NONA 2,8 ) (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, α-aminoisobutyric acid; OMe, methoxy) and of the singly spin-labelled peptide FmocAib-TOAC-Aib-OMe (TRI 2 ) with both X-band (9 GHz) and W-band (95 GHz) ESR [23].…”