Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra

Abstract

A model for the calculation of amide I FTIR and 2DIR spectra taking into account fluctuations in hydrogen bonding and structure from molecular dynamics (MD) simulations is tested on three systems. It is found that although the homogeneous lineshape approximation yields satisfactory FTIR spectra, 2DIR spectra are sensitive to the inhomogeneity naturally present in any solvated protein and the common approximations of a static structure and averaged-effect solvent are invalid. By building on the local amide Hamiltonian and incorporating site energy variation with electrostatic-based models and disorder from MD trajectories, good agreement is obtained between calculated and measured 2DIR spectra. The largest contribution to the observed inhomogeneity is found to be the fluctuating site energies, which in turn are most sensitive to the water solvent. With the ability to accurately predict 2DIR spectra from atomistic simulations, new opportunities to test force fields and mechanistic predictions from MD are revealed.

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

“…This Z-shape like structure is much less pronounced than observed for the ideal β-sheet structure [18,19]. Such features were also found in the studies of other β-hairpin peptides [24,29]. In the 2D spectra in Fig.…”

“…The 2DIR technique distinguishes β-sheet structures by producing Z shape like spectra [18,19] when this particular structural motif is present. In the past decades a number of 2DIR studies have been reported of peptides and proteins in solution [16,[20][21][22][23][24][25][26][27][28][29][30][31][32][33] or confined in membranes [34][35][36][37][38], revealing structural details and conformational changes from femtosecond (fs) to nanosecond (ns) time scales, and the nature of dynamic environments. For the structure determination of peptides that are in gas phase or micro-solvated (surrounded by few solvent molecules) the mid-infrared spectroscopic technique has become a promising tool [39][40][41][42].…”

Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment

“…29 Early models for amide I frequencies employed simple geometric criteria such as hydrogen bond count and length; 9,[30][31][32][33] although these models have proven intuitively useful and reasonably accurate for simple calculations, 34 they are generally regarded as insufficient for detailed spectral simulations. 35 Most current vibrational frequency models are based on a linear mapping of frequency against various combinations of electrostatic variables evaluated at different positions within the peptide group…”

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

“…[16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] This method exploits the linear correlation found between the C=O bond length, stretching frequency and electrostatic potential at the atoms of NMA, 18,31,32 which provides a link between perturbation of molecular (and electronic) structure by the electric field of the solvent and the resulting shift of the vibrational frequency. Parametrized electrostatic calculations using the building block approach have been used in protein amide I sim-ulations of ubiquitin, 10,33 other proteins 34 as well as polypeptides in membrane environment. 29,35 These calculations are generally combined with MD simulations that provide coordinate trajectories, which are then utilized for calculating instantaneous normal modes and the resulting spectral line shapes.…”