Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution

Abstract

We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550 -1720 cm -1 ). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured twodimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.

Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins

“…Our choice was restricted to proteins for which experimental FTIR and 2DIR data are readily available 17,21 and proteins with well determined crystal structures. These restrictions lead us to choose the following four proteins: myoglobin (Mb, 153 residues, Protein Data Bank Identification (PDB ID) 5MBN; 99 0% β-sheet, 89% α-helix structure, 11% coils) that has no β-sheets; lysozyme (Lys, 129 residues, PDB ID 1AKI; 100 10% β-sheet, 52% α-helix structure, 38% coils) that has a small three-stranded β-sheet region; ribonuclease A (RNse A, 124 residues, PDB ID 1FS3; 101 40% β-sheet, 26% α-helix structure, 34% coils) that has two domains that vary from two-to four-stranded regions; and concanavalin A (Con A, 237 residues, PDB ID 1NLS; 102 55% β-sheet, 8% α-helix structure, 37% coils), the most extended system, with two relatively flat six-stranded anti-parallel β-sheets.…”

Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

“…18 . The spectra are characterized by their peak positions and lineshape, which are related with secondary structure.…”

“…[1][2][3][4][5][6][7][8][9] Probing fast dynamics along the reaction coordinate can, thus, provide deeper knowledge of structure-activity relationships of biological systems. [10][11][12][13][14][15][16][17][18] The amide I band is the most probed mode in infrared (IR) spectroscopy of proteins, due to its sensitivity to solvation and secondary structure. It is dominated by the CO stretch vibrations in the peptide backbone, and located in the frequency range from 1600 to 1700 cm −1 .…”

Engineering mid-infrared nanoantennas for surface enhanced infrared absorption spectroscopy

“…Understanding this relationship is not only significant within the context of fundamental biophysical studies [1], but also is of immense practical importance to disease diagnostics and treatment [2][3][4]. While fluorescence or refractive index change based biosensors are essential for rapid and sensitive detection [5,6], vibrational spectroscopy methods are unparalleled as optical probes of molecular structure [1,[7][8][9][10][11][12][13][14][15][16].…”