3.1.2 Bio-Molecular Structure from Quasi-Static 2D IR Spectra
2D IR spectroscopy can be used to elucidate detailed molecular structure also for
molecules as large as proteins. Such systems exhibit dynamics that can range from
picoseconds up to milliseconds and longer. Therefore, the method can shed light on
all of the dynamics of a protein itself, as well as on its dynamic environment such as
biological water molecules. The latter is believed to be a crucial aspect in
developing an understanding of a relationship between bio-molecular structure and
biological function [30]. The inherent capability of resolving lineshapes, couplings
and dynamics thereof makes 2D IR spectroscopy unique among the many existing
methods for structural biology. As a particularly powerful combination, 2D IR is
often used in conjunction with isotope-labelling and mutational approaches to study
protein structure [30, 47, 86, 87]. Such studies generally look at the amide-I region
of the proteins (about 1700–1600 cm
-1 ), which is largely composed of CO-stretch
(and some additional NH-wagging contributions). In many cases, the amide-I modes
are delocalized over many residues, thus giving a detailed structural fingerprint of
the protein backbone. Less common is the investigation of the amide-II region
(1600–1500 cm
-1 ) for this purpose. Alternatively, also other vibrational labels can
be introduced by help of unnatural amino acids or protein-bound ligands [88, 89].
2D IR in combination with FT IR spectra for comparison can be advantageously
used to determine particularly the secondary structure of proteins (helices, sheets,
coils, turns), due to the quadratic scaling of the signal intensity on the absorption
coefficient (Sect. 2). This effect enhances the spectral contrast over FT IR signals.
Moreover, structural information is contained in the resolution of cross peaks
between different residues that originate from vibrational excitons (Sect. 3.1.1).
Such couplings can be particularly well resolved by applying specific combinations
of pump and probe polarizations [25, 78]. Finally, experimental data can often be
compared to detailed structural simulations, thereby helping to clarify even faint
details of bio-macromolecules.
Of particular interest with regard to protein structure is the elucidation of
misfolding. The reason for this is that misfolded protein structures are often
responsible for diseases in living organisms. The identification of molecular origin
of the misfolding is expected to reveal routes to potential drugs and therapies. 2D IR
spectroscopy has been demonstrated as an ideal analytical tool for studying
structural defects in proteins, such as partial unfolding or aggregations [30, 86]. Of
particular interest is the formation of so-called amyloid fibrils, which have been
identified as origins for several distinct human diseases. Zanni et al. have shown
how to use 2D IR spectroscopy in combination with isotope-labelling to identify
specific intermediates in amyloid formation and thereby getting access to the
mechanism of the process [90]. That group investigated the kinetics and the
mechanism by which the human islet amyloid polypeptide (hIAPP) forms fibrils via
an intermediate that exhibits a parallel beta-sheet structure. In particular, the authors
exploited the characteristic features of beta-sheets and disordered peptides in 2D IR
spectra to uncover the backbone structure [86].
Figure 7a shows the sequence, as well as a solid-state NMR model structure of
the investigated hIAPP with 37 residues. The colored letters refer to amino acids
Top Curr Chem (Z) (2017) 375:86
123
131
Reprinted from the journal
2D IR spectroscopy can be used to elucidate detailed molecular structure also for
molecules as large as proteins. Such systems exhibit dynamics that can range from
picoseconds up to milliseconds and longer. Therefore, the method can shed light on
all of the dynamics of a protein itself, as well as on its dynamic environment such as
biological water molecules. The latter is believed to be a crucial aspect in
developing an understanding of a relationship between bio-molecular structure and
biological function [30]. The inherent capability of resolving lineshapes, couplings
and dynamics thereof makes 2D IR spectroscopy unique among the many existing
methods for structural biology. As a particularly powerful combination, 2D IR is
often used in conjunction with isotope-labelling and mutational approaches to study
protein structure [30, 47, 86, 87]. Such studies generally look at the amide-I region
of the proteins (about 1700–1600 cm
-1 ), which is largely composed of CO-stretch
(and some additional NH-wagging contributions). In many cases, the amide-I modes
are delocalized over many residues, thus giving a detailed structural fingerprint of
the protein backbone. Less common is the investigation of the amide-II region
(1600–1500 cm
-1 ) for this purpose. Alternatively, also other vibrational labels can
be introduced by help of unnatural amino acids or protein-bound ligands [88, 89].
2D IR in combination with FT IR spectra for comparison can be advantageously
used to determine particularly the secondary structure of proteins (helices, sheets,
coils, turns), due to the quadratic scaling of the signal intensity on the absorption
coefficient (Sect. 2). This effect enhances the spectral contrast over FT IR signals.
Moreover, structural information is contained in the resolution of cross peaks
between different residues that originate from vibrational excitons (Sect. 3.1.1).
Such couplings can be particularly well resolved by applying specific combinations
of pump and probe polarizations [25, 78]. Finally, experimental data can often be
compared to detailed structural simulations, thereby helping to clarify even faint
details of bio-macromolecules.
Of particular interest with regard to protein structure is the elucidation of
misfolding. The reason for this is that misfolded protein structures are often
responsible for diseases in living organisms. The identification of molecular origin
of the misfolding is expected to reveal routes to potential drugs and therapies. 2D IR
spectroscopy has been demonstrated as an ideal analytical tool for studying
structural defects in proteins, such as partial unfolding or aggregations [30, 86]. Of
particular interest is the formation of so-called amyloid fibrils, which have been
identified as origins for several distinct human diseases. Zanni et al. have shown
how to use 2D IR spectroscopy in combination with isotope-labelling to identify
specific intermediates in amyloid formation and thereby getting access to the
mechanism of the process [90]. That group investigated the kinetics and the
mechanism by which the human islet amyloid polypeptide (hIAPP) forms fibrils via
an intermediate that exhibits a parallel beta-sheet structure. In particular, the authors
exploited the characteristic features of beta-sheets and disordered peptides in 2D IR
spectra to uncover the backbone structure [86].
Figure 7a shows the sequence, as well as a solid-state NMR model structure of
the investigated hIAPP with 37 residues. The colored letters refer to amino acids
Top Curr Chem (Z) (2017) 375:86
123
131
Reprinted from the journal