Martin T. Zanni

Two-dimensional IR spectroscopy can be designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure determination

The power of two-dimensional (2D) IR spectroscopy as a structural method with unprecedented time resolution is greatly improved by the introduction of IR polarization conditions that completely eliminate diagonal peaks from the spectra and leave only the crosspeaks needed for structure determination. This approach represents a key step forward in the applications of 2D IR to proteins, peptides, and other complex molecules where crosspeaks are often obscured by diagonal peaks. The technique is verified on the model compound 1,3-cyclohexanedione and subsequently used to clarify the distribution of structures that the acetylproline-NH2 dipeptide adopts in chloroform. In both cases, crosspeaks are revealed that were not observed before, which, in the case of the dipeptide, has led to additional information about the structure of the amino group end of the peptide.

Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution

There is considerable interest in uncovering the pathway of amyloid formation because the toxic properties of amyloid likely stems from prefibril intermediates and not the fully formed fibrils. Using a recently invented method of collecting 2-dimensional infrared spectra and site-specific isotope labeling, we have measured the development of secondary structures for 6 residues during the aggregation process of the 37-residue polypeptide associated with type 2 diabetes, the human islet amyloid polypeptide (hIAPP). By monitoring the kinetics at 6 different labeled sites, we find that the peptides initially develop well-ordered structure in the region of the chain that is close to the ordered loop of the fibrils, followed by formation of the 2 parallel β-sheets with the N-terminal β-sheet likely forming before the C-terminal sheet. This experimental approach provides a detailed view of the aggregation pathway of hIAPP fibril formation as well as a general methodology for studying other amyloid forming proteins without the use of structure-perturbing labels.

Automated 2D IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide

The capability of 2D IR spectroscopy to elucidate time-evolving structures is enhanced by a programmable mid-IR pulse shaper that greatly improves the ease, speed, and accuracy of data collection. Traditional ways of collecting 2D IR spectra are difficult to implement, cause distorted peak shapes, and result in poor time resolution and/or phase problems. We report on several methods for collecting 2D IR spectra by using a computer-controlled germanium acoustooptic modulator that overcomes the above problems. The accuracy and resolution of each method is evaluated by using model metal carbonyl compounds that have well defined lineshapes. Furthermore, phase cycling can now be employed to largely alleviate background scatter from heterogeneous samples. With these methods in hand, we apply 2D IR spectroscopy to study the structural diversity in amyloid fibers of aggregated human islet amyloid polypeptide (hIAPP), which is involved with type 2 diabetes. The 2D IR spectra reveal that the β-sheet fibers have a large structural distribution, as evidenced by an inhomogeneously broadened β-sheet peak and strong coupling to random coil conformations. Structural diversity is an important characteristic of hIAPP because it may be that partly folded peptides cause the disease. This experiment on hIAPP is an example of how computer generation of 2D IR pulse sequences is a key step toward automating 2D IR spectroscopy, so that new pulse sequences can be implemented quickly and a diverse range of systems can be studied more easily.

Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures

Recently, new methods for determining time-evolving structures using infrared analogs of NMR spectroscopy have been introduced that have outstanding potential in structural biology. Already, within the past two years, structures of dipeptides, tripeptides and pentapeptides have been determined on much faster timescales than the conformational dynamics. Also, two-dimensional infrared correlation spectra of some proteins and isotopically edited alanine-rich helices have been examined.

Two-dimensional heterodyned and stimulated infrared photon echoes of N-methylacetamide-D

The stimulated infrared photon echo of N-methylacetamide-D [NMAD; CH3(CO)ND(CH3)] was measured and used to determine the vibrational frequency correlation function. The correlation function was modeled as a single exponential plus a constant, and it was found that most of the NMAD vibrational frequency distribution is motionally narrowed with a pure dephasing time of 1.12 ps. The two-dimensional infrared (2D IR) spectrum of NMAD was also obtained by heterodyning the echo field with a weak local oscillator pulse. The real and imaginary portions of the 2D IR spectrum exhibit multiple peaks due to υ=0–1 and 1–2 coherences that are excited, which are not resolved in the absolute magnitude of the 2D IR spectrum. Using the correlation function determined from the stimulated photon echo, the 2D IR spectrum was accurately simulated. Resolution enhancement of the 2D IR spectrum was performed by manipulating the photon echo field with window functions. The enhanced experimental and simulated 2D IR spectra are drama...

Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

While amyloid formation has been implicated in the pathology of over twenty human diseases, the rational design of amyloid inhibitors is hampered by a lack of structural information about amyloid-inhibitor complexes. We use isotope labeling and two-dimensional infrared spectroscopy to obtain a residue-specific structure for the complex of human amylin, the peptide responsible for islet amyloid formation in type 2 diabetes, with a known inhibitor, rat amylin. Based on its sequence, rat amylin should block formation of the C-terminal β-sheet, but at 8 hours after mixing rat amylin blocks the N-terminal β-sheet instead. At 24 hours after mixing, rat amylin blocks neither β-sheet and forms its own β-sheet most likely on the outside of the human fibrils. This is striking because rat amylin is natively disordered and not previously known to form amyloid β-sheets. The results show that even seemingly intuitive inhibitors may function by unforeseen and complex structural processes.

Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides

Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.

Adding a dimension to the infrared spectra of interfaces using heterodyne detected 2D sum-frequency generation (HD 2D SFG) spectroscopy

In the last ten years, two-dimensional infrared spectroscopy has become an important technique for studying molecular structures and dynamics. We report the implementation of heterodyne detected two-dimensional sum-frequency generation (HD 2D SFG) spectroscopy, which is the analog of 2D infrared (2D IR) spectroscopy, but is selective to noncentrosymmetric systems such as interfaces. We implement the technique using mid-IR pulse shaping, which enables rapid scanning, phase cycling, and automatic phasing. Absorptive spectra are obtained, that have the highest frequency resolution possible, from which we extract the rephasing and nonrephasing signals that are sometimes preferred. Using this technique, we measure the vibrational mode of CO adsorbed on a polycrystalline Pt surface. The 2D spectrum reveals a significant inhomogenous contribution to the spectral line shape, which is quantified by simulations. This observation indicates that the surface conformation and environment of CO molecules is more complicated than the simple “atop” configuration assumed in previous work. Our method can be straightforwardly incorporated into many existing SFG spectrometers. The technique enables one to quantify inhomogeneity, vibrational couplings, spectral diffusion, chemical exchange, and many other properties analogous to 2D IR spectroscopy, but specifically for interfaces.

Facile collection of two-dimensional electronic spectra using femtosecond pulse-shaping technology

This letter reports a straightforward means of collecting two-dimensional electronic (2D-E) spectra using optical tools common to many research groups involved in ultrafast spectroscopy and quantum control. In our method a femtosecond pulse shaper is used to generate a pair of phase stable collinear laser pulses which are then incident on a gas or liquid sample. The pulse pair is followed by an ultrashort probe pulse that is spectrally resolved. The delay between the collinear pulses is incremented using phase and amplitude shaping and a 2D-E spectrum is generated following Fourier transformation. The partially collinear beam geometry results in perfectly phased absorptive spectra without phase twist. Our approach is much simpler to implement than standard non-collinear beam geometries, which are challenging to phase stabilize and require complicated calibrations. Using pulse shaping, many new experiments are now also possible in both 2D-E spectroscopy and coherent control.

Femtosecond pulse shaping directly in the mid-IR using acousto-optic modulation

Pulse shaping directly in the mid-IR is accomplished by using a germanium acousto-optic modulator (Ge AOM) capable of programmable phase and amplitude modulation for IR light between 2 and 18 microm. Shaped waveforms centered at 4.9 microm are demonstrated in both the frequency and the time domains. With a 50% throughput efficiency, the Ge AOM can generate much more intense pulses with higher resolution than can indirect shaping methods. Furthermore, the phase stability of the shaped pulse proved sufficient for cross correlation with unshaped mid-IR pulses. Thus, phase- and amplitude-tailored pulses can now be readily incorporated into phase-sensitive experiments, such as heterodyned 2D IR spectroscopy.