Vibrational dynamics of thiocyanate and selenocyanate bound to horse heart myoglobin

Structural and dynamical changes observed when transitioning from an ionic liquid to a deep eutectic solvent

The microscopic molecular structure and dynamics of a new deep eutectic solvent (DES) composed of an ionic liquid (1-hexyl-3-methylimidazolium chloride) and an amide (trifluoroacetamide) at various molar ratios were investigated using linear and non-linear infrared spectroscopy with a vibrational probe. The use of the ionic liquid allows us to investigate the changes that the system undergoes with the addition of the amide or, equivalently, the changes from an ionic liquid to a DES. Our studies revealed that the vibrational probe in the DES senses a very similar local environment irrespective of the cation chemical structure. In addition, the amide also appears to perceive the same molecular environment. The concentration dependence studies also showed that the amide changes from being isolated from other amides in the ionic liquid environment to an environment where the amide-amide interactions are favored. In the case of the vibrational probe, the addition of the amide produced significant changes in the slow dynamics associated with the making and breaking of the ionic cages but did not affect the rattling-in-cage motions perceived by it. Furthermore, the concentration dependence of slow dynamics showed two regimes which are linked to the changes in the overall structure of the solution. These observations are interpreted in the context of a nanoscopic heterogeneous environment in the DES which, according to the observed dynamical regimes, appears at very large concentrations of the amide (molar ratio of greater than 1:1) since for lower amide molar ratios, the amide appears to be not segregated from the ionic liquid. This proposed molecular picture is supported by small angle x-ray scattering experiments.

Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis

Ultrafast infrared vibrational spectroscopy is widely used for the investigation of dynamics in systems from water to model membranes. Because the experimental observation window is limited to a few times the probe's vibrational lifetime, a frequent obstacle for the measurement of a broad time range is short molecular vibrational lifetimes (typically a few to tens of picoseconds). Five new long-lifetime aromatic selenocyanate vibrational probes have been synthesized and their vibrational properties characterized. These probes are compared to commercial phenyl selenocyanate. The vibrational lifetimes range between ∼400 and 500 ps in complex solvents, which are some of the longest room-temperature vibrational lifetimes reported to date. In contrast to vibrations that are long-lived in simple solvents such as CCl₄, but become much shorter in complex solvents, the probes discussed here have ∼400 ps lifetimes in complex solvents and even longer in simple solvents. One of them has a remarkable lifetime of 1235 ps in CCl₄. These probes have a range of molecular sizes and geometries that can make them useful for placement into different complex materials due to steric reasons, and some of them have functionalities that enable their synthetic incorporation into larger molecules, such as industrial polymers. We investigated the effect of a range of electron-donating and electron-withdrawing para-substituents on the vibrational properties of the CN stretch. The probes have a solvent-independent linear relationship to the Hammett substituent parameter when evaluated with respect to the CN vibrational frequency and the ipso ¹³C NMR chemical shift.

Transparent window 2D IR spectroscopy of proteins

Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.

Protein Dynamics by Two-Dimensional Infrared Spectroscopy

Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.

Cardiac myoglobin participates in the metabolic pathway of selenium in rats

As an essential micronutrient, selenium deficiency is a leading cause of cardiovascular diseases. The heart is continuously beating to deliver blood to the entire body, and this requires a high amount of energy. An adult heart normally obtains 50-70% of its adenosine 5'-triphosphate from fatty acid β-oxidation. An increase in fatty acid oxidation activity induces the generation of larger amounts of by-products (reactive oxygen species, ROS) from mitochondrial oxidative phosphorylation. Selenium-dependent glutathione peroxidases play a critical role in the removal of these ROS, especially organic hydroperoxides, from the heart. The definitive transport and/or detailed metabolic pathways from the selenium-source compounds to the selenoproteins in the heart still remain unclear. We explored the selenium-binding proteins in a rat cardiac cell lysate using its reactive metabolic intermediate, selenotrisulfide (STS), and MALDI TOF-mass spectrometry. Several proteins with a free cysteine (Cys) thiol were found to be reactive with STS through a thiol-exchange reaction. The most distinctive Cys-containing protein in the cardiac cell lysate was identified as myoglobin (Mb) from a rat protein database search and tryptic fragmentation experiments. When separately examined in selenium adequate rats, selenium-binding to the cardiac Mb was verified using selenium-specific fluorometry. Cardiac Mb is thought to participate in the selenium metabolic pathway in the heart.

Do Osmolytes Impact the Structure and Dynamics of Myoglobin?

Osmolytes are small organic compounds that can affect the stability of proteins in living cells. The mechanism of osmolytes' protective effects on protein structure and dynamics has not been fully explained, but in general, two possibilities have been suggested and examined: a direct interaction of osmolytes with proteins (water replacement hypothesis), and an indirect interaction (vitrification hypothesis). Here, to investigate these two possible mechanisms, we studied myoglobin-osmolyte systems using FTIR, UV-vis, CD, and femtosecond IR pump-probe spectroscopy. Interestingly, noticeable changes are observed in both the lifetime of the CO stretch of CO-bound myoglobin and the spectra of UV-vis, CD, and FTIR upon addition of the osmolytes. In addition, the temperature-dependent CD studies reveal that the protein's thermal stability depends on molecular structure, hydrogen-bonding ability, and size of osmolytes. We anticipate that the present experimental results provide important clues about the complicated and intricate mechanism of osmolyte effects on protein structure and dynamics in a crowded cellular environment.

Water Structure at the Lipid Multibilayer Surface: Anionic Versus Cationic Head Group Effects

Membrane water interface is a potential reaction site for many biochemical reactions. Therefore, a molecular level understanding of water structure and dynamics that strongly depend on the chemical structure of lipid is prerequisite for elucidating the role of water in biological reactions on membrane surface. Recently, we carried out femtosecond infrared pump-probe studies of water structure and dynamics at multibilayer surfaces of zwitterionic phosphatidylcholine-analogue lipid ( J. Phys. Chem. Lett. 2016 , 7 , 741 ). Here, to further elucidate the anionic and cationic headgroup effects on water, we study vibrational dynamics of water on lipid multibilayers formed by anionic phospho-glycerol lipid molecules as well as by cationic choline-derivatized lipid molecules. We observed two significantly different vibrational lifetime components (very fast 0.5 ps and slow 1.9 ps) of the OD stretch mode of HOD molecules at the negatively charged phospho-lipid multibilayer whereas only one vibrational lifetime component (1.6 ps) was observed at the positively charged choline-derivatized lipid multibilayer. From the detailed analyses about the vibrational energy and rotational relaxations of HOD molecules in lipid multibilayers composed of anionic lipid with phosphate and cationic lipid without phosphate, the role of phosphate group in structuring water molecules at phospholipid membrane interface is revealed.

Applications of two-dimensional infrared spectroscopy

Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.

Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids

Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.