Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids

Anharmonically Coupled Vibrational Scaffolds for Energy Dissipation in a Terpyridine-Aldehyde Ligand

The role of intramolecular vibrational energy redistribution is critical when considering the thermal properties of coordination complexes. The interactions and redistribution of vibrational energy can be uncovered through the use of two-dimensional infrared (2D IR) spectroscopy by observing the cross-peaks between different vibrational signatures. In this study, the energetic landscape consisting of the vibrations of [6,2':6',2″-terpyridine]-2-carbaldehyde (terpyCHO) is studied directly in the region between 1400 and 1740 cm-1. Information on the anharmonic coupling between different groups of vibrations estimates the delocalization in the detected normal modes. The delocalization of the aldehyde stretch is directly comparable to that calculated from density functional theory (DFT) calculations and local mode analysis via the LModeA program, a freeware that can characterize the normal modes in terms of a nonredundant set of local modes. Tracking of the relative cross-peak intensities as a function of the waiting time reveals a complex network of energy exchange pathways responsible for energy dissipation and vibrational dephasing. These dynamics reveal the aldehyde to be an efficient inlet and outlet of vibrational energy flow and the C-H bends as energetic dumps with the pyridine ring stretches acting as bridging modes between them. Finally, signatures of vibrational coherences are observed in the diagonal peak dynamics of the 2D IR data, further revealing a network of couplings to lower energy modes that mediate this energy exchange. These findings provide new insights into the energetic landscape of organic molecules potentially useful as ligands in single molecule magnets.

Ultrafast Dynamics in Flavocytochrome C by Using Transient Absorption and Femtosecond Fluorescence Lifetime Spectroscopy

Flavocytochrome c sulfide dehydrogenase (FCC) is an important enzyme of sulfur metabolism in sulfur-oxidizing bacteria, and its catalytic properties have been extensively studied. However, the ultrafast dynamics of FCC is not well understood. We present ultrafast transient absorption and fluorescence spectroscopy measurements to unravel the early events upon excitation of the heme and flavin chromophores embedded in the flavocytochrome c (FccAB) from the bacterium Thiocapsa roseopersicina. The fluorescence kinetics of FccAB suggests that the majority of the photoexcited species decay nonradiatively within the first few picoseconds. Transient absorption spectroscopy supports these findings by suggesting two major dynamic processes in FccAB, internal conversion occurring in about 400 fs and the vibrational cooling occurring in about 4 ps, mostly affecting the heme moiety.

Coherent Vibrational Dynamics in an Isolated Peptide Captured with Two-Dimensional Infrared Spectroscopy

Quantum mechanical vibrational coherence transfer processes play important roles in energy relaxation, charge transfer, and reaction dynamics in chemical and biological systems but are difficult to directly measure using traditional condensed-phase nonlinear spectroscopies. Recently, we developed a new experimental capability to obtain two-dimensional infrared (2D IR) spectra of molecular systems in the gas phase that enables the direct measurement of coherence pathways. Herein, we report ultrafast 2D IR spectroscopy of the peptide glutathione (GSH) isolated and cryogenically cooled in the gas phase. Six vibrational modes were simultaneously excited within the amide I and II region. The spectral dynamics of both diagonal and off-diagonal cross peak features exhibit long-lived oscillatory behavior consistent with the presence of coherent vibrational dynamics. The oscillatory signatures deviate significantly from the expected quantum beating pathways predicted from standard nonlinear response theories. These deviations indicate the presence of additional nonlinear pathways, including coherence transfer processes. Quantum chemistry calculations indicate large anharmonic couplings between the excited vibrational modes in GSH and, critically, strong coupling between the excited modes and numerous low-frequency modes that act as a bath to mediate coherence transfer. The data provide important new benchmarks for modeling coherence transfer dynamics and system-bath interactions in open quantum systems free from solvent effects.

Temperature Dependence of Thermal Conductivity of Proteins: Contributions of Thermal Expansion and Grüneisen Parameter

The thermal conductivity of many materials depends on temperature due to several factors, including variation of heat capacity with temperature, changes in vibrational dynamics with temperature, and change in volume with temperature. For proteins some, but not all, of these influences on the variation of thermal conductivity with temperature have been investigated in the past. In this study, we examine the influence of change in volume, and corresponding changes in vibrational dynamics, on the temperature dependence of the thermal conductivity. Using a measured value for the coefficient of thermal expansion and recently computed values for the Grüneisen parameter of proteins we find that the thermal conductivity increases with increasing temperature due to change in volume with temperature. We compare the impact of thermal expansion on the variation of the thermal conductivity with temperature found in this study with contributions of heat capacity and anharmonic coupling examined previously. Using values of thermal transport coefficients computed for proteins we also model heating of water in a protein solution following photoexcitation.

Thermal Energy Transport through Nonbonded Native Contacts in Protein

Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.

Vibrational Energy Landscapes and Energy Flow in GPCRs

We construct and analyze disconnectivity graphs to provide the first graphical representation of the vibrational energy landscape of a protein, in this study β2AR, a G-protein coupled receptor (GPCR), in active and inactive states. The graphs, which indicate the relative free energy of each residue and the minimum free energy barriers for energy transfer between them, reveal important composition, structural and dynamic properties that mediate the flow of energy. Prolines and glycines, which contribute to GPCR plasticity and function, are identified as bottlenecks to energy transport along the backbone from which alternative pathways for energy transport via nearby noncovalent contacts emerge, seen also in the analysis of first passage time (FPT) distributions presented here. Striking differences between the disconnectivity graphs and FPT distributions for the inactive and active states of β2AR are found where structural and dynamic changes occur upon activation, contributing to allosteric regulation.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase

Murine adenosine deaminase (mADA) is a prototypic system for studying the thermal activation of active site chemistry within the TIM barrel family of enzyme reactions. Previous temperature-dependent hydrogen deuterium exchange studies under various conditions have identified interconnected thermal networks for heat transfer from opposing protein-solvent interfaces to active site residues in mADA. One of these interfaces contains a solvent exposed helix-loop-helix moiety that presents the hydrophobic face of its long α-helix to the backside of bound substrate. Herein we pursue the time and temperature dependence of solvation dynamics at the surface of mADA, for comparison to established kinetic parameters that represent active site chemistry. We first created a modified protein devoid of native tryptophans with close to native kinetic behavior. Single site-specific tryptophan mutants were back inserted into each of the four positions where native tryptophans reside. Measurements of nanosecond fluorescence relaxation lifetimes and Stokes shift decays, that reflect time dependent environmental reoroganization around the photo-excited state of Trp*, display minimal temperature dependences. These regions serve as controls for the behavior of a new single tryptophan inserted into a solvent exposed region near the helix-loop-helix moiety located behind the bound substrate, Lys54Trp. This installed Trp displays a significantly elevated value for Ea ( k Stokes shift ) ; further, when Phe61 within the long helix positioned behind bound substrate is replaced by a series of aliphatic hydrophobic side chains, the trends in Ea ( k Stokes shift ) mirror the earlier reported impact of the same series of function-altering hydrophobic side chains on the activation energy of catalysis, Ea ( k cat ) .The reported experimental findings implicate a solvent initiated and rapid (>ns) protein restructuring that contributes to the enthalpic activation barrier to catalysis in mADA.

Intermolecular Protein-Water Coupling Impedes the Coupling Between the Amide A and Amide I Mode in Interfacial Proteins

The coupling between different vibrational modes in proteins is essential for chemical dynamics and biological functions and is linked to the propagation of conformational changes and pathways of allosteric communication. However, little is known about the influence of intermolecular protein-H2O coupling on the vibrational coupling between amide A (NH) and amide I (C═O) bands. Here, we investigate the NH/CO coupling strength in various peptides with different secondary structures at the lipid cell membrane/H2O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy (SFG-VS) in which a femtosecond infrared pump is used to excite the amide A band, and SFG-VS is used to probe transient spectral evolution in the amide A and amide I bands. Our results reveal that the NH/CO coupling strength strongly depends on the bandwidth of the amide I mode and the coupling of proteins with water molecules. A large extent of protein-water coupling significantly reduces the delocalization of the amide I mode along the peptide chain and impedes the NH/CO coupling strength. A large NH/CO coupling strength is found to show a strong correlation with the high energy transfer rate found in the light-harvesting proteins of green sulfur bacteria, which may understand the mechanism of energy transfer through a molecular system and assist in controlling vibrational energy transfer by engineering the molecular structures to achieve high energy transfer efficiency.

Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer

Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient. Here, we introduce two novel donor ncAAs based on an iminothioindoxyl (ITI) chromophore. The dimethylamino-ITI (DMA-ITI) and julolidine-ITI (J-ITI) moieties overcome the limitation of AzAla with a 50 times higher Vis extinction coefficient. While ITI moieties are known for ultrafast photoswitching, DMA-ITI and J-ITI exclusively form a hot ground state on the sub-ps timescale instead, which is essential for their usage as vibrational energy donor. In VET measurements of donor-sensor dipeptides we investigate the performance of the new donors. We observe 20 times larger signals compared to the established AzAla donor, which opens unprecedented possibilities for the study of VET in proteins.

Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry

It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need in molecular biology and drug discovery to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme glycogen phosphorylase is a clinical target of great interest to treat type II diabetes and metastatic cancers. Here, we developed a time-resolved nonequilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach capable of precisely locating dynamic structural changes during allosteric activation and inhibition of glycogen phosphorylase. We resolved obligate transient changes in the localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect with a common structurally dynamic motif. This mass spectrometry approach uniquely stands to discover local transient structural dynamics and could be used broadly to identify features that influence the structural transitions of proteins.

Biomolecular infrared spectroscopy: making time for dynamics

Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.

Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra

Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.

Noncovalent π Interactions in Mutated Aquomet-Myoglobin Proteins: A QM/MM and Local Vibrational Mode Study

Protein dynamics and function is strongly connected to the energy flow taking place. Myoglobin (Mb) and its mutations are ideal systems to study the process of vibrational energy transfer (VET) at the molecular level. Anti-Stokes ultraviolet resonance Raman studies using a tryptophan (Trp) probe, introduced at different Mb positions by amino acid replacement, have suggested that the amount of VET depends on the position of the Trp probe relative to the heme group. Inspired by this experimental work, we explored the strength of noncovalent π interactions, as well as covalent interactions for both the axial and distal ligands bound to iron in aquomet-Mb with the local vibrational mode analysis (LMA), originally developed by Konkoli and Cremer. Two sets of noncovalent interactions were investigated: (1) the interaction between the water ligand and Trp rings and (2) the interaction between the Trp and the porphyrin rings of the heme group. We assessed the strength of these noncovalent interactions via a special local mode force constant. Various Trp-modified water-bound ferric Mb proteins in the ground state were studied (6 in total) using gas-phase and QM/MM calculations followed by LMA. Our results disclose that VET is indeed dependent on the position of the Trp probe relative to the heme group but also on the tautomeric nature of distal histidine. They provide new guidelines on how to assess noncovalent π interactions in proteins utilizing LMA and how to use these data to explore VET, and more generally protein dynamics and function.

Influence of a Methyl Group on the Unidirectional Flow of Vibrational Energy in an Adenine-Thymine Base Pair

The role of a methyl group in intramolecular vibrational energy redistribution (IVR) of the hydrogen-bonded adenine-thymine base pair has been studied using classical dynamics procedures. Energy transferred to the doorway bond thymine-NH from the vibrationally excited H₂O(v) efficiently redistributes among various bonds of the base pair through vibration-to-vibration coupling, depositing a large fraction of the available energy in the terminal bond adenine-NH. On the other hand, the extent of energy flow in the reverse direction from the excited adenine-NH to thymine-NH is insignificant, indicating IVR in adenine-thymine resulting from the intermolecular interaction with a vibrationally excited H₂O molecule, is direction-specific. The unidirectional flow is due to the coupling of stretch-torsion vibrations of a methyl group with conjugated bonds on the thymine ring, when the methyl rotor is present and is adjacent to the vibrationally excited thymine-NH. The insignificance of energy flow from the terminal-to-terminal bond in the reverse direction is attributed to the absence of a methyl group on the adenine moiety, even though the molecule has many CC and CN bonds coupled to their neighbors.

Locating dynamic contributions to allostery via determining rates of vibrational energy transfer

Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β₂-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.

Time-resolved spectroscopic mapping of vibrational energy flow in proteins: Understanding thermal diffusion at the nanoscale

Vibrational energy exchange between various degrees of freedom is critical to barrier-crossing processes in proteins. Hemeproteins are well suited for studying vibrational energy exchange in proteins because the heme group is an efficient photothermal converter. The released energy by heme following photoexcitation shows migration in a protein moiety on a picosecond timescale, which is observed using time-resolved ultraviolet resonance Raman spectroscopy. The anti-Stokes ultraviolet resonance Raman intensity of a tryptophan residue is an excellent probe for the vibrational energy in proteins, allowing the mapping of energy flow with the spatial resolution of a single amino acid residue. This Perspective provides an overview of studies on vibrational energy flow in proteins, including future perspectives for both methodologies and applications.

Energy Transport and Its Function in Heptahelical Transmembrane Proteins

Photoproteins such as bacteriorhodopsin (bR) and rhodopsin (Rho) need to effectively dissipate photoinduced excess energy to prevent themselves from damage. Another well-studied seven transmembrane (TM) helices protein is the β₂ adrenergic receptor (β₂AR), a G protein-coupled receptor for which energy dissipation paths have been linked with allosteric communication. To study the vibrational energy transport in the active and inactive states of these proteins, a master equation approach [J. Chem. Phys.2020, 152, 045103] is employed, which uses scaling rules that allow us to calculate energy transport rates solely based on the protein structure. Despite their overall structural similarity, the three 7TM proteins reveal quite different strategies to redistribute excess energy. While bR quickly removes the energy using the TM7 helix as a "lightning rod", Rho exhibits a rather poor energy dissipation, which might eventually require the hydrolysis of the Schiff base between the protein and the retinal chromophore to prevent overheating. Heating the ligand adrenaline of β₂AR, the resulting energy transport network of the protein is found to change significantly upon switching from the active state to the inactive state. While the energy flow may highlight aspects of the inter-residue couplings of β₂AR, it seems not particularly suited to explain allosteric phenomena.

Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation

We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.

Intramolecular vibrational energy redistribution in nucleobases: Excitation of NH stretching vibrations in adenine–uracil + H2O

Redistribution of vibrational energy in the adenine–uracil base pair is studied when the base pair undergoes an intermolecular interaction with an overtone-bending vibration excited H2O(2[Formula: see text]bend) molecule. Energy transfer is calculated using the structural information obtained from density functional theory in the solution of the equations of motion. Intermolecular vibrational energy transfer (VET) from H2O(2[Formula: see text]bend) to the uracil–NH stretching mode is efficient and rapidly followed by intramolecular vibrational energy redistribution (IVR) resulting from coupling between vibrational modes. An important pathway is IVR carrying energy to the NH-stretching mode of the adenine moiety in a subpicosecond scale, the energy build-up being sigmoidal, when H2O interacts with the uracil–NH bond. The majority of intermolecular hydrogen bonds between the base pair and H2O are weakened but unbroken during the ultrafast energy redistribution period. Lifetimes of intermolecular HB are on the order of 0.5 ps. The efficiency of IVR in the base pair is due to near-resonance between coupled CC and CN vibrations. The resonance also exists between the frequencies of H2O bend and NH stretch, thus facilitating VET. When H2O interacts with the NH bond at the adenine end of the base pair, energy flow in the reverse direction to the uracil–NH stretch is negligible, the unidirectionality discussed in terms of the effects of uracil CH stretches. The energy distributed in the CH bonds is found to be significant. The IVR process is found to be nearly temperature independent between 200 and 400 K.

Versatile Vibrational Energy Sensors for Proteins

Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.

Computational Study on the Thermal Conductivity of a Protein

Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m^-1 K^-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.

Origin of thiocyanate spectral shifts in water and organic solvents

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.

High-precision background correction and artifact suppression for ultrafast spectroscopy by quasi-simultaneous measurements in a split-sample cell

Alternating acquisition of background and sample spectra is often employed in conventional Fourier-transform infrared spectroscopy or ultraviolet-visible spectroscopy for accurate background subtraction. For example, for solvent background correction, typically a spectrum of a cuvette with solvent is measured and subtracted from a spectrum of a cuvette with solvent and solute. Ultrafast spectroscopies, though, come with many peculiarities that make the collection of well-matched, subtractable background and sample spectra challenging. Here, we present a demountable split-sample cell in combination with a modified Lissajous scanner to overcome these challenges. It allows for quasi-simultaneous measurements of background and sample spectra, mitigating the effects of drifts of the setup and maintaining the beam and sample geometry when swapping between background and sample measurements. The cell is moving between subsequent laser shots to refresh the excited sample volume. With less than 45 μl of solution for 150 μm optical thickness, sample usage is economical. Cell assembly is a key step and covered in an illustrated protocol.

Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases

In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.

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.