β-Azidoalanine as an IR Probe: Application to Amyloid Aβ(16-22) Aggregation

Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity

2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins.

β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes

An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump–probe spectroscopy.

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.

Infrared Pump-Probe Study of Nanoconfined Water Structure in Reverse Micelle

The influence of nanoconfinement on water structure is studied with time- and frequency-resolved vibrational spectroscopy of hydrazoic acid (HN3) encapsulated in reverse micelle. The azido stretch mode of HN3 is found to be a promising infrared probe for studying the structure and local hydrogen-bond environment of confined and interfacial water in reverse micelle due to its narrow spectral bandwidth and large transition dipole moment. The results show a clear separation between the core and shell spectral components, making it advantageous over the previously studied infrared probes. The measured vibrational lifetimes appear to be substantially different for the interfacial and bulk-like environments but show no remarkable size dependency, which indicates that water structures around this IR probe are distinctively different in the core and shell regions. The influence of local hydrogen bond network in the first and higher solvation shells on the vibrational dynamics of HN3 is further discussed.

Ester carbonyl vibration as a sensitive probe of protein local electric field

The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6.

Carbon-deuterium bonds as non-perturbative infrared probes of protein dynamics, electrostatics, heterogeneity, and folding

Vibrational spectroscopy is uniquely able to characterize protein dynamics and microenvironmental heterogeneity because it possesses an inherently high temporal resolution and employs probes of ultimately high structural resolution-the bonds themselves. The use of carbon-deuterium (C-D) bonds as vibrational labels circumvents the spectral congestion that otherwise precludes the use of vibrational spectroscopy to proteins and makes the observation of single vibrations within a protein possible while being wholly non-perturbative. Thus, C-D probes can be used to site-specifically characterize conformational heterogeneity and thermodynamic stability. C-D probes are also uniquely useful in characterizing the electrostatic microenvironment experienced by a specific residue side chain or backbone due to its effect on the C-D absorption frequency. In this chapter we describe the experimental procedures required to use C-D bonds and FT IR spectroscopy to characterize protein dynamics, structural and electrostatic heterogeneity, ligand binding, and folding.

Vibrational solvatochromism: towards systematic approach to modeling solvation phenomena

Vibrational solvatochromic frequency shift of IR probe is an effect of interaction between local electric field and IR probe in condensed phases. Despite prolonged efforts to develop empirical maps for vibrational frequency shifts and transition dipoles of IR probes, a systematic approach to ab initio calculation of vibrational solvatochromic charges and multipoles has not been developed. Here, we report on density functional theory (DFT) calculations of N-methylacetamide (NMA) frequency shifts using implicit and coarse-grained models. The solvatochromic infrared spectral shifts are estimated based on the distributed multipole analysis of electronic densities calculated for gas-phase equilibrium structure of NMA. Thus obtained distributed solvatochromic multipole parameters are used to calculate the amide I vibrational frequency shifts of NMA in water clusters that mimic the instantaneous configurations of the liquid water. Our results indicate that the spectral shifts are primarily electrostatic in nature and can be quantitatively reproduced using the proposed model with semi-quantitative accuracy when compared to the corresponding DFT results.

Computational infrared and two-dimensional infrared photon echo spectroscopy of both wild-type and double mutant myoglobin-CO proteins

The CO stretching mode of both wild-type and double mutant ( T67R / S92D ) MbCO (carbonmonoxymyoglobin) proteins is an ideal infrared (IR) probe for studying the local electrostatic environment inside the myoglobin heme pocket. Recently, to elucidate the conformational switching dynamics between two distinguishable states, extensive IR absorption, IR pump-probe, and two-dimensional (2D) IR spectroscopic studies for various mutant MbCO's have been performed by the Fayer group. They showed that the 2D IR spectroscopy of the double mutant, which has a peroxidase enzyme activity, reveals a rapid chemical exchange between two distinct states, whereas that of the wild-type does not. Despite the fact that a few simulation studies on these systems were already performed and reported, such complicated experimental results have not been fully reproduced nor described in terms of conformational state-to-state transition processes. Here, we first develop a distributed vibrational solvatochromic charge model for describing the CO stretch frequency shift reflecting local electric potential changes. Then, by carrying out molecular dynamic simulations of the two MbCO's and examining their CO frequency trajectories, it becomes possible to identify a proper reaction coordinate consisting of His64 imidazole ring rotation and its distance to the CO ligand. From the 2D surfaces of the resulting potential of mean forces, the spectroscopically distinguished A1 and A3 states of the wild-type as well as two more substates of the double mutant are identified and their vibrational frequencies and distributions are separately examined. Our simulated IR absorption and 2D IR spectra of the two MbCO's are directly compared with the previous experimental results reported by the Fayer group. The chemical exchange rate constants extracted from the two-state kinetic analyses of the simulated 2D IR spectra are in excellent agreement with the experimental values. On the basis of the quantitative agreement between the simulated spectra and experimental ones, we further examine the conformational differences in the heme pockets of the two proteins and show that the double mutation, T67R / S92D , suppresses the A1 population, restricts the imidazole ring rotation, and increases hydrogen-bond strength between the imidazole Nε-H and the oxygen atom of the CO ligand. It is believed that such delicate change of distal His64 imidazole ring dynamics induced by the double mutation may be responsible for its enhanced peroxidase catalytic activity as compared to the wild-type myoglobin.

Sensitive, site-specific, and stable vibrational probe of local protein environments: 4-azidomethyl-L-phenylalanine

We have synthesized the unnatural amino acid (UAA), 4-azidomethyl-L-phenylalanine (pN₃CH₂Phe), to serve as an effective vibrational reporter of local protein environments. The position, extinction coefficient, and sensitivity to local environment of the azide asymmetric stretch vibration of pN₃CH₂Phe are compared to the vibrational reporters: 4-cyano-L-phenylalanine (pCNPhe) and 4-azido-L-phenylalanine (pN₃Phe). This UAA was genetically incorporated in a site-specific manner utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity into two distinct sites in superfolder green fluorescent protein (sfGFP). This allowed for the dependence of the azide asymmetric stretch vibration of pN₃CH₂Phe to different protein environments to be measured. The photostability of pN₃CH₂Phe was also measured relative to the photoreactive UAA, pN₃Phe.

Expanding the scope of replicable unnatural DNA: stepwise optimization of a predominantly hydrophobic base pair

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventually in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs exemplified by d5SICS-dMMO2 and d5SICS-dNaM. When incorporated into DNA, the latter is replicated and transcribed with greater efficiency and fidelity than the former; however, previous optimization efforts identified the para and methoxy-distal meta positions of dMMO2 as particularly promising for further optimization. Here, we report the stepwise optimization of dMMO2 via the synthesis and evaluation of 18 novel para-derivatized analogs of dMMO2, followed by further derivatization and evaluation of the most promising analogs with meta substituents. Subject to size constraints, we find that para substituents can optimize replication via both steric and electronic effects and that meta methoxy groups are unfavorable, while fluoro substituents can be beneficial or deleterious depending on the para substituent. In addition, we find that improvements in the efficiency of unnatural triphosphate insertion translate most directly into higher fidelity replication. Importantly, we identify multiple, unique base pair derivatives that when incorporated into DNA are well replicated. The most promising, d5SICS-dFEMO, is replicated under some conditions with greater efficiency and fidelity than d5SICS-dNaM. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new SAR data, and importantly identify multiple new candidates for eventual in vivo evaluation.

Vibrational solvatochromism and electrochromism. II. Multipole analysis

Small infrared probe molecules have been widely used to study local electrostatic environment in solutions and proteins. Using a variety of time- and frequency-resolved vibrational spectroscopic methods, one can accurately measure the solvation-induced vibrational frequency shifts and the timescales and amplitudes of frequency fluctuations of such IR probes. Since the corresponding frequency shifts are directly related to the local electric field and its spatial derivatives of the surrounding solvent molecules or amino acids in proteins, one can extract information on local electric field around an IR probe directly from the vibrational spectroscopic results. Here, we show that, carrying out a multipole analysis of the solvatochromic frequency shift, the solvatochromic dipole contribution to the frequency shift is not always the dominant factor. In the cases of the nitrile-, thiocyanato-, and azido-derivatized molecules, the solvatochromic quadrupole contributions to the corresponding stretch mode frequency shifts are particularly large and often comparable to the solvatochromic dipole contributions. Noting that the higher multipole moment-solvent electric field interactions are short range effects in comparison to the dipole interaction, the H-bonding interaction-induced vibrational frequency shift can be caused by such short-range multipole-field interaction effects. We anticipate that the present multipole analysis method specifically developed to describe the solvatochromic vibrational frequency shifts will be useful to understand the intermolecular interaction-induced vibrational property changes and to find out a relationship between vibrational solvatochromism and electrochromism of IR probes in condensed phases.

Nitrile group as infrared probe for the characterization of the conformation of bovine serum albumin solubilized in reverse micelles

Infrared spectroscopy is a powerful technique for structure characterization. For a protein hosted in a reversed micellar medium, the spectral features of the protein are always interfered by the IR absorption bands of the medium in addition to the congestion in their IR spectra. Fortunately, there is a transparent window in the 2500-2200 cm(-1) region. Incorporation of a vibrational probe with IR absorption frequencies in this region into proteins represents a promising strategy for the study of the conformation of a protein in a reverse micelle. In the present work, we incorporated 4-cyanobenzyl group (CN) into bovine serum albumin (BSA) via cysteine alkylation reactions under mild conditions. Circular dichroism spectroscopy showed that the CN modified BSA (CNBSA) could retain its conformation. When CNBSA was hosted in AOT reverse micelle, it was found that the nitrile group on BSA was sensitive to the conformational change of BSA induced by urea as an additive in the reverse micelle. The peak splitting of nitrile group was also observed when the size of AOT reverse micelle and the concentration of an electrolyte were varied. Obviously, the shift of the IR absorption peak and/or peak splitting of nitrile group on BSA are correlated with the change of BSA conformation in AOT reverse micelle. So we conclude that the nitrile infrared probe can be used to study protein conformation in a reverse micelle.

Spectroscopic evidence for polymorphic aggregates formed by amyloid-β fragments

Understanding the structure of amyloid-β (Aβ) aggregates is a key step towards elucidating the pathology of Alzheimer's disease. In this work, three fragments of the Aβ(1-42) protein, Aβ(1-25) (DAEFRHDSGYEVHHQKLVFFAEDVG), Aβ(25-35) (GSNKGAIIGLM), and Aβ(33-42) (GLMVGGVVIA), were synthesized, and their aggregated structures were examined by linear infrared spectroscopy in the amide-I (mainly the C=O stretching) region. The structures of the formed aggregates were found to be both sequence and pH dependent. The results suggest that instead of forming matured fibrils, as in the case of full-length Aβ(1-42), both Aβ(1-25) and Aβ(33-42) form a mixture of threadlike β-sheet fibril, soluble β-sheet oligomer, and random coil structures. The β-sheet conformations were found to be mainly antiparallel for the former and both parallel and antiparallel for the latter. However, the Aβ(25-35) fragment was found to form assembled fibrils containing predominantly parallel β-sheets. The conformation and morphology of the aggregates were also confirmed by circular dichroism measurements and transmission electron microscopy. Factors influencing the structures of the aggregates formed by the Aβ fragments were discussed.

Phase networks of cross-β peptide assemblies

Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.

Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy

The polarity pattern of a macromolecule is of utmost importance to its structure and function. For example, one of the main driving forces for protein folding is the burial of hydrophobic residues. Yet polarity remains a difficult property to measure experimentally, due in part to its non-uniformity in the protein interior. Herein, we show that FTIR linewidth analysis of noninvasive 1-(13)C=(18)O labels can be used to obtain a reliable measure of the local polarity, even in a highly multi-phasic system, such as a membrane protein. We show that in the Influenza M2 H(+) channel, residues that line the pore are located in an environment that is as polar as fully solvated residues, while residues that face the lipid acyl chains are located in an apolar environment. Taken together, FTIR linewidth analysis is a powerful, yet chemically non-perturbing approach to examine one of the most important properties in proteins - polarity.

Introduction and technical survey: protein aggregation and fibrillogenesis

In this chapter we provided the overall background to the subject of protein aggregation and fibrillogenesis in amyloidogenesis, with introduction and brief discussion of the various topics that are included with the coming chapters. The division of the book into basic science and clinical science sections enables correlation of the topics to be made. The many proteins and peptides that have currently been found to undergo fibrillogenesis are tabulated. A broad technical survey is made, to indicate the vast array of techniques currently available to study aspects of protein oligomerization, aggregation and fibrillogenesis. These are split into three groups and tabulated, as the microscopical techniques, the analytical and biophysical methods, and the biochemical and cellular techniques. A few techniques are discussed, but in most cases only a link to relevant recent literature is provided.

Using infrared spectroscopy of cyanylated cysteine to map the membrane binding structure and orientation of the hybrid antimicrobial peptide CM15

The synthetic antimicrobial peptide CM15, a hybrid of N-terminal sequences from cecropin and melittin peptides, has been shown to be extremely potent. Its mechanism of action has been thought to involve pore formation based on prior site-directed spin labeling studies. This study examines four single-site β-thiocyanatoalanine variants of CM15 in which the artificial amino acid side chain acts as a vibrational reporter of its local environment through the frequency and line shape of the unique CN stretching band in the infrared spectrum. Circular dichroism experiments indicate that the placements of the artificial side chain have only small perturbative effects on the membrane-bound secondary structure of the CM15 peptide. All variant peptides were placed in buffer solution, in contact with dodecylphosphatidylcholine micelles, and in contact with vesicles formed from Escherichia coli polar lipid extract. At each site, the CN stretching band reports a different behavior. Time-dependent attenuated total reflectance infrared spectra were also collected for each variant as it was allowed to remodel the E. coli lipid vesicles. The results of these experiments agree with the previously proposed formation of toroidal pores, in which each peptide finds itself in an increasingly homogeneous and curved local environment without apparent peptide-peptide interactions. This work also demonstrates the excellent sensitivity of the SCN stretching vibration to small changes in the peptide-lipid interfacial structure.

Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand

Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein.

Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules

Elucidating the underlying molecular mechanisms of protein folding and function is a very exciting and active research area, but poses significant challenges. This is due in part to the fact that existing experimental techniques are incapable of capturing snapshots along the 'reaction coordinate' in question with both sufficient spatial and temporal resolutions. In this regard, recent years have seen increased interests and efforts in development and employment of site-specific probes to enhance the structural sensitivity of spectroscopic techniques in conformational and dynamical studies of biological molecules. In particular, the spectroscopic and chemical properties of nitriles, thiocyanates, and azides render these groups attractive for the interrogation of complex biochemical constructs and processes. Here, we review their signatures in vibrational, fluorescence and NMR spectra and their utility in the context of elucidating chemical structure and dynamics of protein and DNA molecules.

Azido Homoalanine is a Useful Infrared Probe for Monitoring Local Electrostatistics and Sidechain Solvation in Proteins

The use of IR probes to monitor protein structure, deduce local electric field, and investigate the mechanism of enzyme catalysis and protein folding has attracted increasing attention. Here, the azidohomoalanine (Aha) is considered as a useful IR probe. The intricate details of the distinct effects of backbone peptide bonds and H-bonded water molecules on the azido stretch mode of the IR probe Aha were revealed by carrying out QM/MM MD simulations of two variants of the protein NTL9, NTL9-Met1Aha and NTL9-Ile4Aha and comparing the resulting simulated IR spectra with experiments.

Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water

Mid-IR active analogs of enzyme cofactors have the potential to be important spectroscopic reporters of enzyme active site dynamics. Azido-nicotinamide adenine dinucleotide (NAD(+)), which has been recently synthesized in our laboratory, is a mid-IR active analog of NAD(+), a ubiquitous redox cofactor in biology. In this study, we measure the frequency-frequency time correlation function for the antisymmetric stretching vibration of the azido group of azido-NAD(+) in water. Our results are consistent with previous studies of pseudohalides in water. We conclude that azido-NAD(+) is sensitive to local environmental fluctuations, which, in water, are dominated by hydrogen-bond dynamics of the water molecules around the probe. Our results demonstrate the potential of azido-NAD(+) as a vibrational probe and illustrate the potential of substituted NAD(+)-analogs as reporters of local structural dynamics that could be used for studies of protein dynamics in NAD-dependent enzymes.

Modulating Accidental Fermi Resonance: What a Difference a Neutron Makes

Vibrational reporters have shown significant promise as sensitive probes of local environments in proteins and nucleic acids. The utility of two potential vibrational probes, the cyanate and azide groups in phenyl cyanate and 3-azidopyridine, respectively, has been hindered by accidental Fermi resonance. Anharmonic coupling, between the fundamental -OCN or -N(3) asymmetric stretch vibration with a near resonant combination band, results in an extremely broad and complex absorption profile for each of these probes. A total of eight phenyl cyanate and six 3-azidopyridine isotopomers were synthesized and studied. Isotopic editing effectively modulated the accidental Fermi resonance - the absorption profiles of several isotopomers were greatly simplified while others remained complex. The origins of the observed profiles are discussed. Addition of a single neutron to the middle atom of the oscillator converted the absorption profile to essentially a single band resulting from either the cyanate or azide asymmetric stretch vibration.

A direct comparison of azide and nitrile vibrational probes

The synthesis of 2'-azido-5-cyano-2'-deoxyuridine, N(3)CNdU (1), from trityl-protected 2'-amino-2'-deoxyuridine was accomplished in four steps with a 12.5% overall yield. The IR absorption positions and profiles of the azide and nitrile group of N(3)CNdU were investigated in 14 different solvents and water/DMSO solvent mixtures. The azide probe was superior to the nitrile probe in terms of its extinction coefficient, which is 2-4 times larger. However, the nitrile IR absorbance profile is generally less complicated by accidental Fermi resonance. The IR frequencies of both probes undergo a substantial red shift upon going from water to aprotic solvents such as THF or DMSO. DFT calculations supported the hypothesis that the molecular origin of the higher observed frequency in water is primarily due to hydrogen bonds between the probes and water molecules.

Probing structural transitions in the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by vibrational spectroscopy of cyanylated cysteines

Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) were cyanylated at cysteine and their infrared spectra in the C triple bond N stretching region were recorded both in the absence and in the presence of one of the physiological partners of N(TAIL), namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within N(TAIL), the C triple bond N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level.

A sensitive multispectroscopic probe for nucleic acids

Azides have recently been used as vibrational probes of proteins, but their incorporation into nucleic acids has been limited to photo-cross-linking or click chemistry applications. The utility of 2'-azido-2'-deoxyuridine (N(3)-dU, 1) as an IR and (15)N NMR spectroscopic probe of the sugar phosphate backbone region of nucleic acids was investigated by measuring the effects of solvent, heterodimer formation, and temperature on peak frequencies and IR bandwidth. The azide IR asymmetric stretching band (nu(N(3))) of N(3)-dU was sensitive to its environment, undergoing a blue shift of 13.5 cm(-1) when changing the solvent from THF to water. The solvent effects on (15)N chemical shifts (delta((15)N)) of each of the nitrogen atoms in the azido group was studied, and the terminal nitrogen atom was the most sensitive to solvent, shifting downfield by 3.8 ppm when changing the solvent from THF-d(8) to D(2)O. Formation of a base-pair-like heterodimer between 3 (a silyl ether analogue of 1) and 2,6-diheptanamidopyridine (4) in chloroform resulted in minimal changes in the IR and (15)N NMR spectral frequency and chemical shift, respectively, as expected given the location of the azido moiety. The intrinsic temperature dependence of nu(N(3)) and delta((15)N) were found to be minimal over the temperature range studied especially compared to the solvent dependence of these spectral observables. The analysis of the experimental studies was complemented by density functional theory (DFT) calculations on model systems.

2D IR photon echo of azido-probes for biomolecular dynamics

The vibrations in the azido-, N(3), asymmetric stretching region of 2'-azido-2'-deoxyuridine (N(3)dU) are examined by two-dimensional infrared spectroscopy. In water and tetrahydrofuran (THF), the spectra display a single sharp diagonal peak that shows solvent sensitivity. The frequency-frequency correlation time in water is 1.5 ps, consistent with H-bond making and breaking dynamics. The 2D IR spectrum is reproduced for N(3)dU in water based on a model correlation function and known linear response functions. Its large extinction coefficient, vibrational frequency outside the protein and nucleic acid IR absorption, and sensitivity to water dynamics render -N(3) a very useful probe for 2D IR and other nonlinear IR studies: its signal is ca. 100 times that of nitriles.

A concise and scalable route to L-azidohomoalanine

A concise and highly efficient synthetic route to L-azidohomoalanine (L-Aha) and its homologues is presented here. These chemically modified amino acids are used for the introduction of bioorthogonal handles into proteins. The described route avoids major problems of previously reported methods including expensive starting materials, low efficiency, and lack of scalability. Starting from inexpensive N-Boc-O-Bn-L-aspartic acid, gram quantities of L-Aha hydrochloride can be prepared with high purity. The reactions can be completed within 1 week and the products can be incorporated into proteins using L-methionine auxotrophs.

Ultrafast vibrational spectroscopy of cyanophenols

Aromatic compounds with electron-donating or -accepting substituents exhibit interesting resonance effects on a variety of chemical reactivities and optical properties. To understand such effects and the possible relationship between vibrational energy dissipation pathways and resonance structures of aromatic compounds, we studied ortho-, meta-, and para-substituted cyanophenols and their anionic forms in methanol by using time- and frequency-resolved pump-probe and two-dimensional IR spectroscopy, where the nitrile group acts as an IR probe. From the measured transient spectra and singular-value decomposition analyses, we found that there is a combination band whose frequency is very close to that of the nitrile stretch mode. Due to the difference in the lifetimes of these two mode excited states, the transient pump-probe spectra commonly show notable blue-shifting behaviors in time. Comparing the vibrational lifetimes of neutral cyanophenols and cyanophenoxide anions in methanol and carrying out quantum mechanical/molecular mechanical molecular dynamics simulations to study hydrogen-bonding dynamics, we found that the vibrational energy of the nitrile stretch mode initially relaxes to intramolecular degrees of freedom instead of solvent modes. Also, the vibrational anharmonic frequency shifts, intrinsic lifetimes, and bandwidths of the nitrile stretch mode and the combination mode in these molecular systems are fully characterized, and their relationships with resonance structures are discussed. It is believed that the present work sheds light on the intrinsic vibrational relaxation process of the nitrile stretch mode in cyanophenols, even in the case when their IR spectra are congested by the spectrally overlapping combination bands, and the resonance effects of aromatic compounds on vibrational dynamics and relaxation processes.