Nitrile Probe Research Articles

Experimental two-dimensional infrared spectra of methyl thiocyanate in water and organic solvents.

Thiocyanates, nitriles, and azides represent a versatile set of vibrational probes to measure the structure and dynamics in biological systems. The probes are minimally perturbative, the nitrile stretching mode appears in an otherwise uncongested spectral region, and the spectra report on the local environment around the probe. Nitrile frequencies and lineshapes, however, are difficult to interpret, and theoretical models that connect local environments with vibrational frequencies are often necessary. However, the development of both more accurate and intuitive models remains a challenge for the community. The present work provides an experimentally consistent collection of experimental measurements, including IR absorption and ultrafast two-dimensional infrared (2D IR) spectra, to serve as a benchmark in the development of future models. Specifically, we catalog spectra of the nitrile stretching mode of methyl thiocyanate (MeSCN) in fourteen different solvents, including non-polar, polar, and protic solvents. Absorption spectra indicate that π-interactions may be responsible for the line shape differences observed between aromatic and aliphatic alcohols. We also demonstrate that a recent Kamlet-Taft formulation describes the center frequency MeSCN. Furthermore, we report cryogenic infrared spectra that may lead to insights into the peak asymmetry in aprotic solvents. 2D IR spectra measured in protic solvents serve to connect hydrogen bonding with static inhomogeneity. We expect that these insights, along with the publicly available dataset, will be useful to continue advancing future models capable of quantitatively describing the relation between local environments, line shapes, and dynamics in nitrile probes.

Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields.

Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.

Electrostatic Impact of Brefeldin A on Thiocyanate Probes Surrounding the Interface of Arf1-BFA-ARNO4M, a Protein-Drug-Protein Complex.

Protein-protein interactions regulate many cellular processes, making them ideal drug candidates. Design of such drugs, however, is hindered by a lack of understanding of the factors that contribute to the interaction specificity. Specific protein-protein complexes possess both structural and electrostatic complementarity, and while structural complementarity of protein complexes has been extensively investigated, fundamental understanding of the complicated networks of electrostatic interactions at these interfaces is lacking, thus hindering the rational design of orthosterically binding small molecules. To better understand the electrostatic interactions at protein interfaces and how a small molecule could contribute to and fit within that environment, we used a model protein-drug-protein system, Arf1-BFA-ARNO4M, to investigate how small molecule brefeldin A (BFA) perturbs the Arf1-ARNO4M interface. By using nitrile probe labeled Arf1 sites and measuring vibrational Stark effects as well as temperature dependent infrared shifts, we measured changes in the electric field and hydrogen bonding at this interface upon BFA binding. At all five probe locations of Arf1, we found that the vibrational shifts resulting from BFA binding corroborate trends found in Poisson-Boltzmann calculations of surface potentials of Arf1-ARNO4M and Arf1-BFA-ARNO4M, where BFA contributes negative electrostatic potential to the protein interface. The data also corroborate previous hypotheses about the mechanism of interfacial binding and confirm that alternating patches of hydrophobic and polar interactions lead to BFA binding specificity. These findings demonstrate the impact of BFA on this protein-protein interface and have implications for the design of other interfacial drug candidates.

AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies.

Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as pKa shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM (r = 0.88) and the FTLS (r = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.

Distinguishing between the Electrostatic Effects and Explicit Ion Interactions in a Stark Probe

Vibrational Stark probes are incisive tools for measuring local electric fields in a wide range of chemical environments. The interpretation of the frequency shift often gets complicated due to the specific interactions of the probe, such as hydrogen bonding and Lewis bonding. Therefore, it is important to distinguish between the pure electrostatic response and the response due to such specific interactions. Here we report a molecular system that is sensitive to both the Stark effect from a single ion and the explicit Lewis bonding of ions with the probe. The molecule consists of a crown ether with an appended benzonitrile. The crown captures cations of various charges, and the electric field from the ions is sensed by the benzonitrile probe. Additionally, the lone pair of the benzonitrile can engage in Lewis interactions with some of the ions by donating partial charge density to the ions. Our system exhibits both of these effects and therefore is a suitable test bed for distinguishing between the pure electrostatic and the Lewis interactions. Our computational results show that the electrostatic influence of the ion is operative at large distances, while the Lewis interaction becomes important only within distances that permit orbital overlap. Our results may be useful for using the nitrile probe for measuring electrostatic and coordination effects in complex ionic environments such as the electrode-electrolyte interfaces.

Protein protic and aprotic interactions systematically mapped via IR spectroscopy and polarizable molecular dynamics.

Nitrile vibrational frequencies can readily report on the environmental electric field except in hydrogen bonding (H-bonding) environments, where factors other than the field contribute to frequency shifts; these environments are very commonly found in proteins, among other forms of condensed phase matter, so an alternative observable for unambiguous field determination is desirable. We previously showed that the nitrile's transition dipole moment (TDM) – and therefore peak area – experiences a new vibrational Stark effect that linearly correlates with the field in all environments, unlike frequencies. As a proof-of-concept, we demonstrated this relationship using nitrile probes in solvents and applied it to four variants of photoactive yellow protein (PYP) with nitrile-containing ortho-cyanophenylalanine residues introduced via amber suppression (JACS, 144, 7562-7567 (2022)). Eight further PYP mutants were constructed from one variant to modify the H-bonding/electric fields experienced by the nitrile probe. IR spectroscopy yielded four consistent IR lineshapes, interpreted as environmental phenotypes, which included mixtures of protic and aprotic environments. TDM-based electric fields were assessed, and high-resolution crystal structures were obtained to further interpretation of the spectroscopic data. The structures showed that either the mutated residue or newly accessible waters around the nitrile serve as the H-bond donor(s) and could explain the environmental phenotypes on a qualitative level. For a more quantitative assessment, we performed molecular dynamics (MD) on PYPs with polarizable AMOEBA force fields: a strong correlation is found between average electric fields from simulation and experimental TDM analysis, further establishing that the field-TDM relationship extends to complex protein environments. Also, characterizations of the nitrile environment (average structure, H-bond donor identities, etc.) correlated well with environmental phenotype, implying that polarizable force fields realistically model local protein interactions.

Carbon-deuterium bonds as reporters of electric fields in solvent and protein environments.

Use of vibrational probes to measure electric fields inside proteins has illuminated the role of electrostatics in biological applications ranging from binding interactions to enzyme catalysis. While prior work focused on strongly absorbing carbonyl and nitrile probes, more recent work has begun exploring weakly absorbing carbon-hydrogen bonds, beginning with measurements of electric fields inside oxidoreductases using the vibrational Stark effect (VSE). Originally, an alcohol dehydrogenase inhibitor containing a deuterated aldehyde was used to measure the field in two directions—on carbonyl and carbon-deuterium (C-D) bonds—in the enzyme active site. Now, several more distinct cases demonstrate how C-D probes map electric fields to vibrational frequency shifts, with new implications for our understanding of the VSE. To probe the field along a different dimension in oxidoreductases, we consider singly deuterated NAD(P)H which reports fields along the hydride transfer axis and whose frequency detection is facilitated by advancements in quantum cascade laser (QCL) technology for infrared spectroscopy. Unusually, the solvatochromic shift for this C-D probe appears opposite to that observed for carbonyls and nitriles; that is, the probe blueshifts in more polar solvents. In another example, the chromophore of green fluorescent protein (GFP) with a deuterated bridge carbon demonstrates similarly unusual frequency shifts in solvent and protein environments, with stronger fields parallel to the C-D dipole causing blueshifts. Observed Stark tuning rates for these molecules are recapitulated by in silico Stark calculations at the B3LYP or ωB97X-D/6-31+G(d) level. Stark tuning rate comparison with other C-D containing molecules including deuterated aldehydes and chloroform-d indicates a large sensitivity of the Stark tuning rate to molecular structure. We demonstrate how properly calibrated C-D probes can be effective reporters of electric fields in applications such as enzyme-catalyzed hydride transfer, biological photophysics and beyond.

Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis.

The contribution of ligand–ligand electrostatic interaction to transition state formation during enzyme catalysis has remained unexplored, even though electrostatic forces are known to play a major role in protein functions and have been investigated by the vibrational Stark effect (VSE). To monitor electrostatic changes along important steps during catalysis, we used a nitrile probe (T46C-CN) inserted proximal to the reaction center of three dihydrofolate reductases (DHFRs) with different biophysical properties, Escherichia coli DHFR (EcDHFR), its conformationally impaired variant (EcDHFR-S148P), and Geobacillus stearothermophilus DHFR (BsDHFR). Our combined experimental and computational approach revealed that the electric field projected by the substrate toward the probe negates those exerted by the cofactor when both are bound within the enzymes. This indicates that compared to previous models that focus exclusively on subdomain reorganization and protein–ligand contacts, ligand–ligand interactions are the key driving force to generate electrostatic environments conducive for catalysis.

Mapping solvation heterogeneity in live cells by hyperspectral stimulated Raman scattering microscopy.

Water provides a dynamic matrix in which all biochemical processes occur in living organisms. The structure and dynamics of intracellular water constitute the cornerstone for understanding all aspects of cellular function. Fundamentally, direct visualization of subcellular solvation heterogeneity is essential but remains challenging with commonly used nuclear magnetic resonance methods due to poor spatial resolution. To explore this question, we demonstrate a vibrational-shift imaging approach by combining the spectral-focusing hyperspectral stimulated Raman scattering technique with an environmentally sensitive nitrile probe. The sensing ability of a near-infrared nitrile-containing molecule is validated in the solution phase, microscopic droplets, and cellular environments. Finally, we quantitatively measure the subcellular solvation variance between the cytoplasm (29.5%, S.E. 1.8%) and the nucleus (57.3%, S.E. 1.0%), which is in good agreement with previous studies. This work sheds light on heterogeneous solvation in live systems using coherent Raman microscopy and opens up new avenues to explore environmental variance in complex systems with high spatiotemporal resolution.

Beyond pKa: Experiments and Simulations of Nitrile Vibrational Probes in Staphylococcal Nuclease Show the Importance of Local Interactions.

Electric fields are fundamentally important to biological phenomena, but are difficult to measure experimentally or predict computationally. Changes in pKa of titratable residues have long been used to report on local electrostatic fields in proteins. Alternatively, nitrile vibrational probes are potentially less disruptive and more direct reporters of local electrostatic field, but quantitative interpretation is clouded by the ability of the nitrile to accept a hydrogen bond. To this end, we incorporated nitrile probes into 10 locations of staphylococcal nuclease (SNase) where pKa shifts had already been determined. We characterized the local environment of each nitrile probe experimentally, through temperature-dependent spectroscopy, and computationally, through molecular dynamics simulations, and show that hydrogen bonding interactions dominate the spectral line shapes. We demonstrate that the information provided by the line shape of the nitrile spectra, compared to scalar values of pKa shift or nitrile frequency shift, better describes local environments in proteins in a manner that will be useful for future computational efforts to predict electrostatics in complex biological systems.

Local Acid Strength of Solutions and Its Quantitative Evaluation Using Excess Infrared Nitrile Probes.

We propose the concept of local acidity in condensed-phase chemistry in this work. The feature is demonstrated in trifluoroethanol (TFE) by employing two Fourier-transform infrared spectroscopy (FTIR) nitrile probes, acetonitrile (CH3CN) and benzonitrile (PhCN). Specifically, three positive excess peaks were found in the binary systems composed of TFE and a probe using excess spectroscopy. To characterize the local acidity quantitatively, we have tried to correlate the wavenumbers of the positive excess peaks of the probes and the pKa values in water of a series of XH-containing compounds (X = O, N, and C). Good linear relationships were discovered. Accordingly, three different pKa values of TFE were determined based on the three positive excess infrared peaks, which are attributed to the monomer, dimer, and trimer of TFE with the help of quantum-chemical calculations. The concept of local acidity and its quantitative evaluation enrich our knowledge of acid-base chemistry and will shed light on a better understanding of microstructures of solutions.

Quantifying the Effects of Hydrogen Bonding on Nitrile Frequencies in GFP: Beyond Solvent Exposure.

Vibrational spectroscopy is a powerful tool for characterizing the complex noncovalent interactions that arise in biological systems. The nitrile stretching frequency has proven to be a particularly convenient biological probe, but the interpretation of nitrile spectroscopy is complicated by its sensitivity to local hydrogen bonding interactions. This often inhibits the straightforward interpretation of nitrile spectra by requiring knowledge of the molecular-level details of the local environment surrounding the probe. While the effect of hydrogen bonds on nitrile frequencies has been well-documented for small molecules in solution, there have been relatively few studies of these effects in a complex protein system. To address this, we introduced a nitrile probe at nine locations throughout green fluorescent protein (GFP) and compared the mean vibrational frequency of each probe to the specific hydrogen bonding geometries observed in molecular dynamics (MD) simulations. We show that a continuum of hydrogen bonding angles is found depending on the particular location of each nitrile, and that the differences in these angles account for the differences in the measured nitrile frequency. We further observed that the temperature dependence of the nitrile frequencies (measured as a frequency-temperature line slope, FTLS) was a good indicator of the hydrogen bonding interactions of the probe, even in scenarios where the nitrile was involved in complex and restricted hydrogen bonds, both from protein and from water. While constant offsets to the nitrile frequency to all hydrogen bonding environments have been applied before to interpret shifts in nitrile frequency, we show that this is insufficient in systems where the hydrogen bonds may be restricted by the surrounding medium. However, the strength of the observed correlation between nitrile frequency and hydrogen bonding angle suggests that it may be possible to disentangle electrostatic effects and effects of the orientation of hydrogen bonding on the nitrile stretching frequency. Meanwhile, the experimental measurement of the FTLS of the nitrile is an excellent tool to identify changes in the hydrogen bonding interactions for a particular probe.

Measuring Electric Fields in Biological Matter Using the Vibrational Stark Effect of Nitrile Probes.

Measurement of the electrostatic interactions that give rise to biological functions has been a longstanding challenge in biophysics. Advances in spectroscopic techniques over the past two decades have allowed for the direct measurement of electric fields in a wide variety of biological molecules and systems via the vibrational Stark effect (VSE). The frequency of the nitrile stretching oscillation has received much attention as an electric field reporter because of its sensitivity to electric fields and its occurrence in a relatively transparent region of the infrared spectrum. Despite these advantages and its wide use as a VSE probe, the nitrile stretching frequency is sensitive to hydrogen bonding in a way that complicates the straightforward relationship between measured frequency and environmental electric field. Here we highlight recent applications of nitrile VSE probes with an emphasis on experiments that have helped shape our understanding of the determinants of nitrile frequencies in both hydrogen bonding and nonhydrogen bonding environments.

Probing Substrate Sequestration in Carrier Proteins using Vibrational Spectroscopy Labels and Molecular Dynamic Simulations

Carrier proteins are considered “lynchpin” enzymes of biosynthetic pathways. The E. coli acyl carrier protein (ACP) has multiple alpha helices that form a hydrophobic, solvent-protected pocket and can provide a hiding spot to protect growing substrates bound to the ACP's phosphopantetheine (Ppant) arm. The action of “chain sequestration” is thought to be important for driving the acyl chain biosynthetic process. Site specific vibrational spectroscopy techniques are being used to investigate Ppant arm dynamics via nitrile probes on unnatural amino acids incorporated into the sequestration cavity. Molecular dynamics simulations in aim to characterize the Ppant arm's shifting conformational distribution and substrate-loading selectivity by analyzing geometric quantities and the solvent exposed surface area (SASA) of specific pieces of the arm. Ultimately, incorporating a nitrile probe group into the simulation will provide a direct connection to experimental data through the CN infrared spectroscopic lineshape. A thorough understanding of Ppant arm dynamics will inform further characterization of experimental data from carrier proteins and efforts to manipulate ACP's interactions with partner enzymes.

Evaluation of p-(13C,15N-Cyano)phenylalanine as an Extended Time Scale 2D IR Probe of Proteins.

Two-dimensional infrared (2D IR) spectroscopy provides a powerful approach for the direct study of molecular dynamics with high spatial and temporal resolution. Its application for investigating specific locations in proteins requires the incorporation of IR probe groups with spectrally isolated absorptions to avoid the congestion inherent to protein spectra. This has motivated extensive efforts toward the development of new IR probes, but there remains a need for those that can extend the experimental time range, which is limited by their vibrational lifetimes. Toward this goal, isotopically labeled p-(13C15N-cyano)phenylalanine was synthesized, site-selectively incorporated into the protein plastocyanin, and evaluated for its potential as a 2D IR probe. The isotopic labeling increases the vibrational lifetime about 2-fold, which results in larger signals at longer time scales. However, isotopic labeling simultaneously shifts the absorption to a spectral region with greater water absorbance, which results in greater heating-induced signals in the background that overlap those of the nitrile probe. The study demonstrates the use of a new 2D IR probe to measure the side chain dynamics in a protein and also illustrates the multiple factors to consider in development of 2D IR probes for studying proteins.

Probing Substrate Sequestration in Carrier Proteins using Vibrational Spectroscopy Labels

Carrier proteins are considered “lynchpin” enzymes of biosynthetic pathways. The E. coli acyl carrier protein (ACP) is composed of multiple alpha helices that form a hydrophobic, solvent-protected pocket that sometimes provides a cavernous hiding spot to protect substrates bound to the ACP's phosphopantetheine (Ppant) arm. The action of “chain sequestration” is thought to be important for driving the biosynthetic process. In this study, selected amino acid residues inside the ACP sequestration channel were targeted as possible incorporation sites for para-substituted aromatic nitrile or alkyne vibrational spectroscopic probes. Using stop codon suppression, non-canonical amino acids were incorporated into the ACP via a co-transformed aminoacyl tRNA synthetase. In addition, artificial substrates containing unique vibrational labeling groups like nitriles were covalently ligated to the ACP's Ppant arm. The vibrational frequencies of these labeling groups, measured via IR absorption or Raman scattering, report on mainly the solvent exposure of the CN group, and the lineshape reports the distribution of environments around the label on either the protein or the growing substrate. IR and Raman results that report on the sequestration of substrates of different length, as well as methodological advances that enable this spectroscopic approach, will be discussed.

Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding.

There is growing interest in using the nitrile vibrational oscillation as a site-specific probe of local environment to study dynamics, folding, and electrostatics in biological molecules such as proteins. Nitrile probes have been used extensively as reporters of electric field using vibrational Stark effect spectroscopy. However, the analysis of frequencies in terms of electric fields is potentially complicated by the large ground state dipole moment of the nitrile, which may irrevocably perturb the protein under investigation, and the ability of nitriles to accept hydrogen bonds, which causes frequency shifts that are not described by the Stark effect. The consequence of this is that vibrational spectroscopy of nitriles in biomolecules could be predominately sensitive to their local hydration status, not electrostatic environment, and have the potential to be particularly destabilizing to the protein. Here, we introduce green fluorescent protein (GFP) as a model system for addressing these concerns using biosynthetically incorporated p-cyanophenylalanine (pCNF) residues in the interior of GFP and measuring absorption energies of both the intrinsic GFP fluorophore and pCNF residues in response to a series of amino acid mutations. We show that observed changes in emission energy of GFP due to the mutations strongly correlate with changes in electric field experienced by both the nitrile probes and the intrinsic fluorophore. Additionally, we show that changes in electric field measured from the intrinsic fluorophore due to amino acid mutations are unperturbed by the addition of pCNF residues inserted nearby. Finally, we show that changes in electric field experienced by the vibrational probes trend monotonically with changes in field experienced by the native fluorophore even though the nitrile probe is engaged in moderate hydrogen bonding to nearby water molecules, indicated by the temperature dependence of the nitrile's absorption energy. Together these results demonstrate that even in the presence of hydrogen bonding it is possible to relate nitrile absorption frequencies to electrostatic environment by comparing highly similar environments. GFP's intrinsic linear sensitivity to electric fields makes it a convenient model system for studying electrostatics in proteins that offers lessons for proteins without this visible fluorophore.

Vibrational and Electronic Stark Effects in Green Fluorescent Protein

The use of unnatural amino acids to probe non-covalent interactions, dynamics, and folding in proteins is growing rapidly. Specifically, para-cyanophenylalanine (pCNF) is an attractive probe of electrostatics because of its sensitivity to electric fields and its minimal structural perturbation when replacing phenylalanine or tyrosine. However, due to the potential for hydrogen bonding to the nitrile moiety there is potential for the introduction of nonnative interactions, which can cloud our understanding of native proteins. Usual attempts to quantify the extent of nitrile perturbation include functional assays or structural measurements. While structure and function are undoubtedly linked to electrostatic environment, they are not direct reporters of it. An intrinsic reporter of electrostatic environment would allow for the direct comparison of environments with and without an extrinsic nitrile probe. Boxer and coworkers have shown that the intrinsic fluorophore of green fluorescent protein (GFP) is sensitive to electric fields in a manner consistent with a linear Stark effect. Here we incorporate multiple pCNF probes into buried sites near the GFP fluorophore and measure changes in the electric field environment from both the nitriles and the fluorophore in response to a series of amino acid mutations. Our results show that pCNF probes can be incorporated near the GFP fluorophore without affecting the electric field changes experienced by the fluorophore. Additionally, changes in electric field measured from the nitrile are in agreement with those measured from the fluorophore. These results suggest that, for this model system, nitrile probes do not significantly perturb the native electrostatic environment. The agreement of changes in electric field from vibrational and electronic Stark effect probes inside the beta barrel of GFP suggests nitrile frequencies can be interpreted in terms of the Stark effect even when they participate in hydrogen bonding.

Measurement of the membrane dipole electric field in DMPC vesicles using vibrational shifts of p-cyanophenylalanine and molecular dynamics simulations.

The magnitude of the membrane dipole field was measured using vibrational Stark effect (VSE) shifts of nitrile oscillators placed on the unnatural amino acid p-cyanophenylalanine (p-CN-Phe) added to a peptide sequence at four unique positions. These peptides, which were based on a repeating alanine-leucine motif, intercalated into small unilamellar DMPC vesicles which formed an α-helix as confirmed by circular dichroic (CD) spectroscopy. Molecular dynamics simulations of the membrane-intercalated helix containing two of the nitrile probes, one near the headgroup region of the lipid (αLAX(25)) and one buried in the interior of the bilayer (αLAX(16)), were used to examine the structure of the nitrile with respect to the membrane normal, the assumed direction of the dipole field, by quantifying both a small tilt of the helix in the bilayer and conformational rotation of the p-CN-Phe side chain at steady state. Vibrational absorption energies of the nitrile oscillator at each position showed a systematic blue shift as the nitrile was stepped toward the membrane interior; for several different concentrations of peptide, the absorption energy of the nitrile located in the middle of the bilayer was ∼3 cm(-1) greater than that of the nitrile closest to the surface of the membrane. Taken together, the measured VSE shifts and nitrile orientations within the membrane resulted in an absolute magnitude of 8-11 MV/cm for the dipole field, at the high end of the range of possible values that have been accumulated from a variety of indirect measurements. Implications for this are discussed.

Site-selective Characterization of Src Homology 3 Domain Molecular Recognition with Cyanophenylalanine Infrared Probes.

Local heterogeneity of microenvironments in proteins is important in biological function, but difficult to characterize experimentally. One approach is the combination of infrared (IR) spectroscopy and site-selective incorporation of probe moieties with spectrally resolved IR absorptions that enable characterization within inherently congested protein IR spectra. We employed this method to study molecular recognition of a Src homology 3 (SH3) domain from the yeast protein Sho1 for a peptide containing the proline-rich recognition sequence of its physiological binding partner Pbs2. Nitrile IR probes were introduced at four distinct sites in the protein by selective incorporation of p-cyanophenylalanine via the amber codon suppressor method and characterized by IR spectroscopy. Variation among the IR absorption bands reports on heterogeneity in local residue environments dictated by the protein structure, as well as on residue-dependent changes upon peptide binding. The study informs on the molecular recognition of SH3 Sho1 and illustrates the speed and simplicity of this approach for characterization of select microenvironments within proteins.