13C-Labeled Tyrosine Residues as Local IR Probes for Monitoring Conformational Changes in Peptides and Proteins

UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction

Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.

Easy Production of "Difficult Peptides" Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site

Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.

Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy

Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm^-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

An investigation of inactivation mechanisms of Bacillus amyloliquefaciens spores in non-thermal plasma of ambient air

BACKGROUND

To utilize the potential of non-thermal plasma technologies for food safety control and sanitation, the inactivation mechanisms of Bacillus amyloliquefaciens spores by non-thermal plasma of ambient air (NTP-AA) were investigated using scanning electron microscopy, atomic force microscopy, attenuated total reflectance Fourier transform infrared spectroscopy with chemometric analysis and proton nuclear magnetic resonance spectroscopy, aiming to probe both the morphological and biochemical changes occurring in spores during the kinetic inactivation process.

RESULTS

Kinetic analysis indicates that there is no intrinsic D-value (i.e. time required to inactivate 90% of the spores) in spore inactivation by NTP-AA because we observed non-linear (biphasic) inactivation kinetics and, in addition, the inactivation rate depended on the initial spore concentration and how the spores were exposed to the reactive species in the NTP-AA. The presence of suitable amount of water in the NTP-AA field accelerates spore inactivation.

CONCLUSION

Progressive erosion of spore surface by NTP-AA with ensuing or concomitant biochemical damage, which includes the alteration of structural proteins, internal lipids and the loss of dipicolinic acid content from the spore core, represent the main mechanisms of inactivation, and there is evidence that reactive NTP-AA species could penetrate the cortex and reach the core of spores to cause damage. © 2018 Society of Chemical Industry.

Design of peptidase-resistant peptide inhibitors of myosin light chain kinase

Myosin light chain kinase (MLCK) is a key regulator of various forms of cell motility including smooth muscle contraction, cell migration, cytokinesis, receptor capping, secretion, etc. Inhibition of MLCK activity in endothelial and epithelial monolayers using cell-permeant peptide Arg-Lys-Lys-Tyr-Lys-Tyr-Arg-Arg-Lys (PIK, Peptide Inhibitor of Kinase) allows protecting the barrier capacity, suggesting a potential medical use of PIK. However, low stability of L-PIK in a biological milieu prompts for development of more stable L-PIK analogues for use as experimental tools in basic and drug-oriented biomedical research. Previously, we designed PIK1, H-(N^α Me)Arg-Lys-Lys-Tyr-Lys-Tyr-Arg-Arg-Lys-NH₂ , that was 2.5-fold more resistant to peptidases in human plasma in vitro than L-PIK and equal to it as MLCK inhibitor. In order to further enhance proteolytic stability of PIK inhibitor, we designed the set of six site-protected peptides based on L-PIK and PIK1 degradation patterns in human plasma as revealed by ¹ H-NMR analysis. Implemented modifications increased half-live of the PIK-related peptides in plasma about 10-fold, and these compounds retained 25-100% of L-PIK inhibitory activity toward MLCK in vitro. Based on stability and functional activity ranking, PIK2, H-(N^α Me)Arg-Lys-Lys-Tyr-Lys-Tyr-Arg-D-Arg-Lys-NH₂ , was identified as the most stable and effective L-PIK analogue. PIK2 was able to decrease myosin light chain phosphorylation in endothelial cells stimulated with thrombin, and this effect correlated with the inhibition by PIK2 of thrombin-induced endothelial hyperpermeability in vitro. Therefore, PIK2 could be used as novel alternative to other cell-permeant inhibitors of MLCK in cell culture-based and in vivo studies where MLCK catalytic activity inhibition is required. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

The Role of Electrostatic Interactions in Folding of β-Proteins

Atomic-level molecular dynamic simulations are capable of fully folding structurally diverse proteins; however, they are limited in their ability to accurately represent electrostatic interactions. Here we have experimentally tested the role of charged residues on stability and folding kinetics of one of the most widely simulated β-proteins, the WW domain. The folding of wild type Pin1 WW domain, which has two positively charged residues in the first turn, was compared to the fast folding mutant FiP35 Pin1, which introduces a negative charge into the first turn. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the amide I region. The relaxation dynamics of the peptide backbone, β-sheets and β-turns, and negatively charged aspartic acid side chain of FiP35 were measured independently by probing the corresponding bands assigned in the amide I region. Folding is initiated in the turns and the β-sheets form last. While the global folding mechanism is in good agreement with simulation predictions, we observe changes in the protonation state of aspartic acid during folding that have not been captured by simulation methods. The protonation state of aspartic acid is coupled to protein folding; the apparent pKa of aspartic acid in the folded protein is 6.4. The dynamics of the aspartic acid follow the dynamics of the intermediate phase, supporting assignment of this phase to formation of the first hairpin. These results demonstrate the importance of electrostatic interactions in turn stability and formation of extended β-sheet structures.

WW domain folding complexity revealed by infrared spectroscopy

Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescence spectroscopy, to study the folding of the FBP28 WW domain. Laser-induced temperature jumps coupled with fluorescence or infrared spectroscopy have been used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding IR bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe three kinetics phases, with the fastest process corresponding to the relaxation kinetics of the turns. In contrast, fluorescence measurements of the wild-type WW domain and tryptophan mutants exhibit single-exponential kinetics with a lifetime that corresponds to the slowest phase observed by infrared spectroscopy. Mutant sequences provide evidence of an intermediate dry molten globule state. The slowest step in the folding of this WW domain is the tight packing of the side chains in the transition from the dry molten globule intermediate to the native structure. This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.

Dynamics of an ultrafast folding subdomain in the context of a larger protein fold

Small fast folding subdomains with low contact order have been postulated to facilitate the folding of larger proteins. We have tested this idea by determining how the fastest folding linear β-hairpin, CLN025, which folds on the nanosecond time scale, folds within the context of a two-hairpin WW domain system, which folds on the microsecond time scale. The folding of the wild type FBP28 WW domain was compared to constructs in which each of the loops was replaced by CLN025. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the peptide backbone. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding bands assigned in the amide I region. The folding rate of the CLN025 β-hairpin is unchanged within the larger protein. Insertion of the β-hairpin into the second loop results in an overall stabilization of the WW domain and a relaxation lifetime five times faster than the parent WW domain. In both mutants, folding is initiated in the turns and the β-sheets form last. These results demonstrate that fast folding subdomains can be used to speed the folding of more complex proteins, and that the folding dynamics of the subdomain is unchanged within the context of the larger protein.

Monitoring protein-ligand interactions by time-resolved FTIR difference spectroscopy

Time-resolved FTIR difference spectroscopy is a valuable tool to monitor the dynamics and exact molecular details of protein-ligand interactions. FTIR difference spectroscopy selects, out of the background absorbance of the whole sample, the absorbance bands of the protein groups and of the ligands that are involved in the protein reaction. The absorbance changes can be monitored with time-resolutions down to nanoseconds and followed for time periods ranging over nine orders of magnitude even in membrane proteins with a size of 100,000 Da. Here, we discuss the various experimental setups. The rapid scan technique allows a time resolution in the millisecond regime, whereas the step scan technique allows nanosecond time resolution. We show appropriate sample cells and how to trigger a reaction within these cells. The kinetic analysis of the data is discussed. A crucial step in the data analysis is the reliable assignment of bands to chemical groups of the protein and the ligand. This is done either by site directed mutagenesis, where the absorbance bands of the exchanged amino acids disappear or by isotopically labeling, where the band of the labelled group is frequency shifted.

A solid-state (17)O NMR study of L-tyrosine in different ionization states: implications for probing tyrosine side chains in proteins

We report experimental characterization of (17)O quadrupole coupling (QC) and chemical shift (CS) tensors for the phenolic oxygen in three l-tyrosine (l-Tyr) compounds: l-Tyr, l-Tyr.HCl, and Na(2)(l-Tyr). This is the first time that these fundamental (17)O NMR tensors are completely determined for phenolic oxygens in different ionization states. We find that, while the (17)O QC tensor changes very little upon phenol ionization, the (17)O CS tensor displays a remarkable sensitivity. In particular, the isotropic (17)O chemical shift increases by approximately 60 ppm upon phenol ionization, which is 6 times larger than the corresponding change in the isotropic (13)C chemical shift for the C(zeta) nucleus of the same phenol group. By examining the CS tensor orientation in the molecular frame of reference, we discover a "cross-over" effect between delta(11) and delta(22) components for both (17)O and (13)C CS tensors. We demonstrate that the knowledge of such "cross-over" effects is crucial for understanding the relationship between the observed CS tensor components and chemical bonding. Our results suggest that solid-state (17)O NMR can potentially be used to probe the ionization state of tyrosine side chains in proteins.

The depsipeptide method for solid-phase synthesis of difficult peptides

After about one century of peptide chemistry, the main limitation to the accessibility of peptides and proteins via chemosynthesis is the arising of folding and aggregation phenomena. This is true not only for sequences above a critical length but also for several biologically relevant substrates that are relatively short yet form either highly folded structures (e.g. WW domains) or fibrils and aggregates after final deprotection (beta-amyloid peptide). Such so-called difficult sequences may be more easily obtained via their corresponding depsipeptides (O-acyl isopeptides), ester isomers that are often easier to assemble and purify, and are smoothly converted to the parent amides under mild conditions. The depsipeptide method is the most recent technique to improve the outcome of difficult syntheses, applicable to sequences containing residues of serine or threonine. A brief overview is presented about chemical aspects of the method, the steps that have been undertaken for its optimization, and the evaluation of its efficiency. Further applications of analogous principles to other critical topics in peptide synthesis such as condensation of peptide segments and solid-phase synthesis of naturally occurring cyclodepsipeptides are addressed as well.

Interactions of tyrosine in Leu-enkephalin at a membrane-water interface: an ultrafast two-dimensional infrared study combined with density functional calculations and molecular dynamics simulations

The interactions of neuropeptides and membranes play an important role in peptide hormone function. Our current understanding of peptide-membrane interactions remains limited due to the paucity of experimental techniques capable of probing such interactions. In this work, we study the nature of opioid peptide-membrane interactions using ultrafast two-dimensional infrared (2D IR) spectroscopy. The high temporal resolution of 2D IR is particularly suited for studying highly flexible opioid peptides. We investigate the location of the tyrosine (Tyr) side chain of leucine-enkephalin (Lenk) in lipid bilayer membranes by measuring spectral diffusion of the phenolic ring vibrational mode in three different systems: Lenk in lipid bilayer membranes (bicelles), Lenk in deuterated water, and p-cresol in deuterated water. Frequency-frequency correlation functions obtained from waiting-time-dependent 2D IR spectra reveal an ultrafast decaying component with an approximately 1 ps time constant that is common for all three systems. On the basis of density functional theory calculations and molecular dynamics simulations, this spectral diffusion component is attributed to hydrogen-bond dynamics of the phenolic hydroxyl group interacting with bulk water. Unlike p-cresol in water, both Lenk systems exhibit static spectral inhomogeneity, which can be attributed to conformational distributions of Lenk that do not interconvert within 4 ps. Our results suggest that the Tyr side chain of Lenk in bicelles is located at the water-abundant region at the membrane-water interface and not embedded into the hydrophobic core.

Multivariate prediction of the thermal-induced weak interaction changes of poly(n-isopropylacrylamide) film by the interconversion between middle and near-infrared spectra

The use of a novel spectral interconversion scheme to probe weak molecular interactions of a polymer system is reported. Based on the multivariate regression model using partial least squares (PLS), the thermally induced changes in the weak interaction of poly(n-isopropylacrylamide) (PNiPA) film was studied by the interconversion between mid-infrared (MIR) and near-infrared (NIR) spectra measured at temperatures between 40 and 220 degrees C. It was demonstrated that not only NIR spectra but also well-resolved MIR spectra of PNiPA film, either in narrow or wide spectral ranges, can be predicted from each other based on the proposed scheme. The thermally induced weak interaction changes of PNiPA, expressed as either the band shift or intensity changes at a specific region, can be probed properly. Meanwhile, the effect of several important factors such as the selected spectral range, correlation between the specific bands, and especially the multiple scattering corrections (MSC) on the accuracy of the spectral prediction were also investigated in detail. This study provides a novel method for the analysis of weak interactions in complex systems.

Early stages of misfolding and association of beta2-microglobulin: insights from infrared spectroscopy and dynamic light scattering

Conformational changes associated with the assembly of recombinant beta 2-microglobulin in vitro under acidic conditions were investigated using infrared spectroscopy and static and dynamic light scattering. In parallel, the morphology of the different aggregated species obtained under defined conditions was characterized by electron microscopy. The initial salt-induced aggregate form of beta 2-microglobulin, composed of small oligomers (dimers to tetramers), revealed the presence of beta-strands organized in an intramolecular-like fashion. Further particle growth was accompanied by the formation of intermolecular beta-sheet structure and led to short curved forms. An increase in temperature by only 25 degrees C was able to disaggregate these assemblies, followed by the formation of longer filamentous structures. In contrast, a rise in temperature up to 100 degrees C was associated with a reorganization of the short curved forms at the level of secondary structure and the state of assembly, leading to a species with a characteristic infrared spectrum different from those of all the other aggregates observed before, suggesting a unique overall structure. The infrared spectral features of this species were nearly identical to those of beta 2-microglobulin assemblies formed at low ionic strength with agitation, indicating the presence of fibrils, which was confirmed by electron microscopy. The observed spectroscopic changes suggest that the heat-triggered conversion of the short curved assemblies into fibrils involves a reorganization of the beta-strands from an antiparallel arrangement to a parallel arrangement, with the latter being characteristic of amyloid fibrils of beta 2-microglobulin.

Solid-phase peptide synthesis: from standard procedures to the synthesis of difficult sequences

This protocol for solid-phase peptide synthesis (SPPS) is based on the widely used Fmoc/tBu strategy, activation of the carboxyl groups by aminium-derived coupling reagents and use of PEG-modified polystyrene resins. A standard protocol is described, which was successfully applied in our lab for the synthesis of the corticotropin-releasing factor (CRF), >400 CRF analogs and a countless number of other peptides. The 41-mer peptide CRF is obtained within approximately 80 working hours. To achieve the so-called difficult sequences, special techniques have to be applied in order to reduce aggregation of the growing peptide chain, which is the main cause of failure for peptide chemosynthesis. Exemplary application of depsipeptide and pseudoproline units is shown for synthesizing an extremely difficult sequence, the Asn(15) analog of the WW domain FBP28, which is impossible to obtain using the standard protocol.

Depsipeptide Methodology for Solid-Phase Peptide Synthesis: Circumventing Side Reactions and Development of an Automated Technique via Depsidipeptide Units,

The depsipeptide technique is a recently developed method for peptide synthesis which is applicable to difficult sequences when the synthetic difficulty arises because of aggregation phenomena. In the present work, application of the depsipeptide method to extremely difficult sequences has been demonstrated and a serious side reaction involving diketopiperazine formation uncovered and subsequently avoided by the appropriate use of the Bsmoc protecting group. Many other aspects of the technique have been investigated, such as the stability of the depsi units during assembly and workup procedures, the completeness of the O-acylation step, the occurrence of epimerization of the amino acid activated during O-acylation, and the nature of side products formed. In addition, the method was modified so as to allow for completely automated syntheses of long-chain depsipeptides without the need for any interruption by manual esterification procedures. Finally, the synthesis efficiency of the new depsipeptide technique was shown to be comparable to that of the well-known pseudoproline technique.

Probing the Ligand-Binding Specificity and Analyzing the Folding State of SPOT-Synthesized FBP28 WW Domain Variants

The WW domains are known as the smallest naturally occurring, monomeric, triple-stranded, antiparallel beta-sheet domains. Hence, we chose the FBP28 WW domain as a model to investigate the stability of the beta-sheet structure at the amino acid level in the context of its function (ligand binding). The structure-function relationship was investigated through a complete substitution analysis of the FBP28 WW domain, with variants synthesized as a cellulose-bound peptide array. The functionality of the FBP28 WW domain variants was examined by probing the peptide array for ligand binding. In addition, selected FBP28 WW domain variants were investigated by CD measurements to determine the stability of the antiparallel beta-sheet structure. We discuss the correlation between structure stability and functionality for the FBP28 WW domain, as well as the effect of ligand-induced structure stabilization.