A conformation-selective IR-UV study of the dipeptides Ac-Phe-Ser-NH2 and Ac-Phe-Cys-NH2: probing the SH···O and OH···O hydrogen bond interactions

Engineered reversible inhibition of SpyCatcher reactivity enables rapid generation of bispecific antibodies

The precise regulation of protein function is essential in biological systems and a key goal in chemical biology and protein engineering. Here, we describe a straightforward method to engineer functional control into the isopeptide bond-forming SpyTag/SpyCatcher protein ligation system. First, we perform a cysteine scan of the structured region of SpyCatcher. Except for two known reactive and catalytic residues, none of these mutations abolish reactivity. In a second screening step, we modify the cysteines with disulfide bond-forming small molecules. Here we identify 8 positions at which modifications strongly inhibit reactivity. This inhibition can be reversed by reducing agents. We call such a reversibly inhibitable SpyCatcher "SpyLock". Using "BiLockCatcher", a genetic fusion of wild-type SpyCatcher and SpyLock, and SpyTagged antibody fragments, we generate bispecific antibodies in a single, scalable format, facilitating the screening of a large number of antibody combinations. We demonstrate this approach by screening anti-PD-1/anti-PD-L1 bispecific antibodies using a cellular reporter assay.

Modulation of the strength of weak S-H⋯O hydrogen-bond: Spectroscopic study of the complexes of 2-flurothiophenol with methanol and ethanol

Spectroscopic exploration of sulfur-centered hydrogen bonding involving a thiol group (S-H) as the hydrogen bond donor is scarce in the literature. Herein, we have investigated 1:1 complexes of 2-fluorothiophenol (2-FTP) with methanol (MeOH) and ethanol (EtOH) in the gas phase to examine the physical characteristics and strength of the S-H⋯O hydrogen bond. Structures, conformations, and the strength of the S-H⋯O interaction are investigated by measuring the electronic and Infrared (IR) spectra of the two complexes employing resonant two-photon ionization, UV-UV hole-burning, and IR-UV double resonance spectroscopic techniques combined with quantum chemical calculations. Three conformers of 2-FTP⋯MeOH and two conformers of 2-FTP⋯EtOH have been detected in the experiment. A comparison of the IR spectra obtained from the experiment with those of the low-energy conformers of 2-FTP⋯MeOH and 2-FTP⋯EtOH predicted from the theory confirms that all the observed conformers of the two complexes are primarily S-H⋯O hydrogen bonded. The IR red-shifts found in the S-H stretching frequencies in 2-FTP⋯MeOH and 2-FTP⋯EtOH concerning that in 2-FTP are ∼76 and ∼88 cm-1, respectively, which are much larger than that was reported earlier in the 2-FTP⋯H2O complex (30 cm-1). The strength and physical nature of different noncovalent interactions, including the S-H⋯O hydrogen bond existing in the complexes, are further analyzed using natural bond orbital analysis, quantum theory of atoms in molecules, and localized molecular orbital-energy decomposition analysis. The current investigation reveals that the S-H⋯O hydrogen bond can be strengthened by judicial choices of the hydrogen bond acceptors of higher proton affinities.

Unraveling the ultrafast dynamics of thermal-energy chemical reactions

In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.

An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide

The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD-γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD-γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.

Cryogenic infrared spectroscopy reveals remarkably short NH+⋯F hydrogen bonds in fluorinated phenylalanines

In past decades, hydrogen bonds involving organic fluorine have been a highly disputed topic. Obtaining clear evidence for the presence of fluorine-specific interactions is generally difficult because of their weak nature. Today, the existence of hydrogen bonds with organic fluorine is widely accepted and supported by numerous studies. However, strong bonds with short H⋯F distances remain scarce and are primarily found in designed model compounds. Using a combination of cryogenic gas-phase infrared spectroscopy and density functional theory, we here analyze a series of conformationally unrestrained fluorinated phenylalanine compounds as protonated species. The results suggest proximal NH+⋯F hydrogen bonds with an exceptionally close H⋯F distance (1.79 Å) in protonated ortho-fluorophenylalanine.

Coupling and decoupling CH stretching vibration of methylene and methine in serine conformers

In the molecules of the early Earth, as a building block of proteins, serine has enormous chemical and biological significance. The vibrational spectroscopy of CH bonds plays an important role in probing biomolecules. Whether the CH stretching vibration bands can be accurately assigned will affect the accuracy of the detection results. In this study, we employed the MP2/cc-pVTZ method to calculate the Raman spectra of 85 serine conformers and the corresponding species with deuterium in the CH stretching region from 2800 cm^-1 to 3050 cm^-1 and then recorded the movement of each atom and the dihedral angles, CH bond lengths, and Raman shifts before and after deuterium for each conformer. We directly observed that the stretching vibration of two CH bonds in the methylene group decoupled to vibrate independently in some conformers, and the stretching vibrations of methylene and methine could be strongly coupled in some conformers. Those results are inconsistent with the traditional understanding, which is generally believed that the CH stretching vibrations are mutually coupled in a single methyl or methylene group to generate symmetric and antisymmetric stretching vibrations, while for different methyl, methylene or methine groups, the CH stretching vibrations cannot be mutually coupled. Through the statistical analysis between several factors, we found that the level of local coupling in serine methylene was correlated with the bond length difference between two CH bonds. Our work provides a new understanding of the vibrational modes of hydrocarbon bonds and the coupling between different hydrocarbon groups.

Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry

The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6^δ and inter-residue 7^δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm⁻¹ spectral shift of the NH stretch engaged in a 7^δ NH⋯S/Se bond.

A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine

S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).

An intraresidue H-bonding motif in selenocysteine and cysteine, revealed by gas phase laser spectroscopy and quantum chemistry calculations

Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences. Experimental data, complemented by quantum chemistry calculations and natural bonding orbital (NBO) analyses, are interpreted in terms of the formation of a so-called 5γ intra-residue motif, which bridges the acceptor chalcogen atom of the side chain to the NH bond of the same residue. This local structure, in which the O/S/Se atom is close to the plane of the N-terminal side amide, is constrained by local backbone-side chain hyperconjugation effects involving the S and Se atoms. Theoretical investigations of the Cys/Sec side chain show that (i) this 5γ motif is an intrinsic feature of these residues, (ii) the corresponding H-bond is strongly non-linear and intrinsically weak, (iii) but enhanced by γ- and β-turn secondary structures, which promote a more favorable 5γ H-bonding approach and distance. The resulting H-bonds are slightly stronger in selenocysteine than in cysteine, but nearly inexistent in serine, whose side chain in contrast behaves as a H-bonding donor. The modest spectral shifts of the Cys/Sec NH stretches measured experimentally reflect the moderate strength of the 5γ H-bonding, in agreement with the correlation obtained with a NBO-based H-bond strength indicator. The evolution along the Ser, Cys and Sec series emphasizes the compromise between the several factors that control the H-bonding in a hyperconjugation-constrained geometry, among them the chalcogen van der Waals and covalent radii. It also illustrates the 5γ H-bond enhancements with the Sec and Cys residues favoured by the constraints imposed by the γ- and β-turn structures of the peptide chain.

Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group

A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Conformation control through concurrent N-H⋯S and N-H⋯O[double bond, length as m-dash]C hydrogen bonding and hyperconjugation effects

In addition to the classical N-H⋯O[double bond, length as m-dash]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N-H⋯S interactions (C6^γ), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H⋯O[double bond, length as m-dash]C interactions (C5) to provide a C5-C6^γ feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6^γ features in the planar dimer implicate an unprecedented three-centre H-bond of the type C[double bond, length as m-dash]O⋯H(N)⋯SR₂, while the trimer adopts two C5-C6^γ features separated by a Ramachandran α-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Modulating amyloid fibrillation in a minimalist model peptide by intermolecular disulfide chemical reduction

Peptide structural transformation and aggregation is associated with a large number of outsider aetiology diseases, and it is intrinsically linked to amyloid peptide aggregation. Diphenylalanine self-assembled structures are used as robust minimalist beta amyloids not only to elucidate protein aggregation but also to generate hydrogels. Herein, we employed a neutral model peptide Ac-Phe-Phe-Cys-NH2 (Ac-FFC-NH2) to elucidate the role of intermolecular disulfide bonds in protein fibrillation. The Ac-FFC-NH2 peptide initially self-assembles into nanospheres that evolve to amyloid type fibrils under mild oxidative conditions. Incubation of the peptide in the presence of the chemical reduction agent TCEP inhibits the formation of the fibrils, detecting only spherical nanostructures with no secondary structure. Importantly, we triggered the transformation of the preformed linear straight amyloid fibrils to non-fibrillar structures by TCEP treatment. Under this condition, the amyloid bundles are transformed into rings, which evolve to a new spherical microstructure. We showed that the chemical reduction of intermolecular S-S in internal amyloid sequences might favour the off-path intermediates of amyloid fibril growth, even when the fibrils are formed. Our findings demonstrated that in internal amyloid sequences, the formation of intermolecular S-S promotes the formation of amyloid type fibrils; meanwhile, its reduction stabilises non-fibrillar structures. Altogether, this work provides fundamental understanding at the molecular and supramolecular level, thus facilitating the rational design of therapeutic tools for protein aggregation diseases.

Spatially Separating the Conformers of a Dipeptide

Atomic-resolution-imaging approaches for single molecules, such as coherent X-ray diffraction at free-electron lasers, require the delivery of high-density beams of identical molecules. However, even very cold beams of biomolecules typically have multiple conformational states populated. We demonstrate the production of very cold (T_rot ≈2.3 K) molecular beams of intact dipeptide molecules, which were then spatially separated into the individual populated conformational states. This is achieved using the combination of supersonic expansion laser-desorption vaporization with electrostatic deflection in strong inhomogeneous fields. This represents the first demonstration of a conformer-separated and rotationally cold molecular beam of a peptide, which enables the investigation of conformer-specific chemistry using inherently non-conformer-specific techniques. It furthermore represents a milestone toward the direct structural imaging of individual biological molecules with atomic resolution by ultrafast diffractive-imaging methods.

Dimerization of the Benzyl Radical in a High-Temperature Pyrolysis Reactor Investigated by IR/UV Ion Dip Spectroscopy

We investigate the self-reaction of benzyl, C₇ H₇ , in a high-temperature pyrolysis reactor. The work is motivated by the observation that resonance-stabilized benzyl radicals can accumulate in reactive environments and contribute to the formation of polycyclic aromatic hydrocarbons (PAHs) and soot. Reaction products are detected by IR/UV ion dip spectroscopy, using infrared radiation from the free electron laser FELIX, and are identified by comparison with computed spectra. Among the reaction products identified by their IR absorption are several PAHs linked to toluene combustion such as bibenzyl, phenanthrene, diphenylmethane, and fluorene. The identification of 9,10-dihydrophenanthrene provides evidence for a mechanism of phenanthrene formation from bibenzyl that proceeds by initial cyclization rather than an initial hydrogen loss to stilbene.

On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins

The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.

The new competitive mechanism of hydrogen bonding interactions and transition process for the hydroxyphenyl imidazo [1, 2-a] pyridine in mixed liquid solution

The new competitive mechanism of intermolecular and intramolecular hydrogen bond can be proposed with an improved mixed model. Upon the photoinduced process, the twisting intramolecular charge transfer (TICT) structure of the hydroxyphenyl imidazo [1, 2-a] pyridine (HPIP) can be obtained. TICT character prompts the fluorescent inactivation via non-radiative decay process. For exploring the photochemical and photophysical properties, the electronic spectra and the infrared (IR) vibrational spectra of titled compounds have been detailedly investigated. In addition, the frontier molecular orbitals (MOs) analysis visually reveals that the unbalanced electron population can give rise to the torsion of molecular structure. To further give an attractive insight into the non-radiative decay process, the potential energy curves have been depicted on the ground state (S₀), the first excited state (S₁) and the triple excited state (T₁). Minimum energy crossing point (MECP) has been found in the S₁ and T₁ state. On the MECP, the intersystem crossing (ISC) might be dominant channel. The density functional theory (DFT) and the time-dependent density functional theory (TDDFT) methods have been throughout employed in the S₀ state, T₁ state and S₁ state, respectively. The theoretical results are consistent with experiment in mixed and PCM model.

Unifying the microscopic picture of His-containing turns: from gas phase model peptides to crystallized proteins

The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, is assessed by the comparison of protein structures with relevant isolated model peptides.

Mapping gas phase dipeptide motions in the far-infrared and terahertz domain

Vibrational signatures of Ac-Phe-AA-NH₂ dipeptides are recorded and analysed in the far IR/THz spectral domain (100–800 cm⁻¹, 3–24 THz), with the ‘AA’ amino acid chosen within the series ‘AA’ = Gly, Ala, Pro, Cys, Ser, Val. Phe stands for phenylalanine.

Fourier transform microwave spectroscopy of Ac-Ser-NH2: the role of side chain interactions in peptide folding

Serine capped dipeptide N-acetyl-l-serinamide (Ac-Ser-NH2) has been investigated using Fourier transform microwave spectroscopic techniques combined with laser ablation sources. Spectral signatures originating from one dominant species have been detected in the supersonic expansion. Rotational and nuclear quadrupole coupling constants of the two (14)N nuclei have been used in the characterization of a C/γ-turn structure, which is stabilized by a CO∙∙∙HN intramolecular hydrogen bond closing a seven-membered ring. Two extra hydrogen bonds involving the polar side chain (-CH2OH) further stabilize the structure. The non-observation of C5 species, attributed to the presence of the polar side chain, is in contrast with the previous gas phase observation of the related dipeptides containing glycine or alanine residues. The A-E splitting pattern arising from the internal rotation of the methyl group has been analyzed and the internal rotation barrier has been determined.

Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.

Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides

Gas phase conformer-selective IR spectroscopy combined and relevant quantum chemistry methods document the NH–π interactions in Phe residues.

Cβ–H stretching vibration as a new probe for conformation of n-propanol in gaseous and liquid states

The CH₂ symmetric stretching mode at the β-carbon position can be used as a new probe for the five conformations of n-propanol.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

Can far-IR action spectroscopy combined with BOMD simulations be conformation selective?

The combination of conformation selective far-IR/UV double resonance spectroscopy with Born–Oppenheimer molecular dynamics (BOMD) simulations is presented here for the structural characterization of the Ac-Phe-Pro-NH₂ peptide in the far-infrared spectral domain, i.e. for radiation below 800 cm⁻¹.

Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides

Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.