Toward detecting the formation of a single helical turn by 2D IR cross peaks between the amide-I and -II modes

Artificial Intelligence-based Amide-II Infrared Spectroscopy Simulation for Monitoring Protein Hydrogen Bonding Dynamics

The structurally sensitive amide II infrared (IR) bands of proteins provide valuable information about the hydrogen bonding of protein secondary structures, which is crucial for understanding protein dynamics and associated functions. However, deciphering protein structures from experimental amide II spectra relies on time-consuming quantum chemical calculations on tens of thousands of representative configurations in solvent water. Currently, the accurate simulation of amide II spectra for whole proteins remains a challenge. Here, we present a machine learning (ML)-based protocol designed to efficiently simulate the amide II IR spectra of various proteins with an accuracy comparable to experimental results. This protocol stands out as a cost-effective and efficient alternative for studying protein dynamics, including the identification of secondary structures and monitoring the dynamics of protein hydrogen bonding under different pH conditions and during protein folding process. Our method provides a valuable tool in the field of protein research, focusing on the study of dynamic properties of proteins, especially those related to hydrogen bonding, using amide II IR spectroscopy.

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

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

Distinct electrostatic frequency tuning rates for amide I and amide I' vibrations

Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D₂O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I' spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm^-1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I' data. We here analyze amide I and amide I' peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I' comparison. While we find an excellent linear correlation between amide I and amide I' peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H₂O/D₂O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear "map" for translating between amide I and amide I' frequencies.

Protein Dynamics by Two-Dimensional Infrared Spectroscopy

Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.

Computational Study of Helical and Helix-Hinge-Helix Conformations of an Anti-Microbial Peptide in Solution by Molecular Dynamics and Vibrational Analysis

Many classical antimicrobial peptides adopt an amphipathic helical structure at a water-membrane interface. Prior studies led to the hypothesis that a hinge near the middle of a helical peptide plays an important role in facilitating peptide-membrane interactions. Here, dynamics and vibrations of a designed hybrid antimicrobial peptide LM7-2 in solution were simulated to investigate its hinge formation. Molecular dynamics simulation results on the basis of the CHARMM36 force field showed that the α-helix LM7-2 bent around two or three residues near the middle of the peptide, stayed in a helix-hinge-helix conformation for a short period of time, and then returned to a helical conformation. High-resolution computational vibrational techniques were applied on the LM7-2 system when it has α-helical and helix-hinge-helix conformations to understand how this structural change affects its inherent vibrations. These studies concentrated on the calculation of frequencies that correspond to backbone amide bands I, II, and III: vibrational modes that are sensitive to changes in the secondary structure of peptides and proteins. To that end, Fourier transforms were applied to thermal fluctuations in C-N-H angles, C-N bond lengths, and C═O bond lengths of each amide group. In addition, instantaneous all-atom normal mode analysis was applied to monitor and detect the characteristic amide bands of each amide group within LM7-2 during the MD simulation. Computational vibrational results indicate that shapes and frequencies of amide bands II and especially III were altered only for amide groups near the hinge. These methods provide high-resolution vibrational information that can complement spectroscopic vibrational studies. They assist in interpreting spectra of similar systems and suggest a marker for the presence of the helix-hinge-helix motif. Moreover, radial distribution functions indicated an increase in the probability of hydrogen bonding between water and a hydrogen atom connected to nitrogen (HN) in such a hinge. The probability of intramolecular hydrogen bond formation between HN and an amide group oxygen atom within LM7-2 was lower around the hinge. No correlation has been found between the presence of a hinge and hydrogen bonds between amide group oxygen atoms and the hydrogen atoms of water molecules. This result suggests a mechanism for hinge formation wherein hydrogen bonds to oxygen atoms of water replace intramolecular hydrogen bonds as the peptide backbone folds.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala

Characterizing ensembles of intrinsically disordered proteins is experimentally challenging because of the ill-conditioned nature of ensemble determination with limited data and the intrinsic fast dynamics of the conformational ensemble. Amide I two-dimensional infrared (2D IR) spectroscopy has picosecond time resolution to freeze structural ensembles as needed for probing disordered-protein ensembles and conformational dynamics. Also, developments in amide I computational spectroscopy now allow a quantitative and direct prediction of amide I spectra based on conformational distributions drawn from molecular dynamics simulations, providing a route to ensemble refinement against experimental spectra. We performed a Bayesian ensemble refinement method on Ala-Ala-Ala against isotope-edited Fourier-transform infrared spectroscopy and 2D IR spectroscopy and tested potential factors affecting the quality of ensemble refinements. We found that isotope-edited 2D IR spectroscopy provides a stringent constraint on Ala-Ala-Ala conformations and returns consistent conformational ensembles with the dominant ppII conformer across varying prior distributions from many molecular dynamics force fields and water models. The dominant factor influencing ensemble refinements is the systematic frequency uncertainty from spectroscopic maps. However, the uncertainty of conformer populations can be significantly reduced by incorporating 2D IR spectra in addition to traditional Fourier-transform infrared spectra. Bayesian ensemble refinement against isotope-edited 2D IR spectroscopy thus provides a route to probe equilibrium-complex protein ensembles and potentially nonequilibrium conformational dynamics.

Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition

Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.

Simple Quantum Dynamics with Thermalization

In this paper, we introduce two simple quantum dynamics methods. One is based on the popular surface-hopping method, and the other is based on rescaling of the propagation on the bath ground-state potential surface. The first method is special, as it avoids specific feedback from the simulated quantum system to the bath and can be applied for precalculated classical trajectories. It is based on the equipartition theorem to determine if hops between different potential energy surfaces are allowed. By comparing with the formally exact Hierarchical Equations Of Motion approach for four model systems we find that the method generally approximates the quantum dynamics toward thermal equilibrium very well. The second method is based on rescaling of the nonadiabatic coupling and also neglect the effect of the state of the quantum system on the bath. By the nature of the approximations, they cannot reproduce the effect of bath relaxation following excitation. However, the methods are both computationally more tractable than the conventional fewest switches surface hopping, and we foresee that the methods will be powerful for simulations of quantum dynamics in systems with complex bath dynamics, where the system-bath coupling is not too strong compared to the thermal energy.

The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study

We present a joint experimental and computational study of the dynamic interactions of dialanine (Ala-Ala) with water, comparing the results of ultrafast 2D IR and infrared transient absorption spectroscopy of its amide I vibration with spectra modeled from molecular dynamics (MD) simulations. The experimental data are analyzed to describe vibrational frequency fluctuations, vibrational energy relaxation, and chemical exchange processes. The origin of these processes in the same underlying fluctuating forces allows a common description in terms of the fluctuations and conformational dynamics of the peptide and associated solvent. By comparing computational spectroscopy from MD simulations with multiple force fields and water models, we describe how the dynamics of water hydrogen bond fluctuations and switching processes act as a source of friction that governs the dephasing and vibrational relaxation, and provide a description of coupled water and peptide motions that give rise to spectroscopic exchange processes.

Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy

Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.

An alternative structural isoform in amyloid-like aggregates formed from thermally denatured human γD-crystallin

The eye lens protein γD-crystallin contributes to cataract formation in the lens. In vitro experiments show that γD-crystallin has a high propensity to form amyloid fibers when denatured, and that denaturation by acid or UV-B photodamage results in its C-terminal domain forming the β-sheet core of amyloid fibers. Here, we show that thermal denaturation results in sheet-like aggregates that contain cross-linked oligomers of the protein, according to transmission electron microscopy and SDS-PAGE. We use two-dimensional infrared spectroscopy to show that these aggregates have an amyloid-like secondary structure with extended β-sheets, and use isotope dilution experiments to show that each protein contributes approximately one β-strand to each β-sheet in the aggregates. Using segmental (13) C labeling, we show that the organization of the protein's two domains in thermally induced aggregates results in a previously unobserved structure in which both the N-terminal and C-terminal domains contribute to β-sheets. We propose a model for the structural organization of the aggregates and attribute the recruitment of the N-terminal domain into the fiber structure to intermolecular cross linking.

2D IR cross peaks reveal hydrogen-deuterium exchange with single residue specificity

A form of chemical exchange, hydrogen-deuterium exchange (HDX), has long been used as a method for studying the secondary and tertiary structure of peptides and proteins using mass spectrometry and NMR spectroscopy. Using two-dimensional infrared (2D IR) spectroscopy, we resolve cross peaks between the amide II band and a (13)C(18)O isotope-labeled amide I band, which we show measures HDX with site-specific resolution. By rapidly scanning 2D IR spectra using mid-IR pulse shaping, we monitor the kinetics of HDX exchange on-the-fly. For the antimicrobial peptide ovispirin bound to membrane bilayers, we find that the amide II peak decays with a biexponential with rate constants of 0.54 ± 0.02 and 0.12 ± 0.01 min(-1), which is a measure of the overall HDX in the peptide. The cross peaks between Ile-10-labeled ovispirin and the amide II mode, which specifically monitor HDX kinetics at Ile-10, decay with a single rate constant of 0.36 ± 0.1 min(-1). Comparing this exchange rate to theoretically determined exchange rates of Ile-10 for ovispirin in a solution random coil configuration, the exchange rate at Ile-10 is at least 100 times slower, consistent with the known α-helix structure of ovispirin in bilayers. Because backbone isotope labels produce only a very small shift of the amide II band, site-specific HDX cannot be measured with FTIR spectroscopy, which is why 2D IR spectroscopy is needed for these measurements.

Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment

The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm(-1) for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm(-1). These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.

Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.

Spectroscopic studies of protein folding: linear and nonlinear methods

Although protein folding is a simple outcome of the underlying thermodynamics, arriving at a quantitative and predictive understanding of how proteins fold nevertheless poses huge challenges. Therefore, both advanced experimental and computational methods are continuously being developed and refined to probe and reveal the atomistic details of protein folding dynamics and mechanisms. Herein, we provide a concise review of recent developments in spectroscopic studies of protein folding, with a focus on new triggering and probing methods. In particular, we describe several laser-based techniques for triggering protein folding/unfolding on the picosecond and/or nanosecond timescales and various linear and nonlinear spectroscopic techniques for interrogating protein conformations, conformational transitions, and dynamics.

Modeling the vibrational dynamics and nonlinear infrared spectra of coupled amide I and II modes in peptides

The amide vibrational modes play an important role in energy transport and relaxation in polypeptides and proteins and provide us with spectral markers for structure and structural dynamics of these macromolecules. Here, we present a detailed model to describe the dynamic properties of the amide I and amide II modes and the resulting linear and nonlinear spectra. These two modes have large oscillator strengths, and their mutual coupling plays an important role in their relaxation. Using first-principles calculations of NMA-d(7) and a dipeptide in a fluctuating bath described by molecular dynamics simulations, we model the frequencies of the local vibrations as well as the coupling between them. Both the coherent couplings and the fluctuations induced by contact with their environment are taken into account. We apply the resulting model of interacting fluctuating oscillators to study the collective vibrations and the partially coherent transport of vibrational energy through a model α-helix. We find that the instantaneous vibrations are delocalized over a few (up to four) amide units, while the coherences in the helix survive for 0.5-1 ps, leading to coherent transport on a similar time scale.

Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations

Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I' beta-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 degrees C, the fraction of population with a type I' turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides.