Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy

The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy

Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process has been a white whale for material scientists due to its potential in biomimetic applications, ranging from medical to microelectronic fields. Replicating diatom biosilicification will depend on a thorough understanding of the silaffin peptide structure during the reaction, yet existing models in the literature offer conflicting views on peptide folding during silicification. In our study, we employed two-dimensional infrared spectroscopy (2DIR) within the amide I region to determine the secondary structure of the silaffin repeat unit 5 (R5), both pre- and post-interaction with silica. The 2DIR experiments are complemented by molecular dynamics (MD) simulations of pure R5 reacting with silicate. Subsequently, theoretical 2DIR spectra calculated from these MD trajectories allowed us to compare calculated spectra with experimental data, and to determine the diverse structural poses of R5. Our findings indicate that unbound R5 predominantly forms β-strand structures alongside various atypical secondary structures. Post-silicification, there's a noticeable shift: a decrease in β-strands coupled with an increase in turn-type and bend-type configurations. We theorize that this structural transformation stems from silicate embedding within R5's hydrogen-bond network, prompting the peptide backbone to contract and adapt around the biosilica precursors.

Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions

Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.

Inconsistent hydrogen bond-mediated vibrational coupling of amide I

Using infrared spectroscopy and density functional theory (DFT) calculations, we scrutinized an amide (dimethylformamide) as a "model" compound to interpret the interactions of amide 1 with different phenol derivatives (para-chlorophenol (PCP) and para-cresol (CP)) as "model guest molecules". We established the involvement of amide I in vibrational coupling with symmetric and asymmetric C[double bond, length as m-dash]C modes of different phenolic derivatives and how their coupling was dependent upon different guest aromatic phenolic compounds. Interestingly, substitution of phenol perturbed the pattern of vibrational coupling with amide I. The symmetric and asymmetric C[double bond, length as m-dash]C modes of PC were coupled significantly with amide 1. For PCP, the symmetric C[double bond, length as m-dash]C mode coupled significantly, but the asymmetric mode coupled negligibly, with amide I. Here, we reveal the nature of vibrational coupling based on the structure of a guest molecule hydrogen-bonded with amide I. Our conclusions could be valuable for depiction of the unusual dynamics of coupled amide-I modes as well as the dependency of vibrational coupling on altered factors.

AIM: A Mapping Program for Infrared Spectroscopy of Proteins

Here, we present a new analysis program, AIM, that allows extracting the vibrational amide-I Hamiltonian using molecular dynamics trajectories for protein infrared spectroscopy modeling. The constructed Hamiltonians can be used as input for spectral calculations allowing the calculation of infrared absorption spectra, vibrational circular dichroism, and two-dimensional infrared spectra. These spectroscopies allow the study of the structure and dynamics of proteins. We will explain the essence of how AIM works and give examples of the information and spectra that can be obtained with the program using the Trypsin Inhibitor as an example. AIM is freely available from GitHub, and the package contains a demonstration allowing easy introduction to the use of the program.

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

Fabrication, characterization and cytocompatibility assessment of gelatin nanofibers coated with a polymer thin film by initiated chemical vapor deposition

The presence of various functional groups in the structure of gelatin nanofibers (GNFs) has made it a suitable candidate for biomedical applications, yet its fast dissolution in aqueous media has been a real challenge for years. In the present work, we propose an efficient procedure to improve the durability of the GNFs. The electrospun GNFs were coated with poly(ethylene glycol dimethacrylate) (pEGDMA) using initiated chemical vapor deposition (iCVD) as a completely dry polymerization method. Morphological and chemical analysis revealed that an ultrathin layer formed around nanofibers (iCVD-GNFs) which has covalently bonded to gelatin chains. Against the instant dissolution of GNFs, the in vitro biodegradability test showed the iCVD-GNFs, to a large extent, preserve their morphology after 14 days of immersion and did not lose its integrity even after 31 days. In vitro cell culture studies, also, revealed cytocompatibility of the iCVD-GNFs for human fibroblast cells (hFC), as well as higher cell proliferation on the iCVD-GNFs compared to control made from tissue culture plate (TCP). Furthermore, contact angle measurements indicated that the hydrophilic GNFs became hydrophobic after the iCVD, yet FE-SEM images of cell-seeded iCVD-GNFs showed satisfactory cell adhesion. Taken together, the proposed method paves a promising way for the production of water-resistant GNFs utilized in biomedical applications; for instance, tissue engineering scaffolds and wound dressings.

Temperature-Induced Collapse of Elastin-like Peptides Studied by 2DIR Spectroscopy

Elastin-like peptides are hydrophobic biopolymers that exhibit a reversible coacervation transition when the temperature is raised above a critical point. Here, we use a combination of linear infrared spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations to study the structural dynamics of two elastin-like peptides. Specifically, we investigate the effect of the solvent environment and temperature on the structural dynamics of a short (5-residue) elastin-like peptide and of a long (450-residue) elastin-like peptide. We identify two vibrational energy transfer processes that take place within the amide I' band of both peptides. We observe that the rate constant of one of the exchange processes is strongly dependent on the solvent environment and argue that the coacervation transition is accompanied by a desolvation of the peptide backbone where up to 75% of the water molecules are displaced. We also study the spectral diffusion dynamics of the valine(1) residue that is present in both peptides. We find that these dynamics are relatively slow and indicative of an amide group that is shielded from the solvent. We conclude that the coacervation transition of elastin-like peptides is probably not associated with a conformational change involving this residue.

Site-specific detection of protein secondary structure using 2D IR dihedral indexing: a proposed assembly mechanism of oligomeric hIAPP

Human islet amyloid polypeptide (hIAPP) aggregates into fibrils through oligomers that have been postulated to contain α-helices as well as β-sheets. We employ a site-specific isotope labeling strategy that is capable of detecting changes in dihedral angles when used in conjunction with 2D IR spectroscopy. The method is analogous to the chemical shift index used in NMR spectroscopy for assigning protein secondary structure. We introduce isotope labels at two neighbouring residues, which results in an increased intensity and positive frequency shift if those residues are α-helical versus a negative frequency shift in β-sheets and turns. The 2D IR dihedral index approach is demonstrated for hIAPP in micelles for which the polypeptide structure is known, using pairs of 13C18O isotope labels L12A13 and L16V17, along with single labeled control experiments. Applying the approach to aggregation experiments performed in buffer, we show that about 27-38% of hIAPP peptides adopt an α-helix secondary structure in the monomeric state at L12A13, prior to aggregation, but not at L16V17 residues. At L16V17, the kinetics are described solely by the monomer and fiber conformations, but at L12A13 the kinetics exhibit a third state that is created by an oligomeric intermediate. Control experiments performed with a single isotope label at A13 exhibit two-state kinetics, indicating that a previously unknown change in dihedral angle occurs at L12A13 as hIAPP transitions from the intermediate to fiber structures. We propose a mechanism for aggregation, in which helices seed oligomer formation via structures analogous to leucine rich repeat proteins.

Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide

Intrinsically disordered proteins play an important role in biology, and unraveling their labile structure presents a vital challenge. However, the dynamical structure of such proteins thwarts their study by standard techniques such as X-ray diffraction and NMR spectroscopy. Here, we use a neat liquid composed of N-methylacetamide molecules as a model system to elucidate dynamical and structural properties similar to those one can expect to see in intrinsically disordered proteins. To examine the structural dynamics in the neat liquid, we combine molecular dynamics, response-function-based spectral simulations, and two-dimensional polarization-resolved infrared spectroscopy in the amide I (CO stretch) region. The two-dimensional spectra reveal a delicate interplay between hydrogen bonding and intermolecular vibrational coupling effects, observed through a fast anisotropy decay. The present study constitutes a general platform for understanding the structure and dynamics of highly disordered proteins.

Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.

A new interpretation of the meaning of the center of line slope from a two-dimensional infrared spectrum

This article presents a new approximation to understand the connection between the center of line slope from a single peak of a two-dimensional (2D) infrared spectrum and the frequency-frequency correlation function. This approximation which goes beyond the short-time approximation includes explicitly pure dephasing mechanisms by introducing a time parameter that separates the fast fluctuations and slow fluctuations. While in the short-time approximation, the center of line slope is given by the normalized frequency fluctuations auto-correlation function, I show using this new approximation that the center of line slope measures on long time scales a shifted and scaled correlation function. The results present a new interpretation of the meaning of the center of line slope that allows for a better understanding of what 2D experiments can measure. To illustrate these findings, I compare this approximation with the short-time approximation for several examples of frequency-frequency correlation functions. I also give an estimate of the value of the time separation parameter for a correlation function with a simple exponential decay.

Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins

In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.

Two-Dimensional Vibrational Spectroscopy of a Dissipative System with the Optimized Mean-Trajectory Approximation

The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions representing radiation-matter interactions. Here we apply this method to an anharmonic chromophore coupled to a harmonic bath. A forward-backward trajectory implementation of the OMT method is described that addresses the numerical challenges of applying the OMT to large systems with disparate frequency scales. The OMT is shown to well reproduce line shapes and waiting time dynamics in the pure dephasing limit of weak coupling to an off-resonant bath. The OMT is also shown to describe a case where energy transfer is the predominant source of line broadening.

Vibrational coherence and energy transfer in two-dimensional spectra with the optimized mean-trajectory approximation

The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions that represent radiation-matter interactions. Here, we extend the OMT to include additional vibrational coherence and energy transfer processes. This generalized approximation is applied to a pair of anharmonic chromophores coupled to a bath. The resulting 2D spectra are shown to reflect coherence transfer between normal modes.

Linear absorption and two-dimensional infrared spectra of N-methylacetamide in chloroform revisited: polarizability and multipole effects

The effect of solvent polarizability and multipole effects on the amide I vibrational spectra of a peptide unit is investigated. Four molecular dynamics force fields of increasing complexity for the solvent are used to model both the linear absorption and two-dimensional infrared spectra. It is observed that, at least in chloroform solution, the predicted solvent shift is considerably improved when accounting for the polarizabiltiy and multipole effects. The latter are typically connected with halogen bonding. Significant deviations are still observed for more sensitive line shape parameters such as the spectral width and line skewness. However, the findings demonstrate that previously observed deviations have an origin in the force field treatment rather than in the electrostatic mapping procedure frequently employed to simulate linear absorption and two-dimensional infrared spectroscopy.

How quickly can a β-hairpin fold from its transition state?

Understanding the structural nature of the free energy bottleneck(s) encountered in protein folding is essential to elucidating the underlying dynamics and mechanism. For this reason, several techniques, including Φ-value analysis, have previously been developed to infer the structural characteristics of such high free-energy or transition states. Herein we propose that one (or few) appropriately placed backbone and/or side chain cross-linkers, such as disulfides, could be used to populate a thermodynamically accessible conformational state that mimics the folding transition state. Specifically, we test this hypothesis on a model β-hairpin, Trpzip4, as its folding mechanism has been extensively studied and is well understood. Our results show that cross-linking the two β-strands near the turn region increases the folding rate by an order of magnitude, to about (500 ns)⁻¹, whereas cross-linking the termini results in a hyperstable β-hairpin that has essentially the same folding rate as the uncross-linked peptide. Taken together, these findings suggest that cross-linking is not only a useful strategy to manipulate folding free energy barriers, as shown in other studies, but also, in some cases, it can be used to stabilize a folding transition state analogue and allow for direct assessment of the folding process on the downhill side of the free energy barrier. The calculated free energy landscape of the cross-linked Trpzip4 also supports this picture. An empirical analysis further suggests, when folding of β-hairpins does not involve a significant free energy barrier, the folding time (τ) follows a power law dependence on the number of hydrogen bonds to be formed (n_H), namely, τ = τ₀n_H^α, with τ₀ = 20 ns and α = 2.3.

Aggregation gatekeeper and controlled assembly of Trpzip β-hairpins

Protein and peptide aggregation is an important issue both in vivo and in vitro. Herein, we examine the aggregation behaviors of two well-studied β-hairpins, Trpzip1 and Trpzip2. Previous studies suggested that Trpzip2 remains monomeric up to a concentration of ~15 mM whereas Trpzip1 readily aggregates at micromolar concentrations at acidic or neutral pH. This disparity is puzzling considering that these two peptides differ only in their turn sequences (i.e., GN vs NG). We hypothesize that these peptides can aggregate from their folded states via native edge-to-edge interactions and that the Lys8 residue in Trpzip2 is a more effective aggregation gatekeeper, because of a more favorable orientation. In support of this hypothesis, we find that increasing the pH to 13 or replacing Lys8 with a hydrophobic and photolabile Lys analogue, Lys(nvoc), leads to a significant increase in the aggregation propensity of Trpzip2, and that the aggregation of this Trpzip2 mutant can be reversed upon restoring the native Lys side chain via photocleavage of the nvoc moiety. In addition, we find that while both Trpzip1 and Trpzip2 form parallel β-sheet aggregates, the Lys(nvoc) Trpzip2 mutant forms antiparallel β-sheets and more stable fibrils. Taken together, these findings provide another example showing how sensitive peptide and protein aggregation is to minor sequence variation and that it is possible to use a photolabile non-natural amino acid, such as Lys(nvoc), to tune the rate of peptide aggregation and to control fibrillar structure.

Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study

We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.

Molecular mechanics force field-based general map for the solvation effect on amide I probe of peptide in different micro-environments

A general electrostatic potential map based on molecular mechanics force field for modeling the amide I frequency is presented. This map is applied to N-methylacetamide (NMA) and designed to be transferable in different micro-environments. The electrostatic potentials from solvent and peptide side chain are projected on the amide unit of NMA to induce the frequency shift of amide I mode. It is shown that the predicted amide I frequency reproduces the experimental data satisfactorily, especially when NMA in polar solvents. The amide I frequency shift is largely determined by the solvents in aqueous solution while it is dominated by the local structure of peptide in other solvent environments. The map parameters are further applied on NMA-MeOH system and the obtained IR spectra show doublet peak profile with negligible deviation from the experimental data, suggesting the usefulness of this general map for providing information about vibrational parameters of amide motions of peptide in different environments.

Amide-I characteristics of helical β-peptides by linear infrared measurement and computations

In this work, we have examined the amide-I characteristics of three β-peptide oligomers in typical helical conformations (two in 14-helix and one in 12/10-helix), solvated in water, methanol, and chloroform, respectively. Local-mode frequencies and their distributions were computed using a molecular-mechanics force field based frequency map that was constructed on the basis of molecular dynamics simulations. The local-mode frequencies were found to be determined primarily by peptide backbone and side chain, rather by solvent, suggesting their local structural sensitivities. Intermode vibrational couplings computed using a transition dipole scheme were found to be very sensitive to peptide conformation, with their signs and magnitudes varying periodically along the peptide chain. Linear infrared absorption spectra of the three peptides, simulated using a frequency-frequency time-correlation function method, were found to be in fair agreement with experimental results. Normalized potential energy distribution analysis indicated that the amide-I mode can delocalize over a few amide units. However, the IR band structure appears to be more sophisticated in helical β-peptides than in helical α-peptides.

Two-dimensional spectroscopy of coupled vibrations with the optimized mean-trajectory approximation

The optimized mean-trajectory (OMT) approximation is a semiclassical representation of the nonlinear vibrational response function used to compute multidimensional infrared spectra. In this method, response functions are calculated from a sequence of classical trajectories linked by discontinuities representing the effects of radiation-matter interactions, thus providing an approximation to quantum dynamics using classical inputs. This approach was previously formulated and assessed numerically for a single anharmonic degree of freedom. Our previous work is generalized here in two respects. First, the derivation of the OMT is extended to any number of coupled anharmonic vibrations by determining semiclassical approximations for pairs of double-sided Feynman diagrams. Second, an efficient numerical procedure is developed for calculating two-dimensional infrared spectra of coupled anharmonic vibrations in the OMT approximation. The OMT approximation is shown to reproduce the fundamental features of the quantum response function including both coherence and population dynamics.

Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy

Protein folding is one of the most fundamental problems in modern molecular biology. Uncovering the detailed folding mechanism requires methods that can monitor the structures at high temporal and spatial resolution. Two-dimensional infrared (2DIR) spectroscopy is a new tool for studying protein structures and dynamics with high time resolution. Using atomistic molecular dynamics simulations, we illustrate the folding process of Trp-cage along the dominant pathway on the free energy landscape by analyzing nonchiral and chiral coherent 2DIR spectra along the pathway. Isotope labeling is used to reveal residue-specific information. We show that the high resolution structural sensitivity of 2DIR can differentiate the ensemble evolution of protein and thus provides a microscopic picture of the folding process.

An optimized semiclassical approximation for vibrational response functions

The observables of multidimensional infrared spectroscopy may be calculated from nonlinear vibrational response functions. Fully quantum dynamical calculations of vibrational response functions are generally impractical, while completely classical calculations are qualitatively incorrect at long times. These challenges motivate the development of semiclassical approximations to quantum mechanics, which use classical mechanical information to reconstruct quantum effects. The mean-trajectory (MT) approximation is a semiclassical approach to quantum vibrational response functions employing classical trajectories linked by deterministic transitions representing the effects of the radiation-matter interaction. Previous application of the MT approximation to the third-order response function R(3)(t3, t2, t1) demonstrated that the method quantitatively describes the coherence dynamics of the t3 and t1 evolution times, but is qualitatively incorrect for the waiting-time t2 period. Here we develop an optimized version of the MT approximation by elucidating the connection between this semiclassical approach and the double-sided Feynman diagrams (2FD) that represent the quantum response. Establishing the direct connection between 2FD and semiclassical paths motivates a systematic derivation of an optimized MT approximation (OMT). The OMT uses classical mechanical inputs to accurately reproduce quantum dynamics associated with all three propagation times of the third-order vibrational response function.

Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy

We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR spectroscopy. The amide I' vibrations of three Trpzip2 isotopologues are used as a local probe of the midstrand contacts, β-turn, and overall β-sheet content. Our experiments distinguish between a folded state with a type I' β-turn and a misfolded state with a bulged turn, providing evidence for distinct conformations of the peptide backbone. Transient 2D IR spectroscopy at 45 °C following a laser temperature jump tracks the nanosecond and microsecond kinetics of unfolding and the exchange between conformers. Hydrogen bonds to the peptide backbone are loosened rapidly compared with the 5-ns temperature jump. Subsequently, all relaxation kinetics are characterized by an observed 1.2 ± 0.2-μs exponential. Our time-dependent 2D IR spectra are explained in terms of folding of either native or nonnative contacts from a common compact disordered state. Conversion from the disordered state to the folded state is consistent with a zip-out folding mechanism.

Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation

Vibrationally resolved fluorescence spectra of the β-hairpin trpzip2 peptide at two temperatures as well as during a T-jump unfolding process are simulated on the basis of a combination of Markov state models and quantum chemistry schemes. The broad asymmetric spectral line shape feature is reproduced by considering the exciton-phonon couplings. The temperature dependent red shift observed in the experiment has been attributed to the state population changes of specific chromophores. Through further theoretical study, it is found that both the environment's electric field and the chromophores' geometry distortions are responsible for tryptophan fluorescence shift.

Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding

Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.

Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations

The infrared optical response of amyloid fibrils Aβ(1-40) is investigated. Simulations of two models corresponding to different protonation states are compared with experiment. The simulations reveal that vibrational frequency distributions inside the fibrils are dominated by side chain fluctuations. We further confirm earlier suggestions based on 2D-IR measurements that water molecules can be trapped inside the fibrils.

2DIR spectroscopy of human amylin fibrils reflects stable β-sheet structure

The aggregation of human amylin to form amyloid contributes to islet β-cell dysfunction in type 2 diabetes. Studies of amyloid formation have been hindered by the low structural resolution or relatively modest time resolution of standard methods. Two-dimensional infrared (2DIR) spectroscopy, with its sensitivity to protein secondary structures and its intrinsic fast time resolution, is capable of capturing structural changes during the aggregation process. Moreover, isotope labeling enables the measurement of residue-specific information. The diagonal line widths of 2DIR spectra contain information about dynamics and structural heterogeneity of the system. We illustrate the power of a combined atomistic molecular dynamics simulation and theoretical and experimental 2DIR approach by analyzing the variation in diagonal line widths of individual amide I modes in a series of labeled samples of amylin amyloid fibrils. The theoretical and experimental 2DIR line widths suggest a "W" pattern, as a function of residue number. We show that large line widths result from substantial structural disorder and that this pattern is indicative of the stable secondary structure of the two β-sheet regions. This work provides a protocol for bridging MD simulation and 2DIR experiments for future aggregation studies.

Development and validation of transferable amide I vibrational frequency maps for peptides

Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.

Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach

We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and two-dimensional IR (2DIR) spectra based on the Markov state model (MSM) and nonlinear exciton propagation (NEP) methods. MSMs partition the conformation space into a set of nonoverlapping metastable states, and we can calculate spectra signal for each of these states using the NEP method. Thus the overall spectroscopic observable for a given system is simply the sum of spectra of different metastable states weighted by their populations. We show that results from MSMs constructed from a large number of simulations have a much better agreement with the equilibrium experimental 2DIR spectra compared to that generated from straightforward MD simulations starting from the folded state. This indicates that a sufficient sampling of important relevant conformational states is critical for calculating the accurate spectroscopic observables. MSMs are also capable of simulating the unfolding relaxation dynamics upon the temperature jump. The agreement of the simulation using MSMs and NEP with the experiment not only provides a justification for our protocol, but also provides the physical insight of the underlying spectroscopic observables. The protocol we developed has the potential to be extended to simulate a wide range of fast triggering plus optical detection experiments for biomolecules.

Molecular theory and simulation of coherence transfer in metal carbonyls and its signature on multidimensional infrared spectra

We present a general and comprehensive theoretical and computational framework for modeling ultrafast multidimensional infrared spectra of a vibrational excitonic system in liquid solution. Within this framework, we describe the dynamics of the system in terms of a quantum master equation that can account for population relaxation, dephasing, coherence-to-coherence transfer, and coherence-to-population transfer. A unique feature of our approach is that, in principle, it does not rely on any adjustable fitting parameters. More specifically, the anharmonic vibrational Hamiltonian is derived from ab initio electronic structure theory, and the system-bath coupling is expressed explicitly in terms of liquid degrees of freedom whose dynamics can be obtained via molecular dynamics simulations. The applicability of the new approach is demonstrated by employing it to model the recently observed signatures of coherence transfer in the two-dimensional spectra of dimanganese decacarbonyl in liquid cyclohexane. The results agree well with experiment and shed new light on the nature of the molecular interactions and dynamics underlying the spectra and the interplay between dark and bright states, their level of degeneracy, and the nature of their interactions with the solvent.

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.