Photothermal studies of pH induced unfolding of apomyoglobin

Folding Kinetics and Volume Variation of the β-Hairpin Peptide Chignolin upon Ultrafast pH-Jumps

In-depth characterization of fundamental folding steps of small model peptides is crucial for a better understanding of the folding mechanisms of more complex biomacromolecules. We have previously reported on the folding/unfolding kinetics of a model α-helix. Here, we study folding transitions in chignolin (GYDPETGTWG), a short β-hairpin peptide previously used as a model to study conformational changes in β-sheet proteins. Although previously suggested, until now, the role of the Tyr2-Trp9 interaction in the folding mechanism of chignolin was not clear. In the present work, pH-dependent conformational changes of chignolin were characterized by circular dichroism (CD), nuclear magnetic resonance (NMR), ultrafast pH-jump coupled with time-resolved photoacoustic calorimetry (TR-PAC), and molecular dynamics (MD) simulations. Taken together, our results present a comprehensive view of chignolin's folding kinetics upon local pH changes and the role of the Tyr2-Trp9 interaction in the folding process. CD data show that chignolin's β-hairpin formation displays a pH-dependent skew bell-shaped curve, with a maximum close to pH 6, and a large decrease in β-sheet content at alkaline pH. The β-hairpin structure is mainly stabilized by aromatic interactions between Tyr2 and Trp9 and CH-π interactions between Tyr2 and Pro4. Unfolding of chignolin at high pH demonstrates that protonation of Tyr2 is essential for the stability of the β-hairpin. Refolding studies were triggered by laser-induced pH-jumps and detected by TR-PAC. The refolding of chignolin from high pH, mainly due to the protonation of Tyr2, is characterized by a volume expansion (10.4 mL mol-1), independent of peptide concentration, in the microsecond time range (lifetime of 1.15 μs). At high pH, the presence of the deprotonated hydroxyl (tyrosinate) hinders the formation of the aromatic interaction between Tyr2 and Trp9 resulting in a more disorganized and dynamic tridimensional structure of the peptide. This was also confirmed by comparing MD simulations of chignolin under conditions mimicking neutral and high pH.

Role of Ultrafast Internal Conversion and Intersystem Crossing in the Nonadiabatic Relaxation Dynamics of ortho-Nitrobenzaldehyde

ortho-Nitrobenzaldehyde (oNBA) is a well-known photoactivated acid and a prototypical photolabile nitro-aromatic compound. Despite extensive investigations, the ultrafast relaxation dynamics of oNBA is still not properly understood, especially concerning the role of the triplet states. In this work, we provide an in-depth picture of this dynamics by combining single- and multireference electronic structure methods with potential energy surface exploration and nonadiabatic dynamics simulations using the Surface Hopping including ARbitary Couplings (SHARC) approach. Our results reveal that the initial decay from the bright ππ* state to the S₁ minimum is barrierless. It involves three changes in electronic structure from ππ* (ring) to nπ* (nitro group), to nπ* (aldehyde group), and then to another nπ* (nitro group). The decay of the ππ* takes 60-80 fs and can be tracked with time-resolved luminescence spectroscopy, where we predict for the first time a short-lived coherence of the luminescence energy with a 25 fs period. Intersystem crossing can occur already during the S₄ → S₁ deactivation cascade but also from S₁, with a time constant of about 2.4 ps and such that first a triplet ππ* state localized on the nitro group is populated. The triplet population first evolves into an nπ* and then quickly undergoes hydrogen transfer to form a biradical intermediate, from where the ketene is eventually produced. The majority of the excited population decays from S₁ through two conical intersections of equal utilization, a previously unreported one involving a scissoring motion of the nitro group that leads back to the oNBA ground state and the one involving hydrogen transfer that leads to the ketene intermediate.

Excited states of ortho-nitrobenzaldehyde as a challenging case for single- and multi-reference electronic structure theory

We present a large set of vertical excitation calculations for the ortho-nitrobenzaldehyde (oNBA) molecule, which exhibits a very challenging excited-state electronic structure like other nitroaromatic compounds. The single-reference methods produce mostly consistent results up to about 5.5 eV. By contrast, the CAS second-order perturbation theory (CASPT2) results depend sensitively on the employed parameters. At the CAS self-consistent field level, the energies of the bright ππ * $$ {\pi \pi}^{\ast } $$ states are strongly overestimated while doubly excited states appear too low and mix with these ππ * $$ {\pi \pi}^{\ast } $$ states. This mixing hampers the CASPT2 step, leading to inconsistent results. Only by increasing the number of states in the state-averaging step to about 40-to cover all bright ππ * $$ {\pi \pi}^{\ast } $$ states embedded in the double excitations-and employing extended multistate CASPT2 could CASPT2 results consistent with experiment be obtained. We assign the four bands in the molecule's spectrum: The weakest band at 3.7 eV arises from the n NO 2 π * $$ {n}_{\mathrm{NO}2}{\pi}^{\ast } $$ states, the second one at 4.4 eV from the ππ * $$ {\pi \pi}^{\ast } $$ ( L b $$ {L}_b $$ ) state, the shoulder at 5.2 eV from the ππ * $$ {\pi \pi}^{\ast } $$ ( L a $$ {L}_a $$ ) state, and the maximum at 5.7 eV from the ππ * $$ {\pi \pi}^{\ast } $$ ( B a / B b $$ {B}_a/{B}_b $$ ) states. We also highlight the importance of modern wave function analysis techniques in elucidating the absorption spectrum of challenging molecules.

Ultrafast pH-jump two-dimensional infrared spectroscopy

We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.

One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics

The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. ¹H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol^-1, 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol^-1, ∼1.7 μs). The essential role of two discrete side chain interactions, a salt bridge, and in particular a single cation-π interaction in the folding dynamics of a naturally occurring α-helix peptide is uniquely revealed by these data.

Time resolved thermodynamics associated with ligand photorelease in heme peroxidases and globins: Open access channels versus gated ligand release

Heme proteins represent a diverse class of biomolecules responsible for an extremely diverse array of physiological functions including electron transport, monooxygenation, ligand transport and storage, cellular signaling, respiration, etc. An intriguing aspect of these proteins is that such functional diversity is accomplished using a single type of heme macrocycle based upon iron protoporphyrin IX. The functional diversity originates from a delicate balance of inter-molecular interactions within the protein matrix together with well choreographed dynamics that modulate the heme electronic structure as well as ligand entry/exit pathways from the bulk solvent to the active site. Of particular interest are the dynamics and energetics associated with the entry/exit of ligands as this process plays a significant role in regulating the rates of heme protein activity. Time-resolved photoacoustic calorimetry (PAC) has emerged as a powerful tool through which to probe the underlying energetics associated with small molecule dissociation and release to the bulk solvent in heme proteins on time scales from tens of nanoseconds to several microseconds. In this review, the results of PAC studies on various classes of heme proteins are summarized highlighting how different protein structures affect the thermodynamics of ligand migration. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

Spectroscopic study on acid-induced unfolding and refolding of apo-neuroglobin

pH-induced unfolding and refolding of apo-neuroglobin (apo-Ngb) were investigated by UV, fluorescence, circular dichroism (CD) spectra and light scattering measurements. Results revealed that apo-Ngb became partially unfolded at around pH 5.0, with evidences from a red shift in the fluorescence spectra, a decrease in the far-UV CD and a sharp peak in the light scattering intensity. Further lowering of the pH reversed these effects, suggesting that apo-Ngb folds back to a compact state. At pH 2.0, the apo-Ngb forms a folding intermediate known as molten globule (MG), which is possessed of native-like secondary structure and almost complete loss of tertiary structure. Based on these results, the acid-induced denaturation pathway of apo-Ngb can be illustrated from the native state (N), via a partially unfolded state (U(A)) to the molten globule state (MG).

Acid-induced unfolding of myoglobin triggered by a laser pH jump method

Using 1-(2-nitrophenyl)ethyl sulfate (caged sulfate) as a photoactivatable caged proton, we could induce complete acid unfolding of myoglobin with a single nanosecond laser pulse. This was possible because of the high ( approximately mM) concentration of protons released by the photolabile compound. The ability of the compound to produce a large pH jump arises because the other photoproducts (2-nitrosoacetophenone and sulfate ion) do not buffer the released protons. The complete time course of the unfolding kinetics, spanning a range from milliseconds to several seconds, could be accurately reproduced by monitoring absorbance changes in the visible spectrum at 633 nm.

Effects of Turn Stability on the Kinetics of Refolding of a Hairpin in a β-sheet

As part of our continuing study of the effects of the turn sequence on the conformational stability as well as the mechanism of folding of a beta-sheet structure, we have undertaken a parallel investigation of the solution structure, conformational stability, and kinetics of refolding of the beta-sheet VFIVDGOTYTEV(D)PGOKILQ. The latter peptide is an analogue of the original Gellman beta-sheet VFITS(D)PGKTYTEV(D)PGOKILQ, wherein the TS(D)PGK turn sequence in the first hairpin has been replaced by VDGO. Thermodynamics studies revealed comparable conformational stability of the two peptides. However, unlike the Gellman peptide, which showed extremely rapid refolding of the first hairpin, early kinetic events associated with the refolding of the corresponding hairpin in the VDGO mutant were found to be significantly slower. A detailed study of the conformation of the modified peptide suggested that hydrophobic interactions might be contributing to its stability. Accordingly, we surmise that the early kinetic events are sensitive to whether the formation of the hairpin is nucleated at the turn or by sequestering of the hydrophobic residues across the strand, before structural rearrangements to produce the nativelike topology. Nucleation of the hairpin at the turn is expected to be intrinsically rapid for a strong turn. However, if the process must involve collapse of hydrophobic side chains, the nucleation should be slower as solvent molecules must be displaced to sequester the hydrophobic residues. These findings reflect the contribution of different forces toward nucleation of hairpins in the mechanism of folding of beta-sheets.