Reaction volume of water formation detected by time-resolved photoacoustics: photoinduced proton transfer between o-nitrobenzaldehyde and hydroxyls in water

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.

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.

Synthesis and self-assembly of photoacid-containing block copolymers based on 1-naphthol

Photoacids experience a strong increase in acidity when absorbing light and, hence, can be considered as molecular switches. The incorporation into amphiphilic block copolymers leads to novel stimuli-responsive materials with great potential.

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.

Structures of the kinetically trapped i-motif DNA intermediates

In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast + ΔHslow = 43 ± 7 kcal mol-1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = ±3 to ±5) at low pH conditions. As solution pH increases, the cytosine neutralization leads to the loss of cytosine-cytosine+ (C·CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = -6 to -9). Collisional induced activation prior to TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = -6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = -7 and z = -8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.

Molten Globule Formation in Apomyoglobin Monitored by the Fluorescent Probe Nile Red

The interaction of nile red (NR) with apomyoglobin (ApoMb) in the native (pH 7) and molten globule (pH 4) states was investigated using experimental and computational methods. NR binds to hydrophobic locations in ApoMb with higher affinity (K(d) = 25 +/- 5 microM) in the native state than in the molten globule state (K(d) = 52 +/- 5 microM). In the molten globule state, NR is located in a more hydrophobic environment. The dye does not bind to the holoprotein, suggesting that the binding site is located at the heme pocket. In addition to monitoring steady-state properties, the fluorescence emission of NR is capable of tracking submillisecond, time-resolved structural rearrangements of the protein, induced by a nanosecond pH jump. Molecular dynamics simulations were run on ApoMb at neutral pH and at pH 4. The structure obtained for the molten globule state is consistent with the experimentally available structural data. The docking of NR with the crystal structure shows that the ligand binds into the binding pocket of the heme group, with an orientation bringing the planar ring system of NR to overlap with the position of two of the heme porphyrin rings in Mb. The docking of NR with the ApoMb structure at pH 4 shows that the dye binds to the heme pocket with a slightly less favorable binding energy, in keeping with the experimental K(d) value. Under these conditions, NR is positioned in a different orientation, reaching a more hydrophobic environment in agreement with the spectroscopic data.

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.

Kinetics of proton release after flash photolysis of 1-(2-nitrophenyl)ethyl sulfate (caged sulfate) in aqueous solution

The kinetics of proton release after laser photolysis of 1-(2-nitrophenyl)ethyl sulfate (caged sulfate) have been characterized by time-resolved absorbance and photoacoustic methods. The absorbance at approximately 400 nm is observed to rise with a biphasic behavior in which a prompt component (formation of the nitronic acid) is followed by a slower (tau approximately 63 +/- 6 ns) phase (deprotonation of the nitronic acid). The decay of this intermediate occurs with a lifetime which is affected by the pH of the solution and the laser pulse energy. In buffered aqueous solution at pH 7, 20 degrees C the aci-nitro decay rate is 18 +/- 4 s(-1). Protons are released to the solution with rate (1.58 +/- 0.09) x 10(7) s(-1) at neutral pH from the nitronic acid intermediate. From the numerical analysis of the protonation kinetics of suitable pH indicators, we could estimate the pK(a) of the nitronic acid as 3.69 +/- 0.05. At acidic pH, a substantial fraction of the aci-nitro intermediate is in the protonated form and this leads to a biphasic release of protons, with the slower phase being characterized by an apparent rate constant strongly dependent on the pH. The strongly acidic character of the final photoproduct (sulfate ion) means that there is negligible buffering of photoreleased protons.

Kinetics of Acid-Induced Spectral Changes in the GFPmut2 Chromophore

We have used a nanosecond pH-jump technique, coupled with simultaneous transient absorption and fluorescence emission detection, to characterize the dynamics of the acid-induced spectral changes in the GFPmut2 chromophore. Disappearance of the absorbance at 488 nm and the green fluorescence emission occurs with a thermally activated, double exponential relaxation. To understand the source of the two transients we have introduced mutations in amino acid residues that interact with the chromophore (H148G, T203V, and E222Q). Results indicate that the faster transient is associated with proton binding from the solution, while the second process, smaller in amplitude, is attributed to structural rearrangement of the amino acids surrounding the chromophore. The protonation rate shows a 3-fold increase for the H148G mutant, demonstrating that His148 plays a key role in protecting the chromophore from the solvent. The deprotonation rate for T203V is an order of magnitude smaller, showing that the hydrogen bond with the hydroxyl of Thr203 is important in stabilizing the deprotonated form of the chromophore. A kinetic model suggests that, in addition to protecting the chromophore from the solvent, His148 may act as the primary acceptor for the protons on the way to the chromophore.

Time-resolved photothermal methods: accessing time-resolved thermodynamics of photoinduced processes in chemistry and biology

Photothermal methods are currently being employed in a variety of research areas, ranging from materials science to environmental monitoring. Despite the common term which they are collected under, the implementations of these techniques are as diverse as the fields of application. In this review, we concentrate on the recent applications of time-resolved methods in photochemistry and photobiology.

Deprotonation yields, pKa, and aci-nitro decay rates in some substituted o-nitrobenzaldehydes

In this paper we report the deprotonation yields, the pKa, and decay kinetics of the aci-nitro intermediates of some substituted 2-nitrobenzaldehydes that can be used as photoactivatable caged proton compounds. The decay of the aci-nitro absorbance for 2-nitrobenzaldehyde occurs within a few nanoseconds from photoexcitation. Addition of electron donating methoxy substituents at positions 4 and 5 leads to lower deprotonation yields, higher pKa, and slower decays of the aci-nitro intermediates. On the contrary, the decay rate is accelerated by the introduction of an electron-withdrawing Cl atom at position 4 in the phenyl ring, with little influence on the deprotonation yield and pKa of the aci-nitro intermediate.

Two-photon photoacoustic calorimetry and the absolute measurement of molar absorption coefficients of transient species in solution

The theory of two-photon photoacoustic calorimetry (PAC) is developed for the case of a homogeneously irradiated volume and it is shown that the laser-intensity dependence of the photoacoustic signals can be used to determine the molar absorption coefficient of transient species. The application of the method is illustrated via the measurement of the absorption coefficients of benzophenone and acetophenone triplets using a front-face PAC cell. The very high sensitivity exhibited by this cell strongly recommends the inclusion of laser-intensity dependence studies in the procedure for measuring heat depositions. Only extrapolation to zero laser intensity can afford reliable enthalpies of formation for very short-lived species.

Photoreaction of caged ATP studied by the time-resolved transient grating method

The photoreaction of caged ATP, P3-[1-(2-nitrophenyl)ethyl]adenosine-5'-triphosphate, has been investigated using the time-resolved transient grating (TG) method. We found that a feature of the TG signal time profile depends sensitively on the grating wavenumber (q) after the photoexcitation of caged ATP. This q-dependent feature of the TG signal was interpreted based on a model where the ATP release rate is comparable to the molecular diffusion process. We found that the TG signals at various q can be consistently analyzed based on this model and the ATP release rate determined. The enthalpy and volume changes of the reaction have been determined by quantitative measurement of the grating and photoacoustic signals.

Characterization of a new caged proton capable of inducing large pH jumps

A new caged proton, 1-(2-nitrophenyl)ethyl sulfate (caged sulfate), is characterized by infrared spectroscopy and compared with a known caged, proton 2-hydroxyphenyl 1-(2-nitrophenyl)ethyl phosphate (caged HPP). In contrast to caged HPP, caged sulfate can induce large pH jumps and protonate groups that have pK values as low as 2.2. The photolysis mechanism of caged sulfate is analogous to that of P(3)-[1-(2-nitrophenyl)ethyl] ATP (caged ATP), and the photolysis efficiency is similar. The utility of this new caged compound for biological studies was demonstrated by its ability to drive the acid-induced conformational change of metmyoglobin. This transition from the native conformation to a partially unfolded form takes place near pH 4 and was monitored by near-UV absorption spectroscopy.

Kinetics of histidine deligation from the heme in GuHCl-unfolded Fe(III) cytochrome C studied by a laser-induced pH-jump technique

We have developed an instrumental setup that uses transient absorption to monitor protein folding/unfolding processes following a laser-induced, ultrafast release of protons from o-nitrobenzaldehyde. The resulting increase in [H(+)], which can be more than 100 microM, is complete within a few nanoseconds. The increase in [H(+)] lowers the pH of the solution from neutrality to approximately 4 at the highest laser pulse energy used. Protein structural rearrangements can be followed by transient absorption, with kinetic monitoring over a broad time range (approximately 10 ns to 500 ms). Using this pH-jump/transient absorption technique, we have examined the dissociation kinetics of non-native axial heme ligands (either histidine His26 or His33) in GuHCl-unfolded Fe(III) cytochrome c (cyt c). Deligation of the non-native ligands following the acidic pH-jump occurs as a biexponential process with different pre-exponential factors. The pre-exponential factors markedly depend on the extent of the pH-jump, as expected from differences in the pK(a) values of His26 and His33. The two lifetimes were found to depend on temperature but were not functions of either the magnitude of the pH-jump or the pre-pulse pH of the solution. The activation energies of the deligation processes support the suggestion that GuHCl-unfolded cyt c structures with non-native histidine axial ligands represent kinetic traps in unfolding.

Kinetics of local helix formation in poly-L-glutamic acid studied by time-resolved photoacoustics: neutralization reactions of carboxylates in aqueous solutions and their relevance to the problem of protein folding

Photoactivatable caged protons have been used to trigger proton transfer reactions in aqueous solutions of acetate, glutamate, and poly-L-glutamic acid, and the volumetric and enthalpic changes have been detected and characterized by means of time-resolved photoacoustics. Neutralization of carboxylates in aqueous solutions invariably results in an expansion of the solution due to the disappearance of two charges and is accompanied by little enthalpic change. The reactions occur with thermally activated, apparent bimolecular rates on the order of 10(10) M(-1)s(-1). In the case of aqueous solutions of poly-L-glutamic acid at pH around the pK(a) of the coil-to-helix transition, diffusional binding of a proton by carboxylates is followed by a sequential reaction with rate 1.06 (+/- 0.05) x 10(7)s(-1). This step is not thermally activated in the temperature range we have investigated and is likely related to local formation of hydrogen bonds near the protonation site. This structural event may constitute a rate-limiting step in helix propagation.

Photodecarboxylation of ketoprofen in aqueous solution. A time-resolved laser-induced optoacoustic study

The photodecarboxylation reaction of 2-(3-benzoylphenyl)propionate (ketoprofen anion, KP-) was studied in water and in 0.1 M phosphate buffer solutions in the pH range 5.7-11.0 by laser-induced optoacoustic spectroscopy (LIOAS, T range 9.5-31.6 degrees C). Upon exciting KP- with 355 nm laser pulses under anaerobic conditions, two components in the LIOAS signals with well-separated lifetimes were found (tau 1 < 20 ns; 250 < tau 2 < 500 ns) in the whole pH range, whereas a long-lived third component (4 < tau 3 < 10 microseconds) was only detected at pH < or = 6.1. The heat and structural volume changes accompanying the first step did not depend on pH or on the presence of buffer. The carbanion resulting from prompt decarboxylation within the nanosecond pulse (< 10 ns) drastically reduces its molar volume ([-18.9 +/- 2.0] cm3/mol) with respect to KP- and its enthalpy content is (256 +/- 10) kJ/mol. At acid pH (ca 6), a species is formed with a lifetime in the hundreds of ns. The enthalpy and structural volume change for this species with respect to KP- are (181 +/- 15) kJ/mol and (+0.6 +/- 2.0) cm3/mol, respectively. This species is most likely a neutral biradical formed by protonation of the decarboxylated carbanion, and decays to the final product 3-ethylbenzophenone in several microsecond. At basic pH (ca 11), direct formation of 3-ethylbenzophenone occurs in hundreds of ns involving a reaction with the solvent. The global decarboxylation reaction is endothermic ([45 +/- 15] kJ/mol) and shows an expansion of (+14.5 +/- 0.5) cm3/mol with respect to KP-. At low pH, the presence of buffer strongly affects the magnitude of the structural volume changes associated with intermolecular proton-transfer processes of the long-lived species due to reactions of the buffer anion with the decarboxylated ketoprofen anion.

Fast events in protein folding: structural volume changes accompanying the early events in the N-->I transition of apomyoglobin induced by ultrafast pH jump

Ultrafast, laser-induced pH jump with time-resolved photoacoustic detection has been used to investigate the early protonation steps leading to the formation of the compact acid intermediate (I) of apomyoglobin (ApoMb). When ApoMb is in its native state (N) at pH 7.0, rapid acidification induced by a laser pulse leads to two parallel protonation processes. One reaction can be attributed to the binding of protons to the imidazole rings of His24 and His119. Reaction with imidazole leads to an unusually large contraction of -82 +/- 3 ml/mol, an enthalpy change of 8 +/- 1 kcal/mol, and an apparent bimolecular rate constant of (0.77 +/- 0.03) x 10(10) M(-1) s(-1). Our experiments evidence a rate-limiting step for this process at high ApoMb concentrations, characterized by a value of (0. 60 +/- 0.07) x 10(6) s(-1). The second protonation reaction at pH 7. 0 can be attributed to neutralization of carboxylate groups and is accompanied by an apparent expansion of 3.4 +/- 0.2 ml/mol, occurring with an apparent bimolecular rate constant of (1.25 +/- 0.02) x 10(11) M(-1) s(-1), and a reaction enthalpy of about 2 kcal/mol. The activation energy for the processes associated with the protonation of His24 and His119 is 16.2 +/- 0.9 kcal/mol, whereas that for the neutralization of carboxylates is 9.2 +/- 0.9 kcal/mol. At pH 4.5 ApoMb is in a partially unfolded state (I) and rapid acidification experiments evidence only the process assigned to carboxylate protonation. The unusually large contraction and the high energetic barrier observed at pH 7.0 for the protonation of the His residues suggests that the formation of the compact acid intermediate involves a rate-limiting step after protonation.

An experimental methodology for measuring volume changes in proton transfer reactions in aqueous solutions

A fast perturbation in proton concentration can be induced in aqueous solution using a pulsed ultraviolet laser and suitable photolabile compounds which, upon photoexcitation, irreversibly release protons. The volume change and the rate constant for the reaction of the photodetached protons with proton-accepting groups in solution can be monitored using time resolved photoacoustics. A typical proton concentration jump of 1 microM can be obtained with a 200-microJ laser pulse at 308 nm. Reaction dynamics from 20 ns to 5 micros can be easily followed. The methodology we establish represents a direct, time-resolved measurement of the reaction volume in proton transfer processes and an extension to the nanosecond-microsecond range of traditional relaxation techniques, such as stopped-flow. We report example applications to reactions involving simple molecules and polypeptides.