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

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.

Photoacid Generators for Biomedical Applications

Photoacid generators (PAGs) are compounds capable of producing hydrogen protons (H+ ) upon irradiation, including irreversible and reversible PAGs, which have been widely studied in photoinduced polymerization and degradation for a long time. In recent years, the applications of PAGs in the biomedical field have attracted more attention due to their promising clinical value. So, an increasing number of novel PAGs have been reported. In this review, the recent progresses of PAGs for biomedical applications is systematically summarized, including tumor treatment, antibacterial treatment, regulation of protein folding and unfolding, control of drug release and so on. Furthermore, a concept of water-dependent reversible photoacid (W-RPA) and its antitumor effect are highlighted. Eventually, the challenges of PAGs for clinical applications are discussed.

Dual Excited State Proton Transfer Pathways in the Bifunctional Photoacid 6-Amino-2-naphtol

This study investigates the photoacidity and excited state proton transfer (ESPT) pathways of a bifunctional molecule, 6-amino-2-naphthol (6N2OH), using absorption, steady-state fluorescence, time-resolved fluorescence, and theoretical calculations. 6N2OH attains four different prototropic forms in the excited state (cation, neutral, anion, or zwitterion) depending on pH of the solution. Interestingly, ESPT at the OH site of the molecule can be controlled by the protonation state of the amino substituent. Conversion of the electron donating NH2 group to the electron withdrawing NH3+ group brings about a reduction of more than 7 pKa units for the deprotonation of OH in the excited state. Further, the position of the NH2 substituent on the naphthalene framework is found to play an important role in dictating the ESPT pathways of aminonaphthols. Unlike most aminonaphthol derivatives that undergo ESPT only at the OH site, akin to substituted naphthols, 6N2OH undergoes ESPT at both OH and NH3+ sites, indicating its similarity to substituted naphthols and substituted naphthylamines. ESPT at the NH3+ site resulting in cation ↔ neutral equilibrium of 6N2OH in the excited state is well-corroborated by comparative studies with another reference photoacid, 6-amino-2-methoxynaphthalene (6N2M). Correlation of the acidity constants of 6N2OH with the σp parameters according to the Hammett model reveals that while 6N2OH can be treated either as naphthol or as naphthylamine in the ground state, the structure-function correlation cannot be extrapolated directly in the excited state, thus highlighting the rich and complex photophysics of bifunctional photoacids.

A red-green photochromic bacterial protein as a new contrast agent for improved photoacoustic imaging

The GAF3 domain of the cyanobacteriochrome Slr1393 from Synechocystis sp. PCC6803, binding phycocyanobilin as a chromophore, shows photochromicity between two stable, green- and red-absorbing states, characterized by relatively high photoconversion yields. Using nanosecond-pulsed excitation by red or green light, respectively, and suitable cw photoconversion beams, we demonstrate that the light-modulatable photoacoustic waveforms arising from GAF3 can be easily distinguished from background signals originating from non-modulatable competitive absorbers and scattering media. It is demonstrated that this effect can be exploited to identify the position of the photochromic molecule by using as a phantom a cylindrical capillary tube filled with either a GAF3 solution or with an E.coli suspension overexpressing GAF3. These properties identify the high potential of GAF3 to be included in the palette of genetically encoded photochromic probes for photoacoustic imaging.

Quinoline Photobasicity: Investigation within Water-Soluble Light-Responsive Copolymers

Quinoline photobases exhibit a distinctly higher pKa in their electronically excited state than in the ground state, thereby enabling light-controlled proton transfer reactions, for example, in molecular catalysis. The absorption of UV light translates to a pKa jump of approximately 10 units, as established for small-molecule photobases. This contribution presents the first synthesis of quinoline-based polymeric photobases prepared by reversible addition-fragmentation chain-transfer (RAFT) polymerization. The integration of quinolines as photobase chromophores within copolymers offers new possibilities for light-triggered proton transfer in nanostructured materials, that is, in nanoparticles, at surfaces, membranes and interfaces. To exploit the light-triggered reactivity of photobases within such materials, we first investigated how the ground- and excited-state properties of the quinoline unit changes upon polymer integration. To address this matter, we combined absorption and emission spectroscopy with time-resolved transient-absorption studies to reveal photoinduced proton-transfer dynamics in various solvents. The results yield important insights into the thermodynamic and kinetic properties of these polymeric quinoline photobases.

Photodynamic action of Hypericum perforatum hydrophilic extract against Staphylococcus aureus

Hypericin (Hyp) is one of the most effective, naturally occurring photodynamic agents, which proved effective against a wide array of microorganisms.

A new visible light triggered Arrhenius photobase and its photo-induced reactions

Visible light triggered Arrhenius photobases are of potential use for excited state hydroxide ion dissociation (ESHID), photo-induced pOH jump experiments, and base-catalyzed reactions.

Kinetic Evidence for the Necessity of Two Proton Donor Molecules for Successful Excited State Proton Transfer by a Photobase

Photobases are molecules that convert light to proton transfer drive and therefore have potential applications in many areas of chemistry. Previously, we studied the photobasicity of quinolines and explored their applications. While it is possible to tether a photobase near a target proton donor, for the sake of versatility it is desirable to explore their capability to deprotonate molecules dispersed in a solution. Previous evidence suggested that in this scenario at least two proton donors were necessary for successful excited state proton transfer: one to donate a proton and the second to stabilize the photogenerated donor anion. Here we report kinetic evidence from transient absorption (TA) and time-correlated single photon counting (TCSPC) in support of this hypothesis. We used 5-methoxyquinoline as the photobase and 2,2,2-trifluoroethanol (TFE), a low pK_a alcohol, as the proton donor. A constant concentration of the photobase was used for a range of proton-donor dilutions spanning several orders of magnitude in an aprotic background solvent. Absorption spectra confirm that over most of the studied range the majority of the photobase population is hydrogen bonded to at least one donor. Short-pulse TA was used to measure the faster (2-500 ps) dynamics, while TSCPC was used to measure the slower (>500 ps) dynamics. The measured proton transfer time constants varied as a function of donor concentration over a wide range. A log-log plot of the proton transfer rate constant as a function of proton-donor concentration shows two regimes: nondiffusive at high donor concentrations where multiple proton donors are near the photobase and diffusive at low donor concentrations where proton donors are more dilute. The nondiffusive regime has a slope of approximately one, suggesting that the proton transfer process is dependent on one donor molecule in addition to the donor molecule already hydrogen bonded with the photobase. The diffusive regime reasonably follows diffusion kinetics. We propose a model for how the second proton-donor molecule may interact with the photogenerated alkoxide to stabilize it. This work highlights the importance of inducing irreversible changes, in this case solvation of the alkoxide, after proton transfer. Understanding of such details is likely to be important in applications of photobases.

Chloromethyl-modified Ru(ii) complexes enabling large pH jumps at low concentrations through photoinduced hydrolysis

Photo-induced hydrolysis of benzyl chlorides was first utilized to fabricate PAGs with high photoacid quantum yields and large photoacid capacities.

Photoacid generators (PAGs) are finding increasing applications in spatial and temporal modulation of biological events in vitro and in vivo. In these applications, large pH jumps at low PAG concentrations are of great importance to achieve maximal expected manipulation but minimal unwanted interference. To this end, both high photoacid quantum yield and capacity are essential, where the capacity refers to the proton number that a PAG molecule can release. Up to now, most PAGs only produce one proton for each molecule. In this work, the hydrolysis reaction of benzyl chlorides was successfully leveraged to develop a novel type of PAG. Upon visible light irradiation, Ru(ii) polypyridyl complexes modified with chloromethyl groups can undergo full hydrolysis with photoacid quantum yield as high as 0.6. Depending on the number of the chloromethyl groups, the examined Ru(ii) complexes can release multiple protons per molecule, leading to large pH jumps at very low PAG concentrations, a feature particularly favorable for bio-related applications.

Enhanced photosensitizing properties of protein bound curcumin

AIMS

The naturally occurring compound curcumin has been proposed for a number of pharmacological applications. In spite of the promising chemotherapeutic properties of the molecule, the use of curcumin has been largely limited by its chemical instability in water. In this work, we propose the use of water soluble proteins to overcome this issue in perspective applications to photodynamic therapy of tumors.

MATERIALS AND METHODS

Curcumin was bound to bovine serum albumin and its photophysical properties was studied as well as its effect on cell viability after light exposure through MTT assay and confocal imaging.

KEY FINDINGS

Bovine serum albumin binds curcumin with moderate affinity and solubilizes the hydrophobic compound preserving its photophysical properties for several hours. Cell viability assays demonstrate that when bound to serum albumin, curcumin is an effective photosensitizer for HeLa cells, with better performance than curcumin alone. Confocal fluorescence imaging reveals that when curcumin is delivered alone, it preferentially associates with mitochondria, whereas curcumin bound to bovine serum albumin is found in additional locations within the cell, a fact that may be related to the higher phototoxicity observed in this case.

SIGNIFICANCE

The higher bioavailability of the photosensitizing compound curcumin when bound to serum albumin may be exploited to increase the efficiency of the drug in photodynamic therapy of tumors.

Apomyoglobin is an efficient carrier for zinc phthalocyanine in photodynamic therapy of tumors

The spectral and the photophysical properties of phthalocyanines have made these dyes attractive for applications in photodynamic therapy of cancer. One important known issue of these compounds is their tendency to aggregate in aqueous media, which decreases their fluorescence, triplet, and singlet oxygen quantum yields. We report on the use of apomyoglobin as a carrier for zinc phthalocyanine (ZnPc) to overcome solubility limitations of the dye. We show that the protein is able to bind ZnPc in monomeric form, preserving its photophysics. Confocal fluorescence imaging of PC3 and HeLa cells, treated with the complex between ZnPc and apomyoglobin, demonstrates that the photosensitizer is uptaken quickly by cells. Illumination of treated cells strongly decreases viability, as demonstrated by live/dead fluorescence assay.

Donor-acceptor preassociation, excited state solvation threshold, and optical energy cost as challenges in chemical applications of photobases

Photobases are molecules with increased pKa in the excited state that can serve to transduce light energy into proton removal capability. They can be used to control chemical reactions using light, such as removing protons from a catalytic site in reactions that are rate-limited by proton transfer. We identify and explore several major challenges toward their practical applications. Two important challenges are the need for pre-association (or ground state hydrogen bonding) between the proton donor and the photobase, and the need for excited state solvation of the photogenerated products. We investigate these two challenges with the photobase 5-methoxyquinoline as the proton acceptor and a low-pKa alcohol, 2,2,2-trifluoroethanol, as the proton donor. We vary the concentration of the donor in a background non-hydrogen-bonding solvent. Using absorption spectroscopy, we have identified that the donor-acceptor concentration ratio must exceed 100 : 1 to achieve appreciable ground state hydrogen bonding. Interestingly, emission spectroscopy reveals that the onset of ground state hydrogen bonding does not guarantee successful excited state proton transfer. It takes an additional order of magnitude increase in donor-acceptor ratio to achieve that goal, revealing that it is necessary to have excess donor molecules to reach the solvation threshold for the photogenerated products. The next challenge is reducing the large ground-excited state energy gap, which often requires UV photons to drive proton transfer. We show experimental and computational data comparing the photobasicity and optical energy gap for a few N-aromatic heterocyclic photobases. In general, we find that reducing the energy gap by increasing the conjugation size necessarily reduces photobasicity, while adding substituents of varying electron-withdrawing strength allows some fine-tuning of this effect. The combination of these two factors provide a preliminary design space for creating new photobasic molecules.

Ultrafast Dynamics of a "Super" Photobase

Molecular reactivity can change dramatically with the absorption of a photon due to the difference of the electronic configurations between the excited and ground states. Here we report on the discovery of a modular system (Schiff base formed from an aldehyde and an amine) that upon photoexcitation yields a more basic imine capable of intermolecular proton transfer from protic solvents. Ultrafast dynamics of the excited state conjugated Schiff base reveals the pathway for proton transfer, culminating in a 14-unit increase in pK_a to give the excited state pK_a ^* >20 in ethanol.

Remote activation of nanoparticulate biomimetic activity by light triggered pH-jump

By incorporating flash photolysis reagents, a facile and versatile method for the photo-regulation of pH-dependent activities of artificial enzymes is presented.

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.

Directly monitor protein rearrangement on a nanosecond-to-millisecond time-scale

In order to directly observe the refolding kinetics from a partially misfolded state to a native state in the bottom of the protein-folding funnel, we used a "caging" strategy to trap the β-sheet structure of ubiquitin in a misfolded conformation. We used molecular dynamics simulation to generate the cage-induced, misfolded structure and compared the structure of the misfolded ubiquitin with native ubiquitin. Using laser flash irradiation, the cage can be cleaved from the misfolded structure within one nanosecond, and we monitored the refolding kinetics of ubiquitin from this misfolded state to the native state by photoacoustic calorimetry and photothermal beam deflection techniques on nanosecond to millisecond timescales. Our results showed two refolding events in this refolding process. The fast event is shorter than 20 ns and corresponds to the instant collapse of ubiquitin upon cage release initiated by laser irradiation. The slow event is ~60 μs, derived from a structural rearrangement in β-sheet refolding. The event lasts 10 times longer than the timescale of β-hairpin formation for short peptides as monitored by temperature jump, suggesting that rearrangement of a β-sheet structure from a misfolded state to its native state requires more time than ab initio folding of a β-sheet.

Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o-NBA photo-acid interaction with BSA

Serum albumins present reversible pH dependent conformational transitions. A sudden laser induced pH-jump is a methodology that can provide new insights on localized protein (un)folding processes that occur within the nanosecond to microsecond time scale. To generate the fast pH jump needed to fast-trigger a protein conformational event, a photo-triggered acid generator as o-nitrobenzaldehyde (o-NBA) can be conveniently used. In order to detect potential specific or nonspecific interactions between o-NBA and BSA, we have performed ligand-binding studies using fluorescence spectroscopy, saturation transfer difference (STD) NMR, molecular docking and semi-empirical calculations. Fluorescence quenching indicates the formation of a non-fluorescent complex in the ground-state between the fluorophore and the quencher, but o-NBA does not bind much effectively to the protein (Ka~4.34×10(3)M(-1)) and thus can be considered a relatively weak binder. The corresponding thermodynamic parameters: ΔG°, ΔS° and ΔH° showed that the binding process is spontaneous and entropy driven. Results of (1)H STD-NMR confirm that the photo-acid and BSA interact, and the relative intensities of the signals in the STD spectra show that all o-NBA protons are equally involved in the binding process, which should correspond to a nonspecific interaction. Molecular docking and semi-empirical calculations suggest that the o-NBA binds preferentially to the Trp-212-containing site of BSA (FA7), interacting via hydrogen bonds with Arg-217 and Tyr-149 residues.

A caged substrate peptide for matrix metalloproteinases

Based on the widely applied fluorogenic peptide FS-6 (Mca-Lys-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2; Mca = methoxycoumarin-4-acetyl; Dpa = N-3-(2,4-dinitrophenyl)l-α,β-diaminopropionyl) a caged substrate peptide Ac-Lys-Pro-Leu-Gly-Lys*-Lys-Ala-Arg-NH2 (*, position of the cage group) for matrix metalloproteinases was synthesized and characterized. The synthesis implies the modification of a carbamidated lysine side-chain amine with a photocleavable 2-nitrobenzyl group. Mass spectrometry upon UV irradiation demonstrated the complete photolytic cleavage of the protecting group. Time-resolved laser-flash photolysis at 355 nm in combination with transient absorption spectroscopy determined the biphasic decomposition with τa = 171 ± 3 ms (79%) and τb = 2.9 ± 0.2 ms (21%) at pH 6.0 of the photo induced release of the 2-nitrobenzyl group. The recombinantly expressed catalytic domain of human membrane type I matrix metalloproteinase (MT1-MMP or MMP-14) was used to determine the hydrolysis efficiency of the caged peptide before and after photolysis. It turned out that the cage group sufficiently shields the peptide from peptidase activity, which can be thus controlled by UV light.

The carbonate/bicarbonate system as a pH indicator for infrared spectroscopy

Caged compounds capable of inducing large pH-jumps upon UV illumination have represented a breakthrough in time-resolved infrared spectroscopy of acidification-triggered phenomena, but their use is hampered by the inability to control the initial pH as well as to measure the final pH in μL volumes. We have developed an experimental approach that accurately measures the initial and final pH values in pH-jump experiments. Our approach exploits the concomitant presence of two or more inorganic ions, such as carbonate and bicarbonate, that are added to the sample at a known concentration. The difference spectrum obtained in the infrared measurement is fitted to isolate the bands arising from the appearance or disappearance of either protonation state, and is then compared to a synthetic library of difference spectra generated using both qualitative (band position and width, extinction coefficient, pK) and quantitative (concentration, pathlength) parameters of the reporter ions. We have tested this approach in UV-photolysis experiments of 1-(2-nitrophenyl)ethyl sulfate in the presence of different concentrations of Na2CO3 and successfully used the infrared absorption of the carbonate and the bicarbonate ions to determine the initial and final pH values before and after the pH-jump, respectively.

Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function

Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.

A photoinduced nanoparticle separation in microchannels via pH-sensitive surface traps

A microfluidic surface trap was developed for capturing pH-sensitive nanoparticles via a photoinitiated proton-releasing reaction of o-nitrobenzaldehyde (o-NBA) that reduces the solution pH in microchannels. The surface trap and nanoparticles were both modified with a pH-responsive polymer-poly(N-isorpopylacylamide-co-propylacrylic acid), P(NIPAAm-co-PAA). The o-NBA-coated microchannel walls demonstrated rapid proton release upon UV light irradiation, allowing the buffered solution pH in the microchannel to decrease from 7.4 to 4.5 in 60 s. The low solution pH switched the polymer-modified surfaces to be more hydrophobic, which enabled the capture of the pH-sensitive nanobeads onto the trap. When a photomask was utilized to limit the UV irradiation to a specific channel region, we were able to restrict the particle separation to only the exposed region. Via control of the UV irradiation, this technique enables not only prompt pH changes within the channel but also the capture of target molecules at specific channel locations.

Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations

Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.

A perfusion-based micro opto-fluidic system (PMOFS) for continuously in-situ immune sensing

This paper proposes a novel perfusion-based micro opto-fluidic system (PMOFS) as a reusable immunosensor for in-situ and continuous protein detection. The PMOFS includes a fiber optic interferometry (FOI) sensor housed in a micro-opto-fluidic chip covered with a microdialysis membrane. It features a surface regeneration mechanism for continuous detection. Gold nanoparticles (GNPs) labeled anti-rabbit IgG were used to enhance the immune conjugation signal by the elongated optical path from GNPs conjugation. Surface regeneration of the sensor was achieved through local pH level manipulation by means of a photoactive molecule, o-Nitrobenzaldehyde (o-NBA), which triggered the elution of immune complexes. Experimental results showed that the pH level of the o-NBA solution can be reduced from 7 to 3.5 within 20 seconds under UV irradiation, sufficient for an effective elution process. The o-NBA molecules, contained within poly(ethylene glycol) diacrylate (PEG) complexes, were trapped within the sensing compartment by the microdialysis membrane and would not leak into the outside environment. The pH variation was also limited in the neighborhood of the sensor surface, resulting in a self-contained sensing system. In-situ immune detection and surface regeneration of the sensing probe has been successfully carried out for two identical cycles by the same sensing probe, and the cycle time can be less than 8 minutes, which is so far the fastest method for continuous monitoring on protein/peptide molecules. In addition, the interference fringe shift of the sensor is linearly related to the concentration of anti-cytochrome C antibody solution and the detection limit approaches 10 ng/ml.

Hydrated and dehydrated tertiary interactions--opening and closing--of a four-helix bundle peptide

The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide was studied with steady-state and time-resolved fluorescence spectroscopy and with circular dichroism (CD). At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations, we can use the lifetime analysis to monitor the change in hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9 degrees C to 23 degrees C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30 degrees C the structural dynamics involve transient openings of the four-helix bundle structure, as evidenced by the emergence of a water-quenched component and less negative CD. Above 60 degrees C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions.

Rapid kinetic techniques

The elementary steps in complex biochemical reaction schemes (isomerization, dissociation, and association reactions) ultimately determine how fast any system can react in responding to incoming signals and in adapting to new conditions. Many of these steps have associated rate constants that result in subsecond responses to incoming signals or externally applied changes. This chapter is concerned with the techniques that have been developed to study such rapidly reacting systems in vitro and to determine the values of the rate constants for the individual steps. We focus principally on two classes of techniques: (1) flow techniques, in which two solutions are mixed within a few milliseconds and the ensuing reaction monitored over milliseconds to seconds, and (2) relaxation techniques, in which a small perturbation to an existing equilibrium is applied within a few microseconds and the response of the system is followed over microseconds to hundreds of milliseconds. These reactions are most conveniently monitored by recording the change in some optical signal, such as absorbance or fluorescence. We discuss the instrumentation that is (commercially) available to study fast reactions and describe a number of optical probes (chromophores) that can be used to monitor the changes. We discuss the experimental design appropriate for the different experimental techniques and reaction mechanisms, as well as the fundamental theoretical concepts behind the analysis of the data obtained.

Photoacoustic spectroscopy of aromatic amino acids in proteins

This paper concerns the use of photoacoustic spectroscopy (PAS) to study the presence of aromatic amino acid in proteins. We examined the aromatic amino acids in six proteins with well-known structures using absorption spectra of near ultraviolet PAS over the wavelength range 240-320 nm. The fundamental understanding of the physical and chemical properties that govern the absorption of light and a subsequent release of heat to generate a transient pressure wave was used to test the concept of monitoring aromatic amino acids with this method. Second derivative spectroscopy in the ultraviolet region of proteins was also used to study the regions surrounding the aromatics and the percentage area in each band was related in order to determine the contribution in function of the respective molar extinction coefficients for each residue. Further investigation was conducted into the interaction between sodium dodecyl sulphate (SDS) and bothropstoxin-I (BthTx-I), with the purpose of identifying the aromatics that participate in the interaction. The clear changes in the second derivative and curve-fitting procedures suggest that initial SDS binding to the tryptophan located in the dimer interface and above 10 SDS an increased intensity between 260 and 320 nm, demonstrating that the more widespread tyrosine and phenylalanine residues contribute to the SDS/BthTx-I interactions. These results demonstrate the potential of near UV-PAS for the investigation of membrane proteins/detergent complexes in which light scattering is significant.

Photoacoustic characterization of protein dynamics following CO photodetachment from fully reduced bovine cytochrome c oxidase

We report a protein conformational change following carbon monoxide photodetachment from fully reduced bovine cytochrome c oxidase that is hypothesized to be associated with changes in ligand mobility through a dioxygen access channel in the protein. Although not resolved by earlier photoacoustic or optical studies on this adduct, utilization of slightly lower temperatures revealed a process with a kinetic lifetime of about 70 ns at 10 degrees C. We measure an enthalpy change of about 8 kcal/mol in 0.050 M HEPES buffer that becomes less endothermic (DeltaH approximately 2 kcal/mol) at higher ionic strength. The volume contraction of about -0.7 mL/mol associated with the process almost doubles in higher ionic strength buffer systems. Measurements of samples in phosphate buffer systems are similar and appear to display the same subtle ionic strength dependence. Both the isolation of this photoacoustic signal component and the possible dependence on ionic strength of the thermodynamic parameters derived from its analysis appear analogous to and consistent with prior photoacoustic results monitoring CO photodetachment from the camphor complex of cytochrome P-450. Accordingly, we consider a similar model in which a conformational change results in movement of an exposed charged group or groups towards the interior of the protein, out of contact with solvent, as in the closing of a salt bridge.

pH-Dependence of extrinsic and intrinsic H(+)-ion mobility in the rat ventricular myocyte, investigated using flash photolysis of a caged-H(+) compound

Passive H(+)-ion mobility within eukaryotic cells is low, due to H(+)-ion binding to cytoplasmic buffers. A localized intracellular acidosis can therefore persist for seconds or even minutes. Because H(+)-ions modulate so many biological processes, spatial intracellular pH (pH(i))-regulation becomes important for coordinating cellular activity. We have investigated spatial pH(i)-regulation in single and paired ventricular myocytes from rat heart by inducing a localized intracellular acid-load, while confocally imaging pH(i) using the pH-fluorophore, carboxy-SNARF-1. We present a novel method for localizing the acid-load. This involves the intracellular photolytic uncaging of H(+)-ions from a membrane-permeant acid-donor, 2-nitrobenzaldehyde. The subsequent spatial pH(i)-changes are consistent with intracellular H(+)-mobility and cell-to-cell H(+)-permeability constants measured using more conventional acid-loading techniques. We use the method to investigate the effect of reducing pH(i) on intrinsic (non-CO(2)/HCO(3)(-) buffer-dependent) and extrinsic (CO(2)/HCO(3)(-) buffer-dependent) components of H(i)(+)-mobility. We find that although both components mediate spatial regulation of pH within the cell, their ability to do so declines sharply at low pH(i). Thus acidosis severely slows intracellular H(+)-ion movement. This can result in spatial pH(i) nonuniformity, particularly during the stimulation of sarcolemmal Na(+)-H(+) exchange. Intracellular acidosis thus presents a window of vulnerability in the spatial coordination of cellular function.

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.

Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with a green fluorescent protein

The kinetics of proton transfer in Green Fluorescent Protein (GFP) have been studied as a model system for characterizing the correlation between dynamics and function of proteins in general. The kinetics in EGFP (a variant of GFP) were monitored by using a laser-induced pH jump method. The pH was jumped from 8 to 5 by nanosecond flash photolysis of the "caged proton," o-nitrobenzaldehyde, and subsequent proton transfer was monitored by following the decrease in fluorescence intensity. The modulation of proton transfer kinetics by external perturbants such as viscosity, pH, and subdenaturing concentrations of GdnHCl as well as of salts was studied. The rate of proton transfer was inversely proportional to solvent viscosity, suggesting that the rate-limiting step is the transfer of protons through the protein matrix. The rate is accelerated at lower pH values, and measurements of the fluorescence properties of tryptophan 57 suggest that the enhancement in rate is associated with an enhancement in protein dynamics. The rate of proton transfer is nearly independent of temperature, unlike the rate of the reverse process. When the stability of the protein was either decreased or increased by the addition of co-solutes, including the salts KCl, KNO(3), and K(2)SO(4), a significant decrease in the rate of proton transfer was observed in all cases. The lack of correlation between the rate of proton transfer and the stability of the protein suggests that the structure is tuned to ensure maximum efficiency of the dynamics that control the proton transfer function of the protein.

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.

Measuring the refolding of beta-sheets with different turn sequences on a nanosecond time scale

Whether turns play an active or passive role in protein folding remains a controversial issue at this juncture. Here we use a photolabile cage strategy in combination with laser-flash photolysis and photoacoustic calorimetry to study the effects of different turns on the kinetics of beta-hairpin refolding on a nanosecond time scale. This strategy opens up a temporal window to allow the observation of early kinetic events in the protein refolding process at ambient temperature and pH without interference from any denaturants. Our results provide direct evidence demonstrating that even a one-residue difference in the turn region can change the refolding kinetics of a peptide. This observation suggests an active role for turn formation in directing protein folding.