Time-Resolved Temperature-Jump Infrared Spectroscopy at a High Repetition Rate

Time-resolved temperature-jump infrared absorption spectroscopy at a 0.5 to 1 kHz repetition rate is presented. A 1 kHz neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pumping an optical parametric oscillator provided >70 µJ, 3.75 µm pump pulses, which delivered a temperature jump via excitation of the O-D stretch of a D₂O solution. A 10 kHz train of mid-infrared probe pulses was used to monitor spectral changes following the temperature jump. Calibration with trifluoroacetic acid solution showed that a temperature jump of 10 K lasting for tens of microseconds was achieved, sufficient to observe fast processes in functionally relevant biomolecular mechanisms. Modeling of heating profiles across ≤10 µm path length cells and subsequent cooling dynamics are used to describe the initial <100 ns cooling at the window surface and subsequent, >10 µs cooling dynamics of the bulk solution.

Enhanced Sensitivity to Local Dynamics in Peptides by Use of Temperature-Jump IR Spectroscopy and Isotope Labeling

Site-specific isotopic labeling of molecules is a widely used approach in IR spectroscopy to resolve local contributions to vibrational modes. The induced frequency shift of the corresponding IR band depends on the substituted masses, as well as on hydrogen bonding and vibrational coupling. The impact of these different factors was analyzed with a designed three-stranded β-sheet peptide and by use of selected ¹³ C isotope substitutions at multiple positions in the peptide backbone. Single-strand labels give rise to isotopically shifted bands at different frequencies, depending on the specific sites; this demonstrates sensitivity to the local environment. Cross-strand double- and triple-labeled peptides exhibited two resolved bands that could be uniquely assigned to specific residues, the equilibrium IR spectra of which indicated only weak local-mode coupling. Temperature-jump IR laser spectroscopy was applied to monitor structural dynamics and revealed an impressive enhancement of the isotope sensitivity to both local positions and coupling between them, relative to that of equilibrium FTIR spectroscopy. Site-specific relaxation rates were altered upon the introduction of additional cross-strand isotopes. Likewise, the rates for the global β-sheet dynamics were affected in a manner dependent on the distinct relaxation behavior of the labeled oscillator. This study reveals that isotope labels provide not only local structural probes, but rather sense the dynamic complexity of the molecular environment.

Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy

The signaling protein calmodulin (CaM) undergoes a well-known change in secondary structure upon binding Ca²⁺, but the structural plasticity of the Ca²⁺-free apo state is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58 °C that are assigned to melting of the C- and N-terminal domains, respectively, but the molecular mechanism of domain unfolding is unknown. We report temperature-jump time-resolved infrared (IR) spectroscopy experiments designed to target the first steps in the C-terminal domain melting transition of human apo-CaM. A comparison of the nonequilibrium relaxation of apo-CaM with the more thermodynamically stable holo-CaM, with 4 equiv of Ca²⁺ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix destabilization. These observations enable the assignment of previously reported dynamics of CaM on hundreds of microsecond time scales to thermally activated melting, producing a complete mechanism for thermal unfolding of CaM.

Isotopically Site-Selected Dynamics of a Three-Stranded β-Sheet Peptide Detected with Temperature-Jump Infrared-Spectroscopy

Infrared detected temperature-jump (T-jump) spectroscopy and site-specific isotopic labeling were applied to study a model three-stranded β-sheet peptide with the goal of individually probing the dynamics of strand and turn structural elements. This peptide had two ^DPro-Gly (pG) turn sequences to stabilize the two component hairpins, which were labeled with ¹³C═O on each of the Gly residues to resolve them spectroscopically. Labeling the second turn on the amide preceding the ^DPro (Xxx-^DPro amide) provided an alternate turn label as a control. Placing ¹³C═O labels on specific in-strand residues gave shifted modes that overlap the Xxx-^DPro amide I' modes. Their impact could be separated from the turn dynamics by a novel difference transient analysis approach. Fourier-transform infrared spectra were modeled with density functional theory-computations which showed the local, isotope-selected vibrations were effectively uncoupled from the other amide I modes. Our T-jump dynamics results, combined with nuclear magnetic resonance structures and equilibrium spectral measurements, showed the first turn to be most stable and best formed with the slowest dynamics, whereas the second turn and first strand (N-terminus) had similar dynamics, and the third strand (C-terminus) had the fastest dynamics and was the least structured. The relative dynamics of the strands, Xxx-^DPro amides, and ¹³C-labeled Gly residues on the turns also qualitatively corresponded to molecular dynamics (MD) simulations of turn and strand fluctuations. MD trajectories indicated the turns to be bistable, with the first turn being Type I' and the second turn flipping from I' to II'. The differences in relaxation times for each turn and the separate strands revealed that the folding process of this turn-stabilized β-sheet structure proceeds in a multistep process.

Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles

The self-assembly and self-organization of small molecules on the surface of nanoparticles constitute a potential route toward the preparation of advanced proteinlike nanosystems. However, their structural characterization, critical to the design of bionanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles (GNPs) is developed using experimentally characterized Cys-Ala-Leu-Asn-Asn (CALNN)- and Cys-Phe-Gly-Ala-Ile-Leu-Ser-Ser (CFGAILSS)-capped GNPs as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated using both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on the peptide capping density and on the nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bionanomaterials.

pH-jump induced leucine zipper folding beyond the diffusion limit

The folding of a pH-sensitive leucine zipper, that is, a GCN4 mutant containing eight glutamic acid residues, has been investigated. A pH-jump induced by a caged proton (o-nitrobenzaldehyde, oNBA) is employed to initiate the process, and time-resolved IR spectroscopy of the amide I band is used to probe it. The experiment has been carefully designed to minimize the buffer capacity of the sample solution so that a large pH jump can be achieved, leading to a transition from a completely unfolded to a completely folded state with a single laser shot. In order to eliminate the otherwise rate-limiting diffusion-controlled step of the association of two peptides, they have been covalently linked. The results for the folding kinetics of the cross-linked peptide are compared with those of an unlinked peptide, which reveals a detailed picture of the folding mechanism. That is, folding occurs in two steps, one on an ∼1-2 μs time scale leading to a partially folded α-helix even in the monomeric case and a second one leading to the final coiled-coil structure on distinctively different time scales of ∼30 μs for the cross-linked peptide and ∼200 μs for the unlinked peptide. By varying the initial pH, it is found that the folding mechanism is consistent with a thermodynamic two-state model, despite the fact that a transient intermediate is observed in the kinetic experiment.

The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone

Recombination of photolysed protein disulfide bonds confirms subdiffusional backbone motion and measures the roughness of the protein's energy landscape.

High-resolution sizing of monolayer-protected gold clusters by differential centrifugal sedimentation

Differential centrifugal sedimentation (DCS) has been applied to accurately size ligand-protected gold hydrosols in the 10 to 50 nm range. A simple protocol is presented to correct for particle density variations due to the presence of the ligand shell, which is formed here by either polyethylene glycol-substituted alkane thiols (PEG-alkane thiols) of different chain length or oligopeptides. The method gives reliable data for all particle sizes investigated and lends itself to rapid routine sizing of nanoparticles. Unlike TEM, DCS is highly sensitive to small changes in the thickness of the organic ligand shell and can be applied to monitor shell thickness variations of as little as 0.1 nm on particles of a given core size.

Stability and folding dynamics of polyglutamic acid

The thermal stability and folding dynamics of polyglutamic acid were studied by equilibrium circular dichroism (CD), Fourier-transform infrared (FTIR), and time-resolved temperature-jump infrared (IR) spectroscopy. Polyglutamic acid (PGA) forms α-helical peptides in aqueous solution and is an ideal model system to study the helix-coil transition. Melting curves were monitored with CD and FTIR as a function of pD. At low pD, PGA aggregates at temperatures above 323 K, whereas at pD >5, unfolding and refolding are reversible. At pD 5.4, a helix-coil transition occurs with a transition temperature T(m) of 307 K. At slightly higher pD of 6.2, the peptide conformation is already in a coil structure and only small conformational changes occur upon heating. We determined the equilibrium constant for the reversible helix-coil transition at pD 5.4. The dynamics of this transition was measured at single IR wavelengths after a nanosecond laser-excited temperature jump of ∆T ~ 10 K. Relaxation constants decreased with increasing peptide temperature. Folding and unfolding rates as well as activation energies were extracted based on a two-state model. Our study shows how equilibrium and time-resolved infrared spectroscopic data can be combined to characterize a structural transition and to analyze folding mechanisms.

Mechanistic studies of peptide self-assembly: transient α-helices to stable β-sheets

The pathologic self-assembly of proteins is associated with typically late-onset disorders such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes. Important mechanistic details of the self-assembly are unknown, but there is increasing evidence supporting the role of transient α-helices in the early events. Islet amyloid polypeptide (IAPP) is a 37-residue polypeptide that self-assembles into aggregates that are toxic to the insulin-producing β cells. To elucidate early events in the self-assembly of IAPP, we used limited proteolysis to identify an exposed and flexible region in IAPP monomer. This region includes position 20 where a serine-to-glycine substitution (S20G) is associated with enhanced formation of amyloid fibrils and early onset type 2 diabetes. To perform detailed biophysical studies of the exposed and flexible region, we synthesized three peptides including IAPP(11-25)WT (wild type), IAPP(11-25)S20G, and IAPP(11-25)S20P. Solution-state NMR shows that all three peptides transiently populate the α-helical conformational space, but the S20P peptide, which does not self-assemble, transiently samples a broken helix. Under similar sample conditions, the WT and S20G peptides populate the α-helical intermediate state and β-sheet end state, respectively, of fibril formation. Our results suggest a mechanism for self-assembly that includes the stabilization of transient α-helices through the formation of NMR-invisible helical intermediates followed by an α-helix to β-sheet conformational rearrangement. Furthermore, our results suggest that reducing intermolecular helix-helix contacts as in the S20P peptide is an attractive strategy for the design of blockers of peptide self-assembly.

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory

The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

Rapid temperature jump by infrared diode laser irradiation for patch-clamp studies

Several thermal TRP ion channels have recently been identified. These channels are directly gated by temperature, but the mechanisms have remained elusive. Studies of their temperature gating have been impeded by lack of methods for rapid alteration of temperature in live cells. As a result, only measurements of steady-state properties have been possible. To solve the problem, we have developed an optical approach that uses recently available infrared diode lasers as heat sources. By restricting laser irradiation around a single cell, our approach can produce constant temperature jumps over 50 degrees C in submilliseconds. Experiments with several heat-gated ion channels (TRPV1-3) show its applicability for rapid temperature perturbation in both single cells and membrane patches. Compared with other laser heating approaches such as those by Raman-shifting of the Nd:YAG fundamentals, our approach has the advantage of being cost effective and applicable to live cells while providing an adequate resolution for time-resolved detection of channel activation.

Two-dimensional infrared spectroscopy of photoswitchable peptides

We present a detailed discussion of the complimentary fields of the application of two-dimensional infrared (2D-IR) spectroscopy in comparison with two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Transient 2D-IR (T2D-IR) spectroscopy of nonequilibrium ensembles is probably one of the most promising strengths of 2D-IR spectroscopy, as the possibilities of 2D-NMR spectroscopy are limited in this regime. T2D-IR spectroscopy uniquely combines ultrafast time resolution with microscopic structural resolution. In this article we summarize our recent efforts to investigate the ultrafast structural dynamics of small peptides, such as the unfolding of peptide secondary structure motifs. The work requires two ingredients: 2D-IR spectroscopy and the possibility of triggering a structural transition of a peptide on an ultrafast timescale using embedded or intrinsic photoswitches. Several photoswitches have been tested, and we discuss our progress in merging these two pathways of research.

Solvation and desolvation dynamics in apomyoglobin folding monitored by time-resolved infrared spectroscopy

Solvation and desolvation dynamics around helices during the kinetic folding process of apomyoglobin (apoMb) were investigated by using time-resolved infrared (IR) spectroscopy based on continuous-flow rapid mixing devices and an IR microscope. The folding of apoMb can be described by the collapse and search mechanism, in which the initial collapse occurring within several hundreds of microseconds is followed by the search for the correct secondary and tertiary structures. The time-resolved IR measurements showed a significant increase in solvated helix possessing a component of amide I' at 1633 cm(-1) within 100 mus after initiating the folding by a pD jump from pD2.2 to 6.0. In contrast, there was a minor increase in buried helices having amide I' at 1652 cm(-1) in this time domain. The observations demonstrate that the initially collapsed conformation of apoMb possesses a large amount of solvated helices, and suggest that much water is retained inside the collapsed domain. The contents of solvated and buried helices decrease and increase, respectively, in the time domain after the collapse, showing that the stepwise desolvation around helices is associated with the conformational search process. Interestingly, the largest changes in solvated and buried helices were observed at the final rate-limiting step of the apoMb folding. The persistence of the solvated helix until the final stage of apoMb folding suggests that the dissociation of hydrogen bonds between water and main-chain amides contributes to the energy barrier in the rate-determining step of the folding.

Infrared Study of the Effect of Hydration on the Amide I Band and Aggregation Properties of Helical Peptides

The amide I' band of a polypeptide is sensitive not only to its secondary structure content but also to its environment. In this study we show how degrees of hydration affect the underlying spectral features of the amide I' band of two alanine-based helical peptides. This is achieved by solubilizing these peptides in the water pool of sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles with different water contents or w0 values. In agreement with several earlier studies, our results show that the amide I' band arising from a group of dehydrated helical amides is centered at approximately 1650 cm-1, whereas hydration shifts this frequency toward lower wavenumbers. More importantly, temperature-dependent infrared studies further show that these helical peptides undergo a thermally induced conformational transition in reverse micelles of low w0 values (e.g., w0=6), resulting in soluble peptide aggregates rich in antiparallel beta-sheets. Interestingly, however, increasing w0 or water content leads to an increase in the onset temperature at which such beta-aggregates begin to form. Therefore, these results provide strong evidence suggesting that dehydration facilitates aggregate formation and that removal of water imposes a free energy barrier to peptide association and aggregation, a feature that has been suggested in recent simulation studies focusing on the mechanism of beta-amyloid formation.

Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds

Using time-resolved IR spectroscopy, we monitored the kinetics of folding and unfolding processes of a photoswitchable 16-residue alanine-based alpha-helical peptide on a timescale from few picoseconds to almost 40 micros and over a large temperature range (279-318 K). The folding and unfolding processes were triggered by an ultrafast laser pulse that isomerized the cross linker within a few picoseconds. The main folding and unfolding times (700 ns and 150 ns, respectively, at room temperature) are in line with previous T-jump experiments obtained from similar peptides. However, both processes show complex, strongly temperature-dependent spectral kinetics that deviate clearly from a single-exponential behavior. Whereas in the unfolding experiment the ensemble starts from a well defined folded state, the starting ensemble in the folding experiment is more heterogeneous, which leads to distinctly different kinetics of the experiments, because they are sensitive to different regions of the energy surface. A qualitative agreement with the experimental data-set can be obtained by a model where the unfolded states act as a hub connected to several separated "misfolded" states with a distribution of rates. We conclude that a rather large spread of rates (k(1) : k(n) approximately 9) is needed to explain the experimentally observed stretched exponential response with stretching factor beta = 0.8 at 279 K.

Elucidation of residue-level structure and dynamics of polypeptides via isotope-edited infrared spectroscopy

Infrared spectroscopy is a powerful tool for analyzing the structure of proteins and peptides. The amide I band is particularly sensitive to the strength and position of the hydrogen bonds that define secondary structure as well as dipole-dipole interactions that are affected by the geometry of the peptide backbone. The introduction of a single (13)C-labeled carbonyl into a peptide backbone results in a resolvable shoulder to the main amide I band, which can be analyzed as a separate peak. Thus, site-specific structural information can be obtained by sequential, systematic labeling of the backbone. This method of isotope-edited infrared spectroscopy is a tool for obtaining medium-resolution information about the backbone conformation and dynamics. This tool has been used to dissect the conformation and dynamics of alpha helices and amyloid aggregates, where the versatility of possible sampling with infrared spectroscopy is well-suited for studies of large-protein aggregates.

The α-Helix Folds More Rapidly at the C-Terminus Than at the N-Terminus

The helix-coil dynamics of different sections of an alpha-helical model peptide were observed separately by nanosecond temperature jump experiments with IR detection on a series of isotopically labeled peptides. The results show that the helix-coil dynamics of the alpha-helical C-terminus are faster than those of the N-terminus.

Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy

Photo-triggered alpha-helix formation of a 16-residue peptide featuring a built-in conformational photoswitch is monitored by time-resolved IR spectroscopy. An experimental approach with 2-ps time resolution and a scanning range up to 30 micros is used to cover all time scales of the peptide dynamics. Experiments are carried out at different temperatures between 281 and 322 K. We observe single-exponential kinetics of the amide I' band at 322 K on a time scale comparable to a recent temperature-jump folding experiment. When lowering the temperature, the kinetics become slower and nonexponential. The transition is strongly activated. Spectrally dispersed IR measurements provide multiple spectroscopic probes simultaneously in one experiment by resolving the amide I' band, isotope-labeled amino acid residues, and side chains. We find differing relaxation dynamics at different spectral positions.