UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting

Protein dynamics of human serum albumin at hypothermic temperatures investigated by temperature jump

Human serum albumin (HSA) is the most abundant protein in human plasma. Most protein dynamics studies of HSA have been performed above the hyperthermia temperature (>42 °C), so information on the dynamics under hypothermic conditions (<35 °C) is lacking. In this work, a tryptophan-based fluorescence temperature jump system was employed to investigate the thermally-induced dynamic process of HSA at a physiological concentration of ca. 45 mg mL^-1 and pH = ca. 7 upon an instantaneous temperature increase from 25 °C to 30-43 °C. The observed kinetics manifested a three-state consecutive feature, . Upon analysis with the Arrhenius model, the rate coefficients k₁ and k₂ manifested piecewise temperature dependence, and the turning-point temperature was found to be ca. 34 °C, coinciding with the upper bound of hypothermic temperature. Meanwhile, the corresponding activation energies of the transitions at 34-43 °C were lower than those at 30-34 °C, suggesting that protein conformational adjustments at 34-43 °C were more feasible than those at hypothermic temperatures. These observations provided a fresh viewpoint on the relationship between the energetics of protein dynamics and the apparent functioning of a given protein at the molecular level.

High-throughput, high-resolution Echelle deep-UV Raman spectrometer

We constructed an ultrahigh-throughput, high-resolution ultraviolet (UV) Raman spectrograph that utilizes a high-efficiency filter-stage monochromator and a high-dispersion Echelle spectrograph. The spectrograph utilizes a total of six mirrors and two gratings, with an overall efficiency at 229 nm of ~18%. The limiting resolution of our spectrometer is 0.6 cm⁻¹ full width half-maximum (FWHM), as measured for 229 nm Rayleigh scattering. Use of a 1 mm-wide entrance slit gives rise to an approximately 10 cm⁻¹ FWHM resolution at 229 nm. The ultrahigh spectrograph throughput enables ultrahigh signal-to-noise ratio, deep UV Raman spectra that allow us to monitor <1% changes in peptide bond composition. The throughput is measured to be 35-fold greater than conventional deep UV Raman spectrometers.

Observation of persistent α-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep-UV resonance Raman spectroscopy

The molten globule state can aide in the folding of a protein to a functional structure and is loosely defined as an increase in structural disorder with conservation of the ensemble secondary structure content. Simultaneous observation of persistent secondary structure content with increased disorder has remained experimentally problematic. As a consequence, modeling how the molten globule state remains stable and how it facilitates proper folding remains difficult due to a lack of amenable spectroscopic techniques to characterize this class of partially unfolded proteins. Previously, deep-UV resonance Raman (dUVRR) spectroscopy has proven useful in the resolution of global and local structural fluctuations in the secondary structure of proteins. In this work, dUVRR was employed to study the molten globule to ordered transition of a model four-helix bundle protein, HP7. Both the average ensemble secondary structure and types of local disorder were monitored, without perturbation of the solvent, pH, or temperature. The molten globule to ordered transition is induced by stepwise coordination of two heme molecules. Persistent dUVRR spectral features in the amide III region at 1295-1301 and 1335-1338 cm-1 confirm previous observations that HP7 remains predominantly helical in the molten globule versus the fully ordered state. Additionally, these spectra represent the first demonstration of conserved helical content in a molten globule protein. With successive heme binding significant losses are observed in the spectral intensity of the amide III3 and S regions (1230-1260 and 1390 cm-1, respectively), which are known to be sensitive to local disorder. These observations indicate that there is a decrease in the structural populations able to explore various extended conformations, with successive heme binding events. DUVRR spectra indicate that the first heme coordination between two helical segments diminishes exploration of more elongated backbone structural conformations in the inter-helical regions. A second heme coordination by the remaining two helices further restricts protein motion.

Impact of ion binding on poly-L-lysine (un)folding energy landscape and kinetics

We utilize T-jump UV resonance Raman spectroscopy (UVRR) to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-L-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix, and turns) of PLL are slower than those of short alanine-based peptides. The PLL pure α-helix folding time is similar to that of short alanine-based peptides. We for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO(4)(-) binding to the Lys side chain -NH(3)(+) groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO(4)(-) binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate(s) differs from the unfolding coordinate(s). The-π helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process.

Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations

We report the first experimental measurements of Ramachandran Ψ-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27S mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond time scale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an α-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the α-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection.

Triplet-triplet energy transfer studies on conformational dynamics in peptides and a protein

Peptides and proteins are highly dynamic systems, which can adopt more or less stable conformations. The dynamics of these molecules, particularly those on the nanosecond to tens of microsecond time scale, are difficult to assess with conventional techniques. This review summarizes experiments using TTET, a technique that reports on van der Waals contact formation between a triplet donor and acceptor group, and which is sensitive in this time range. TTET allows to directly measure the chain dynamics of unstructured model peptides, i.e. large-amplitude fluctuations on the nanosecond time scale. Furthermore, contact formation can be used as irreversible probing reaction to study the kinetics of conformational equilibria. This approach enabled us to measure local α-helix folding and unfolding in helical peptides, which gave new insight into the equilibrium dynamics of this fundamental secondary structure element. TTET has also been applied to study the dynamics both in the native and unfolded state of a protein, the villin headpiece subdomain. The contact formation kinetics between different positions revealed an unlocking and local unfolding reaction in the native state of this model protein, and gave information about the chain dynamics in the unfolded state ensemble.

Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III(3) band and the C(α)-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 3(10)- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures.

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.

Infrared signature and folding dynamics of a helical beta-peptide

Synthetic foldamers consisting of beta-amino acids offer excellent model systems for examining the effect of backbone flexibility on the dynamics of protein folding. Herein, we study the folding-unfolding kinetics of a beta-peptide that folds into a 14-helical structure in water. We find that the T-jump induced relaxation kinetics of this peptide occur on the nanosecond time scale and are noticeably slower than those of alanine-based alpha-helical peptides, and additionally, the relaxation rates show a weaker dependence on temperature. These differences appear to indicate that the folding energy landscapes of these peptides are different. In addition, we find that the amide I' band of this beta-peptide exhibits a sharp feature at approximately 1612 cm(-1), which we believe is a distinct infrared reporter of 14-helix.

Salt dependence of an alpha-helical peptide folding energy landscapes

We used CD, UV resonance Raman spectroscopy, and molecular dynamics simulation to examine the impact of salts on the conformational equilibria and the Ramachandran Psi angle (un)folding Gibbs free energy landscape coordinate of a mainly polyalanine alpha-helical peptide, AP of sequence AAAAA(AAARA)(3)A. NaClO(4) stabilizes alpha-helical-like conformations more than does NaCl, which stabilizes more than Na(2)SO(4) at identical ionic strengths. This alpha-helix stabilization ordering is the reverse of the Hofmeister series of anions in their ability to disorder water hydrogen bonding. Much of the NaClO(4) alpha-helix stabilization results from ClO(4)(-) association with the AP terminal -NH(3)(+) groups and Arg side chains. ClO(4)(-) stabilizes 3(10)-helix conformations but destabilizes turn conformations. The decreased Cl(-) and SO(4)(2-) AP alpha-helix stabilization probably results from a decreased association with the Arg and terminal -NH(3)(+) groups. Cl(-) is expected to have a smaller binding affinity and thus stabilizes alpha-helical conformations intermediately between NaClO(4) and Na(2)SO(4). Electrostatic screening stabilizes pi-bulge conformations.

Local conformational dynamics in alpha-helices measured by fast triplet transfer

Coupling fast triplet-triplet energy transfer (TTET) between xanthone and naphthylalanine to the helix-coil equilibrium in alanine-based peptides allowed the observation of local equilibrium fluctuations in alpha-helices on the nanoseconds to microseconds time scale. The experiments revealed faster helix unfolding in the terminal regions compared with the central parts of the helix with time constants varying from 250 ns to 1.4 micros at 5 degrees C. Local helix formation occurs with a time constant of approximately 400 ns, independent of the position in the helix. Comparing the experimental data with simulations using a kinetic Ising model showed that the experimentally observed dynamics can be explained by a 1-dimensional boundary diffusion with position-independent elementary time constants of approximately 50 ns for the addition and of approximately 65 ns for the removal of an alpha-helical segment. The elementary time constant for helix growth agrees well with previously measured time constants for formation of short loops in unfolded polypeptide chains, suggesting that helix elongation is mainly limited by a conformational search.

Protein dynamics from time resolved UV Raman spectroscopy

Raman spectroscopy can provide unique information on the evolution of structure in proteins over a wide range of time scales; the picosecond to millisecond range can be accessed with pump-probe techniques. Specific parts of the molecule are interrogated by tuning the probe laser to a resonant electronic transition, including the UV transitions of aromatic residues and of the peptide bond. Advances in laser technology have enabled the characterization of transient species at an unprecedented level of structural detail. Applications to protein unfolding and allostery are reviewed.

Barrierless evolution of structure during the submillisecond refolding reaction of a small protein

To determine whether a protein folding reaction can occur in the absence of a dominant barrier is crucial for understanding its complexity. Here direct ultrafast kinetic measurements have been used to study the initial submillisecond (sub-ms) folding reaction of the small protein barstar. The cooperativity of the initial folding reaction has been explored by using two probes: fluorescence resonance energy transfer, through which the contraction of two intramolecular distances is measured, and the binding of 8-anilino-1-naphthalene sulfonic acid, through which the formation of hydrophobic clusters is monitored. A fast chain contraction is shown to precede the formation of hydrophobic clusters, indicating that the sub-ms folding reaction is not cooperative. The observed rate constant of the sub-ms folding reaction monitored by 8-anilino-1-naphthalene sulfonic acid fluorescence has been found to be the same in stabilizing conditions (low urea concentrations), in which specific structure is formed, and in marginally stabilizing conditions (higher urea concentrations), where virtually no structure is formed in the product of the sub-ms folding reaction. The observation that the folding rate is independent of the folding conditions suggests that the initial folding reaction occurs in the absence of a dominant free energy barrier. These results provide kinetic evidence that the formation of specific structure need not be slowed down by any significant free energy barrier during the course of a very fast protein folding reaction.

Dependence of glycine CH2 stretching frequencies on conformation, ionization state, and hydrogen bonding

We experimentally and theoretically examined the conformation, pH, and temperature dependence of the CH2 stretching frequencies of glycine (gly) in solution and in the crystalline state. To separate the effects of the amine and carboxyl groups on the CH2 stretching frequencies we examined the Raman spectra of 2,2,2-d3-ethylamine (CD3-CH2-NH2) and 3,3,3-d3-propionic acid (CD3-CH2-COOH) in D2O. The symmetric (nusCH2) and asymmetric (nuasCH2) stretching frequencies show a significant dependence on gly conformation. We quantified the relation between the frequency splitting (Delta = nuasCH2-nusCH2) and the xi angle which determines the gly conformational geometry. This relation allows us to determine the conformation of gly directly from the Raman spectral frequencies. We observe a large dependence of the nusCH2 and nuasCH2 frequencies on the ionization state of the amine group, which we demonstrate theoretically results from a negative hyperconjugation between the nitrogen lone pair and the C-H antibonding orbitals. The magnitude of this effect is maximized for C-H bonds trans to the nitrogen lone pair. In contrast, a small dependence of the CH2 stretching frequencies on the carboxyl group ionization state arises from delocalization of electron density from carboxyl oxygen to C-H bonding orbitals. According to our experimental observations and theoretical calculations the temperature dependence of the nusCH2 and nuasCH2 of gly is due to the change in the hydrogen-bonding strength of the amine/carboxyl groups to water.

Investigation of polypeptide conformational transitions with two-dimensional Raman optical activity correlation analysis, applying autocorrelation and moving window approaches

The study of conformational transitions in polypeptides is not only important for the understanding of folding mechanisms responsible for the self-assembly of proteins but also for the investigation of the misfolding of proteins that can result in diseases including cystic fibrosis, Alzheimer's, and Parkinson's diseases. Our recent studies developing two-dimensional Raman optical activity (ROA) correlation analysis have proven to be successful in the investigation of polypeptide conformational transitions. However, the complexity of the ROA spectra, and the 2D correlation synchronous and asynchronous plots, makes data analysis detailed and complex, requiring great care in interpretation of 2D correlation rules. By utilizing the 2D correlation approaches of autocorrelation and moving windows it has been possible to gain further information from the ROA spectral data sets in a simpler and more consistent way. The most significant spectral intensity changes have been easily identified, facilitating appropriate interpretation of synchronous plots, and transition phases have been identified in the moving window plots, directly relating spectral intensity changes to the perturbation.

Enthalpic and entropic stages in alpha-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy

The alpha-helix is a ubiquitous structural element in proteins, and a number of studies have addressed the mechanism of helix formation and melting in simple peptides. However, fundamental issues remain to be resolved, particularly the temperature (T) dependence of the rate. In this work, we report application of a novel kHz repetition rate solid-state tunable NIR (pump) and deep UV Raman (probe) laser system to study the dynamics of helix unfolding in Ac-GSPEA3KA4KA4-CO-D-Arg-CONH2, a peptide designed for helix stabilization in aqueous solution. Its T-dependent UV resonance Raman (UVRR) spectra, excited at 197 nm for optimal enhancement of amide vibrations, were decomposed into variable contributions from helix and coil spectra. The helix fractions derived from the UVRR spectra and from far UV CD spectra were coincident at low T but deviated increasingly at high T, the UVRR curve giving higher helix content. This difference is consistent with the greater sensitivity of UVRR spectra to local conformation than CD. After a laser-induced T-jump, the UVRR-determined helix fractions defined monoexponential decays, with time-constants of approximately 120 ns, independent of the final T (Tf = 18-61 degrees C), provided the initial T (Ti) was held constant (6 degrees C). However, there was also a prompt loss of helicity, whose amplitude increased with increasing Tf, thereby defining an initial enthalpic phase, distinct from the subsequent entropic phase. These phases are attributed to disruption of H-bonds followed by reorientation of peptide links, as the chain is extended. When Ti was raised in parallel with Tf (10 degrees C T-jumps), the prompt phase merged into an accelerating slow phase, an effect attributable to the shifting distribution of initial helix lengths. Even greater acceleration with rising Ti has been reported in T-jump experiments monitored by IR and fluorescence spectroscopies. This difference is attributable to the longer range character of these probes, whose responses are therefore more strongly weighted toward the H-bond-breaking enthalpic process.