Multiple pathways on a protein-folding energy landscape: kinetic evidence

Heterogeneity in Protein Folding and Unfolding Reactions

Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.

Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein

To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET methodology. After an initial heterogeneous polypeptide chain collapse, structure formation proceeds on parallel pathways. Kinetic analysis of the population evolution data across various protein segments provides a clear structural distinction between the parallel pathways. The analysis leads to a phenomenological model that describes how and when discrete segments acquire structure independently of each other in different subensembles of protein molecules. When averaged over all molecules, structure formation is seen to progress as α-helix formation, followed by core consolidation, then β-sheet formation, and last end-to-end distance compaction. Parts of the protein that are closer in the primary sequence acquire structure before parts separated by longer sequence.

X-ray snapshots reveal conformational influence on active site ligation during metalloprotein folding

Cytochrome c (cyt c) has long been utilized as a model system to study metalloprotein folding dynamics and the interplay between active site ligation and tertiary structure. However, recent reports regarding the weakness of the native Fe(ii)-S bond (Fe-Met80) call into question the role of the active site ligation in the protein folding process. In order to investigate the interplay between protein conformation and active site structures, we directly tracked the evolution of both during a photolysis-induced folding reaction using X-ray transient absorption spectroscopy and time-resolved X-ray solution scattering techniques. We observe an intermediate Fe-Met80 species appearing on ∼2 μs timescale, which should not be sustained without stabilization from the folded protein structure. We also observe the appearance of a new active site intermediate: a weakly interacting Fe-H2O state. As both intermediates require stabilization of weak metal-ligand interactions, we surmise the existence of a local structure within the unfolded protein that protects and limits the movement of the ligands, similar to the entatic state found in the native cyt c fold. Furthermore, we observe that in some of the unfolded ensemble, the local stabilizing structure is lost, leading to expansion of the unfolded protein structure and misligation to His26/His33 residues.

Disulfide driven folding for a conditionally disordered protein

Conditionally disordered proteins are either ordered or disordered depending on the environmental context. The substrates of the mitochondrial intermembrane space (IMS) oxidoreductase Mia40 are synthesized on cytosolic ribosomes and diffuse as intrinsically disordered proteins to the IMS, where they fold into their functional conformations; behaving thus as conditionally disordered proteins. It is not clear how the sequences of these polypeptides encode at the same time for their ability to adopt a folded structure and to remain unfolded. Here we characterize the disorder-to-order transition of a Mia40 substrate, the human small copper chaperone Cox17. Using an integrated real-time approach, including chromatography, fluorescence, CD, FTIR, SAXS, NMR, and MS analysis, we demonstrate that in this mitochondrial protein, the conformational switch between disordered and folded states is controlled by the formation of a single disulfide bond, both in the presence and in the absence of Mia40. We provide molecular details on how the folding of a conditionally disordered protein is tightly regulated in time and space, in such a way that the same sequence is competent for protein translocation and activity.

Disulfide driven folding for a conditionally disordered protein

Conditionally disordered proteins are either ordered or disordered depending on the environmental context. The substrates of the mitochondrial intermembrane space (IMS) oxidoreductase Mia40 are synthesized on cytosolic ribosomes and diffuse as intrinsically disordered proteins to the IMS, where they fold into their functional conformations; behaving thus as conditionally disordered proteins. It is not clear how the sequences of these polypeptides encode at the same time for their ability to adopt a folded structure and to remain unfolded. Here we characterize the disorder-to-order transition of a Mia40 substrate, the human small copper chaperone Cox17. Using an integrated real-time approach, including chromatography, fluorescence, CD, FTIR, SAXS, NMR, and MS analysis, we demonstrate that in this mitochondrial protein, the conformational switch between disordered and folded states is controlled by the formation of a single disulfide bond, both in the presence and in the absence of Mia40. We provide molecular details on how the folding of a conditionally disordered protein is tightly regulated in time and space, in such a way that the same sequence is competent for protein translocation and activity.

Effect of mammalian kidney osmolytes on the folding pathway of sheep serum albumin

Recently, we had published that urea-induced denaturation curves of optical properties of sheep serum albumin (SSA) are biphasic with a stable intermediate that has characteristics of molten globule (MG) state. In this study, we have extended the work by carrying out urea- and guanidinium chloride (GdmCl)-induced denaturations of SSA in the presence of naturally occurring mammalian kidney osmolytes, namely, sorbitol, myo-inositol and glycine betaine. We have observed that all these osmolytes (i) transform this biphasic transition into a co-operative, two-state transition and (ii) increase the stability of the protein in terms of midpoint of denaturation (C_m) and Gibbs free energy change in the absence of both denaturants (ΔG_D⁰). The relative effectiveness of different osmolytes on the stability of SSA follows the order: glycine betaine>myo-inositol>sorbitol. In this paper, we also report that kidney osmolytes destabilize MG state by shifting the equilibrium, native state↔MG state toward the left. This study will be helpful in understanding the existence of osmolytes in kidney and their role in folding of kidney proteins soaked with urea.

Packing energetics determine the folding routes of the RNase-H proteins

The RNase-H proteins show a diverse range of folding routes with structurally distinct folding nuclei.

Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems

Analysis of molecular dynamics, for example using Markov models, often requires the identification of order parameters that are good indicators of the rare events, i.e. good reaction coordinates. Recently, it has been shown that the time-lagged independent component analysis (TICA) finds the linear combinations of input coordinates that optimally represent the slow kinetic modes and may serve in order to define reaction coordinates between the metastable states of the molecular system. A limitation of the method is that both computing time and memory requirements scale with the square of the number of input features. For large protein systems, this exacerbates the use of extensive feature sets such as the distances between all pairs of residues or even heavy atoms. Here we derive a hierarchical TICA (hTICA) method that approximates the full TICA solution by a hierarchical, divide-and-conquer calculation. By using hTICA on distances between heavy atoms we identify previously unknown relaxation processes in the bovine pancreatic trypsin inhibitor.

Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage

The attempt frequency or prefactor (k0) of the transition-state rate equation of protein folding kinetics has been estimated to be on the order of 10(6) s(-1), which is many orders of magnitude smaller than that of chemical reactions. Herein we use the mini-protein Trp-cage to show that it is possible to significantly increase the value of k0 for a protein folding reaction by rigidifying the transition state. This is achieved by reducing the conformational flexibility of a key structural element (i.e., an α-helix) formed in the transition state via photoisomerization of an azobenzene cross-linker. We find that this strategy not only decreases the folding time of the Trp-cage peptide by more than an order of magnitude (to ∼100 ns at 25°C) but also exposes parallel folding pathways, allowing us to provide, to the best of our knowledge, the first quantitative assessment of the curvature of the transition-state free-energy surface of a protein.

Laser desorption dual spray post-ionization mass spectrometry for direct analysis of samples via two informative channels

A laser desorption dual spray post-ionization mass spectrometry method is described, and its usefulness is demonstrated with the examples of selective detection of food components, manipulation of protein charge state distribution and investigation on the formation of magic number clusters. The method is carried out by adopting two spray emitters for post-ionization of analytes desorbed by a pulsed infrared laser. Various components in a complex sample or distinct behavior of an analyte in two different spray reagents can be rapidly probed by the method quasi-simultaneously, highlighting the potential applications of this method for protein characterization, reaction study and food analysis.

The principle of stationary action in biophysics: stability in protein folding

We conceptualize protein folding as motion in a large dimensional dihedral angle space. We use Lagrangian mechanics and introduce an unspecified Lagrangian to study the motion. The fact that we have reliable folding leads us to conjecture the totality of paths forms caustics that can be recognized by the vanishing of the second variation of the action. There are two types of folding processes: stable against modest perturbations and unstable. We also conjecture that natural selection has picked out stable folds. More importantly, the presence of caustics leads naturally to the application of ideas from catastrophe theory and allows us to consider the question of stability for the folding process from that perspective. Powerful stability theorems from mathematics are then applicable to impose more order on the totality of motions. This leads to an immediate explanation for both the insensitivity of folding to solution perturbations and the fact that folding occurs using very little free energy. The theory of folding, based on the above conjectures, can also be used to explain the behavior of energy landscapes, the speed of folding similar to transition state theory, and the fact that random proteins do not fold.

Probing kinetic mechanisms of protein function and folding with time-resolved natural and magnetic chiroptical spectroscopies

Recent and ongoing developments in time-resolved spectroscopy have made it possible to monitor circular dichroism, magnetic circular dichroism, optical rotatory dispersion, and magnetic optical rotatory dispersion with nanosecond time resolution. These techniques have been applied to determine structural changes associated with the function of several proteins as well as to determine the nature of early events in protein folding. These studies have required new approaches in triggering protein reactions as well as the development of time-resolved techniques for polarization spectroscopies with sufficient time resolution and sensitivity to probe protein structural changes.

Chiral vibrational structures of proteins at interfaces probed by sum frequency generation spectroscopy

We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces.

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

Markov (state) models (MSMs) have attracted a lot of interest recently as they (1) can probe long-term molecular kinetics based on short-time simulations, (2) offer a way to analyze great amounts of simulation data with relatively little subjectivity of the analyst, (3) provide insight into microscopic quantities such as the ensemble of transition pathways, and (4) allow simulation data to be reconciled with measurement data in a rigorous and explicit way. Here we sketch our current perspective of Markov models and explain in short their theoretical basis and assumptions. We describe transition path theory which allows the entire ensemble of protein folding pathways to be investigated and that combines naturally with Markov models. Experimental observations can be naturally linked to Markov models with the dynamical fingerprint theory, by which experimentally observable timescales can be equipped with an understanding of the structural rearrangement processes that take place at these timescales. The concepts of this paper are illustrated by a simple kinetic model of protein folding.

Nanosecond time-resolved polarization spectroscopies: tools for probing protein reaction mechanisms

Polarization methods, introduced in the 1800s, offered one of the earliest ways to examine protein structure. Since then, many other structure-sensitive probes have been developed, but circular dichroism (CD) remains a powerful technique because of its versatility and the specificity of protein structural information that can be explored. With improvements in time resolution, from millisecond to picosecond CD measurements, it has proven to be an important tool for studying the mechanism of folding and function in many biomolecules. For example, nanosecond time-resolved CD (TRCD) studies of the sub-microsecond events of reduced cytochrome c folding have provided direct experimental evidence of kinetic heterogeneity, which is an inherent property of the diffusional nature of early folding dynamics on the energy landscape. In addition, TRCD has been applied to the study of many biochemical processes, such as ligand rebinding in hemoglobin and myoglobin and signaling state formation in photoactive yellow protein and prototropin 1 LOV2. The basic approach to TRCD has also been extended to include a repertoire of nanosecond polarization spectroscopies: optical rotatory dispersion (ORD), magnetic CD and ORD, and linear dichroism. This article will discuss the details of the polarization methods used in this laboratory, as well as the coupling of time-resolved ORD with the temperature-jump trigger so that protein folding can be studied in a larger number of proteins.

Effects of Congo red on aβ(1-40) fibril formation process and morphology

Alzheimer's disease (AD), an age-related neurodegenerative disorder, is the most common form of dementia, and the seventh-leading cause of death in the United States. Current treatments offer only symptomatic relief; thus, there is a great need for new treatments with disease-modifying potential. One pathological hallmark of AD is so-called senile plaques, mainly made up of β-sheet-rich assemblies of 40- or 42-residue amyloid β-peptides (Aβ). Hence, inhibition of Aβ aggregation is actively explored as an option to prevent or treat AD. Congo red (CR) has been widely used as a model antiamyloid agent to prevent Aβ aggregation. Herein, we report detailed morphological studies on the effect of CR as an antiamyloid agent, by circular dichroism spectroscopy, photo-induced cross-linking reactions, and atomic force microscopy. We also demonstrate the effect of CR on a preaggregated sample of Aβ(1-40). Our result suggests that Aβ(1-40) follows a different path for aggregation in the presence of CR.

Probing early events in ferrous cytochrome c folding with time-resolved natural and magnetic circular dichroism spectroscopies

In a 1998 collaboration with Tony Fink, we coupled nanosecond circular dichroism methods (TRCD) with a CO-photolysis system for quickly triggering folding in cytochrome c (cyt c) in order to make the first time-resolved far-UV CD measurement of early secondary structure formation in a protein. The small signal observed in that initial study, approximately 10% of native helicity, became the seed for increasingly robust results from subsequent studies bringing additional natural and magnetic circular polarization dichroism and optical rotatory dispersion detection methods (e.g., TRORD, TRMCD, and TRMORD), coupled to fast photolysis and photoreduction triggers, to the study of early folding events. Nanosecond polarization methods are reviewed here in the context of the range of initiation methods and structure-sensitive probes currently available for fast folding studies. We also review the impact of experimental results from fast polarization studies on questions in folding dynamics such as the possibility of multiple folding pathways implied by energy landscape models, the sequence dependence of ultrafast helix formation, and the simultaneity of chain collapse and secondary structure formation implicit in molten globule models for kinetic folding intermediates.

Poly-N-methylated amyloid beta-peptide (Abeta) C-terminal fragments reduce Abeta toxicity in vitro and in Drosophila melanogaster

Alzheimer's disease (AD), an age related neurodegenerative disorder, threatens to become a major health-economic problem. Assembly of 40- or 42-residue amyloid beta-peptides (Abeta) into neurotoxic oligo-/polymeric beta-sheet structures is an important pathogenic feature in AD, thus, inhibition of this process has been explored to prevent or treat AD. The C-terminal part plays an important role in Abeta aggregation, but most Abeta aggregation inhibitors have targeted the central region around residues 16-23. Herein, we synthesized hexapeptides with varying extents of N-methylation based on residues 32-37 of Abeta, to target its C-terminal region. We measured the peptides' abilities to retard beta-sheet and fibril formation of Abeta and to reduce Abeta neurotoxicity. A penta-N-methylated peptide was more efficient than peptides with 0, 2, or 3 N-methyl groups. This penta-N-methylated peptide moreover increased life span and locomotor activity in Drosophila melanogaster flies overexpressing human Abeta(1-42).

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

Characterizing the equilibrium ensemble of folding pathways, including their relative probability, is one of the major challenges in protein folding theory today. Although this information is in principle accessible via all-atom molecular dynamics simulations, it is difficult to compute in practice because protein folding is a rare event and the affordable simulation length is typically not sufficient to observe an appreciable number of folding events, unless very simplified protein models are used. Here we present an approach that allows for the reconstruction of the full ensemble of folding pathways from simulations that are much shorter than the folding time. This approach can be applied to all-atom protein simulations in explicit solvent. It does not use a predefined reaction coordinate but is based on partitioning the state space into small conformational states and constructing a Markov model between them. A theory is presented that allows for the extraction of the full ensemble of transition pathways from the unfolded to the folded configurations. The approach is applied to the folding of a PinWW domain in explicit solvent where the folding time is two orders of magnitude larger than the length of individual simulations. The results are in good agreement with kinetic experimental data and give detailed insights about the nature of the folding process which is shown to be surprisingly complex and parallel. The analysis reveals the existence of misfolded trap states outside the network of efficient folding intermediates that significantly reduce the folding speed.

An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins

BACKGROUND

The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein.

METHODOLOGY

We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface. Using this algorithm, and the ECEPP/3 potential function, we have made an exhaustive enumeration of the low-energy structures of peptides of different lengths, and have extrapolated these results to larger polypeptides.

CONCLUSIONS AND SIGNIFICANCE

We show that the number of native-like structures for a polypeptide is, in general, an exponential function of its sequence length. The density of these structures in conformational space remains more or less constant and all the increase appears to come from an expansion in the volume of the space. These results are consistent with earlier reports that were based on other models and techniques.

Early events, kinetic intermediates and the mechanism of protein folding in cytochrome C

Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t ≤ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-μs conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 μs timescale to a compact intermediate I_C containing some native-like secondary structure. Although the existence and nature of I_C as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of I_C as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that I_C may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

Single-molecule manipulation techniques have given experimental access to unfolding intermediates of proteins that are inaccessible in conventional experiments. A detailed characterization of the intermediates is a challenging problem that provides new possibilities for directly probing the energy landscape of proteins. We investigated single-molecule mechanical unfolding of a small globular protein, staphylococcal nuclease (SNase), using atomic force microscopy. The unfolding trajectories of the protein displayed sub-molecular and stochastic behavior with typical lengths corresponding to the size of the unfolded substructures. Our results support the view that the single protein unfolds along multiple pathways as suggested in recent theoretical studies. Moreover, we found the drastic change, caused by the ligand and inhibitor bindings, in the mechanical unfolding dynamics.

Folding mechanism of reduced Cytochrome c: equilibrium and kinetic properties in the presence of carbon monoxide

Despite close structural similarity, the ferric and ferrous forms of cytochrome c differ greatly in terms of their ligand binding properties, stability, folding, and dynamics. The reduced heme iron binds diatomic ligands such as CO only under destabilizing conditions that promote weakening or disruption of native methionine-iron linkage. This makes CO a useful conformational probe for detecting partially structured states that cannot be observed in the absence of endogenous ligands. Heme absorbance, circular dichroism, and NMR were used to characterize the denaturant-induced unfolding equilibrium of ferrocytochrome c in the presence and in the absence of CO. In addition to the native state (N), which does not bind CO, and the unfolded CO complex (U-CO), a structurally distinct CO-bound form (M-CO) accumulates to high levels (approximately 75% of the population) at intermediate guanidine HCl concentrations. Comparison of the unfolding transitions for different conformational probes reveals that M-CO is a compact state containing a native-like helical core and regions of local disorder in the segment containing the native Met80 ligand and adjacent loops. Kinetic measurements of CO binding and dissociation under native, partially denaturing, and fully unfolded conditions indicate that a state M that is structurally analogous to M-CO is populated even in the absence of CO. The binding energy of the CO ligand lowers the free energy of this high-energy state to such an extent that it accumulates even under mildly denaturing equilibrium conditions. The thermodynamic and kinetic parameters obtained in this study provide a fully self-consistent description of the linked unfolding/CO binding equilibria of reduced cytochrome c.

Multiple routes and structural heterogeneity in protein folding

Experimental studies show that many proteins fold along sequential pathways defined by folding intermediates. An intermediate may not always be a single population of molecules but may consist of subpopulations that differ in their average structure. These subpopulations are likely to fold via independent pathways. Parallel folding and unfolding pathways appear to arise because of structural heterogeneity. For some proteins, the folding pathways can effectively switch either because different subpopulations of an intermediate get populated under different folding conditions, or because intermediates on otherwise hidden pathways get stabilized, leading to their utilization becoming discernible, or because mutations stabilize different substructures. Therefore, the same protein may fold via different pathways in different folding conditions. Multiple folding pathways make folding robust, and evolution is likely to have selected for this robustness to ensure that a protein will fold under the varying conditions prevalent in different cellular contexts.

The protein folding problem

The "protein folding problem" consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely and moving toward successful applications. The structures of small proteins are now often well predicted by computer methods. And, there is now a testable explanation for how a protein can fold so quickly: A protein solves its large global optimization problem as a series of smaller local optimization problems, growing and assembling the native structure from peptide fragments, local structures first.

Parallel folding pathways in the SH3 domain protein

The transition-state ensemble (TSE) is the set of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an understanding of the folding process. We determined the TSE of the src-SH3 domain protein by using extensive molecular dynamics simulations of the Go model and computing the folding probability of a generated set of TSE candidate conformations. We found that the TSE possesses a well-defined hydrophobic core with variable enveloping structures resulting from the superposition of three parallel folding pathways. The most preferred pathway agrees with the experimentally determined TSE, while the two least preferred pathways differ significantly. The knowledge of the different pathways allows us to design the interactions between amino acids that guide the protein to fold through the least preferred pathway. This particular design is akin to a circular permutation of the protein. The finding motivates the hypothesis that the different experimentally observed TSEs in homologous proteins and circular permutants may represent potentially available pathways to the wild-type protein.

Infrared spectroscopic discrimination between the loop and alpha-helices and determination of the loop diffusion kinetics by temperature-jump time-resolved infrared spectroscopy for cytochrome c

The infrared (IR) absorption of the amide I band for the loop structure may overlap with that of the alpha-helices, which can lead to the misassignment of the protein secondary structures. A resolution-enhanced Fourier transform infrared (FTIR) spectroscopic method and temperature-jump (T-jump) time-resolved IR absorbance difference spectra were used to identify one specific loop absorption from the helical IR absorption bands of horse heart cytochrome c in D2O at a pD around 7.0. This small loop consists of residues 70-85 with Met-80 binding to the heme Fe(III). The FTIR spectra in amide I' region indicate that the loop and the helical absorption bands overlap at 1653 cm(-1) at room temperature. Thermal titration of the amide I' intensity at 1653 cm(-1) reveals that a transition in loop structural change occurs at lower temperature (Tm=45 degrees C), well before the global unfolding of the secondary structure (Tm approximately 82 degrees C). This loop structural change is assigned as being triggered by the Met-80 deligation from the heme Fe(III). T-jump time-resolved IR absorbance difference spectra reveal that a T-jump from 25 degrees C to 35 degrees C breaks the Fe-S bond between the Met-80 and the iron reversibly, which leads to a loop (1653 cm(-1), overlap with the helical absorption) to random coil (1645 cm(-1)) transition. The observed unfolding rate constant interpreted as the intrachain diffusion rate for this 16 residue loop was approximately 3.6x10(6) s(-1).

Conformational equilibration time of unfolded protein chains and the folding speed limit

The speed with which the conformers of unfolded protein chains interconvert is a fundamental question in the study of protein folding. Kinetic evidence is presented here for the time constant for interconversion of disparate unfolded chain conformations of a small globular protein, cytochrome c, in the presence of guanidine hydrochloride denaturant. The axial binding reactions of histidine and methionine residues with the Fe(II) heme cofactor were monitored with time-resolved magnetic circular dichroism spectroscopy after photodissociation of the CO complexes of unfolded protein obtained from horse and tuna and from several histidine mutants of the horse protein. A kinetic model fitting both the reaction rate constants and spectra of the intermediates was used to obtain a quantitative estimate of the conformational diffusion time. The latter parameter was approximated as a first-order time constant for exchange between conformational subensembles presenting either a methionine or a histidine residue to the heme iron for facile binding. The mean diffusional time constant of the wild type and variants was 3 +/- 2 mus, close to the folding "speed limit". The implications of the relatively rapid conformational equilibration time observed are discussed in terms of the energy landscape and classical pathway time regimes of folding, for which the conformational diffusion time can be considered a pivot point.

Direct observation of protein folding in nanoenvironments using a molecular ruler

We observe folding of horse heart cytochrome c in various environments including nano-compartments (micelles and reverse micelles). Using picosecond-resolved Förster resonance energy transfer (FRET) dynamics of an extrinsic covalently attached probe dansyl (donor) at the surface of the protein to a heme group (acceptor) embedded inside the protein, we measured angstrom-resolved donor-acceptor distances in the environments. The overall structural perturbations of the protein revealed from the FRET experiments are in close agreement with our circular dichroism (CD) and dynamic light scattering (DLS) studies on the protein in a variety of solution conditions. The change of segmental motion of the protein due to imposed restriction in the nano-compartments compared to that in bulk buffer is also revealed by temporal fluorescence anisotropy of the dansyl probe.

Population of On-pathway Intermediates in the Folding of Ubiquitin

The role that intermediate states play in protein folding is the subject of intense investigation and in the case of ubiquitin has been controversial. We present fluorescence-detected kinetic data derived from single and double mixing stopped-flow experiments to show that the F45W mutant of ubiquitin (WT*), a well-studied single-domain protein and most recently regarded as a simple two-state system, folds via on-pathway intermediates. To account for the discrepancy we observe between equilibrium and kinetic stabilities and m-values, we show that the polypeptide chain undergoes rapid collapse to an intermediate whose presence we infer from a fast lag phase in interrupted refolding experiments. Double-jump kinetic experiments identify two direct folding phases that are not associated with slow isomerisation reactions in the unfolded state. These two phases are explained by kinetic partitioning which allows molecules to reach the native state from the collapsed state via two possible competing routes, which we further examine using two destabilised ubiquitin mutants. Interrupted refolding experiments allow us to observe the formation and decay of an intermediate along one of these pathways. A plausible model for the folding pathway of ubiquitin is presented that demonstrates that obligatory intermediates and/or chain collapse are important events in restricting the conformational search for the native state of ubiquitin.

The earliest events in protein folding: a structural requirement for ultrafast folding in cytochrome C

The folding dynamics of reduced cytochrome c (redcyt c) obtained from tuna heart, which contains a tryptophan residue at the site occupied by His33 in horse heart cytochrome c, was studied using nanosecond time-resolved optical rotatory dispersion spectroscopy. As observed previously for horse heart redcyt c, two time regimes were observed for secondary structure formation in tuna redcyt c: a fast (microseconds) and a slow (milliseconds) phase. However, the fast phase of tuna redcyt c folding was much slower and smaller in amplitude than the same phase in horse. The differences in the fast folding phases suggest that for horse heart redcyt c, the conformers that undergo the fastest observed folding have the His18-Fe-His33 heme configuration, which appears to be necessary, but not sufficient, to poise an unfolded chain conformation for fastest folding in redcyt c.

Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin

Steady-state and transient conformational changes upon the thermal unfolding of ubiquitin were investigated with nonlinear IR spectroscopy of the amide I vibrations. Equilibrium temperature-dependent 2D IR spectroscopy reveals the unfolding of the beta-sheet of ubiquitin through the loss of cross peaks formed between transitions arising from delocalized vibrations of the beta-sheet. Transient unfolding after a nanosecond temperature jump is monitored with dispersed vibrational echo spectroscopy, a projection of the 2D IR spectrum. Whereas the equilibrium study follows a simple two-state unfolding, the transient experiments observe complex relaxation behavior that differs for various spectral components and spans 6 decades in time. The transient behavior can be separated into fast and slow time scales. From 100 ns to 0.5 ms, the spectral features associated with beta-sheet unfolding relax in a sequential, nonexponential manner, with time constants of 3 micros and 80 micros. By modeling the amide I vibrations of ubiquitin, this observation is explained as unfolding of the less stable strands III-V of the beta-sheet before unfolding of the hairpin that forms part of the hydrophobic core. This downhill unfolding is followed by exponential barrier-crossing kinetics on a 3-ms time scale.

Osmolytes Induce Structure in an Early Intermediate on the Folding Pathway of Barstar

Osmolytes stabilize proteins against denaturation, but little is known about how their stabilizing effect might affect a protein folding pathway. Here, we report the effects of the osmolytes, trimethylamine-N-oxide, and sarcosine on the stability of the native state of barstar as well as on the structural heterogeneity of an early intermediate ensemble, IE, on its folding pathway. Both osmolytes increase the stability of the native protein to a similar extent, with stability increasing linearly with osmolyte concentration. Both osmolytes also increase the stability of IE but to different extents. Such stabilization leads to an acceleration in the folding rate. Both osmolytes also alter the structure of IE but do so differentially; the fluorescence and circular dichroism properties of IE differ in the presence of the different osmolytes. Because these properties also differ from those of the unfolded form in refolding conditions, different burst phase changes in the optical signals are seen for folding in the presence of the different osmolytes. An analysis of the urea dependence of the burst phase changes in fluorescence and circular dichroism demonstrates that the formation of IE is itself a multistep process during folding and that the two osmolytes act by stabilizing, differentially, different structural components present in the IE ensemble. Thus, osmolytes can alter the basic nature of a protein folding pathway by discriminating, through differential stabilization, between different members of an early intermediate ensemble, and in doing so, they thereby appear to channel folding along one route when many routes are available.

Folding barrier in horse cytochrome c: support for a classical folding pathway

Native-state structures and conformations of ferrocytochrome c, nitrosylcytochrome c, and carbonmonoxycytochrome c are very similar. They are, however, immensely different from each other in terms of thermodynamic stability. The dramatic destabilization of ferrocytochrome c to the extent of 12 kcal mol(-1) produces no effect on the folding rate, and this is so in spite of the fact that all three test-tube variants fold in an apparent two-state manner. For all three proteins the folding barrier is early in time, sizable in energy, and is of the same magnitude (approximately 6.5 kcal mol(-1)). These results raise some challenges to the "new view" of protein folding. An early transition state, the search for which consumes most of the observed folding time, is suggested.