Application of the diffusion-collision model to the folding of three-helix bundle proteins

Molecular dynamics and protein function

A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.

Helix stability and hydrophobicity in the folding mechanism of the bacterial immunity protein Im9

Recent models suggest that the mechanism of protein folding is determined by the balance between the stability of secondary structural elements and the hydrophobicity of the sequence. Here we determine the role of these factors in the folding kinetics of Im9* by altering the secondary structure propensity or hydrophobicity of helices I, II or IV by the substitution of residues at solvent exposed sites. The folding kinetics of each variant were measured at pH 7.0 and 10 degrees C, under which conditions wild-type Im9* folds with two-state kinetics. We show that increasing the helicity of these sequences in regions known to be structured in the folding intermediate of Im7*, switches the folding of Im9* from a two- to three-state mechanism. By contrast, increasing the hydrophobicity of helices I or IV has no effect on the kinetic folding mechanism. Interestingly, however, increasing the hydrophobicity of solvent-exposed residues in helix II stabilizes the folding intermediate and the rate-limiting transition state, consistent with the view that this helix makes significant non-native interactions during folding. The results highlight the generic importance of intermediates in folding and show that such species can be populated by increasing helical propensity or by stabilizing inter-helix contacts through non-native interactions.

The role of sequence and structure in protein folding kinetics; the diffusion-collision model applied to proteins L and G

The diffusion-collision model (DCM) is applied to the folding kinetics of protein L and protein G. In the DCM, the two proteins are treated as consisting of two beta-hairpins and one alpha-helix, so that they are isomorphous with the three-helix bundle DCM model. In the absence of sequence dependent factors, both proteins would fold in the same way in the DCM, with the coalescence of the N-terminal hairpin and the helix slightly favored over the C-terminal hairpin and the helix because the former are closer together than the latter. However, sequence dependent factors make the N-terminal hairpin of protein L and the C-terminal hairpin of protein G more stable in the ensemble of unfolded conformations. This difference in the stabilities gives rise to the difference in the calculated folding behavior, in agreement with experiment.

Probing site-specific conformational distributions in protein folding with solid-state NMR

We demonstrate an experimental approach to structural studies of unfolded and partially folded proteins in which conformational distributions are probed at a site-specific level by 2D solid-state 13C NMR spectroscopy of glassy frozen solutions. Experiments on chemical denaturation of the 35-residue villin headpiece subdomain, a model three-helix-bundle protein with a known folded structure, reveal that 13C-labeled residues in the three helical segments of the folded state have markedly different conformational distributions in the unfolded state. Moreover, the 2D solid-state NMR line shapes near the unfolding midpoint do not fit a simple two-state model, in which the conformational distributions of the unfolded component are assumed to be independent of denaturant concentration. Comparison with solid-state NMR spectra of peptides containing the individual helical segments suggests an alternative two-step description of conformational distributions in partially folded states of the helical villin headpiece subdomain, in which chemical denaturation is viewed as a disruption of tertiary contacts followed by equilibration of local secondary structure according to the intrinsic helical propensities of individual segments.

A Minimal Model of Three-State Folding Dynamics of Helical Proteins

A diffusion-collision-like model is proposed for helical proteins with three-state folding dynamics. The model generalizes a previous scheme based on the dynamics of putatively essential parts of the protein (foldons) that was successfully tested on proteins with two-state folding. We show that the extended model, unlike the original one, allows satisfactory calculation of the folding rate and reconstruction of the salient steps of the folding pathway of two proteins with three-state folding (Im7 and p16). The dramatic reduction of variables achieved by focusing on the foldons makes our model a good candidate for a minimal description of the folding process also for three-state folders. Finally, the applicability of the foldon diffusion-collision model to two-state and three-state folders suggests that different folding mechanisms are amenable to conceptually homogeneous descriptions. The implications for a unification of the variety of folding theories so far proposed for helical proteins are discussed in the final discussion.

The folding of spectrin domains II: phi-value analysis of R16

Studies on the folding of helical proteins have shown a wide range of different mechanisms and highlighted the importance of helical propensity as a factor in determining folding mechanism. Here, we contribute to this interesting field with the protein engineering phi-value analysis of the 16th domain of chicken brain alpha-spectrin, R16. The fortuitous curvature seen in the unfolding arm of the chevron plot allows us to investigate both early and late events in folding. R16 is the first two-state helical protein for which this has been possible.

Experimental resolution of early steps in protein folding: testing molecular dynamics simulations

Time-resolved Tyr fluorescence spectroscopy coupled with a laser-induced temperature-jump (T-jump) was employed to follow the folding relaxation dynamics of the B-domain of Staphylococcal protein A. The single Tyr is located in helix 1 (H1) and is a sensitive probe of the structure of this helix and the overall helical bundle structure. The results from this study were compared to those from a complementary infrared T-jump study on this protein [Vu, D. M.; Myers, J. K.; Oas, T. G.; Dyer, R. B. Biochemistry 2004, 43, 3582]. Both methods detect a microsecond process that follows the cooperative relaxation of the helical bundle core. However, a fast process (10-7 s) that follows the relaxation of the individual helices was observed only with the infrared probe. Thus, fast formation of H1 is not observed, but rather H1 forms in the microsecond phase, concomitantly with the docking to (and stabilization by) the other two helices to form the helical bundle structure. This observation validates the results of several previous molecular dynamics simulations that predict H1 formation only in the final assembly of the helix bundle.

Protein folding in high-dimensional spaces: hypergutters and the role of nonnative interactions

We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilizing interactions, and folding rates themselves, leads to a model of the energy hypersurface that is characterized by the structure of diffusive "hypergutters" as well as the familiar "funnels". Several general predictions result: 1), intermediate subspaces of configurations will always be visited; 2), specific but nonnative interactions may be important in stabilizing these low-dimensional diffusive searches on the folding pathway, as well as native interactions; 3), sequential barriers will commonly be found, even in "two-state" proteins; 4), very early times will show characteristic departures from single-exponential kinetics; and 5), contributions of nonnative interactions to Phi-values and "Chevron plots" are calculable, and may be significant. The example of a three-helix bundle is treated in more detail as an illustration. The model also shows that high-dimensional structures provide conceptual relations between different models of protein folding. It suggests that kinetic strategies for fast folding may be encoded rather generally in nonnative as well as in native interactions. The predictions are related to very recent findings in experiment and simulation.

Fast and faster: a designed variant of the B-domain of protein A folds in 3 microsec

We have introduced the mutation glycine 29 to alanine, designed to increase the rate of protein folding, into the B-domain of protein A (BdpA). From NMR lineshape analysis, we find the G29A mutation increases the folding rate constant by threefold; the folding time is 3 microsec. Although wild-type BdpA folds extremely fast, simple-point mutations can still speed up the folding; thus, the folding rate is not evolutionarily maximized. The short folding time of G29A BdpA (the shortest time yet reported) makes it an attractive candidate for an all-atom molecular dynamics simulation that could potentially show a complete folding reaction starting from an extended chain. We also constructed a fluorescent variant of BdpA by mutating phenylalanine 13 to tryptophan, allowing fluorescence-based time-resolved temperature-jump measurements. Temperature jumps and NMR complement each other, and give a very complete picture of the folding kinetics.

The protein folding 'speed limit'

How fast can a protein possibly fold? This question has stimulated experimentalists to seek fast folding proteins and to engineer them to fold even faster. Proteins folding at or near the speed limit are prime candidates for all-atom molecular dynamics simulations. They may also have no free energy barrier, allowing the direct observation of intermediate structures on the pathways from the unfolded to the folded state. Both experimental and theoretical approaches predict a speed limit of approximately N/100micros for a generic N-residue single-domain protein, with alpha proteins folding faster than beta or alphabeta. The predicted limits suggest that most known ultrafast folding proteins can be engineered to fold more than ten times faster.

Using protein folding rates to test protein folding theories

The fastest simple, kinetically two-state protein folds a million times more rapidly than the slowest. Here we review many recent theories of protein folding kinetics in terms of their ability to qualitatively rationalize, if not quantitatively predict, this fundamental experimental observation.

Fast folding of a helical protein initiated by the collision of unstructured chains

To examine whether helix formation necessarily precedes chain collision, we have measured the folding of a fully helical coiled coil that has been specially engineered to have negligible intrinsic helical propensity but high overall stability. The folding rate approaches the diffusion-limited value and is much faster than possible if folding is contingent on precollision helix formation. Therefore, the collision of two unstructured chains is the initial step of the dominant kinetic pathway, whereas helicity exerts its influence only at a later step. Folding from an unstructured encounter complex may be efficient and robust, which has implications for any biological process that couples folding to binding.

Prediction of protein folding rates from the amino acid sequence-predicted secondary structure

We present a method for predicting folding rates of proteins from their amino acid sequences only, or rather, from their chain lengths and their helicity predicted from their sequences. The method achieves 82% correlation with experiment over all 64 "two-state" and "multistate" proteins (including two artificial peptides) studied up to now.

Diffusion-collision model algorithms for protein folding kinetics

The diffusion-collision model (DCM) of protein folding is described qualitatively and quantitatively. The input parameters required to perform a calculation are explained, and the output data are outlined. Three examples are given of calculating DCM folding kinetics: the Engrailed Homeodomain (a three-helix bundle with three helical microdomains, pdb code 1ENH), protein G (with three microdomains having a beta-hairpin-alpha-helix-beta-hairpin motif, pdb code 1PGA), and apomyoglobin (with eight helices and seven strong microdomain-microdomain pairings).

Dynamics of the minimally frustrated helices determine the hierarchical folding of small helical proteins

In this paper we aim at determining the key residues of small helical proteins in order to build up reduced models of the folding dynamics. We start by arguing that the folding process can be dissected into concurrent fast and slow dynamics. The fast events are the quasiautonomous coil-to-helix transitions occurring in the minimally frustrated initiation sites of folding in the early stages of the process. The slow processes consist in the docking of the fluctuating helices formed in these critical sites. We show that a neural network devised to predict native secondary structures from sequence can be used to estimate the probabilities of formation of these helical traits as they are embedded in the protein. The resulting probabilities are shown to correlate well with the experimental helicities measured in the same isolated peptides. The relevance of this finding to the hierarchical character of folding is confirmed within the framework of a diffusion-collision-like mechanism. We demonstrate that thermodynamic and topological features of these critical helices allow accurate estimation of the folding times of five proteins that have been kinetically studied. This suggests that these critical helices determine the fundamental events of the whole folding process. A remarkable feature of our model is that not all of the native helices are eligible as critical helices, whereas the whole set of the native helices has been used so far in other reconstructions of the folding mechanism. This stresses that the minimally frustrated helices of these helical proteins comprise the minimal set of determinants of the folding process.

Testing protein-folding simulations by experiment: B domain of protein A

We have assessed the published predictions of the pathway of folding of the B domain of protein A, the pathway most studied by computer simulation. We analyzed the transition state for folding of the three-helix bundle protein, by using experimental Phi values on some 70 suitable mutants. Surprisingly, the third helix, which has the most stable alpha-helical structure as a peptide fragment, is poorly formed in the transition state, especially at its C terminus. The protein folds around a nearly fully formed central helix, which is stabilized by extensive hydrophobic side chain interactions. The turn connecting the poorly structured first helix to the central helix is unstructured, but the turn connecting the central helix to the third is in the process of being formed as the N-terminal region of the third helix begins to coalesce. The transition state is inconsistent with a classical framework mechanism and is closer to nucleation-condensation. None of the published atomistic simulations are fully consistent with the experimental picture although many capture important features. There is a continuing need for combining simulation with experiment to describe folding pathways, and of continued testing to improve predictive methods.

Towards realistic description of collective motions in the lattice protein folding models

Collective motions and the formation of clusters of residues play an important role in the folding of real proteins. However, existing Monte Carlo (MC) techniques of the protein folding simulations based on highly popular lattice models provide only a schematic representation of collective motions, which is rather far from physical reality. The Clustering Monte Carlo (CMC) algorithm was developed with particular aim to provide a realistic description of collective motions on the lattice. CMC allows modeling the cluster dynamics and the effects of the solvent viscosity, which is impossible in conventional algorithms. In this study two 2D lattice peptides, with the ground states of hierarchical and non-hierarchical design, were investigated comparatively using three methods: Metropolis MC with the local move set, Metropolis MC with unspecific rigid rotations and the CMC algorithm. We present evidence that the folding pathways and kinetics of hierarchically folding clustered sequence are not adequately described in conventional MC simulations, and the account for cluster dynamics provided by CMC allows to capture essential features of the folding process. Our data suggest that the methods, which enable specific cluster motions, such as CMC, should be used for a more realistic description of protein folding.

Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein

Fast relaxation kinetics studies of the B-domain of staphylococcal protein A were performed to characterize the folding and unfolding of this small three-helix bundle protein. The relaxation kinetics were initiated using a laser-induced temperature jump and probed using time-resolved infrared spectroscopy. The kinetics monitored within the amide I' absorbance of the polypeptide backbone exhibit two distinct kinetics phases with nanosecond and microsecond relaxation times. The fast kinetics relaxation time is close to the diffusion limits placed on protein folding reactions. The fast kinetics phase is dominated by the relaxation of the solvated helix (nu = 1632 cm(-1)), which reports on the fast relaxation of the individual helices. The slow kinetics phase follows the cooperative relaxation of the native helical bundle core that is monitored by both solvated (nu = 1632 cm(-1)) and buried helical IR bands (nu = 1652 cm(-1)). The folding rates of the slow kinetics phase calculated over an extended temperature range indicate that the core formation of this protein follows a pathway that is energetically downhill. The unfolding rates are much more strongly temperature-dependent indicating an activated process with a large energy barrier. These results provide significant insight into the primary process of protein folding and suggest that fast formation of helices can drive the folding of helical proteins.

Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump

The small size (58 residues) and simple structure of the B domain of staphylococcal protein A (BdpA) have led to this domain being a paradigm for theoretical studies of folding. Experimental studies of the folding of BdpA have been limited by the rapidity of its folding kinetics. We report the folding kinetics of a fluorescent mutant of BdpA (G29A F13W), named F13W*, using nanosecond laser-induced temperature jump experiments. Automation of the apparatus has permitted large data sets to be acquired that provide excellent signal-to-noise ratio over a wide range of experimental conditions. By measuring the temperature and denaturant dependence of equilibrium and kinetic data for F13W*, we show that thermodynamic modeling of multidimensional equilibrium and kinetic surfaces is a robust method that allows reliable extrapolation of rate constants to regions of the folding landscape not directly accessible experimentally. The results reveal that F13W* is the fastest-folding protein of its size studied to date, with a maximum folding rate constant at 0 M guanidinium chloride and 45 degrees C of 249,000 s(-1). Assuming the single-exponential kinetics represent barrier-limited folding, these data limit the value for the preexponential factor for folding of this protein to at least approximately 2 x 10(6) s(-1).

Peptide Models Provide Evidence for Significant Structure in the Denatured State of a Rapidly Folding Protein: The Villin Headpiece Subdomain

The villin headpiece subdomain is a cooperatively folded 36-residue, three-alpha-helix protein. The domain is one of the smallest naturally occurring sequences which has been shown to fold. Recent experimental studies have shown that it folds on the 10-micros time scale. Its small size, simple topology, and very rapid folding have made it an attractive target for computational studies of protein folding. We present temperature-dependent NMR studies that provide evidence for significant structure in the denatured state of the headpiece subdomain. A set of peptide fragments derived from the headpiece were also characterized in order to determine if there is a significant tendency to form a locally stabilized structure in the denatured state. Peptides corresponding to each of the three isolated helices and to the connection between the first and second helices were largely unstructured. A longer peptide fragment which contains the first and second helices shows considerable structure, as judged by NMR and CD. Concentration-dependent CD measurements and analytical ultracentrifugation experiments indicate that the structure is not due to self-association. NMR studies indicate that the structure is stabilized by tertiary interactions involving phenylalanines and Val 50. A peptide in which two of the three phenylalanines are changed to leucine is considerably less structured, confirming the importance of the phenylalanines. This work indicates that there is significant structure in the denatured state of this rapidly folding protein.

The importance of explicit chain representation in protein folding models: an examination of Ising-like models

A class of models that represents a protein chain as a sequence of "folded" and "unfolded" residues has recently been used to correlate rates and mechanisms of protein folding with the protein native structure. In order to better understand the conditions under which these "Ising-like" models apply, we compare results from this model to those obtained from an off-lattice model which uses the same potential function. We find that Ising-like models by construction impose folding via a highly sequential nucleation-condensation mechanism, which in turn leads to more rugged energy landscapes, fewer "pathways" to the native state, and in the specific case examined here, the cold shock protein A from Escherichia coli, a qualitative difference in the most likely order of events in folding.

Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations

We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.

Unifying features in protein-folding mechanisms

We compare the folding of representative members of a protein superfamily by experiment and simulation to investigate common features in folding mechanisms. The homeodomain superfamily of three-helical, single-domain proteins exhibits a spectrum of folding processes that spans the complete transition from concurrent secondary and tertiary structure formation (nucleation-condensation mechanism) to sequential secondary and tertiary formation (framework mechanism). The unifying factor in their mechanisms is that the transition state for (un)folding is expanded and very native-like, with the proportion and degree of formation of secondary and tertiary interactions varying. There is a transition, or slide, from the framework to nucleation-condensation mechanism with decreasing stability of the secondary structure. Thus, framework and nucleation-condensation are different manifestations of an underlying common mechanism.

Experimental tests of villin subdomain folding simulations

We have used laser temperature-jump to investigate the kinetics and mechanism of folding the 35 residue subdomain of the villin headpiece. The relaxation kinetics are biphasic with a sub-microsecond phase corresponding to a helix-coil transition and a slower microsecond phase corresponding to overall unfolding/refolding. At 300 K, the folding time is 4.3(+/-0.6) micros, making it the fastest folding, naturally occurring protein, with a rate close to the theoretical speed limit. This time is in remarkable agreement with the prediction of 5 (+11,-3) micros by Zagrovic et al. from atomistic molecular dynamics simulations using an implicit solvent model. We test their prediction that replacement of the C-terminal phenylalanine residue with alanine will increase the folding rate by removing a transient non-native interaction. We find that the alanine substitution has no effect on the folding rate or on the equilibrium constant. Implications of this result for the validity of the simulated folding mechanism are discussed.

Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain folds on the microsecond time scale

There is considerable interest in small proteins that fold very rapidly. These proteins have become attractive targets for both theoretical and computational studies. The independently folded 36-residue villin headpiece subdomain has been the subject of a number of such studies and is predicted to fold quickly. We demonstrate using dynamic NMR line-shape analysis that the protein folds on the time scale of 10 mus. Folding rates were directly estimated between 56 and 78 degrees C using resolved protein resonances from three different residues at both 500 and 700 MHz. The rates estimated using different residues and different field strengths agree well with each other. The estimated folding rate lies between 0.5 and 2.0 x 105 s-1 over this temperature range. The folding rate depends only weakly on temperature.

Local secondary structure content predicts folding rates for simple, two-state proteins

Many single-domain proteins exhibit two-state folding kinetics, with folding rates that span more than six orders of magnitude. A quantity of much recent interest for such proteins is their contact order, the average separation in sequence between contacting residue pairs. Numerous studies have reached the surprising conclusion that contact order is well-correlated with the logarithm of the folding rate for these small, well-characterized molecules. Here, we investigate the physico-chemical basis for this finding by asking whether contact order is actually a composite number that measures the fraction of local secondary structure in the protein; viz. turns, helices, and hairpins. To pursue this question, we calculated the secondary structure content for 24 two-state proteins and obtained coefficients that predict their folding rates. The predicted rates correlate strongly with experimentally determined rates, comparable to the correlation with contact order. Further, these predicted folding rates are correlated strongly with contact order. Our results suggest that the folding rate of two-state proteins is a function of their local secondary structure content, consistent with the hierarchic model of protein folding. Accordingly, it should be possible to utilize secondary structure prediction methods to predict folding rates from sequence alone.

The complete folding pathway of a protein from nanoseconds to microseconds

Combining experimental and simulation data to describe all of the structures and the pathways involved in folding a protein is problematical. Transition states can be mapped experimentally by phi values, but the denatured state is very difficult to analyse under conditions that favour folding. Also computer simulation at atomic resolution is currently limited to about a microsecond or less. Ultrafast-folding proteins fold and unfold on timescales accessible by both approaches, so here we study the folding pathway of the three-helix bundle protein Engrailed homeodomain. Experimentally, the protein collapses in a microsecond to give an intermediate with much native alpha-helical secondary structure, which is the major component of the denatured state under conditions that favour folding. A mutant protein shows this state to be compact and contain dynamic, native-like helices with unstructured side chains. In the transition state between this and the native state, the structure of the helices is nearly fully formed and their docking is in progress, approximating to a classical diffusion-collision model. Molecular dynamics simulations give rate constants and structural details highly consistent with experiment, thereby completing the description of folding at atomic resolution.

Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: similarities and differences in the folding of homologous proteins

The bacterial immunity proteins Im7 and Im9 fold with mechanisms of different kinetic complexity. Whilst Im9 folds in a two-state transition at pH 7.0 and 10 degrees C, Im7 populates an on-pathway intermediate under these conditions. In order to assess the role of sequence versus topology in the folding of these proteins, and to analyse the effect of populating an intermediate on the landscape for folding, we have determined the conformational properties of the rate-limiting transition state for Im9 folding/unfolding using Phi(F)-value analysis and have compared the results with similar data obtained previously for Im7. The data show that the rate-limiting transition states for Im9 and Im7 folding/unfolding are similar: both are compact (beta(T)=0.94 and 0.89, respectively) and contain three of the four native helices docked around a specific hydrophobic core. Significant differences are observed, however, in the magnitude of the Phi(F)-values obtained for the two proteins. Of the 20 residues studied in both proteins, ten have Phi(F)-values in Im7 that exceed those in Im9 by more than 0.2, and of these five differ by more than 0.4. The data suggest that the population of an intermediate in Im7 results in folding via a transition state ensemble that is conformationally restricted relative to that of Im9. The data are consistent with the view that topology is an important determinant of folding. Importantly, however, they also demonstrate that while the folding transition state may be conserved in homologous proteins that fold with two and three-state kinetics, the population of an intermediate can have a significant effect on the breadth of the transition state ensemble.

Protein-folding kinetics and mechanisms studied by pulse-labeling and mass spectrometry

The "protein-folding problem" refers to the question of how and why a denatured polypeptide chain can spontaneously fold into a compact and highly ordered conformation. The classical description of this process in terms of reaction pathways has been complemented by models that describe folding as a biased conformational diffusion on a multidimensional energy landscape. The identification and characterization of short-lived intermediates provide important insights into the mechanism of folding. Pulsed hydrogen/deuterium exchange (HDX) methods are among the most powerful tools for studying the properties of kinetic intermediates. Analysis of pulse-labeled proteins by mass spectrometry (MS) provides information that is complementary to that obtained in nuclear magnetic resonance (NMR) studies; NMR data represent an average of entire protein ensembles, whereas MS can detect co-existing protein species. MS-based pulse-labeling experiments can distinguish between folding scenarios that involve parallel pathways, and those where folding is channeled through obligatory intermediates. The proteolytic digestion/MS technique provides spatially resolved information on the HDX pattern of folding intermediates. This method is especially important for proteins that are too large to be studied by NMR. Although traditional pulsed HDX protocols are based on quench-flow techniques, it is also possible to use electrospray (ESI) MS to analyze the reaction mixture on-line and "quasi-instantaneously" after labeling. This approach allows short-lived protein conformations to be studied by their HDX level, their ESI charge-state distribution, and their ligand-binding state. Covalent labeling of free cysteinyl residues provides an alternative approach to pulsed HDX experiments. Another promising development is the use of synchrotron X-rays to induce oxidation at specific sites within a protein for studying their solvent accessibility during folding.

The topomer search model: A simple, quantitative theory of two-state protein folding kinetics

Most small, single-domain proteins fold with the uncomplicated, single-exponential kinetics expected for diffusion on a smooth energy landscape. Despite this energetic smoothness, the folding rates of these two-state proteins span a remarkable million-fold range. Here, we review the evidence in favor of a simple, mechanistic description, the topomer search model, which quantitatively accounts for the broad scope of observed two-state folding rates. The model, which stipulates that the search for those unfolded conformations with a grossly correct topology is the rate-limiting step in folding, fits observed rates with a correlation coefficient of approximately 0.9 using just two free parameters. The fitted values of these parameters, the pre-exponential attempt frequency and a measure of the difficulty of ordering an unfolded chain, are consistent with previously reported experimental constraints. These results suggest that the topomer search process may dominate the relative barrier heights of two-state protein-folding reactions.

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

We have used laser temperature jump spectroscopy to measure the folding speed of the 20-residue Trp-cage, the smallest polypeptide known to exhibit truly cooperative folding behavior. The observed folding time (4 mus at room temperature) makes this not only the smallest foldable protein, but also the fastest, with a folding speed that exceeds contact-order predictions and approaches anticipated diffusional "speed limits" for protein folding.