Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity

Transient On- and Off-Pathway Protein Folding Intermediate States Characterized with NMR Relaxation Dispersion

The earliest events in the folding of a protein are in general poorly understood. We used NMR R2 relaxation dispersion experiments to study transient local collapse events in the unfolded-state (U) conformational ensemble of apomyoglobin (apoMb). Local residual secondary structure (seen in regions corresponding to the A, D, E, and H helices of the folded protein) is largely unchanged over the pH range of 2.3-2.75, yet a significant pH-dependent increase in the conformational exchange contribution to the R2 relaxation rate (Rex) indicates that transient intramolecular contacts occur on a microsecond to millisecond time scale at pH 2.75. A comparison of 15N and 13CO relaxation dispersion data at pH 2.75 for residues in the A, B, G, and H regions, which participate in the earliest folding intermediates, indicates that chain collapse and secondary structure formation are rapid and concomitant. Increasingly stabilizing conditions (lower temperature, higher pH) result in the observation of a relaxation dispersion in the C, CD, and E regions of the protein, which are known to fold at later stages. Mutation of Trp14 in the A-helix region to Ala eliminates conformational exchange throughout the protein, and the mutation of hydrophobic residues in other regions results in the selective inhibition of conformational exchange in the B, G, or H regions. The R2 dispersion data for WT apoMb at pH 2.75 and 10 °C are best fit to a four-state model ABGH ⇆ AGH ⇆ U ⇆ ABCD that includes on-pathway (AGH and ABGH) and off-pathway (ABCD) transiently folded states, both of which are required to explain the behavior of the mutant proteins. The off-pathway intermediate is destabilized at higher temperatures. Our analysis provides insights into the earliest stages of apoMb folding where the collapsing polypeptide chain samples both productive and nonproductive states with stabilized secondary structure.

Thermodynamic, kinetic and conformational analysis of proteins diffusion-sorption on a solid surface

In this paper we examine particularly some of the more fundamental properties of protein conformational changes at a solid surface coupled with diffusion from the bulk of an aqueous solution and with the adsorption-desorption processes. We focus our attention on adsorbed protein monolayers upon a solid surface using a thermodynamic and kinetic analytical development. Account is also taken of the effects on the overall rate of the conformational change on a solid surface of deviation from ideality, of protein flexibility, of surface free energy and of interaction with reactive solid sites. Our theory applied to steady states is illustrated by examples such as folding-misfolding-unfolding of RNase and SNase on a solid surface after diffusion and adsorption from an aqueous solution. For this purpose, we put forward the determining steps which shall lead to the steady state. The existence of three situations is highlighted according to the values of the typical constants relevant for the protein considered: reaction rate determining step, diffusion and sorption determining steps, mixed adsorption diffusion and reaction rate. Finally, we have tried to link the developments of our theories to a large literature based on experimental results encountered during proteins diffusion-sorption-reaction processes, fundamental topics that has been since long investigated by Miller's team in MPKG.

Transient non-native helix formation during the folding of β-lactoglobulin

In ideal proteins, only native interactions are stabilized step-by-step in a smooth funnel-like energy landscape. In real proteins, however, the transient formation of non-native structures is frequently observed. In this review, the transient formation of non-native structures is described using the non-native helix formation during the folding of β-lactoglobulin as a prominent example. Although β-lactoglobulin is a predominantly β-sheet protein, it has been shown to form non-native helices during the early stage of folding. The location of non-native helices, their stabilization mechanism, and their role in the folding reaction are discussed.

Protein evolution along phylogenetic histories under structurally constrained substitution models

MOTIVATION

Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes.

RESULTS

We developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process.

The use of supramolecular structures as protein ligands

Congo red dye as well as other eagerly self-assembling organic molecules which form rod-like or ribbon-like supramolecular structures in water solutions, appears to represent a new class of protein ligands with possible wide-ranging medical applications. Such molecules associate with proteins as integral clusters and preferentially penetrate into areas of low molecular stability. Abnormal, partly unfolded proteins are the main binding target for such ligands, while well packed molecules are generally inaccessible. Of particular interest is the observation that local susceptibility for binding supramolecular ligands may be promoted in some proteins as a consequence of function-derived structural changes, and that such complexation may alter the activity profile of target proteins. Examples are presented in this paper.

Geometric parameters defining the structure of proteins--relation to early-stage folding step

Two geometrical parameters describing the structure of a polypeptide: V-dihedral angle between two sequential peptide bond planes and R-radius of curvature are used for structural classification of polypeptide structure in proteins. The relation between these two parameters was the basis for the definition of the conformational sub-space for early-stage structural forms. The cluster analysis of V and lnR, applied to the selected proteins of well-defined secondary structure (according to DSSP classification) and to proteins without any introductory classified analysis, revealed that several of the discriminated groups of proteins agree with the assumed model of early-stage conformational sub-space. This analysis shows that protein structures may be represented in VR space instead of Phi, Psi angles space, thus lowering the conformational space dimensionality. The VR model allows classification of traditional secondary structure elements as well as different Random Coil motifs, which broadens the range of recognized structural categories (compared to standard secondary structure elements).

Time-dependent changes in side-chain solvent accessibility during cytochrome c folding probed by pulsed oxidative labeling and mass spectrometry

The current work employs a novel approach for characterizing structural changes during the refolding of acid-denatured cytochrome c (cyt c). At various time points (ranging from 10 ms to 5 min) after a pH jump from 2 to 7, the protein is exposed to a microsecond hydroxyl radical (.OH) pulse that induces oxidative labeling of solvent-exposed side chains. Most of the covalent modifications appear as +16-Da adducts that are readily detectable by mass spectrometry. The overall extent of labeling decreases as folding proceeds, reflecting dramatic changes in the accessibility of numerous residues. Peptide mapping and tandem mass spectrometry reveal that the side chains of C14, C17, H33, F46, Y48, W59, M65, Y67, Y74, M80, I81, and Y97 are among the dominant sites of oxidation. Temporal changes in the accessibility of these residues are consistent with docking of the N- and C-terminal helices as early as 10 ms. However, structural reorganization at the helix interface takes place up to at least 1 s. Initial misligation of the heme iron by H33 leads to distal crowding, giving rise to low solvent accessibility of the displaced (native) M80 ligand and the adjacent I81. W59 retains a surprisingly high level of accessibility long into the folding process, indicating the presence of packing defects in the hydrophobically collapsed core. Overall, the results of this work are consistent with previous hydrogen/deuterium exchange studies that proposed a foldon-mediated mechanism. The structural data obtained by .OH labeling monitor the packing and burial of side chains, whereas hydrogen/deuterium exchange primarily monitors the formation of secondary structure elements. Hence, the two approaches yield complementary information. Considering the very short time scale of pulsed oxidative labeling, an extension of the approach used here to sub-millisecond folding studies should be feasible.

Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants

Metals are the most commonly encountered protein cofactors, and they play important structural and functional roles in biology. In many cases, metal binding provides a major driving force for a polypeptide chain to fold. While there are many studies on the structure, stability, and function of metal-binding proteins, there are few studies focusing on understanding the kinetic mechanism of metal-induced folding. Herein, the Zn(2+)-induced folding kinetics of a small zinc-binding protein are studied; the CH1(1) peptide is derived from the first cysteine/histidine-rich region (CH1 domain) of the protein interaction domains of the transcriptional coregulator CREB-binding protein. Computational design is used to introduce tryptophan and histidine mutations that are structurally consistent with CH1(1); these mutants are studied using stopped-flow tryptophan fluorescence experiments. The Zn(2+)-induced CH1(1) folding kinetics are consistent with two parallel pathways, where the initial binding of Zn(2+) occurs at two sites. However, the initially formed Zn(2+)-bound complexes can proceed either directly to the folded state where zinc adopts a tetrahedral coordination or to an off-pathway misligated intermediate. While elimination of those ligands responsible for misligation simplifies the folding kinetics, it also leads to a decrease in the zinc binding constant. Therefore, these results suggest why these nonnative zinc ligands in the CH1(1) motif are conserved in several distantly related organisms and why the requirement for function can lead to kinetic frustration in folding. In addition, the loop closure rate of the CH1(1) peptide is determined based on the proposed model and temperature-dependent kinetic measurements.

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.

Protein folding: independent unrelated pathways or predetermined pathway with optional errors

The observation of heterogeneous protein folding kinetics has been widely interpreted in terms of multiple independent unrelated pathways (IUP model), both experimentally and in theoretical calculations. However, direct structural information on folding intermediates and their properties now indicates that all of a protein population folds through essentially the same stepwise pathway, determined by cooperative native-like foldon units and the way that the foldons fit together in the native protein. It is essential to decide between these fundamentally different folding mechanisms. This article shows, contrary to previous supposition, that the heterogeneous folding kinetics observed for the staphylococcal nuclease protein (SNase) does not require alternative parallel pathways. SNase folding kinetics can be fit equally well by a single predetermined pathway that allows for optional misfolding errors, which are known to occur ubiquitously in protein folding. Structural, kinetic, and thermodynamic information for the folding intermediates and pathways of many proteins is consistent with the predetermined pathway-optional error (PPOE) model but contrary to the properties implied in IUP models.

Paradigm-shifters: phosphorylated prolactin and short prolactin receptors

Since the discovery of physiologically-regulated prolactin (PRL) phosphorylation, one focus of the laboratory has been an examination of the different functions of the unmodified and phosphorylated hormone. In the mammary gland, unmodified PRL promotes growth activities, whereas phosphorylated or pseudophosphorylated PRL antagonizes this while also being a superior agonist for changes that favor differentiation. Phosphorylated PRL also increases expression of the short forms of the PRL receptor. These short forms of the receptor have functions beyond the accepted dominant negative and in mammary epithelial cells are capable of generating an intracellular signal leading to increased tight junction formation and beta-casein expression.

The foldon substructure of staphylococcal nuclease

To search for submolecular foldon units, the spontaneous reversible unfolding and refolding of staphylococcal nuclease under native conditions was studied by a kinetic native-state hydrogen exchange (HX) method. As for other proteins, it appears that staphylococcal nuclease is designed as an assembly of well-integrated foldon units that may define steps in its folding pathway and may regulate some other functional properties. The HX results identify 34 amide hydrogens that exchange with solvent hydrogens under native conditions by way of large transient unfolding reactions. The HX data for each hydrogen measure the equilibrium stability (Delta G(HX)) and the kinetic unfolding and refolding rates (k(op) and k(cl)) of the unfolding reaction that exposes it to exchange. These parameters separate the 34 identified residues into three distinct HX groupings. Two correspond to clearly defined structural units in the native protein, termed the blue and red foldons. The remaining HX grouping contains residues, not well separated by their HX parameters alone, that represent two other distinct structural units in the native protein, termed the green and yellow foldons. Among these four sets, a last unfolding foldon (blue) unfolds with a rate constant of 6 x 10(-6) s(-1) and free energy equal to the protein's global stability (10.0 kcal/mol). It represents part of the beta-barrel, including mutually H-bonding residues in the beta 4 and beta 5 strands, a part of the beta 3 strand that H-bonds to beta 5, and residues at the N-terminus of the alpha2 helix that is capped by beta 5. A second foldon (green), which unfolds and refolds more rapidly and at slightly lower free energy, includes residues that define the rest of the native alpha2 helix and its C-terminal cap. A third foldon (yellow) defines the mutually H-bonded beta1-beta2-beta 3 meander, completing the native beta-barrel, plus an adjacent part of the alpha1 helix. A final foldon (red) includes residues on remaining segments that are distant in sequence but nearly adjacent in the native protein. Although the structure of the partially unfolded forms closely mimics the native organization, four residues indicate the presence of some nonnative misfolding interactions. Because the unfolding parameters of many other residues are not determined, it seems likely that the concerted foldon units are more extensive than is shown by the 34 residues actually observed.

Protein folding and misfolding: mechanism and principles

Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding.

Multiple tryptophan probes reveal that ubiquitin folds via a late misfolded intermediate

Much of our understanding of protein folding mechanisms is derived from experiments using intrinsic fluorescence of natural or genetically inserted tryptophan (Trp) residues to monitor protein refolding and site-directed mutagenesis to determine the energetic role of amino acids in the native (N), intermediate (I) or transition (T) states. However, this strategy has limited use to study complex folding reactions because a single fluorescence probe may not detect all low-energy folding intermediates. To overcome this limitation, we suggest that protein refolding should be monitored with different solvent-exposed Trp probes. Here, we demonstrate the utility of this approach by investigating the controversial folding mechanism of ubiquitin (Ub) using Trp probes located at residue positions 1, 28, 45, 57, and 66. We first show that these Trp are structurally sensitive and minimally perturbing fluorescent probes for monitoring folding/unfolding of the protein. Using a conventional stopped-flow instrument, we show that ANS and Trp fluorescence detect two distinct transitions during the refolding of all five Trp mutants at low concentrations of denaturant: T(1), a denaturant-dependent transition and T(2), a slower transition, largely denaturant-independent. Surprisingly, some Trp mutants (Ub(M1W), Ub(S57W)) display Trp fluorescence changes during T(1) that are distinct from the expected U-->N transition suggesting that the denaturant-dependent refolding transition of Ub is not a U-->N transition but represents the formation of a structurally distinct I-state (U-->I). Alternatively, this U-->I transition could be also clearly distinguished by using a combination of two Trp mutations Ub(F45W-T66W) for which the two Trp probes that display fluorescence changes of opposite sign during T(1) and T(2) (Ub(F45W-T66W)). Global fitting of the folding/unfolding kinetic parameters and additional folding-unfolding double-jump experiments performed on Ub(M1W), a mutant with enhanced fluorescence in the I-state, demonstrate that the I-state is stable, compact, misfolded, and on-pathway. These results illustrate how transient low-energy I-states can be characterized efficiently in complex refolding reactions using multiple Trp probes.

Branching in the sequential folding pathway of cytochrome c

Previous results indicate that the folding pathways of cytochrome c and other proteins progressively build the target native protein in a predetermined stepwise manner by the sequential formation and association of native-like foldon units. The present work used native state hydrogen exchange methods to investigate a structural anomaly in cytochrome c results that suggested the concerted folding of two segments that have little structural relationship in the native protein. The results show that the two segments, an 18-residue omega loop and a 10-residue helix, are able to unfold and refold independently, which allows a branch point in the folding pathway. The pathway that emerges assembles native-like foldon units in a linear sequential manner when prior native-like structure can template a single subsequent foldon, and optional pathway branching is seen when prior structure is able to support the folding of two different foldons.

Folding versus aggregation: polypeptide conformations on competing pathways

Protein aggregation has now become recognised as an important and generic aspect of protein energy landscapes. Since the discovery that numerous human diseases are caused by protein aggregation, the biophysical characterisation of misfolded states and their aggregation mechanisms has received increased attention. Utilising experimental techniques and computational approaches established for the analysis of protein folding reactions has ensured rapid advances in the study of pathways leading to amyloid fibrils and amyloid-related aggregates. Here we describe recent experimental and theoretical advances in the elucidation of the conformational properties of dynamic, heterogeneous and/or insoluble protein ensembles populated on complex, multidimensional protein energy landscapes. We discuss current understanding of aggregation mechanisms in this context and describe how the synergy between biochemical, biophysical and cell-biological experiments are beginning to provide detailed insights into the partitioning of non-native species between protein folding and aggregation pathways.

A unified mechanism for protein folding: predetermined pathways with optional errors

There is a fundamental conflict between two different views of how proteins fold. Kinetic experiments and theoretical calculations are often interpreted in terms of different population fractions folding through different intermediates in independent unrelated pathways (IUP model). However, detailed structural information indicates that all of the protein population folds through a sequence of intermediates predetermined by the foldon substructure of the target protein and a sequential stabilization principle. These contrary views can be resolved by a predetermined pathway--optional error (PPOE) hypothesis. The hypothesis is that any pathway intermediate can incorporate a chance misfolding error that blocks folding and must be reversed for productive folding to continue. Different fractions of the protein population will then block at different steps, populate different intermediates, and fold at different rates, giving the appearance of multiple unrelated pathways. A test of the hypothesis matches the two models against extensive kinetic folding results for hen lysozyme which have been widely cited in support of independent parallel pathways. The PPOE model succeeds with fewer fitting constants. The fitted PPOE reaction scheme leads to known folding behavior, whereas the IUP properties are contradicted by experiment. The appearance of a conflict with multipath theoretical models seems to be due to their different focus, namely on multitrack microscopic behavior versus cooperative macroscopic behavior. The integration of three well-documented principles in the PPOE model (cooperative foldons, sequential stabilization, optional errors) provides a unifying explanation for how proteins fold and why they fold in that way.

A backbone-based theory of protein folding

Under physiological conditions, a protein undergoes a spontaneous disorder order transition called "folding." The protein polymer is highly flexible when unfolded but adopts its unique native, three-dimensional structure when folded. Current experimental knowledge comes primarily from thermodynamic measurements in solution or the structures of individual molecules, elucidated by either x-ray crystallography or NMR spectroscopy. From the former, we know the enthalpy, entropy, and free energy differences between the folded and unfolded forms of hundreds of proteins under a variety of solvent/cosolvent conditions. From the latter, we know the structures of approximately 35,000 proteins, which are built on scaffolds of hydrogen-bonded structural elements, alpha-helix and beta-sheet. Anfinsen showed that the amino acid sequence alone is sufficient to determine a protein's structure, but the molecular mechanism responsible for self-assembly remains an open question, probably the most fundamental open question in biochemistry. This perspective is a hybrid: partly review, partly proposal. First, we summarize key ideas regarding protein folding developed over the past half-century and culminating in the current mindset. In this view, the energetics of side-chain interactions dominate the folding process, driving the chain to self-organize under folding conditions. Next, having taken stock, we propose an alternative model that inverts the prevailing side-chain/backbone paradigm. Here, the energetics of backbone hydrogen bonds dominate the folding process, with preorganization in the unfolded state. Then, under folding conditions, the resultant fold is selected from a limited repertoire of structural possibilities, each corresponding to a distinct hydrogen-bonded arrangement of alpha-helices and/or strands of beta-sheet.

Molecular statistics of cytochrome c: structural plasticity and molecular environment

Nuclear magnetic resonance experiments performed on yeast mitochondrial cytochrome c (Cytc), a paradigmatic electron transfer protein, reveal that the two oxidation states have similar structures, but different mobility: despite the few structural differences compared with the reduced form, the oxidized form displays a larger unfolding propensity. Molecular dynamics simulations performed on both NMR reduced and NMR oxidized forms show that the reduced form has a larger solvent-accessible surface area (SASA). Starting from this observation, a molecular statistical approach was then applied in order to correlate the molecular surface to molecular mobility. Simulations started from biased initial conditions corresponding to different molecular sizes were combined with the maximal constrained entropy method. The NMR structure of oxidized Cytc is more suited to expose a smaller SASA than the NMR structure of the reduced form, but the accessible conformational landscape at 300 K around the NMR oxidized structure is flatter than for the NMR reduced structure. Protein configurations of smaller SASA and size display larger plasticity when they resemble the NMR oxidized structure, whereas they are more rigid when they resemble the NMR reduced structure. Implications of the results for the protein properties during its functional process are discussed.

Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction

Discovering the mechanism of protein folding, in molecular biology, is a great challenge. A key step to this end is to find factors that correlate with protein folding rates. Over the past few years, many empirical parameters, such as contact order, long-range order, total contact distance, secondary structure contents, have been developed to reflect the correlation between folding rates and protein tertiary or secondary structures. However, the correlation between proteins' folding rates and their amino acid compositions has not been explored. In the present work, we examined systematically the correlation between proteins' folding rates and their amino acid compositions for two-state and multistate folders and found that different amino acids contributed differently to the folding progress. The relation between the amino acids' molecular weight and degeneracy and the folding rates was examined, and the role of hydrophobicity in the protein folding process was also inspected. As a consequence, a new indicator called composition index was derived, which takes no structure factors into account and is merely determined by the amino acid composition of a protein. Such an indicator is found to be highly correlated with the protein's folding rate (r > 0.7). From the results of this work, three points of concluding remarks are evident. (1) Two-state folders and multistate folders have different rate-determining amino acids. (2) The main determining information of a protein's folding rate is largely reflected in its amino acid composition. (3) Composition index may be the best predictor for an ab initio protein folding rate prediction directly from protein sequence from the standpoint of practical application.

Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism

Previous work used hydrogen exchange (HX) experiments in kinetic and equilibrium modes to study the reversible unfolding and refolding of cytochrome c (Cyt c) under native conditions. Accumulated results now show that Cyt c is composed of five individually cooperative folding units, called foldons, which unfold and refold as concerted units in a stepwise pathway sequence. The first three steps of the folding pathway are linear and sequential. The ordering of the last two steps has been unclear because the fast HX of the amino acid residues in these foldons has made measurement difficult. New HX experiments done under slower exchange conditions show that the final two foldons do not unfold and refold in an obligatory sequence. They unfold separately and neither unfolding obligately contains the other, as indicated by their similar unfolding surface exposure and the specific effects of destabilizing and stabilizing mutations, pH change, and oxidation state. These results taken together support a sequential stabilization mechanism in which folding occurs in the native context with prior native-like structure serving to template the stepwise formation of subsequent native-like foldon units. Where the native structure of Cyt c requires sequential folding, in the first three steps, this is found. Where structural determination is ambiguous, in the final two steps, alternative parallel folding is found.

Alternate pathways for folding in the flavodoxin fold family revealed by a nucleation-growth model

A recent study of experimental results for flavodoxin-like folds suggests that proteins from this family may exhibit a similar, signature pattern of folding intermediates. We study the folding landscapes of three proteins from the flavodoxin family (CheY, apoflavodoxin, and cutinase) using a simple nucleation and growth model that accurately describes both experimental and simulation results for the transition state structure, and the structure of on-pathway and misfolded intermediates for CheY. Although the landscape features of these proteins agree in basic ways with the results of the study, the simulations exhibit a range of folding behaviours consistent with two alternate folding routes corresponding to nucleation and growth from either side of the central beta-strand.

Identification of native and non-native structure in kinetic folding intermediates of apomyoglobin

Site-directed mutagenesis has been used to probe the interactions that stabilize the equilibrium and burst phase kinetic intermediates formed by apomyoglobin. Nine bulky hydrophobic residues in the A, E, G and H helices were replaced by alanine, and the effects on protein stability and kinetic folding pathways were determined. Hydrogen exchange pulse-labeling experiments, with NMR detection, were performed for all mutants. All of the alanine substitutions resulted in changes in proton occupancy or an increased rate of hydrogen-deuterium exchange for amides in the immediate vicinity of the mutation. In addition, most mutations affected residues in distant parts of the amino acid sequence, providing insights into the topology of the burst phase intermediate and the interactions that stabilize its structure. Differences between the pH 4 equilibrium molten globule and the kinetic intermediate are evident: the E helix region plays no discernible role in the equilibrium intermediate, but contributes significantly to stabilization of the ensemble of compact intermediates formed during kinetic refolding. Mutations that interfere with docking of the E helix onto the preformed A/B/G/H helix core substantially decrease the folding rate, indicating that docking and folding of the E helix region occurs prior to formation of the apomyoglobin folding transition state. The results of the mutagenesis experiments are consistent with rapid formation of an ensemble of compact burst phase intermediates with an overall native-like topological arrangement of the A, B, E, G, and H helices. However, the experiments also point to disorder in docking of the E helix and to non-native contacts in the kinetic intermediate. In particular, there is evidence for translocation of the H helix by approximately one helical turn towards its N terminus to maximize hydrophobic interactions with helix G. Thus, the burst phase intermediate observed during kinetic refolding of apomyoglobin consists of an ensemble of compact, kinetically trapped states in which the helix docking appears to be topologically correct, but in which there are local non-native interactions that must be resolved before the protein can fold to the native structure.

Sequence determinants of a protein folding pathway

Local hydrophobic collapse of the polypeptide chain and transient long-range interactions in unfolded states of apomyoglobin appear to occur in regions of the amino acid sequence which, upon folding, bury an above-average area of hydrophobic surface. To explore the role of these interactions in protein folding, we prepared and characterized apomyoglobins with compensating point mutations designed to change the average buried surface area in local regions of the sequence, while conserving as much as possible the constitution of the hydrophobic core. The behavior of the mutants in quench-flow experiments to determine the folding pathway was exactly as predicted by the changes in the buried surface area parameter calculated from the amino acid sequence. In addition, spin label experiments with acid-unfolded mutant apomyoglobin showed that the transient long-range contacts that occur in the wild-type protein are abolished in the mutant, while new contacts are observed between areas that now have above-average buried surface area. We conclude that specific groupings of amino acid side-chains, which can be predicted from the sequence, are responsible for early hydrophobic interactions in the first phase of folding in apomyoglobin, and that these early interactions determine the subsequent course of the folding process.

A protein folding pathway with multiple folding intermediates at atomic resolution

Using native-state hydrogen-exchange-directed protein engineering and multidimensional NMR, we determined the high-resolution structure (rms deviation, 1.1 angstroms) for an intermediate of the four-helix bundle protein: Rd-apocytochrome b562. The intermediate has the N-terminal helix and a part of the C-terminal helix unfolded. In earlier studies, we also solved the structures of two other folding intermediates for the same protein: one with the N-terminal helix alone unfolded and the other with a reorganized hydrophobic core. Together, these structures provide a description of a protein folding pathway with multiple intermediates at atomic resolution. The two general features for the intermediates are (i) native-like backbone topology and (ii) nonnative side-chain interactions. These results have implications for important issues in protein folding studies, including large-scale conformation search, -value analysis, and computer simulations.

The role of detergent in refolding of GdnHCl-denatured arginine kinase from shrimpFenneropenaeus Chinensis: the solubilization of aggregate and refolding in detergent solutions

Strong aggregation occurred in the refolding route of arginine kinase (AK) denatured with 3 mol GdnHCl/L (GdnHCl, guanidine hydrochloride). The activity recovery of GdnHCl-denatured AK was very low and dependent on the protein concentration in the process of refolding. For denatured AK at 1.2 µmol/L concentration, the recovered activity yield was about 45.2% of the native enzyme, whereas at 5.2 µmol/L the activity recovery yield was only 20% of native activity. The nonionic detergent Triton X-100 and Tween 20 (≤100 mmol/L concentration) not only effectively blocked the aggregation but also enabled the denatured AK to recover most of its native activity. The kinetics of aggregate solubilization showed that there was an induction phase dependent on the detergent, but there was no dependency when detergent was absent. The apparent activity recovery had a cooperative relation with detergents in the process of refolding, which suggested the existence of some interaction between the detergent and the refolding intermediate. On the basis of the study results, a scheme of refolding was proposed.Key words: arginine kinase, guanidine-denatured, refolding, detergent, aggregation.

ATP specifically drives refolding of non-native conformations of cytochrome c

An increasing body of evidence ascribes to misfolded forms of cytochrome c (cyt c) a role in pathophysiological events such as apoptosis and disease. Here, we examine the conformational changes induced by lipid binding to horse heart cyt c at pH 7 and study the ability of ATP (and other nucleotides) to refold several forms of unfolded cyt c such as oleic acid-bound cyt c, nicked cyt c, and acid denatured cyt c. The CD and fluorescence spectra demonstrate that cyt c unfolded by oleic acid has an intact secondary structure, and a disrupted tertiary structure and heme environment. Furthermore, evidence from the Soret CD, electronic absorption, and resonance Raman spectra indicates the presence of an equilibrium of at least two low-spin species having distinct heme-iron(III) coordination. As a whole, the data indicate that binding of cyt c to oleic acid leads to a partially unfolded conformation of the protein, resembling that typical of the molten globule state. Interestingly, the native conformation is almost fully recovered in the presence of ATP or dATP, while other nucleotides, such as GTP, are ineffective. Molecular modeling of ATP binding to cyt c and mutagenesis experiments show the interactions of phosphate groups with Lys88 and Arg91, with adenosine ring interaction with Glu62 explaining the unfavorable binding of GTP. The finding that ATP and dATP are unique among the nucleotides in being able to turn non-native states of cyt c back to native conformation is discussed in the light of cyt c involvement in cell apoptosis.

The N-terminal to C-terminal motif in protein folding and function

Essentially all proteins known to fold kinetically in a two-state manner have their N- and C-terminal secondary structural elements in contact, and the terminal elements often dock as part of the experimentally measurable initial folding step. Conversely, all N-C no-contact proteins studied so far fold by non-two-state kinetics. By comparison, about half of the single domain proteins in the Protein Data Bank have their N- and C-terminal elements in contact, more than expected on a random probability basis but not nearly enough to account for the bias in protein folding. Possible reasons for this bias relate to the mechanisms for initial protein folding, native state stability, and final turnover.