Nucleation mechanisms in protein folding

Disordered C-terminal domain of tyrosyl-tRNA synthetase: secondary structure prediction

The C-terminal domain (residues 320-419) of tyrosyl-tRNA synthetase (TyrRS) from Bacillus stearothermophilus is disordered in the crystal structure and involved in the binding of the anticodon arm of tRNA(Tyr). The sequences of 11 TyrRSs of prokaryotic or mitochondrial origins were aligned and the alignment showed the existence of conserved residues in the sequences of the C-terminal domains. A consensus could be deduced from the application of five programs of secondary structure prediction to the 11 sequences of the query set. These results suggested that the sequences of the C-terminal domains determined a precise and conserved secondary structure. They predicted that the C-terminal domain would have a mixed fold (alpha/beta or alpha+beta), with the alpha-helices in the first half of the sequence and the beta-strands mainly in its second half. Several programs of fold recognition from sequence alone, by threading onto known structures, were applied but none of them identified a type of fold that would be common to the different sequences of the query set. Therefore, the fold of the C-terminal, anticodon binding domain might be novel.

Experimental evolution of a dense cluster of residues in tyrosyl-tRNA synthetase: quantitative effects on activity, stability and dimerization

A dense cluster of eight residues was identified at the crossing of two alpha-helices in tyrosyl-tRNA synthetase (TyrRS) from the thermophile Bacillus stearothermophilus. Its mechanism of evolution was characterized. Four residues of this cluster are not conserved in TyrRS from the mesophile Escherichia coli. The corresponding mutations were constructed in TyrRS(Delta1), a derivative of TyrRS from B. stearothermophilus in which the anticodon binding domain is deleted. Mutations I52L (i.e. Ile52 into Leu), M55L and L105V did not affect the activity of TyrRS(Delta1) in the pyrophosphate exchange reaction whereas T51P increased it. The kinetic stabilities of TyrRS(Delta1) and its mutant derivatives at 68.5 degreesC were determined from experiments of irreversible thermal precipitation. They were in the order L105V<I52L<T51P<Wild Type</=M55L; mutation I52L partially compensated L105V in these experiments whereas M55L was coupled neither to I52L nor to L105V. Mutations I52L and L105V affected the stability of the dimeric TyrRS(Delta1) at different steps of its unfolding by urea, monitored under equilibrium conditions by spectrofluorometry or size exclusion chromatography. I52L destabilized the association between the subunits even though residue Ile52 is more than 20 A away from the subunit interface. L105V destabilized the monomeric intermediate of unfolding. The two mutational pathways, going from the wild-type TyrRS(Delta1) to the I52L-L105V double mutant through each of the single mutants were not equivalent for the stability of the monomeric intermediate and for the total stability of the dimer. One pathway contained two neutral steps whereas the other pathway contained a destabilizing step followed by a stabilizing step. Mutation I52L allowed L105V along the first pathway and compensated it along the second pathway. Thus, the effects of I52L and L105V on stability depended on the structural context. The gain in activity due to T51P was at the expense of a slight destabilization.

Thermodynamics and kinetics of folding of common-type acylphosphatase: comparison to the highly homologous muscle isoenzyme

The thermodynamics and kinetics of folding of common-type acylphosphatase have been studied under a variety of experimental conditions and compared with those of the homologous muscle acylphosphatase. Intrinsic fluorescence and circular dichroism have been used as spectroscopic probes to follow the folding and unfolding reactions. Both proteins appear to fold via a two-state mechanism. Under all the conditions studied, common-type acylphosphatase possesses a lower conformational stability than the muscle form. Nevertheless, common-type acylphosphatase folds more rapidly, suggesting that the conformational stability and the folding rate are not correlated in contrast to recent observations for a number of other proteins. The unfolding rate of common-type acylphosphatase is much higher than that of the muscle enzyme, indicating that the differences in conformational stability between the two proteins are primarily determined by differences in the rate of unfolding. The equilibrium m value is markedly different for the two proteins in the pH range of maximum conformational stability (5. 0-7.5); above pH 8.0, the m value for common-type acylphosphatase decreases abruptly and becomes similar to that of the muscle enzyme. Moreover, at pH 9.2, the dependencies of the folding and unfolding rate constants of common-type acylphosphatase on denaturant concentration (mf and mu values, respectively) are notably reduced with respect to pH 5.5. The pH-induced decrease of the m value can be attributed to the deprotonation of three histidine residues that are present only in the common-type isoenzyme. This would decrease the positive net charge of the protein, leading to a greater compactness of the denatured state. The folding and unfolding rates of common-type acylphosphatase are not, however, significantly different at pH 5.5 and 9.2, indicating that this change in compactness of the denatured and transition states does not have a notable influence on the rate of protein folding.

Folding pathway of a lattice model for proteins

The folding of a protein-like heteropolymer is studied by using direct simulation of a lattice model that folds rapidly to a well-defined "native" structure. The details of each molecular folding event depend on the random initial conformation as well as the random thermal fluctuations of the polymer. By analyzing the statistical properties of hundreds of folding events, a classical folding "pathway" for such a polymer is found that includes partially folded, on-pathway intermediates that are shown to be metastable equilibrium states of the polymer. These results are discussed in the context of the "classical" and "new" views of folding.

Fast events in protein folding: the time evolution of primary processes

Most experimental studies on the dynamics of protein folding have been confined to timescales of 1 ms and longer. Yet it is obvious that many phenomena that are obligatory elements of the folding process occur on much faster timescales. For example, it is also now clear that the formation of secondary and tertiary structures can occur on nanosecond and microsecond times, respectively. Although fast events are essential to, and sometimes dominate, the overall folding process, with a few exceptions their experimental study has become possible only recently with the development of appropriate techniques. This review discusses new approaches that are capable of initiating and monitoring the fast events in protein folding with temporal resolution down to picoseconds. The first important results from those techniques, which have been obtained for the folding of some globular proteins and polypeptide models, are also discussed.

Trimeric domain-swapped barnase

The structure of a trimeric domain-swapped form of barnase (EC 3.1. 27.3) was determined by x-ray crystallography at a resolution of 2.2 A from crystals of space group R32. Residues 1-36 of one molecule associate with residues 41-110 from another molecule related through threefold symmetry. The resulting cyclic trimer contains three protein folds that are very similar to those in monomeric barnase. Both swapped domains contain a nucleation site for folding. The formation of a domain-swapped trimer is consistent with the description of the folding process of monomeric barnase as the formation and subsequent association of two foldons.

The fundamentals of protein folding: bringing together theory and experiment

Experimental and theoretical studies together are providing insights into the mechanism by which proteins fold. Our present knowledge of the essential aspects of the folding reaction is outlined and some approaches, both theoretical and experimental, that are being developed to obtain a more detailed understanding of this complex process are described.

Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments

We are examining possible roles of native and non-native interactions in early events in protein folding by a systematic analysis of the structures of fragments of proteins whose folding pathways are well characterised. Seven fragments of the 110-residue protein barnase, corresponding to the progressive elongation from its N terminus, have been characterised by a battery of biophysical and spectroscopic methods. Barnase is a multi-modular protein that folds via an intermediate in which the C-terminal region of its major alpha-helix (alpha-helix1, residues Thr6-His18) is substantially formed as is also its anti-parallel beta-sheet, centred around a beta-hairpin (residues Ser92-Leu95). Fragments up to, and including, residues 1-95 (fragment B95), appeared to be mainly disordered, although a small amount of helical secondary structure in each was inferred from far-UV CD experiments, and fluorescence studies indicated some native-like tertiary interactions in B95. The largest fragment (residues 1-105, B105) is compactly folded. The secondary structure in alpha-helix1 in the seven fragments was found by NMR to increase with increasing chain length faster than the build-up of tertiary interactions, indicating that alpha-helix1 is being stabilised by non-native interactions. This behaviour contrasts with that in fragments of the 64-residue chymotrypsin inhibitor 2 (CI2), in which tertiary and secondary structures build up in parallel with increasing length. CI2 consists of a single module of structure that folds without a detectable intermediate. The largest fragment of barnase, B105, has interactions that resemble its folding intermediate, whereas one of the largest fragments of CI2 (residues 1-60) resembles the folding transition state. The folding pathways of both proteins are consistent with a scheme in which there are low levels of native-like secondary structure in the denatured state that become stabilised by long-range interactions as folding proceeds. Neither protein forms a stable fold when lacking the last ten residues at the C terminus. Since at least 20 amino acid residues are bound to the ribosome during protein biosynthesis, these small proteins do not fold until they have left the ribosome, and so the studies of the folding of such proteins in vitro may be relevant to their folding in vivo, especially as the molecular chaperone GroEL binds only weakly to denatured CI2 and does not discernibly alter the folding mechanism of barnase.

Sequential domain refolding of pig muscle 3-phosphoglycerate kinase: kinetic analysis of reactivation

BACKGROUND

Slow refolding of 3-phosphoglycerate kinase is supposed to be caused mainly by its domain structure: folding of the C-terminal domain and/or domain pairing has been suggested to be the rate-limiting step. A slow isomerization has been observed during refolding of the isolated C-terminal proteolytic fragment (larger than the C-domain of about 22 kDa by 5 kDa) of the pig muscle enzyme. Here, the role of this step in the reformation of the active enzyme species is investigated.

RESULTS

The time course of reactivation during refolding of 3-phosphoglycerate kinase or its complementary proteolytic fragments (residues 1-155 and 156-416) exhibits a pronounced lag-phase indicating the formation of an inactive folding intermediate. The whole process, which leads to a high (60-85%) recovery of the enzyme activity, can be described by two consecutive first-order steps (with rate constants 0.012+/-0.0035 and 0.007+/-0.0020 s(-1)). A prior renaturation of the C-fragment restores MgATP binding by the C-domain and abolishes the faster step, allowing the separate observation of the slower step. In accordance with this, refolding of the C-domain as monitored by a change in Trp fluorescence occurs at a rate similar to that of the faster step.

CONCLUSIONS

In addition to the previously observed slow refolding step (0.012 s(-1)) within the C-domain, the occurrence of another slow step (0.007 s(-1)), probably within the N-domain, is detected. The independence of the folding of the C-domain is demonstrated whereas, from the comparative kinetic analysis, independent folding of the N-domain looks less probable. Our data are more compatible with a sequential, rather than random, mechanism and suggest that folding of the C-domain, leading to an inactive intermediate, occurs first, followed by folding of the N-domain.

The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models

BACKGROUND

Recent studies have proposed various sources for the origin of cooperativity in simplified protein folding models. Important contributions to cooperativity that have been discussed include backbone hydrogen bonding, sidechain packing and hydrophobic interactions. Related work has also focused on which interactions are responsible for making the free energy of the native structure a pronounced global minimum in the free energy landscape. In addition, two-flavor bead models have been found to exhibit poor folding cooperativity and often lack unique native structures. We propose a simple multibody description of hydration with expectations that it might modify the free energy surface in such a way as to increase the cooperativity of folding and improve the performance of two-flavor models.

RESULTS

We study the thermodynamics and kinetics of folding for designed 36-mer sequences on a cubic lattice using both our solvation model and the corresponding model without solvation terms. Degeneracies of the native states are studied by enumerating the maximally compact states. The histogram Monte Carlo method is used to obtain folding temperatures, densities of states and heat capacity curves. Folding kinetics are examined by accumulating mean first-passage times versus temperature. Sequences in the proposed solvation model are found to have more unique ground states, fold faster and fold with more cooperativity than sequences in the nonsolvation model.

CONCLUSIONS

We find that the addition of a multibody description of solvation can improve the poor performance of two-flavor lattice models and provide an additional source for more cooperative folding. Our results suggest that a better description of solvation will be important for future theoretical protein folding studies.

Identification of kinetically hot residues in proteins

A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for identifying the kinetically hot residues in folded structures. These are the residues involved in the highest frequency fluctuations near the native state coordinates. Their high frequency is a manifestation of the steepness of the energy landscape near their native state positions. The theory is applied to a series of proteins whose kinetically important residues have been extensively explored: chymotrypsin inhibitor 2, cytochrome c, and related C2 proteins. Most of the residues previously pointed out to underlie the folding process of these proteins, and to be critically important for the stabilization of the tertiary fold, are correctly identified, indicating a correlation between the kinetic hot spots and the early forming structural elements in proteins. Additionally, a strong correlation between kinetically hot residues and loci of conserved residues is observed. Finally, residues that may be important for the stability of the tertiary structure of CheY are proposed.

Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain

The transition state for the folding pathway of the activation domain of human procarboxypeptidase A2 (ADA2h) has been analyzed by the protein engineering approach. Recombinant ADA2h is an 81-residue globular domain with no disulfide bridges or cis-prolyl bonds, which follows a two-state folding transition. Its native fold is arranged in two alpha-helices packing against a four-stranded beta-sheet. Application of the protein engineering analysis for 20 single-point mutants spread throughout the whole sequence indicates that the transition state for this molecule is quite compact, possessing some secondary structure and a hydrophobic core in the process of being consolidated. The core (folding nucleus) is made by the packing of alpha-helix 2 and the two central beta-strands. The other two strands, at the edges of the beta-sheet, and alpha-helix 1 seem to be completely unfolded. These results, together with previous analysis of ADA2h with either of its two alpha-helices stabilized through improved local interactions, suggest that alpha-helix 1 does not contribute to the folding nucleus, even though it is partially folded in the denatured state under native conditions. On the other hand, alpha-helix 2 folds partly in the transition state and is part of the folding nucleus. It is suggested that a good strategy to improve folding speed in proteins would be to stabilize the helices that are not folded in the denatured state but are partly present in the transition state. Comparison with other proteins shows that there is no clear relationship between fold and/or size with folding speed and level of structure in the transition state of proteins.

Structural characterization of the transition state for folding of muscle acylphosphatase

The transition state for folding of a small protein, muscle acylphosphatase, has been studied by measuring the rates of folding and unfolding under a variety of solvent conditions. A strong dependence of the folding rate on the concentration of urea suggests the occurrence in the transition state of a large shielding of those groups that are exposed to interaction with the denaturant in the unfolded state (mainly hydrophobic moieties and groups located on the polypeptide backbone). The heat capacity change upon moving from the unfolded state to the transition state is small and is indicative of a substantial solvent exposure of hydrophobic groups. The solvent-accessibility of such groups in the transition state has also been found to be significant by measuring the rates of folding and unfolding in the presence of sugars. These rates have also been found to be accelerated by the addition of small quantities of alcohols. Trifluoroethanol and hexafluoroisopropanol were particularly effective, suggesting that stabilisation of local hydrogen bonds lowers the energy of the transition state relative to the folded and unfolded states. Finally, a study with a competitive inhibitor of acylphosphatase has provided evidence for the complete loss of ligand binding affinity in the transition state, indicating that specific long-range interactions at the level of the active site are not yet formed at this stage of the folding reaction. A model of the transition state for acylphosphatase folding, in which beta-turns and one or both alpha-helices are formed to a significant extent but in which the persistent long-range interactions characteristic of the folded state are largely absent, accounts for all our data. These results are broadly consistent with models of the transition states for folding of other small proteins derived from mutagenesis studies, and suggest that solvent perturbation methods can provide complementary information about the transition region of the energy surfaces for protein folding.

Slow folding of muscle acylphosphatase in the absence of intermediates

The folding of a 98 residue protein, muscle acylphosphatase (AcP), has been studied using a variety of techniques including circular dichroism, fluorescence and NMR spectroscopy following transfer of chemically denatured protein into refolding conditions. A low-amplitude phase, detected in concurrence with the main kinetic phase, corresponds to the folding of a minor population (13%) of molecules with one or both proline residues in a cis conformation, as shown from the sensitivity of its rate to peptidyl prolyl isomerase. The major phase of folding has the same kinetic characteristics regardless of the technique employed to monitor it. The plots of the natural logarithms of folding and unfolding rate constants versus urea concentration are linear over a broad range of urea concentrations. Moreover, the initial state formed rapidly after the initiation of refolding is highly unstructured, having a similar circular dichroism, intrinsic fluorescence and NMR spectrum as the protein denatured at high concentrations of urea. All these results indicate that AcP folds in a two-state manner without the accumulation of intermediates. Despite this, the folding of the protein is extremely slow. The rate constant of the major phase of folding in water, kfH2O, is 0.23 s-1 at 28 degreesC and, at urea concentrations above 1 M, the folding process is slower than the cis-trans proline isomerisation step. The slow refolding of this protein is therefore not the consequence of populated intermediates that can act as kinetic traps, but arises from a large intrinsic barrier in the folding reaction.

How homologs can help to predict protein folds even though they cannot be predicted for individual sequences

At present, one cannot predict the 3D structure of a protein directly from its sequence alone mainly because of errors in the energy estimates. However, a recently developed simple analytical theory (Finkelstein, 1998) shows that using a set of homologs (i.e., chains with numerous amino acid mutations but with equal 3D folds) one can average the interaction energies over the homologs and predict their common 3D fold even when predictions for individual sequences are wrong because the energy parameters are known only approximately. In this work we verify this theoretical conclusion by computer simulations performed with simplified models of protein chains.

Folding mechanism of three structurally similar beta-sheet proteins

The folding mechanism of cellular retinoic acid binding protein I (CRABP I), cellular retinol binding protein II (CRBP II), and intestinal fatty acid binding protein (IFABP) were investigated to determine if proteins with similar native structures have similar folding mechanisms. These mostly beta-sheet proteins have very similar structures, despite having as little as 33% sequence similarity. The reversible urea denaturation of these proteins was characterized at equilibrium by circular dichroism and fluorescence. The data were best fit by a two-state model for each of these proteins, suggesting that no significant population of folding intermediates were present at equilibrium. The native states were of similar stability with free energies (linearly extrapolated to 0 M urea, deltaGH2O) of 6.5, 8.3, and 5.5 kcal/mole for CRABP I, CRBP II, and IFABP, respectively. The kinetics of the folding and unfolding processes for these proteins was monitored by stopped-flow CD and fluorescence. Intermediates were observed during both the folding and unfolding of all of these proteins. However, the overall rates of folding and unfolding differed by nearly three orders of magnitude. Further, the spectroscopic properties of the intermediate states were different for each protein, suggesting that different amounts of secondary and/or tertiary structure were associated with each intermediate state for each protein. These data show that the folding path for proteins in the same structural family can be quite different, and provide evidence for different folding landscapes for these sequences.

Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism

The nature of the nucleation-collapse mechanism in protein folding is probed using 27-mer and 36-mer lattice models. Three different forms for the interaction potentials are used. Three of the four 27-mer sequences have maximally compact and identical native state while the other has a non-compact native conformation. All the sequences fold thermodynamically and kinetically by a two-state process. Analysis of individual trajectories for each sequence using a self-organizing neural net algorithm shows that upon formation of a critical set of contacts the polypeptide chain rapidly reaches the native conformation which is consistent with a nucleation-collapse mechanism. The algorithm, which reduces the identification of the folding nucleus for each trajectory to one of pattern recognition, is used to show that there are multiple folding nuclei. There is a distribution of nucleation contacts in the transition states with some of them occurring with more probability (when averaged over the denatured ensemble) than others. We also show that there is a distribution in the size of the nuclei with the average number of residues in the folding nuclei being less than about one-third of the chain size. The fluctuations in the sizes of the nuclei are large, suggestive of a broad transition region. The folding nuclei, the structures of each are the corresponding transition states, have varying degree of overlap with the native conformation. The distribution of the radius of gyration of the transition states shows that these structures are an expanded form (by about 25% in the radius of gyration) of the native conformation. Local contacts are most dominant in the folding nuclei while a certain fraction of non-local contacts is necessary to stabilize the transition states. The search for the critical nuclei initially involves the formation of local contacts, while non-local contacts are formed later. The fractional values of PhiF for the two 27-mer mutants found by using the protein engineering protocol are consistent with the microscopic picture of partial formation of structures involving these residues in the transition state. These observations lead to a multiple folding nuclei (MFN) model for nucleation-collapse mechanism in protein folding. The major implication of the MFN model is that, even if the residues whose tertiary interactions are formed nearly completely in the transition state are mutated, it does not disrupt the nature of the nucleation-collapse mechanism. We analyze the experiments on chymotrypsin inhibitor 2 and alpha-spectrin SH3 domain and two circular permutants in light of the MFN model. It is shown that the PhiF-value analysis for these proteins gives considerable support to the MFN model. The theoretical and experimental studies give a coherent picture of the nucleation-collapse mechanism in which there is a distribution of folding nuclei with some more probable than others. The formation of any specific nucleus is not necessary for efficient two-state folding.

A descriptive analysis of populations of three-dimensional structures calculated from primary sequences of proteins by OSIRIS

Among different ab initio approaches to calculate 3D-structures of proteins out of primary sequences, a few are using restricted dihedral spaces and empirical equations of energy as is OSIRIS. All those approaches were calibrated on a few proteins or fragments of proteins. To optimize the calculation over a larger diversity of structures, we need first to define for each sequence what are good conditions of calculations in order to choose a consensus procedure fitting most 3D-structures best. This requires objective classification of calculated 3D-structures. In this work, populations of avian and bovine pancreatic polypeptides (APP, BPP) and of calcium-binding protein (CaBP) are obtained by varying the rate of the angular dynamics of the second step of OSIRIS. Then, 3D-structures are clustered using a nonhierarchical method, SICLA, using rmsd as a distance parameter. A good clustering was obtained for four subpopulations of APP, BPP and CaBP. Each subpopulation was characterized by its barycenter, relative frequency and dispersion. For the three alpha-helix proteins, after the step 1 of OSIRIS, most secondary structures were correct but molecules have a few atomic contacts. Step 2, i.e., the angular dynamics, resolves those atomic contacts and clustering demonstrates that it generates subpopulations of topological conformers as the barycenter topologies show.

Contribution of individual residues to formation of the native-like tertiary topology in the alpha-lactalbumin molten globule

Molten globules are partially folded forms of proteins that have native-like secondary structure and a compact geometry, but often without rigid, specific side-chain packing. Recently, the molten globule of alpha-lactalbumin (alpha-LA) has been shown to adopt a native-like tertiary topology, mainly localized in the alpha-helical domain. This native-like topology is reflected by the high effective concentration (Ceff) for formation of the 28-111 disulfide bond, which is approximately 10 to 40 times higher than the Ceff for formation of any non-native disulfide bond in the alpha-helical domain. In order to understand the mechanism for formation of the native-like tertiary topology, we substituted alanine for each of the 23 buried residues in the alpha-helical domain of alpha-LA and determined the effect of these substitutions on the Ceff for formation of the 28-111 disulfide bond. Our results indicate that a subset of hydrophobic residues is most important for formation of the native-like topology. These residues form a densely packed core in the three-dimensional structure of alpha-LA. In contrast, the less important residues consist of both hydrophobic and hydrophilic amino acids located at peripheral positions. These results suggest that a relatively small number of hydrophobic residues may be sufficient for specifying the overall structure of a protein during early stages of protein folding.

Transition state in the folding of alpha-lactalbumin probed by the 6-120 disulfide bond

The guanidine hydrochloride concentration dependence of the folding and unfolding rate constants of a derivative of alpha-lactalbumin, in which the 6-120 disulfide bond is selectively reduced and S-carboxymethylated, was measured and compared with that of disulfide-intact alpha-lactalbumin. The concentration dependence of the folding and unfolding rate constants was analyzed on the basis of the two alternative models, the intermediate-controlled folding model and the multiple-pathway folding model, that we had proposed previously. All of the data supported the multiple-pathway folding model. Therefore, the molten globule state that accumulates at an early stage of folding of alpha-lactalbumin is not an obligatory intermediate. The cleavage of the 6-120 disulfide bond resulted in acceleration of unfolding without changing the refolding rate, indicating that the loop closed by the 6-120 disulfide bond is unfolded in the transition state. It is theoretically shown that the chain entropy gain on removing the cross-link from a random coil chain with helical stretches can be comparable to that from an entirely random chain. Therefore, the present result is not inconsistent with the known structure in the molten globule intermediate. Based on this result and other knowledge obtained so far, the structure in the transition state of the folding reaction of alpha-lactalbumin is discussed.

Protein design: a perspective from simple tractable models

Recent progress in computational approaches to protein design builds on advances in statistical mechanical protein folding theory. Here, the number of sequences folding into a given conformation is evaluated and a simple condition for a protein model's designability is outlined.

Folding funnels and frustration in off-lattice minimalist protein landscapes

A full quantitative understanding of the protein folding problem is now becoming possible with the help of the energy landscape theory and the protein folding funnel concept. Good folding sequences have a landscape that resembles a rough funnel where the energy bias towards the native state is larger than its ruggedness. Such a landscape leads not only to fast folding and stable native conformations but, more importantly, to sequences that are robust to variations in the protein environment and to sequence mutations. In this paper, an off-lattice model of sequences that fold into a beta-barrel native structure is used to describe a framework that can quantitatively distinguish good and bad folders. The two sequences analyzed have the same native structure, but one of them is minimally frustrated whereas the other one exhibits a high degree of frustration.

Kinetic folding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A missing the [40-95] disulfide bond

The oxidative refolding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A (RNase A) from the fully reduced unfolded form to the native state has been studied by using oxidized and reduced dithiothreitol as the redox reagents at pH 8.0 and 25 degrees C. This mutant was prepared by replacing Cys40 and Cys95 in RNase A with alanines while maintaining the other three native disulfide bonds to mimic one of the two major three-disulfide intermediates (des-[40-95]) observed in the regeneration of wild-type RNase A. The kinetics of refolding of this mutant were measured by quenching the regeneration reaction at various times with a rapid blocking reagent, 2-aminoethyl methanethiosulfonate (AEMTS), fractionating the disulfide intermediates by using cation-exchange HPLC, and analyzing the time course of each group of disulfide species. It was found that the disulfide intermediates formed during regeneration reach a steady-state distribution after a short period of preequilibration similar to that in the regeneration of wild-type RNase A. The experimental data acquired under different redox conditions were fit to a kinetic model with a steady-state treatment. The fitted results indicate that this mutant refolds through a rate-determining step which involves the oxidation of certain two-disulfide species to form a putative three-disulfide species which proceeds rapidly to the native protein. A rough estimation suggests that this pathway could constitute no more than 5% of the major pathway leading to the formation of des-[40-95] (the major three-disulfide intermediate formed) in the regeneration of wild-type RNase A. Several kinetic constants pertaining to the oxidation and reduction of various disulfide intermediates were compared with those obtained in the regeneration studies of wild-type RNase A to gain further understanding about the folding pathways of RNase A. Comparisons are also given for the oxidative refolding studies of several other three disulfide bond proteins, suggesting that the formation of a large number of disulfide-bonded intermediates during oxidative refolding is probably a common feature for most proteins.

Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?

Amino acid sequences of seven subfamilies of cytochromes c (mitochondrial cytochromes c, c1; chloroplast cytochromes c6, cf; bacterial cytochromes c2, c550, c551; in total 164 sequences) have been compared. Despite extensive homology within eukaryotic subfamilies, homology between different subfamilies is very weak. Other than the three heme-binding residues (Cys13, Cys14, His18, in numeration of horse cytochrome c) there are only four positions which are conserved in all subfamilies: Gly/Ala6, Phe/Tyr10, Leu/Val/Phe94 and Tyr/Trp/Phe97. In all 17 cytochromes c with known 3D-structures, these residues form a network of conserved contacts (6-94, 6-97, 10-94, 10-97 and 94-97). Especially strong is the contact between aromatic groups in positions 10 and 97, which corresponds to 13 interatomic contacts. As residues 6, 10 and residues 94, 97 are in (i, i+4) and (i, i+3) positions in the N and C-terminal helices, respectively, the above mentioned system of conserved contacts consists mainly of contacts between one turn of N-terminal helix and one turn of C-terminal helix. The importance of the contacts between interfaces of these helices has been confirmed by the existence of these contacts in both equilibrium and kinetic molten globule-like folding intermediates, as well as by mutational evidence that these contacts are involved in tight packing between the N and C-helices. Since these four residues are not involved in heme binding and have no other apparent functional role, their conservation in highly diverged cytochromes c suggests that they are of a critical importance for protein folding. The author assumes that they are involved in a common folding nucleus of all subfamilies of c-type cytochromes.

Folding rate dependence on the chain length of RNA-like heteropolymers

BACKGROUND

Computer experiments and analytical estimates have shown that protein and RNA chains can reach their most stable folds without an exhaustive search over all their possible conformations. Protein-like chain folding proceeds via a specific nucleus and under conditions optimal for the fastest folding of these chains the dependence of the folding time (t) on the chain length (L) is in accord with the power law t integral of Lb (b is a constant).

RESULTS

Using Monte-Carlo folding simulations for a simple model of RNA secondary structure formation, we estimated the RNA chain length dependence of the time necessary to reach the lowest energy fold. Our results are compatible with a relatively weak power dependence of the folding time on the chain length, t integral of Lb. Such dependencies have been observed for different folding conditions, both for random sequences (here, b > 5) and for sequences edited to stabilize their lowest energy folds (for extremely edited sequences b < 2). Although folding transitions in RNA chains are not an all-or-none type in terms of thermodynamics, they proceed via a folding nucleus in terms of kinetics. The peculiarity (compared with protein folding) is that the RNA critical nucleus is big and non-specific.

CONCLUSIONS

We have obtained a general scaling for the dependence of the RNA secondary structure on the chain length. The obtained power dependence is very weak compared with an exponential dependence for an exhaustive sorting.

Reversible denaturation, self-aggregation, and membrane activity of Escherichia coli alpha-hemolysin, a protein stable in 6 M urea

Escherichia coli alpha-hemolysin (HlyA) is an extracellular protein toxin (107 kDa) whose cell lytic activity may be preserved for months at -20 degreesC in the presence of 6 M urea, although it decays rapidly in urea-free buffers. This paper describes experiments addressed to unravel the role of urea in HlyA stabilization. Urea up to 8 M inhibits the Ca2+-binding and hemolytic activities of the protein, alters its secondary and tertiary structures, and reduces its tendency to self-aggregation. All these changes are largely reversed upon urea removal by dilution or dialysis, suggesting that they are interrelated. Furthermore, the extent of recovery of the native activities and structural features of alpha-hemolysin that follows urea removal increases with the concentration of urea during the previous phase. Thus, it seems that urea elicits the reversible transition of HlyA to a less active but more stable state whose structure differs significantly from that of the native protein. Moreover dialysis equilibration of the protein with buffers containing 3 M urea induces the formation of a molecular form of HlyA 5-10 times more active than the native protein in the absence of urea. This hyperactive intermediate appears to keep the native secondary structure of HlyA, but with a less compact tertiary structure, that increases the number of exchangeable Ca2+ ions under these conditions. Changes in the intrinsic fluorescence of HlyA also support the notion of a conformational change in the high-activity intermediate. The intermediate is only detected when assayed in the presence of Ca2+ and 3 M urea and can bind a large number of calcium ions (approximately 12 vs approximately 3 for the native protein); it shows a large tendency to self-aggregation and presumably, in the presence of membranes, a similar tendency to irreversible insertion, which may be the reason for its high lytic activity.

Evidence for barrier-limited protein folding kinetics on the microsecond time scale

Although important structural events in protein folding are known to occur on the submillisecond time scale, the limited time resolution of conventional kinetic methods has precluded direct observation of the initial collapse of the polypeptide chain. A continuous-flow capillary mixing method recently developed by us made it possible to account for the entire fluorescence change associated with refolding of cytochrome c from approximately 5-10(-5)-10(2) s, including the previously unresolved quenching of Trp 59 fluorescence (burst phase) indicative of the formation of compact states. The kinetics of folding exhibits a major exponential process with a time constant of approximately 50 micros, independent of initial conditions and heme ligation state, indicating that a common free energy barrier is encountered during the initial collapse of the polypeptide chain. The resulting loosely packed intermediate accumulates prior to the rate-limiting formation of specific tertiary interactions, confirming previous indications that folding involves at least two distinct stages.

Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond

Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion-collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion-collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be simulated in several days on current supercomputers. Furthermore, such simulations yield folding times that are in the range of time scales observed in experiments.

Molecular dynamics simulations of hydrophobic collapse of ubiquitin

Nine nonnative conformations of ubiquitin, generated during two different thermal denaturation trajectories, were simulated under nearly native conditions (62 degrees C). The simulations included all protein and solvent atoms explicitly, and simulation times ranged from 1-2.4 ns. The starting structures had alpha-carbon root-mean-square deviations (RMSDs) from the crystal structure of 4-12 A and radii of gyration as high as 1.3 times that of the native state. In all but one case, the protein collapsed when the temperature was lowered and sampled conformations as compact as those reached in a control simulation beginning from the crystal structure. In contrast, the protein did not collapse when simulated in a 60% methanol:water mixture. The behavior of the protein depended on the starting structure: during simulation of the most native-like starting structures (<5 A RMSD to the crystal structure) the RMSD decreased, the number of native hydrogen bonds increased, and the secondary and tertiary structure increased. Intermediate starting structures (5-10 A RMSD) collapsed to the radius of gyration of the control simulation, hydrophobic residues were preferentially buried, and the protein acquired some native contacts. However, the protein did not refold. The least native starting structures (10-12 A RMSD) did not collapse as completely as the more native-like structures; instead, they experienced large fluctuations in radius of gyration and went through cycles of expansion and collapse, with improved burial of hydrophobic residues in successive collapsed states.

Simulations of protein folding and unfolding

The 'new view' of protein folding is based on a statistical analysis of the landscape for protein folding. This perspective leads to the investigation of the statistical distributions of protein conformations as the folding protein approaches the native state from unfolded states. Molecular dynamics simulations of both the thermodynamics of protein folding and the kinetics of unfolding are beginning to explore the statistical nature of these distributions. They also provide connections between the theory of protein folding landscapes and the experimental observations of the properties of key ensembles of the conformations populated as folding progresses.

Folding intermediates of wild-type and mutants of barnase. I. Use of phi-value analysis and m-values to probe the cooperative nature of the folding pre-equilibrium

It is difficult to determine whether transient folding intermediates have a cooperative (or first-order) folding transition without measuring their rates of formation directly. An intermediate I could be formed by a second-order transition from a denatured state D that is progressively changed into I as conditions are changed. We have not been able to monitor the rate of formation of the folding intermediate of barnase directly, but have analysed its reactivity and the equilibrium constant for its formation over a combination of wide ranges of temperature, concentration of denaturant and structural variation. Phase diagrams have been constructed for wild-type and 16 mutant proteins to map out the nature of the energy landscape of the denatured state. The free energy of unfolding of I, delta GD-I, changes with [urea] according to a highly cooperative transition. Further, mD-I (= delta delta GD-I/delta [urea]) for wild-type and several mutants is relatively insensitive to temperature, as would be expected for an intermediate that is formed cooperatively, rather than one that melts out according to a second-order transition. The phi-values for the formation of I change abruptly through the folding transitions rather than have the smooth changes expected for a second-order transition. There is a subset of mutants for which both mD-I and phi-value analysis indicate that a second intermediate becomes populated close to the melting temperatures of the native proteins. The folding intermediate of barnase is, thus, a relatively discrete and compact entity which is formed cooperatively.

Pathways for protein folding: is a new view needed?

Theoretical studies using simplified models of proteins have shed light on the general heteropolymeric aspects of the folding problem. Recent work has emphasized the statistical aspects of folding pathways. In particular, progress has been made in characterizing the ensemble of transition state conformations and elucidating the role of intermediates. These advances suggest a reconciliation between the new ensemble approaches and the classical view of a folding pathway.

Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate

The folding/unfolding pathway of barnase has been studied extensively using the protein engineering method, which has provided indirect structural information for the transition state and the major folding intermediate. To further characterize the structural properties of the intermediate, we have simulated the thermal denaturation of barnase beginning from the average NMR structure. Our results indicate that there are at least two intermediates on the unfolding pathway. The three hydrophobic cores are partially formed in the major intermediate (I1), with core1 and core3 being slightly stronger than core2. Helix alpha 1 is substantially formed, with the center being stronger than the termini. The first turn of alpha 2 is lost and alpha 3 is unfolded. The center of the beta-sheet is substantially formed, but the edges are disrupted. These structural characteristics are in good qualitative agreement with the experimental data. For semi-quantitative comparison with experimental data, the extent of native structure of individual residues is characterized by a structure index, S, that reflects both secondary and tertiary structure. There is good agreement between S and the experimentally measured phi values, which are based on energetics, except for three residues. These residues are polar and non-conservative mutations were made to obtain phi values, which can complicate structural interpretations. These residues make strong side-chain interactions in I1, but the backbone structure is disrupted, leading to low S values. Thus, this discordance highlights possible limitations in both the phi value and S value analyses: strong polar interactions in the intermediate may give rise to high phi values that are not reflective of structure per se; however, due to sampling limitations, any one simulation is not expected to capture all of the features of the true conformational ensemble. In any case, these simulations provide an experimentally testable, atomic-level structural model for the major folding intermediate of barnase, as well as the detailed pathway from the native to the intermediate state.

Structure and stability of the N-terminal domain of the ribosomal protein L9: evidence for rapid two-state folding

The N-terminal domain, residues 1-56, of the ribosomal protein L9 has been chemically synthesized. The isolated domain is monomeric as judged by analytical ultracentrifugation and concentration-dependent CD. Complete 1H chemical shift assignments were obtained using standard methods. 2D-NMR experiments show that the isolated domain adopts the same structure as seen in the full-length protein. It consists of a three-stranded antiparallel beta-sheet sandwiched between two helixes. Thermal and urea unfolding transitions are cooperative, and the unfolding curves generated from different experimental techniques, 1D-NMR, far-UV CD, near-UV CD, and fluorescence, are superimposable. These results suggest that the protein folds by a two-state mechanism. The thermal midpoint of folding is 77 +/- 2 degrees C at pD 8.0, and the domain has a delta G degree folding = 2.8 +/- 0.8 kcal/mol at 40 degrees C, pH 7.0. Near the thermal midpoint of the unfolding transition, the 1D-NMR peaks are significantly broadened, indicating that folding is occurring on the intermediate exchange time scale. The rate of folding was determined by fitting the NMR spectra to a two-state chemical exchange model. Similar folding rates were measured for Phe 5, located in the first beta-strand, and for Tyr 25, located in the short helix between strands two and three. The domain folds extremely rapidly with a folding rate constant of 2000 s-1 near the midpoint of the equilibrium thermal unfolding transition.

Slow cooperative folding of a small globular protein HPr

The folding of an 85-residue protein, the histidine-containing phosphocarrier protein HPr, has been studied using a variety of techniques including DSC, CD, ANS fluorescence, and NMR spectroscopy. In both kinetic and equilibrium experiments the unfolding of HPr can be adequately described as a two-state process which does not involve the accumulation of intermediates. Thermodynamic characterization of the native and the transition states has been achieved from both equilibrium and kinetic experiments. The heat capacity change from the denatured state to the transition state (3. 2 kJ mol-1 K-1) is half of the heat capacity difference between the native and denatured states (6.3 kJ mol-1 K-1), while the solvent accessibility of the transition state (0.36) indicates that its compactness is closer to that of the native than that of the denatured state. The high value for the change in heat capacity upon unfolding results in the observation of cold denaturation at moderate denaturant concentrations. Refolding from high denaturant concentrations is, however, slow. The rate constant of folding in water, (14.9 s-1), is small compared to that reported for other proteins of similar size under similar conditions. This indicates that very fast refolding is not a universal character of small globular proteins which fold in the absence of detectable intermediates.

Theory of protein folding: the energy landscape perspective

The energy landscape theory of protein folding is a statistical description of a protein's potential surface. It assumes that folding occurs through organizing an ensemble of structures rather than through only a few uniquely defined structural intermediates. It suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure. This statistical description has been developed using tools from the statistical mechanics of disordered systems, polymers, and phase transitions of finite systems. We review here its analytical background and contrast the phenomena in homopolymers, random heteropolymers, and protein-like heteropolymers that are kinetically and thermodynamically capable of folding. The connection between these statistical concepts and the results of minimalist models used in computer simulations is discussed. The review concludes with a brief discussion of how the theory helps in the interpretation of results from fast folding experiments and in the practical task of protein structure prediction.

"New view" of protein folding reconciled with the old through multiple unfolding simulations

Twenty-four molecular dynamics trajectories of chymotrypsin inhibitor 2 provide a direct demonstration of the diversity of unfolding pathways. Comparison with experiments suggests that the transition state region for folding and unfolding occurs early with only 25 percent of the native contacts and that the root-mean-square deviations between contributing structures can be as large as 15 angstroms. Nevertheless, a statistically preferred unfolding pathway emerges from the simulations; disruption of tertiary interactions between the helix and a two-stranded portion of the beta sheet is the primary unfolding event. The results suggest a synthesis of the "new" and the classical view of protein folding with a preferred pathway on a funnel-like average energy surface.

Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein

To investigate the role of turns in protein folding, we have characterized the effects of combinatorial and site-directed mutations in the two beta-turns of peptostreptococcal protein L on folding thermodynamics and kinetics. Sequences of folded variants recovered from combinatorial libraries using a phase display selection method were considerably more variable in the second turn than in the first turn. These combinatorial mutants as well as strategically placed point mutants in the two turns had a similar range of thermodynamic stabilities, but strikingly different folding kinetics. A glycine to alanine substitution in the second beta-turn increased the rate of unfolding more than tenfold but had little effect on the rate of folding, while mutation of a symmetrically disposed glycine residue in the first turn had little effect on unfolding but slowed the rate of folding nearly tenfold. These results demonstrate that the role of beta-turns in protein folding is strongly context-dependent, and suggests that the first turn is formed and the second turn disrupted in the folding transition state.

Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway

Residual structure in the denatured state of a protein may contain clues about the early events in folding. We have simulated by molecular dynamics the denatured state of barnase, which has been studied by NMR spectroscopy. An ensemble of 10(4) structures was generated after 2 ns of unfolding and following for a further 2 ns. The ensemble was heterogeneous, but there was nonrandom, residual structure with persistent interactions. Helical structure in the C-terminal portion of helix alpha1 (residues 13-17) and in helix alpha2 as well as a turn and nonnative hydrophobic clustering between beta3 and beta4 were observed, consistent with NMR data. In addition, there were tertiary contacts between residues in alpha1 and the C-terminal portion of the beta-sheet. The simulated structures allow the rudimentary NMR data to be fleshed out. The consistency between simulation and experiment inspires confidence in the methods. A description of the folding pathway of barnase from the denatured to the native state can be constructed by combining the simulation with experimental data from phi value analysis and NMR.

Folding dynamics and mechanism of beta-hairpin formation

Protein chains coil into alpha-helices and beta-sheet structures. Knowing the timescales and mechanism of formation of these basic structural elements is essential for understanding how proteins fold. For the past 40 years, alpha-helix formation has been extensively investigated in synthetic and natural peptides, including by nanosecond kinetic studies. In contrast, the mechanism of formation of beta structures has not been studied experimentally. The minimal beta-structure element is the beta-hairpin, which is also the basic component of antiparallel beta-sheets. Here we use a nanosecond laser temperature-jump apparatus to study the kinetics of folding a beta-hairpin consisting of 16 amino-acid residues. Folding of the hairpin occurs in 6 micros at room temperature, which is about 30 times slower than the rate of alpha-helix formation. We have developed a simple statistical mechanical model that provides a structural explanation for this result. Our analysis also shows that folding of a beta-hairpin captures much of the basic physics of protein folding, including stabilization by hydrogen bonding and hydrophobic interactions, two-state behaviour, and a funnel-like, partially rugged energy landscape.