Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants

A considerable number of functional proteins are unstructured under physiological condition. These "intrinsically disordered" proteins exhibit induced folding when they bind their targets. The induced folding comprises two elementary processes: folding and binding. Two mechanisms are possible for the induced folding: either folding before binding or binding before folding. We found that these two mechanisms can be distinguished by the target-concentration dependence of folding kinetics. We also created two types of mutants of staphylococcal nuclease showing the different inhibitor-concentration dependence of induced folding kinetics. One mutant obeys the scheme of binding before folding, while the other the folding before binding. This is the first experimental evidence demonstrating that both mechanisms are realized for a single protein. Binding before folding is possible, when the protein lacks essential nonlocal interaction to stabilize the native conformation. The results cast light on the protein folding mechanism involved in the intrinsically disordered proteins.     

Effects of disulfide bonds on folding behavior and mechanism of the beta-sheet protein tendamistat

Tendamistat, a small disulfide-bonded beta-sheet protein, and its three single/double-disulfide mutants are investigated by using a modified Gō-like model, aiming to understand the folding mechanism of disulfide-bonded protein as well as the effects of removal of disulfide bond on the folding process. Our simulations show that tendamistat and its two single-disulfide mutants are all two-state folders, consistent with the experimental observations. It is found that the disulfide bonds as well as three hydrogen bonds between the N-terminal loop-0 and strand-6 are of significant importance for the folding of tendamistat. Without these interactions, their two-state behaviors become unstable and the predictions of the model are inconsistent with experiments. In addition, the effect of disulfide bonds on the folding process are studied by comparing the wild-type tendamistat and its two mutants; it is found that the removal of either of the C11-C27 or C45-C73 disulfide bond leads to a large decrease in the thermodynamical stability and loss of structure in the unfolded state, and the effect of the former is stronger than that of the later. These simulation results are in good agreement with experiments and, thus, validate our model. Based on the same model, the detailed folding pathways of the wild-type tendamistat and two mutants are studied, and the effect of disulfide bonds on the folding kinetics are discussed. The obtained results provide a detailed folding picture of these proteins and complement experimental findings. Finally, the folding nuclei predicted to be existent in this protein tendamistat as well as its mutants are firstly identified in this work. The positions of the nucleus are consistent with those argued in experimental studies. Therefore, a nucleation/growth folding mechanism that can explain the two-state folding manner is clearly characterized. Moreover, the effect by the removal of each disulfide bond on the folding thermodynamics and dynamics can also be well interpreted from their influence on the folding nucleus. The implementation of this work indicates that the modified Gō-like model really describes the folding behavior of protein tendamistat and could be used to study the folding of other disulfide-bonded proteins.     

Folding of tandem-linked domains

One of the factors, which influences protein folding in vivo, is a linkage of protein domains into multidomain tandems. However, relatively little is known about the impact of domain connectivity on protein folding mechanisms. In this article, we use coarse grained models of proteins to explore folding of tandem-linked domains (TLD). We found TLD folding to follow two scenarios. In the first, the tandem connectivity produces relatively minor impact on folding and the mechanisms of folding of tandem-linked and single domains remain similar. The second scenario involves qualitative changes in folding mechanism because of tandem linkage. As a result, protein domains, which fold via two-state mechanism as single isolated domains, may form new stable intermediates when inserted into tandems. The new intermediates are created by topological constraints imposed by the linkers between domains. In both cases tandem linkage slows down folding. We propose that the impact of tandem connectivity can be minimized, if the terminal secondary structure elements (SSEs) are flexible. In particular, two factors appear to facilitate TLD folding: (1) the interactions between terminal SSE are poorly ordered in the folding transition state, whereas nonterminal SSE are better structured, (2) the interactions between terminal SSE are weak in the native state. We apply these findings to wild-type proteins by examining experimental phi-value data and by performing all-atom molecular dynamics simulations. We show that immunoglobulin-like domains appear to utilize the factors, which minimize the impact of tandem connectivity on their folding. Several single domain proteins, which are likely to misfold in tandems, are also identified.     

Testing the relationship between foldability and the early folding events of dihydrofolate reductase from Escherichia coli

A "folding element" is a contiguous peptide segment crucial for a protein to be foldable and is a new concept that could assist in our understanding of the protein-folding problem. It is known that the presence of the complete set of folding elements of dihydrofolate reductase (DHFR) from Escherichia coli is essential for the protein to be foldable. Since almost all of the amino acid residues known to be involved in the early folding events of DHFR are located within the folding elements, a close relationship between the folding elements and early folding events is hypothesized. In order to test this hypothesis, we have investigated whether or not the early folding events are preserved in circular permutants and topological mutants of DHFR, in which the order of the folding elements is changed but the complete set of folding elements is present. The stopped-flow circular dichroism (CD) measurements show that the CD spectra at the early stages of folding are similar among the mutants and the wild-type DHFR, indicating that the presence of the complete set of folding elements is sufficient to preserve the early folding events. We have further examined whether or not sequence perturbation on the folding elements by a single amino acid substitution affects the early folding events of DHFR. The results show that the amino acid substitutions inside of the folding elements can affect the burst-phase CD spectra, whereas the substitutions outside do not. Taken together, these results indicate that the above hypothesis is true, suggesting a close relationship between the foldability of a protein and the early folding events. We propose that the folding elements interact with each other and coalesce to form a productive intermediate(s) early in the folding, and these early folding events are important for a protein to be foldable.     

Slow folding kinetics of RNase P RNA.

Understanding the folding mechanisms of large, highly structured RNAs is important for understanding how these molecules carry out their function. Although models for the three-dimensional architecture of several large RNAs have been constructed, the process by which these structures are formed is only now beginning to be explored. The kinetic folding pathway of the Tetrahymena ribozyme involves multiple intermediates and both Mg2+-dependent and Mg2+-independent steps. To determine whether this general mechanism is representative of folding of other large RNAs, a study of RNase P RNA folding was undertaken. We show, using a kinetic oligonucleotide hybridization assay, that there is at least one slow step on the folding pathway of RNase P RNA, resulting in conformational changes in the P7 helix region on the minute timescale. Although this folding event requires the presence of Mg2+, the slow step itself does not involve Mg2+ binding. The P7 and P2 helix regions exhibit distinctly different folding behavior and ion dependence, implying that RNase P folding is likely to be a complex process. Furthermore, there are distinct similarities in the folding of RNase P RNA from both Bacillus subtilis and Escherichia coli, indicating that the folding pathway may also be conserved along with the final structure. The slow folding kinetics, Mg2+-independence of the rate, and existence of intermediates are basic features of the folding mechanism of the Tetrahymena group I intron that are also found in RNase P RNA, suggesting these may be general features of the folding of large RNAs.     

Kinetic coupling between protein folding and prolyl isomerization. I. Theoretical models.

Kinetic models were developed to describe the influence of prolyl peptide bond isomerization on the kinetics of reversible protein folding for cases in which structural intermediates do not occur. In the simulations, the number of prolyl residues and the relative rates of folding and isomerization were varied. The experimentally observed rate constants were found to be identical with the intrinsic rate constants of folding and isomerization only when folding remains much faster than prolyl isomerization throughout the transition region. When the rate of folding becomes similar to or lower than the rate of isomerization, the observed kinetic parameters are complex functions of all microscopic rate constants. In particular, the observed folding rates in the transition region decrease with the number of prolyl residues. Pseudo two-state kinetics with single folding and unfolding reactions are observed in several cases, although the apparent folding rates depend strongly on prolyl isomerization reactions in the unfolded chain. This virtual simplicity can easily lead to misinterpretation of kinetic data. Additional phases can be resolved when refolding is started from the fast-folding species (UF). The coupling between folding and prolyl peptide bond isomerization also modifies the dependence on denaturant concentration of the apparent rate constants of folding. We suggest several tests to detect and characterize the contributions of folding and isomerization steps to the observed folding kinetics.     

Protein folding: matching theory and experiment.

The impact of folding funnels and folding simulations on the way experimentalists interpret results is examined. The image of the transition state has changed from a unique species that has a strained configuration, with a correspondingly high free energy, to a more ordinary folding intermediate, whose balance between limited conformational entropy and stabilizing contacts places it at the top of the free energy barrier. Evidence for a broad transition barrier comes from studies showing that mutations can change the position of the barrier. The main controversial issue now is whether populated folding intermediates are productive on-pathway intermediates or dead-end traps. Direct experimental evidence is needed. Theories suggesting that populated intermediates are trapped in a glasslike state are usually based on mechanisms which imply that trapping would only be extremely short-lived (e.g., nanoseconds) in water at 25 degrees C. There seems to be little experimental evidence for long-lived trapping in monomers, if folding aggregates are excluded. On the other hand, there is good evidence for kinetic trapping in dimers. alpha-Helix formation is currently the fastest known process in protein folding, and incipient helices are present at the start of folding. Fast helix formation has the effect of narrowing drastically the choice of folding routes. Thus helix formation can direct folding. It changes the folding metaphor from pouring liquid down a folding funnel to a train leaving a switchyard with only a few choices of exit tracks.     

Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model

We investigate the effect of structural gatekeepers on the folding of the ribosomal protein S6. Folding thermodynamics and early refolding kinetics are studied for this system utilizing computer simulations of a minimalist protein model. When gatekeepers are eliminated, the thermodynamic signature of a folding intermediate emerges, and a marked decrease in folding efficiency is observed. We explain the prerequisites that determine the "strength" of a given gatekeeper. The investigated gatekeepers are found to have distinct functions, and to guide the folding and time-dependent packing of non-overlapping secondary structure elements in the protein. Gatekeepers avoid kinetic traps during folding by favoring the formation of "productive topologies" on the way to the native state. The trends in folding rates in the presence/absence of gatekeepers observed for our minimalist model of S6 are in very good agreement with experimental data on this protein.     

Glycoprotein folding in the endoplasmic reticulum: a tale of three chaperones?

The endoplasmic reticulum (ER) is a major site of protein synthesis and its inside, or lumen, is a major site of protein folding. The lumen of the ER contains many folding factors and molecular chaperones, which facilitate protein folding by increasing both the rate and the efficiency of this process. Amongst the many ER folding factors, there are three components that specifically modulate the folding glycoproteins bearing N-linked carbohydrate side chains. These components are calnexin, calreticulin and ERp57, and this review focuses on the molecular basis for their capacity to influence glycoprotein folding.     

Matching simulation and experiment: a new simplified model for simulating protein folding.

Simulations of simplified protein folding models have provided much insight into solving the protein folding problem. We propose here a new off-lattice bead model, capable of simulating several different fold classes of small proteins. We present the sequence for an alpha/beta protein resembling the IgG-binding proteins L and G. The thermodynamics of the folding process for this model are characterized using the multiple multihistogram method combined with constant-temperature Langevin simulations. The folding is shown to be highly cooperative, with chain collapse nearly accompanying folding. Two parallel folding pathways are shown to exist on the folding free energy landscape. One pathway contains an intermediate--similar to experiments on protein G, and one pathway contains no intermediates-similar to experiments on protein L. The folding kinetics are characterized by tabulating mean-first passage times, and we show that the onset of glasslike kinetics occurs at much lower temperatures than the folding temperature. This model is expected to be useful in many future contexts: investigating questions of the role of local versus nonlocal interactions in various fold classes, addressing the effect of sequence mutations affecting secondary structure propensities, and providing a computationally feasible model for studying the role of solvation forces in protein folding.     

pH dependence of folding of iso-2-cytochrome c

Starting from a standard unfolded state (3.0 M guanidine hydrochloride, pH 7.2), the kinetics of refolding of iso-2-cytochrome c have been investigated as a function of final pH between pH 3 and pH 10. Absorbance in the ultraviolet and visible spectral regions and tryptophan fluorescence are used to monitor folding. Over most of the pH range, fast and slow folding phases are detected by both fluorescence and absorbance probes. Near neutral pH, the rate of fast folding appears to be the same when monitored by absorbance and fluorescence probes. At higher and lower pH, there are two fast folding reactions, with absorbance-detected fast folding occurring in a slightly faster time range than fluorescence-detected fast folding. The rates of both fast folding reactions pass through broad minima near neutral pH, indicating involvement of ionizable groups in rate-limiting steps. The rates of slow folding also depend on the final pH. At acid pH, there appears to be a single slow folding phase for both fluorescence and absorbance probes. At neutral pH, the absorbance-detected and fluorescence-detected slow folding phases separate into distinct kinetic processes which differ in rate and relative amplitude. At high pH, absorbance-detected slow folding is no longer observed, while fluorescence-detected slow folding is decreased in amplitude. In contrast, the equilibrium and kinetic properties of proline imide bond isomerization, believed to be involved in the slow folding reactions, are largely independent of pH. The results suggest that the pH dependence of slow folding involves coupling of pH-sensitive structure to proline imide bond isomerization.(ABSTRACT TRUNCATED AT 250 WORDS)     

Folding behavior of chaperonin-mediated substrate protein

Chaperonin-mediated protein folding is complex. There have been diverse results on folding behavior, and the chaperonin molecules have been investigated as enhancing or retarding the folding rate. To understand the diversity of chaperonin-mediated protein folding, we report a study based on simulations using a simplified Gō-type model. By considering effects of affinity between the substrate protein and the chaperonin wall and spatial confinement of the chaperonin cavity, we study the thermodynamics and kinetics of folding of an unfrustrated substrate protein encapsulated in a chaperonin cavity. The affinity makes the hydrophobic residues of the protein bind to the chaperonin wall, and a strong (or weak) affinity results in a large (or small) effect of binding. Compared with the folding in bulk, the folding in chaperonin cavity with different strengths of affinity shows two kinds of behaviors: one with less dependence on the affinity but more reliance on the spatial confinement effect and the other relying strongly on the affinity. It is found that the enhancement or retardation of the folding rate depends on the competition between the spatial confinement and the affinity due to the chaperonin cavity, and a strong affinity produces a slow folding while a weak affinity induces a fast folding. The crossover between two kinds of folding behaviors happens in the case that the favorable effect of confinement is balanced by the unfavorable effect of the affinity, and a critical affinity strength is roughly defined. By analyzing the contacts formed between the residues of the protein and the chaperonin wall and between the residues of the protein themselves, the role of the affinity in the folding processes is studied. The binding of the residues with the chaperonin wall reduces the formation of both native contacts and nonnative contact or mis-contacts, providing a loose structure for further folding after allosteric change of the chaperonin cavity. In addition, 15 single-site-mutated mutants are simulated in order to test the validity of our model and to investigate the importance of affinity. Inspiringly, our results of the folding rates have a good correlation with those obtained from experiments. The folding rates are inversely correlated with the strength of the binding interactions, i.e., the weaker the binding, the faster the folding. We also find that the inner hydrophobic residues have larger effects on the folding kinetics than those of the exterior hydrophobic residues. We suggest that, besides the confinement effect, the affinity acts as another important factor to affect the folding of the substrate proteins in chaperonin systems, providing an understanding of the folding mechanism of the molecular chaperonin systems.     

The dynamical contact order: Protein folding rate parameters based on quantum conformational transitions

Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain. According to the quantum theory of conformational dynamics, we propose the dynamical contact order (DCO) defined as a characteristic of the contact described by the moment of inertia and the torsion potential energy of the polypeptide chain between contact residues. Consequently, the protein folding rate can be quantitatively studied from the point of view of dynamics. By comparing theoretical calculations and experimental data on the folding rate of 80 proteins, we successfully validate the view that protein folding is a quantum conformational transition. We conclude that (i) a correlation between the protein folding rate and the contact inertial moment exists; (ii) multi-state protein folding can be regarded as a quantum conformational transition similar to that of two-state proteins but with an intermediate delay. We have estimated the order of magnitude of the time delay; (iii) folding can be classified into two types, exergonic and endergonic. Most of the two-state proteins with higher folding rate are exergonic and most of the multi-state proteins with low folding rate are endergonic. The folding speed limit is determined by exergonic folding.     

Protein Folding in the Cell: On the Mechanisms of Its Acceleration

The mechanisms responsible for protein folding in the cell can be divided in two groups. The ones in the first group would be those preventing the aggregation of unfolded polypeptide chains or of incompletely folded proteins, as well as the mechanisms which provide for the energy-consuming unfolding of incorrectly folded structures, giving them a chance to begin a new folding cycle. Mechanisms of this type do not affect the rate of folding (it occurs spontaneously), yet considerably increase the efficiency of the entire process. By contrast, the mechanisms belonging to second group actually accelerate protein folding by exerting a direct influence on the rate-limiting steps of the overall reaction. Although not a conventional one, such a classification helps define the topic of this review. Its main purpose is to discuss the ability of chaperonins (and that of some chaperones) to interact directly with substrate proteins in the course of their folding and thus accelerate the rate-limiting steps of that process. (Mechanisms of protein folding acceleration produced by the action of enzymes, e.g., peptidyl-prolyl cis/trans isomerase and protein disulfide isomerase, are not considered in this review.) Specific cases demonstrating an accelerated folding of some proteins encapsulated in the bacterial chaperonin GroEL cavity are considered, and the conditions favoring such acceleration are examined. Experimental data supporting the notion that the structure and functional properties of GroEL are not optimal for an effective folding of many of its substrate proteins is discussed. The current status of research on the mechanism behind the active participation of different subunits of eucaryotic cytosol chaperonin (CCT) in the final steps of the folding of actin and tubulin is reviewed. Particular attention is devoted to steric chaperones, which dramatically accelerate the formation of the native structure of their substrate proteins by stabilizing certain folding intermediates. The structural foundations underlying the effect of the subtilisin pro-domain on the folding of the mature enzyme are considered. The prospects of future studies into the mechanisms responsible for accelerating protein folding in the cell are commented upon.     

mRNA环结构对蛋白质折叠速率的影响

前期的相关研究发现mRNA二级结构中存在对蛋白质折叠速率的重要影响因素.而mRNA二级结构中普遍存在着各种复杂的环结构,这些环结构是否对蛋白质折叠速率也有重要的影响呢?不同的环结构对蛋白质折叠速率的影响是否相同呢?基于此想法,建立了一个包含mRNA内部环、发夹环、膨胀环和多分支环等环结构信息和相应蛋白质折叠速率的数据库.对于数据库中的每一个蛋白质,计算了mRNA二级结构中各种环结构碱基含量、配对碱基含量及单链碱基含量等参量,分析了各参量与相应蛋白质折叠速率的相关性.结果显示,各种环结构碱基含量与蛋白质折叠速率均呈极显著或显著正相关.说明mRNA环结构对蛋白质折叠速率有重要的影响.进一步,把蛋白质按照不同折叠类型或不同二级结构类型分组后,对每一组蛋白质重复上述的分析工作.结果表明,对不同类蛋白质,mRNA的各种环结构对其相应蛋白质折叠速率的影响存在着显著差异.上述研究将为进一步开展有关mRNA和蛋白质折叠速率的研究奠定理论基础.     

Protein folding in confined and crowded environments

Confinement and crowding are two major factors that can potentially impact protein folding in cellular environments. Theories based on considerations of excluded volumes predict disparate effects on protein folding stability for confinement and crowding: confinement can stabilize proteins by over 10k_BT but crowding has a very modest effect on stability. On the other hand, confinement and crowding are both predicted to favor conformations of the unfolded state which are compact, and consequently may increase the folding rate. These predictions are largely borne out by experimental studies of protein folding under confined and crowded conditions in the test tube. Protein folding in cellular environments is further complicated by interactions with surrounding surfaces and other factors. Concerted theoretical modeling and test-tube and in vivo experiments promise to elucidate the complexity of protein folding in cellular environments.     

Molecular dynamics simulation of the folding of single alkane chains with different lengths on single-walled carbon nanotubes and graphene

Chain folding is an important step during polymer crystallization. In order to study the effects of the surface on chain folding, molecular dynamics simulations of the folding of different alkane chains on three kinds of single-walled carbon nanotubes (SWCNTs) and graphene were performed. The folding behaviors of the single alkane chains on these surfaces were found to be different from their folding behaviors in vacuum. The end-to-end distances of the chains were calculated to explore the chain folding. An increasing tendency to fold into two or more stems with increasing alkane chain length was observed. This result indicates that the occurrence and the stability of chain folding are related to the surface curvature, the diameter of the SWCNT, and surface texture. In addition, the angle between the direction of the alkane chain segment and the direction of the surface texture was measured on different surfaces.     

A combined kinetic push and thermodynamic pull as driving forces for outer membrane protein sorting and folding in bacteria

In vitro folding studies of outer membrane beta-barrels have been invaluable in revealing the lipid effects on folding rates and efficiencies as well as folding free energies. Here, the biophysical results are summarized, and these kinetic and thermodynamic findings are considered in terms of the requirements for folding in the context of the cellular environment. Because the periplasm lacks an external energy source the only driving forces for sorting and folding available within this compartment are binding or folding free energies and their associated rates. These values define functions for periplasmic chaperones and suggest a biophysical mechanism for the BAM complex.