Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis.

Calreticulin (CRT), a chaperone that possesses both lectin and chaperone domains, is localized in the endoplasmic reticulum (ER). CRT has diverse functions and localizations; thus, CRT is a multifunctional protein. Particularly in the ER, CRT mainly aids in the proper folding of nascent glycoproteins as lectin chaperones. Approximately one-third of cellular proteins, including disease-related proteins, are synthesized in the ER. The lectin chaperones CRT and calnexin facilitate the correct folding of these glycoproteins; hence, these chaperones are essential for cells. Various CRT ligands have been reported, mainly composed of Glc1Man9GlcNAc2-type glycan. However, it remains problematic for the complicated synthesis and preparation, and it interacts with glycoprotein folding-related proteins in the ER other than CRT. This suggests that the development of CRT ligands still can be improved. In this study, we developed a hybrid binding concept, which encompasses concurrent binding of ligands to CRT lectin and chaperone domains. We synthesized a CRT-targeting glycan ligand with a glycan and hydrophobic aglycone for CRT lectin and chaperone domain binding, respectively. The thermal shift assay with the CRT-targeting glycan demonstrated that binding was enhanced by simultaneous glycan and hydrophobic aglycone binding. The affinity of the CRT-targeting ligand showed isothermal titration calorimetry approximately 50-fold stronger than that of the glycan alone, thereby supporting the hybrid binding concept. In addition, the CRT-targeting ligand inhibited chaperone function. Overall, these results indicate that the hybrid binding concept may be useful as a novel strategy for the development of CRT ligands and inhibitors.

Prolyl isomerases catalyze the cis/trans isomerization of peptide bonds preceding proline. Previously, we had determined the specificity toward the residue before the proline for cyclophilin-, FKBP-, and parvulin-type prolyl isomerases by using proline-containing oligopeptides and refolding proteins as model substrates. Here, we report the specificities of members of these three prolyl isomerase families for the residue following the proline, again in short peptide and in refolding protein chains. Human cyclophilin 18 and parvulin 10 from Escherichia coli show high activity, but low specificity, with respect to the residue following the proline. Human FKBP12 prefers hydrophobic residues at this position in the peptide assays and shows a very low activity in the protein folding assays. This activity was strongly improved, and the sequence specificity was virtually eliminated after the insertion of a chaperone domain into the prolyl isomerase domain of human FKBP12.

Proline Isomerization of Histone H3 Regulates Lysine Methylation and Gene Expression

Death-Associated Protein Kinase 1 Phosphorylates Pin1 and Inhibits Its Prolyl Isomerase Activity and Cellular Function

The Na(+)-Ca(2+) exchanger (NCX) is a major Ca(2+) regulating protein. It is almost ubiquitously expressed. Cyclophilins (Cyps) make up a class of proteins that are involved in protein folding via their peptidyl prolyl cis-trans isomerase (PPIase) and chaperone domains. They are also the cellular receptors of cyclosporin A (CsA). Binding of CsA to cyclophilins inhibits both PPIase and chaperone activities. We have shown that treatment of transfected HEK 293 cells expressing the Na(+)-Ca(2+) exchanger NCX1 with CsA results in downregulation of surface expression and transport activity, without any reduction in the total level of cell NCX1 protein [Kimchi-Sarfaty, C., et al. (2002) J. Biol. Chem. 277 (4), 2505-2510]. In this work, we show that knockdown of cell CypA using targeting siRNA (without any CsA treatment) results in a reduction in the level of NCX1 surface expression, a decrease in the level of Na(+)-dependent Ca(2+) uptake, and no change in the total amount of cell NCX1 protein in NCX1.5-transfected HEK 293 cells and nontransfected H9c2 cells that express NCX1.1 naturally. It also reduced Na(+)-dependent Ca(2+) fluxes measured by changes in Fluo-4 AM fluorescence in single NCX1.5-transfected HEK 293 and single H9c2 cells. Knockdown of CypB had no significant effect on either transport activity, surface expression, NCX1 cell protein expression, or Ca(2+) fluxes. Overexpression of CypA or its R55A mutant, which exhibits a substantially reduced PPIase activity, alleviated the reduction of NCX1 surface expression caused by CsA treatment, suggesting that the PPIase domain was probably not mandatory for NCX1 functional expression. We suggest that CypA plays a role in the functional expression of NCX1 protein.

Endosialidases (endoNs), as identified so far, are tailspike proteins of bacteriophages that specifically bind and degrade the alpha2,8-linked polysialic acid (polySia) capsules of their hosts. The crystal structure solved for the catalytic domain of endoN from coliphage K1F (endoNF) revealed a functional trimer. Folding of the catalytic trimer is mediated by an intramolecular C-terminal chaperone domain. Release of the chaperone from the folded protein confers kinetic stability to endoNF. In mutant c(S), the replacement of serine 911 by alanine prevents proteolysis and generates an enzyme that varies in activity from wild type. Using soluble polySia as substrate a 3-times higher activity was detected while evaluation with immobilized polySia revealed a 190-fold reduced activity. Importantly, activity of c(S) did not differ from wild type with tetrameric sialic acid, the minimal endoNF substrate. Furthermore, we show that the presence of the chaperone domain in c(S) destabilizes binding to polySia in a similar way as did selective disruption of a polySia binding site in the stalk domain. The improved catalytic efficiency toward soluble polySia observed in these mutants can be explained by higher dissociation and association probabilities, whereas inversely, an impaired processivity was found. The fact that endoNF is a processive enzyme introduces a new molecular basis to explain capsule degradation by bacteriophages, which until now has been regarded as a result of cooperative interaction of tailspike proteins. Moreover, knowing that release of the chaperone domain confers kinetic stability and processivity, conservation of the proteolytic process can be explained by its importance in phage evolution.

Catalysis of slow folding reactions by peptidyl prolyl cis-trans isomerase (PPI) provides estimates of stabilities of intermediates in folding of normal and mutational variants of yeast iso-2 cytochrome c. A two-state model postulating a rapid preequilibration of intermediates with the unfolded protein is employed to calculate the stabilization free energy of the intermediate from the catalytic efficiency (kcat/Km) of PPI toward slow folding species. Stability measurements have been made for two distinct slow-folding intermediates: the absorbance-detected (IIS) and fluorescence-detected (IIIS) intermediates. Mutation-induced changes in the stability of the intermediates and in the activation free energy for slow folding are compared to changes in equilibrium thermodynamic stability. The results show that (1) for iso-2 the absorbance-detected intermediates (IIS) are slightly more stable than the fluorescence-detected intermediates (IIIS), (2) most mutations have different effects on equilibrium stability and the stability of the IIS or IIIS intermediates, and (3) for both slow folding reactions the mutation-induced changes in the activation free energy are small compared to the magnitude of the activation free energy barrier. Differential effects of mutations on equilibrium stability and the stability of intermediates provides a means of assessing the sequence-encoded structural specificity for folding. Mutations with different effects on intermediate stability and equilibrium stability change the encoded folding information and may alter folding pathways and/or lead to different three-dimensional structures. Identification of mutations which stabilize a folding intermediate relative to the native conformation provides an empirical approach to the design of thermodynamically stable forms of folding intermediates.

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

Cyclophilin and FK506 binding protein (FKBP) accelerate cis-trans peptidyl-prolyl isomerization and bind to and mediate the effects of the immunosuppressants cyclosporin A and FK506. The normal cellular functions of these proteins, however, are unknown. We altered the active sites of FKBP12 and mitochondrial cyclophilin from the yeast Saccharomyces cerevisiae by introducing mutations previously reported to inactivate these enzymes. Surprisingly, most of these mutant enzymes were biologically active in vivo. In accord with previous reports, all of the mutant enzymes had little or no detectable prolyl isomerase activity in the standard peptide substrate-chymotrypsin coupled in vitro assay. However, in a variation of this assay in which the protease is omitted, the mutant enzymes exhibited substantial levels of prolyl isomerase activity (5-20% of wild-type), revealing that these mutations confer sensitivity to protease digestion and that the classic in vitro assay for prolyl isomerase activity may be misleading. In addition, the mutant enzymes exhibited near wild-type activity with two protein substrates, dihydrofolate reductase and ribonuclease T1, whose folding is accelerated by prolyl isomerases. Thus, a number of cyclophilin and FKBP12 "active-site" mutants previously identified are largely active but protease sensitive, in accord with our findings that these mutants display wild-type functions in vivo. One mitochondrial cyclophilin mutant (R73A), and also the wild-type human FKBP12 enzyme, catalyze protein folding in vitro but lack biological activity in vivo in yeast. Our findings provide evidence that both prolyl isomerase activity and other structural features are linked to FKBP and cyclophilin in vivo functions and suggest caution in the use of these active-site mutations to study FKBP and cyclophilin functions.

To fully explore the substrate specificities of prolyl isomerases, we synthesized a library of 20 tetrapeptides that are labeled with a 2-aminobenzoyl (Abz) group at the amino terminus and a p-nitroanilide (pNA) group at the carboxy terminus. In this peptide library of the general formula Abz-Ala-Xaa-Pro-Phe-pNA, the position Xaa before the proline is occupied by all 20 proteinogenic amino acids. A conformational analysis of the peptide by molecular dynamics simulations and by NMR spectroscopy showed that the mutual distance between the Abz and pNA moieties in the peptides depends on the isomeric state of the Xaa-Pro bond. In the cis, but not in the trans form, there are significant chemical shift changes of the Abz and pNA moieties, because their aromatic rings are close to each other. This proximity also leads to a strong quenching of Abz fluorescence, which, in combination with a solvent jump, was used to devise a sensitive assay for prolyl isomerases. Unlike the traditional assay, it is not coupled with peptide proteolysis and thus can be employed for protease-sensitive prolyl isomerases as well. The peptide library was used to provide a complete set of P1-site specificities for prototypic human members of the three prolyl isomerase families, FKBP12, cyclophilin 18, and parvulin 14. In a second application, the substrate specificity of SlyD, a protease-sensitive prolyl isomerase from Escherichia coli, was characterized and compared with that of human FKBP12 as well as with homologues from other bacteria.

FK506 Binding Proteins (FKBPs) are a family of highly conserved and important proteins that possess a peptidyl cis-trans isomerase (PPIases) domain. Human FKBP12 is a prototype of this family and it is involved in many diseases due to its interaction with the immunosuppressive drugs FK506 and rapamycin. They inhibit calcineurin and mTOR complex, respectively, leading to parasite death by inhibiting cell proliferation through cytokinesis blockade being an important target to find new drugs. Tuberculosis is a disease that causes important impacts on public health worldwide. In this context, MtFKBP12 is a putative peptidyl prolyl cis-trans isomerase from Mycobacterium tuberculosis and here we report the NMR chemical shift assignment for 1H, 15N and 13C nuclei in the backbone and side chains of the MtFKBP12. This lays the foundation for further structural studies, backbone dynamics, mapping of interactions and drug screening and development. We have found through the NMR spectrum that the protein is well folded with narrow peaks and almost none overlap in 15N-HSQC. Prediction of secondary structure using Talos-N server showed great similarity with other proteins from this family.

NMR Solution Structure of SlyD from Escherichia coli: Spatial Separation of Prolyl Isomerase and Chaperone Function

The transcriptional antiterminator protein LicT regulates the expression of Bacillus subtilis operons involved in beta-glucoside metabolism. It consists of an N-terminal RNA-binding domain (co-antiterminator (CAT)) and two phosphorylatable phosphotransferase system regulation domains (PRD1 and PRD2). In the activated state, each PRD forms a dimeric unit with the phosphorylation sites totally buried at the dimer interface. Here we present the 1.95 A resolution structure of the inactive LicT PRDs as well as the molecular solution structure of the full-length protein deduced from small angle x-ray scattering. Comparison of native (inactive) and mutant (constitutively active) PRD crystal structures shows massive tertiary and quaternary rearrangements of the entire regulatory domain. In the inactive state, a wide swing movement of PRD2 results in dimer opening and brings the phosphorylation sites to the protein surface. This movement is accompanied by additional structural rearrangements of both the PRD1-PRD1 ' interface and the CAT-PRD1 linker. Small angle x-ray scattering experiments indicate that the amplitude of the PRD2 swing might even be wider in solution than in the crystals. Our results suggest that PRD2 is highly mobile in the native protein, whereas it is locked upon activation by phosphorylation.

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.

New nonbonded parameters of a “6-exp-1” all-atom force field are presented for amines, imidazoles, amides, and carboxylic acids. These results are part of our work to derive a general force field for the prediction of crystal and protein structures (the nonbonded parameters for aliphatic and aromatic hydrocarbons and alcohols were published recently, J. Phys. Chem. B 2003, 107, 7143). The parameters were derived by using our global-optimization-based method (J. Phys. Chem. B 2003, 107, 712) which provides the best possible set of parameters for crystal structure prediction for a given form of the potential. The method consists of two steps. First, an initial set of parameters is derived from ab initio quantum mechanical interaction energies of dimers; then, the initial set is refined to satisfy the following criteria: the parameters should reproduce the observed crystal structures and sublimation enthalpies, and the experimental crystal structure should correspond to the global minimum of the potential. The refinement procedure uses information about the potential energy surface of the crystal obtained by global energy minimization. Vector Monte Carlo (J. Phys. Chem. B 2003, 107, 712) and force-minimization methods are used in the refinement step. The parameters presented in this paper reproduce experimental crystal structures with high accuracy. The experimental structures of all molecules tested were found as the global or one of the lowest-energy minima of the potential.