Review: allostery in chaperonins.

Chaperonins mediate protein folding in an ATP-dependent manner. ATP binding and hydrolysis by chaperonins are subject to both homotropic and heterotropic allosteric regulation. In the case of GroEL and CCT, homotropic regulation by ATP is manifested in nested cooperativity, which involves positive intra-ring cooperativity and negative inter-ring cooperativity in ATP binding. Both types of cooperativity are modulated by various heterotropic allosteric effectors, which include nonfolded proteins, ADP, Mg2+, monovalent ions such as K+, and cochaperonins in the case of type I chaperonins such as GroEL. Here, the allosteric properties of chaperonins are reviewed and new results of ours are presented with regard to allosteric effects of ADP. The role of allostery in the reaction cycle and folding function of chaperonins is discussed.

Nested allosteric interactions in the cytoplasmic chaperonin containing TCP-1.

Initial rates of ATP hydrolysis by the chaperonin containing TCP-1 (CCT) from bovine testis were measured as a function of ATP concentration. Two allosteric transitions are observed: one at relatively low concentrations of ATP (<100 microM) and the second at higher concentrations of ATP. The data suggest that CCT has positive intra-ring cooperativity and negative inter-ring cooperativity in ATP hydrolysis, with respect to ATP, as previously observed in the case of GroEL. It is shown that the relatively weak positive intra-ring cooperativity found in the case of CCT may be due to heterogeneity in its subunit composition. Our results suggest that nested allosteric behavior may be common to chaperone double-ring systems.

In vivo and in vitro function of GroEL mutants with impaired allosteric properties.

Escherichia coli cells that produce only plasmid-encoded wild-type or mutant GroEL were generated by bacteriophage P1 transduction. Effects of mutations that affect the allosteric properties of GroEL were characterized in vivo. Cells containing only GroEL(R197A), which has reduced intra-ring positive cooperativity and inter-ring negative cooperativity in ATP binding, grow poorly upon a temperature shift from 25 to 42 degrees C. This strain supports the growth of phages T4 and T5 but not phage lambda and produces light at 28 degrees C when transformed with a second plasmid containing the lux operon. In contrast, cells containing only GroEL(R13G, A126V) which lacks negative cooperativity between rings but has intact intra-ring positive cooperativity grow normally and support phage growth but do not produce light at 28 degrees C. In vitro refolding of luciferase in the presence of this mutant is found to be less efficient compared with wild-type GroEL or other mutants tested. Our results show that allostery in GroEL is important in vivo in a manner that depends on the physiological conditions and is protein substrate specific.

On the relationship between the Hill coefficients for steady-state and transient kinetic data: a criterion for concerted transitions in allosteric proteins.

A frequently used measure for the extent of cooperativity in ligand binding by allosteric proteins is the Hill coefficient. Hill coefficients can be measured for steady-state kinetic data and also for transient kinetic data. Here, the relationship between the two types of Hill coefficients is analysed. It is shown that a value of 1 for the ratio of the two Hill coefficients is a test for a concerted ligand-induced transition between two conformations of the protein, in accordance with the Monod-Wyman-Changeux model. A value of 1 for this ratio has recently been observed for a series of chaperonin GroEL mutants suggesting that ATP-induced allosteric transitions in this protein are concerted.

Coupling between protein folding and allostery in the GroE chaperonin system.

GroEL is an allosteric protein that facilitates protein folding in an ATP-dependent manner. Herein, the relationship between cooperative ATP binding by GroEL and the kinetics of GroE-assisted folding of two substrates with different GroES dependence, mouse dihydrofolate reductase (mDHFR) and mitochondrial malate dehydrogenase, is examined by using cooperativity mutants of GroEL. Strong intra-ring positive cooperativity in ATP binding by GroEL decreases the rate of GroEL-assisted mDHFR folding owing to a slow rate of the ATP-induced transition from the protein-acceptor state to the protein-release state. Inter-ring negative cooperativity in ATP binding by GroEL is found to affect the kinetic partitioning of mDHFR, but not of mitochondrial malate dehydrogenase, between folding in solution and folding in the cavity underneath GroES. Our results show that protein folding by this "two-stroke motor" is coupled to cooperative ATP binding.

A model of a gp120 V3 peptide in complex with an HIV-neutralizing antibody based on NMR and mutant cycle-derived constraints.

The 0.5beta monoclonal antibody is a very potent strain-specific HIV-neutralizing antibody raised against gp120, the envelope glycoprotein of HIV-1. This antibody recognizes the V3 loop of gp120, which is a major neutralizing determinant of the virus. The antibody-peptide interactions, involving aromatic and negatively charged residues of the antibody 0.5beta, were studied by NMR and double-mutant cycles. A deuterated V3 peptide and a Fab containing deuterated aromatic amino acids were used to assign these interactions to specific V3 residues and to the amino acid type and specific chain of the antibody by NOE difference spectroscopy. Electrostatic interactions between negatively charged residues of the antibody Fv and peptide residues were studied by mutagenesis of both antibody and peptide residues and double-mutant cycles. Several interactions could be assigned unambiguously: F96(L) of the antibody interacts with Pro13 of the peptide, H52(H) interacts with Ile7, Ile9 and Gln10 and D56(H) interacts with Arg11. The interactions of the light-chain tyrosines with Pro13 and Gly14 could be assigned to either Y30a(L) and Y32(L), respectively, or Y32(L) and Y49(L), respectively. Three heavy-chain tyrosines interact with Ile7, Ile20 and Phe17. Several combinations of assignments involving Y32(H), Y53(H), Y96(H) and Y100a(H) may satisfy the NMR and mutagenesis constraints, and therefore at this stage the interactions of the heavy-chain tyrosines were not taken into account. The unambiguous assignments [F96(L), H52(H) and D56(H)] and the two possible assignments of the light-chain tyrosines were used to dock the peptide into the antibody-combining site. The peptide converges to a unique position within the binding site, with the RGPG loop pointing into the center of the groove formed by the antibody complementary determining regions while retaining the beta-hairpin conformation and the type-VI RGPG turn [Tugarinov, V., Zvi, A., Levy, R. & Anglister, J. (1999) Nat. Struct. Biol. 6, 331-335].

Transient kinetic analysis of adenosine 5'-triphosphate binding-induced conformational changes in the allosteric chaperonin GroEL.

GroEL with an intrinsic fluorescent probe was generated by introducing the mutation Phe44 --> Trp. Different concentrations of ATP were rapidly mixed with GroEL containing this mutation, and the time-resolved change in fluorescence emission, upon excitation at 280 nm, was followed. Three kinetic phases were observed: a fast phase with a large amplitude and two slower phases with small amplitudes. The phases were assigned by (i) determining their dependence on ATP concentration; (ii) measuring their sensitivity to the mutation Arg197 --> Ala, which decreases cooperativity in ATP binding; and (iii) by carrying out mixing experiments of GroEL also with ADP, ATPgammaS, and ATP without K+. The apparent rate constant corresponding to the fast phase displays a bi-sigmoidal dependence on ATP concentration with Hill coefficients that are strikingly similar to those determined in steady-state experiments. This phase, which reflects ATP-induced conformational changes, is sensitive to the mutation Arg197 --> Ala in a manner that parallels steady-state experiments. The rate of conformational change in the presence of ATP is >100 sec-1, which is fast relative to most protein folding rates, whereas in the absence of ATP it is approximately 0.7 s-1. The second phase reflects the transition from an ATP-bound state of GroEL to an ADP-bound state. The third phase, with the smallest amplitude, reflects release of residual contaminants. The results in this study are found to be consistent with the nested model for cooperativity in ATP binding by GroEL [Yifrach, O., and Horovitz, A. (1995) Biochemistry 34, 5303-5308].

Structural aspects of GroEL function.

The chaperonin GroEL and its cofactor GroES facilitate protein folding in an ATP-regulated manner. The recently solved crystal structure of the GroEL.GroES.(ADP)7 complex shows that the lining of the cavity in the polypeptide acceptor state is hydrophobic, whereas in the protein-release state it becomes hydrophilic. Other highlights of the past year include the visualization of the allosteric states of GroEL with respect to ATP using cryo-electron microscopy, and an X-ray crystallographic analysis of the interaction between the apical domain of GroEL and a peptide.

GroES promotes the T to R transition of the GroEL ring distal to GroES in the GroEL-GroES complex.

Curves of initial rates of ATP hydrolysis by GroEL as a function of ATP concentration, in the presence of fixed concentrations of GroES, were found to deviate from sigmoidal kinetics. Instead of the lag phase typical of sigmoidal curves, a linear phase is observed at low ATP concentrations. Consequently, a good fit of the data to the Hill equation could not be achieved. Such curves could be simulated using a linear combination of Hill equations, thus indicating that more than one allosteric transition is taking place in the ATP concentration range studied. The data were fitted to a fractional saturation equation for ATP binding to GroEL based on a partition function that includes both GroES and ATP-liganded states of GroEL. Using this equation, it was possible to estimate in a reliable manner the value of the allosteric constant, L2', for the transition of the ring distal to GroES in the GroEL-GroES complex from the low (T)- to the high (R)-affinity state for ATP. The value of L2' is found to be 4 x 10(-5) whereas the value of the allosteric constant, L2, for the transition of the second ring of GroEL from the T to R state is 2 x 10(-9) [Yifrach, O., & Horovitz, A. (1995) Biochemistry 34, 5303-5308]. Comparison of these values shows that GroES promotes the T to R transition of the ring distal to GroES in the GroEL-GroES complex. Owing to the relatively low affinity of the R conformation for nonfolded proteins, this transition will lead to release of protein substrates from trans ternary complexes of GroEL, GroES, and protein substrate. The role of this release mechanism may be to assist the folding of relatively large proteins that cannot form cis ternary complexes and/or to facilitate degradation of damaged proteins which cannot fold.

Detection of changes in pairwise interactions during allosteric transitions: coupling between local and global conformational changes in GroEL.

A protein engineering approach for detecting and measuring local conformational changes that accompany allosteric transitions in proteins is described. Using this approach, we can identify interactions that are made or broken during allosteric transitions. The method is applied to probe for changes in pairwise interactions in the chaperonin GroEL during its ATP-induced allosteric transitions. Two pairwise interactions are investigated: one between subunits (Asp-41 with Thr-522) and the other within subunits (Glu-409 with Arg-501). We find that the intraring intersubunit interaction between Asp-41 and Thr-522 changes little during the allosteric transitions of GroEL, indicating that the hydrogen bond between these residues is maintained. In contrast, the intrasubunit salt bridge between Glu-409 and Arg-501 becomes significantly weaker during the ATP-induced allosteric transitions of GroEL. Our results are consistent with the electron microscopy observations of an ATP-induced hinge movement of the apical domains relative to the equatorial domains.

Thermodynamic analysis of the interaction between the 0.5beta Fv fragment and the RP135 peptide antigen derived from the V3 loop of HIV-1 gp120.

The Fv fragment of the 0.5beta monoclonal antibody has recently been constructed, expressed, and purified. It binds with nanomolar affinity to the immunogenic RP135 peptide that is derived from the principal neutralizing determinant of HIV-1 in the third hypervariable region of gp120. Here, we analyzed the temperature-dependence of binding of the 0.5beta Fv fragment to the RP135 peptide and a series of mutants thereof. Our results show that there is almost complete enthalpy-entropy compensation in the effects of mutations in the peptide on binding to the Fv, indicating that the mutations do not change the binding mechanism. There is good correlation, for residues within the antigenic epitope, between mutational effects on DeltaCp and calculated values of DeltaDeltaCp based on the extent of burial of polar and non-polar surface areas of amino acids. The value of DeltaCp for the binding of the 0.5beta Fv fragment to the wild-type RP135 peptide is found to be -5.0 (+/- 0.9) kcal K-1 mol-1 in the presence of 0.1% Tween-20 but only -0.1 (+/- 0.9) kcal K-1 mol-1 in its absence. This result has important implications for the successful application of the structural parameterization approach to predicting changes in heat capacity that accompany binding reactions carried out in the presence of detergent or protein-stabilizing agents.

Contribution of arginine residues in the RP135 peptide derived from the V3 loop of gp120 to its interaction with the Fv fragment of the 0.5beta HIV-1 neutralizing antibody.

The construction, expression, and purification of an active Fv fragment of the 0.5beta monoclonal human immunodeficiency virus type 1 (HIV-1) neutralizing antibody is reported. The interaction between the Fv fragment and the RP135 peptide derived from the V3 loop of gp120 from HIV-1IIIB was studied by varying the salt concentration and by mutating arginine residues in the peptide. The mutations R4A, R8A and R11A (which correspond to residues 311, 315, and 318 in gp120 of HIV-1IIIB) reduce the binding free energy by 0.22 (+/- 0. 20), 4.32 (+/- 0.16), and 1.58 (+/- 0.17) kcal mol-1, respectively. The salt-dependent components of their contributions to binding are 0.02 (+/- 0.22), -0.55 (+/- 0.18), and -0.97 (+/- 0.19) kcal mol-1, respectively. The magnitudes of the mutational effects and the extent of shielding by 1 M NaCl suggest that Arg-8 is involved in a buried salt bridge in the peptide-Fv fragment complex, whereas Arg-11 is involved in a more solvent-exposed electrostatic interaction.

Inter-ring communication is disrupted in the GroEL mutant Arg13 --> Gly; Ala126 --> Val with known crystal structure.

The crystal structures of the chaperonin GroEL Arg13 --> Gly; Ala126 --> Val double mutant, without and in complex with ATP gamma S, have been determined at atomic resolution. Here, we show that the double mutation Arg13 --> Gly; Ala126 --> Val disrupts negative co-operativity between GroEL rings, with respect to ATP, but has little effect on the positive co-operativity within each ring. Our results help to explain why the double mutation facilitated the crystallization of GroEL and why breaking of dyad symmetry between rings is not observed in crystal structures of this mutant. Our results may also help to explain why the observed structural differences between the GroEL double mutant and its ATP gamma S-bound form are small.

On the choice of reference mutant states in the application of the double-mutant cycle method.

Pairwise interactions in proteins can be detected and, in certain circumstances, their strength measured by applying the method of double-mutant cycles. Such cycles comprise wild type protein, two single mutants and the corresponding double mutant. The analysis of double-mutant cycles is most straightforward when the mutations are to alanine since interactions are mostly removed without new interactions being formed. Here, 'not-to-alanine' double-mutant cycles are analysed. It is shown that a 'not-to-alanine' double-mutant cycle can be decomposed into four double-mutant cycles with mutations only to alanine. The coupling energy corresponding to the 'not-to-alanine' double-mutant cycle is expressed as a function of the coupling energies of these four cycles.

Allosteric control by ATP of non-folded protein binding to GroEL.

Co-operativity in ATP hydrolysis by GroEL can be described by a model in which each ring of GroEL is in equilibrium between a low (T) and high (R) affinity state for ATP. According to this model, the GroEL double-ring is in equilibrium between three states: TT, TR and RR. In order to find out which states bind non-folded proteins, we measured the co-operativity in ATP hydrolysis by GroEL in the absence and presence of non-folded alpha-lactalbumin, under equilibrium conditions between GroEL and the non-folded protein. The non-folded protein is found to bind preferentially the T state of GroEL rings and to stimulate the ATPase activity of GroEL by (1) a direct effect on GroEL rings in the T state and (2) a shift in the equilibrium from the RR state toward the more active TR state. The coupling between co-operativity in ATP hydrolysis by GroEL and protein substrate binding and release by this molecular chaperone is shown.

Double-mutant cycles: a powerful tool for analyzing protein structure and function.

A double-mutant cycle involves wild-type protein, two single mutants and the corresponding double mutant protein. If the change in free energy associated with a structural or functional property of the protein upon a double mutation differs from the sum of changes in free energy due to the single mutations, then the residues at the two positions are coupled. Such coupling reflects either direct or indirect interactions between these residues. Double-mutant cycle analysis can be used to measure the strength of intramolecular and intermolecular pairwise interactions in proteins or protein-ligand complexes with known structure. Double-mutant cycles can also be employed to characterize structures that are inaccessible to NMR and X-ray crystallography, such as those of transition states for protein folding, ligand binding and enzyme catalysis, or of membrane proteins. Multidimensional mutant cycle analysis can be used to measure higher-order cooperativity between intramolecular or intermolecular interactions. In the absence of coupling between residues, prediction of mutational effects is possible by assuming their additivity.

Changes mimicking endometrial neoplasia in postmenopausal, tamoxifen-treated women with breast cancer: a transvaginal Doppler study.

In menopausal patients with breast cancer who receive tamoxifen therapy, transvaginal sonography may show an abnormal endometrium. Our objective was to evaluate the effects of prolonged tamoxifen therapy on endometrial blood flow in postmenopausal patients with breast cancer, and to correlate blood flow characteristics with the sonographic appearance of the endometrium and its pathology. Transvaginal color Doppler ultrasound examinations were performed on 45 postmenopausal women (age range 54-70 years) with breast cancer, who had been treated with tamoxifen for 1-3 years. Twenty women (Group 1) had a thick, irregular, cystic endometrium of > or = 5 mm, and 25 (Group 2) showed a thin endometrium of < 5 mm. The blood flow response was assessed by visualization of arterial waveforms in the endometrial and subendometrial regions with a transvaginal color flow imaging system. Resistance indexes (RI) were calculated for analysis and correlated with endometrial appearance and histology. The mean RI in Group 1 was 0.39 +/- 0.10 (range 0.32-0.54), while the mean RI in Group 2 was 0.79 +/- 0.10 (range 0.54-0.90; p < 0.001). On histology, 12 patients in Group 1 showed atrophic endometria confirmed by hysteroscopy, while in the remaining eight, endometrial polyps were found. In Group 2, all patients had scanty, atrophic endometria. Six of the eight patients with endometrial polyps had an RI of < 0.4 and none had malignant changes. These data suggest that tamoxifen therapy in women with postmenopausal breast cancer induces endometrial, morphological and blood flow changes, mimicking endometrial neoplasia.(ABSTRACT TRUNCATED AT 250 WORDS)