Cooperativity: over the Hill.

Cooperativity, the ability of ligand binding at one site on a macromolecule to influence ligand binding at a different site on the same macromolecule, is a fascinating biological property that is often poorly explained in textbooks. The Hill coefficient is commonly used in biophysical studies of cooperative systems although it is not a quantitative measure of cooperativity. The free energy of interaction between binding sites (delta delta G) is a more stringent definition of cooperativity and provides a direct quantitative measure of how the binding of ligand at one site affects the ligand affinity of another site.

The evolving model of calmodulin structure, function and activation.

Recent high-resolution crystal and solution structures have answered many long-standing questions about calmodulin and its various conformational states. However, there is still much to learn.

Kinetics of Ca2+ binding to calmodulin and its tryptic fragments studied by 43Ca-NMR.

The kinetics of calcium ion binding to bovine testis calmodulin and its tryptic fragments have been studied by 43Ca-NMR. The same subdivision of the Ca2+-binding sites of calmodulin into two with slow exchange (high affinity) and two with fast exchange (low affinity) observed at low ionic strength is also encountered at high ionic strength. The effect of 0.1 M KCl is to reduce the exchange rate of the fast process from 1150 s-1 to 520 s-1 at 25 degrees C. Studies of the tryptic fragments TR1C and TR2C, comprising the N- or C-terminal half of calmodulin, respectively, clearly identified Ca2+-binding domains I and II as those with fast exchange (low affinity) and domains III and IV as those with slow exchange (high affinity). Activation parameters are reported for calmodulin and TR1C. Correlation times have been measured for ions bound to the fragments. The obtained values, 5 and 6 ns for TR1C and TR2C, respectively, are of the same order as rotational correlation times for the entire fragment molecules, indicating that the calcium ions do not have any mobility with a correlation time in the ns range within the sites.

A 35Cl(-)-NMR study of the singular anion-binding properties of dromedary hemoglobin.

35Cl(-)-NMR measurements of chloride binding to carbonmonoxy- and deoxy-dromedary hemoglobin reveal the existence of two classes of chloride-binding sites, one of high and the other of low affinity. Although this situation resembles that described for human hemoglobin, it was found that the number of binding sites as well as the association equilibrium constant for chloride binding are significantly higher in the dromedary protein. This difference may be due to the greater number of basic residues exposed to solvent and to the higher flexibility of dromedary hemoglobin. The two oxygen-linked polyanion-binding sites characteristic of this hemoglobin show competition for some of the high-affinity chloride-binding sites in keeping with their location in the cleft enclosed by the beta chains and between the alpha chains termini. It is suggested that the observed anion-binding properties of dromedary hemoglobin may contribute to the control of the physiological osmotic shock after rehydration.

Calcium.

Ca2+ is involved in an intriguing variety of different biological events. The rapid development of techniques such as region- or organelle-directed fluorescent probes and laser scanning confocal microscopy for studying cellular biological events at a molecular level provides us with a rich daily intake of new results. While detailed three-dimensional structures of many intracellular and extracellular Ca2+-binding proteins have become available, structural information on key membrane proteins is still lacking. An integrated picture of the molecular events behind the multifunctional roles of Ca2+ in biological systems is still pending.

Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo-->(Ca2+)II1-->(Ca2+)I,II2 binding pathway.

The three-dimensional solution structure of (Cd2+)1-calbindin D9k has been determined by distance geometry, restrained molecular dynamics and relaxation matrix calculations using experimental constraints obtained from two-dimensional 1H and 15N-1H NMR spectroscopy. The final input data consisted of 1055 NOE distance constraints and 71 dihedral angle constraints, corresponding to 15 constraints per residue on average. The resulting ensemble of 24 structures has no distance or dihedral angle constraints consistently violated by more than 0.07 A and 1.8 degrees, respectively. The structure is characteristic of an EF-hand protein, with two helix-loop-helix calcium binding motifs joined by a flexible linker, and a short anti-parallel beta-type interaction between the two ion-binding sites. The four helices are well defined with a root mean square deviation from the mean coordinates of 0.35 A for the backbone atoms. The structure of the half-saturated cadmium state was compared with the previously determined solution structures of the apo and fully calcium saturated calbindin D9k. The comparisons were aided by introducing the ensemble averaged distance difference matrix as a tool for analyzing differences between two ensembles of structures. Detailed analyses of differences between the three states in backbone and side-chain dihedral angles, hydrogen bonds, interatomic distances, and packing of the hydrophobic core reveal the reorganization of the protein that occurs upon ion binding. Overall, it was found that (Cd2+)1-calbindin D9k, representing the half-saturated calcium state with an ion in site II, is structurally more similar to the fully calcium-saturated state than the apo state. Thus, for the binding sequence apo-->(Ca2+)II1-->(Ca2+)I,II2, the structural changes occurring upon ion binding are most pronounced for the first binding step, an observation that bears significantly on the molecular basis for cooperative calcium binding in calbindin D9k.

Molecular basis for co-operativity in Ca2+ binding to calbindin D9k. 1H nuclear magnetic resonance studies of (Cd2+)1-bovine calbindin D9k.

The molecular basis for the co-operativity in binding of calcium ions by bovine calbindin D9k has been addressed by carrying out a comparative analysis of the solution conformation and dynamics of the apo, half saturated and fully saturated species using two-dimensional 1H nuclear magnetic resonance spectroscopy. Since the half saturated calcium form of the protein is not significantly populated under equilibrium conditions due to the co-operativity in binding of calcium ions, the half saturated cadmium form of the protein has been substituted for the calcium form. To verify that cadmium forms of calbindin D9k represent viable models for the calcium-bound species, the fully saturated cadmium form has been prepared and compared to the calcium-saturated protein. Virtually complete 1H resonance assignments have been obtained for both the (Cd2+)1 and the (Cd2+)2 states. Secondary structure elements and the global folding pattern were determined from nuclear Overhauser effects, backbone spin-spin coupling constants and slowly exchanging amide protons. Comparisons of the half saturated protein with the apo and calcium-saturated forms of calbindin D9k show that all three structures are highly similar. However, a change in the structural and dynamic properties of the protein does occur upon binding of the first ion; the half saturated form is found to be more similar to the calcium-saturated form than to the apo form. These results have important implications concerning the molecular basis for the co-operativity, and suggest that entropic effects associated with the protein dynamics play an important role.

Backbone dynamics and energetics of a calmodulin domain mutant exchanging between closed and open conformations.

Previous studies have suggested that the Ca2+-saturated E140Q mutant of the C-terminal domain of calmodulin exhibits equilibrium exchange between "open" and "closed" conformations similar to those of the Ca2+-free and Ca2+-saturated states of wild-type calmodulin. The backbone dynamics of this mutant were studied using15N spin relaxation experiments at three different temperatures. Measurements at each temperature of the15N rate constants for longitudinal and transverse auto-relaxation, longitudinal and transverse cross-correlation relaxation, and the1H-15N cross-relaxation afforded unequivocal identification of conformational exchange processes on microsecond to millisecond time-scales, and characterization of fast fluctuations on picosecond to nanosecond time-scales using model-free approaches. The results show that essentially all residues of the protein are involved in conformational exchange. Generalized order parameters of the fast internal motions indicate that the conformational substates are well folded, and exclude the possibility that the exchange involves a significant population of unfolded or disordered species. The temperature dependence of the order parameters offers qualitative estimates of the contribution to the heat capacity from fast fluctuations of the protein backbone, revealing significant variation between the well-ordered secondary structure elements and the more flexible regions. The temperature dependence of the conformational exchange contributions to the transverse auto-relaxation rate constants directly demonstrates that the microscopic exchange rate constants are greater than 2.7x10(3)s-1at 291 K. The conformational exchange contributions correlate with the chemical shift differences between the Ca2+-free and Ca2+-saturated states of the wild-type protein, thereby substantiating that the conformational substates are similar to the open and closed states of wild-type calmodulin. Taking the wild-type chemical shifts to represent the conformational substates of the mutant and populations estimated previously, the microscopic exchange rate constants could be estimated as 2x10(4)to 3x10(4)s-1at 291 K for a subset of residues. The temperature depen dence of the exchange allows the characterization of apparent energy barriers of the conformational transition, with results suggesting a complex process that does not correspond to a single global transition between substates.

Structural dynamics in the C-terminal domain of calmodulin at low calcium levels.

Calmodulin undergoes Ca2+-induced structural rearrangements that are intimately coupled to the regulation of numerous cellular processes. The C-terminal domain of calmodulin has previously been observed to exhibit conformational exchange in the absence of Ca2+. Here, we characterize further the conformational dynamics in the presence of low concentrations of Ca2+ using 15N spin relaxation experiments. The analysis included 1H-15N dipolar/15N chemical shift anisotropy interference cross-correlation relaxation rates to improve the description of the exchange processes, as well as the picosecond to nanosecond dynamics. Conformational transitions on microsecond to millisecond time scales were revealed by exchange contributions to the transverse auto-relaxation rates. In order to separate the effects of Ca2+ exchange from intramolecular conformational exchange processes in the apo state, transverse auto-relaxation rates were measured at different concentrations of free Ca2+. The results reveal a Ca2+-dependent contribution due mainly to exchange between the apo and (Ca2+)1 states with an apparent Ca2+ off-rate of approximately 5115 s(-1), as well as Ca2+-independent contributions due to conformational exchange within the apo state. 15N chemical shift differences estimated from the exchange data suggest that the first Ca2+ binds preferentially to loop IV. Thus, characterization of chemical exchange as a function of Ca2+ concentration has enabled the extraction of unique information on the rapidly exchanging and weakly populated (<10 %) (Ca2+)1 state that is otherwise inaccessible to direct study due to strongly cooperative Ca2+ binding. The conformational exchange within the apo state appears to involve transitions between a predominantly populated closed conformation and a smaller population of more open conformations. The picosecond to nanosecond dynamics of the apo state are typical of a well-folded protein, with reduced amplitudes of motions in the helical segments, but with significant flexibility in the Ca2+-binding loops. Comparisons with order parameters for skeletal troponin C and calbindin D9k reveal key structural and dynamical differences that correlate with the different Ca2+-binding properties of these proteins.

Dynamic and structural properties of the calcium binding site of bovine serine proteases and their zymogens. A multinuclear nuclear magnetic resonance and stopped-flow study.

The combined use of 43Ca and 113Cd nuclear magnetic resonance (n.m.r.) has provided information on the structural and dynamic properties of the calcium binding site located in homologous positions in bovine beta-trypsin, alpha-chymotrypsin and their zymogens. The 43Ca and 113Cd n.m.r. chemical shifts are consistent with an octahedral symmetry of the binding site and with the substitution of one of the two carboxylate ligands present in trypsin(ogen) with a neutral ligand in chymotrypsin(ogen). The constancy of the 113Cd n.m.r. chemical shifts upon binding of the pancreatic trypsin inhibitor and/or the dipeptide Ile-Val to trypsinogen confirms that structural changes in the activation domain do not affect the calcium binding site. The exchange between bound and "free" (solvated) Ca2+ is slow on the 43Ca n.m.r. time-scale for trypsin(ogen), but falls in the intermediate exchange region for chymotrypsin(ogen). In trypsin, the Ca2+ off-rate was measured by stopped-flow making use of the calcium indicator 1,2-bis(o-aminophenoxy)-ethane-N,N,N',N'-tetraacetic acid and was found to be 3(+/- 1) s-1. In chymotrypsin(ogen) the off-rates calculated from the 43Ca n.m.r. data are 70 s-1 and 350 s-1, respectively. The dynamic properties of the calcium binding site of serine (pro)enzymes have been related to the flexibility of the binding site itself and have been compared to those of other extracellular and intracellular calcium binding proteins.

Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography.

In a structure of recombinant bovine calbindin D9k, determined crystallographically to 1.6 A resolution, a proline in mixed, approximately equally populated, cis and trans conformation is observed. Isomers of this kind have not been reported in structure determinations of calbindin D9k to 2.3 A resolution or in any other crystallographically determined protein structure. The cis-trans isomerization occurs at the peptide bond between Gly42 and Pro43, which is in agreement with results from two-dimensional 1H nuclear magnetic resonance spectroscopy experiments on solutions of calbindin D9k. Alternative backbone stretches have been modeled and refined by stereochemical restrained least-squares refinement for the segment Lys41 to Pro43. The final R-value was 0.188. The structural perturbations accompanying the cis-trans isomerization are found to be very localized. The largest positional differences are observed at residue Gly42, in which the alternative positions of the oxygen atom are 3.6 A apart.

Mapping of the immunoglobulin light chain-binding site of protein L.

Protein L is a cell surface protein expressed by some strains of the anaerobic bacterial species Peptostreptococcus magnus. The molecule binds specifically and with high affinity to immunoglobulins (Ig) of a wide range of animal species. The Ig-binding activity is mediated through five highly homologous domains, each 72 to 76 amino acid residues long, which interact with framework regions in the variable domain of Ig light chains. The interaction does not interfere with the antigen binding capacity of the antibody. The fold of the Ig light chain-binding domains of Protein L is comprised of an alpha-helix packed against a four stranded beta-sheet and is similar to the fold of the IgG heavy chain-binding domains of streptococcal protein G, despite the fact that the two proteins show no significant sequence homology. In the present work, heteronuclear NMR spectroscopy has been utilized to define the interaction between the N-terminal Ig-binding domain of Protein L and the variable domain of a human Ig kappa light chain. The Ig-binding region of the Protein L domain involves most of the residues in the second beta-strand, the C-terminal residues of the alpha-helix and the loop connecting the alpha-helix with the third beta-strand. The Ig light chain-binding surface of Protein L thus resembles the surface of Protein G which binds to the C gamma 1 domain of IgG, but is different from the portion of Protein G involved in the contact with the C gamma 2-C gamma 3 interface region. The data suggest that the global fold shared by the Ig-binding domains of Proteins L and G provide bacteria with a flexible template for the evolution of surface structures capable of interacting with different conserved parts of Ig molecules of the infected host.

Comparative structural analysis of the calcium free and bound states of the calcium regulatory protein calbindin D9K.

The solution structure of apo calbindin D9K, a member of the calmodulin superfamily of calcium-binding regulatory proteins, has been investigated by 1H nuclear magnetic resonance spectroscopy and the results compared with a corresponding study of the calcium-loaded protein. On the basis of complete sequence-specific assignments, characteristic patterns of short proton-proton distances have been identified in two-dimensional nuclear Overhauser effect spectra, allowing the elements of secondary structure to be determined. It is found that four helices and a short section of antiparallel beta-sheet are present regardless of the calcium content of the protein. In addition, a preliminary analysis of the long-range nuclear Overhauser effects shows that the global folding patterns are the same and that the tertiary structures of the apo protein is very similar to that of the calcium-loaded protein. These results are in stark contrast to a number of very substantial changes in 1H chemical shift. Preliminary studies of protein dynamics show some very large differences in flexibility and internal mobility. This suggests that protein dynamics may play a role more important than was initially realized in the function of calbindin D9K and other homologous calcium-binding regulatory proteins.

Solution structure of the albumin-binding GA module: a versatile bacterial protein domain.

The albumin-binding GA module is found in a family of surface proteins of different bacterial species. It comprises 45 amino acid residues and represents the first known example of contemporary module shuffling. Using 1H NMR spectroscopy we have determined the solution structure of the GA module from protein PAB, a protein of the anaerobic human commensal and pathogen Peptostreptococcus magnus. This structure, the first three-dimensional structure of an albumin-binding protein domain described, was shown to be composed of a left-handed three-helix-bundle. Sequence differences between GA modules with different affinities for albumin indicated that a conserved region in the C-terminal part of the second helix and the flexible sequence between helices 2 and 3 could contribute to the albumin-binding activity. The effect on backbone amide proton exchange rates upon binding to albumin support this assumption. The GA module has a fold that is strikingly similar to the immunoglobulin-binding domains of staphylococcal protein A but it shows no resemblance to the fold shared by the immunoglobulin-binding domains of streptococcal protein G and peptostreptococcal protein L. When the gene sequences, binding properties and thermal stability of these four domains are analysed in relation to their global folds an evolutionary pattern emerges. Thus, in the evolution of novel binding properties mutations are allowed only as long as the energetically favourable global fold is maintained.

NMR analysis of the interaction between protein L and Ig light chains.

Protein L is a cell wall protein expressed by some strains of the anaerobic bacterial species Peptostreptococcus magnus. It binds to immunoglobulin (Ig) light chains predominantly of the kappa subtype from a wide range of animal species. This binding is mediated by five highly homologous repeats designated as B1-B5, each of which comprises 72 to 76 amino acid residues. The fold of the Ig light chain-binding B1 domain of protein L has previously been shown to comprise an alpha-helix packed against a four-stranded beta-sheet. The Ig-binding region of the protein L domain involves most of the residues in the second beta-strand, the C-terminal residues of the alpha-helix, and residues in the loop connecting the alpha-helix with the third beta-strand. In the present study, we have identified the protein L-binding site of an Ig light chain by use of stable isotope-assisted NMR spectroscopy. The light chain of a murine monoclonal anti-17alpha-hydroxy-progesterone Fab fragment (IgG2b, kappa) was selectively labeled with 13C at carbonyl groups of Ala, Arg, Cys, Ile, Lys, Met, Phe, Trp, or Tyr. The residues in which the carbonyl 13C chemical shift was significantly perturbed upon binding of the protein L B1 domain were preferentially found in the second beta-strand of the variable kappa domain and parts of its flanking beta-strands. None of these residues were affected by the addition of the antigen against which the monoclonal Fab fragment is directed. Therefore, we conclude that protein L binds to the outer surface of the framework region of the V(L) domain, primarily involving the V(L) second strand, and that this binding is independent of antigen-binding. The present NMR data, in combination with sequence comparisons between kappa light chains with and without protein L affinity, suggest that the amino acid substitutions at positions 9, 20, and/or 74 of the kappa light chains could crucially affect the interaction between protein L and the V(L) domain.

A calbindin D9k mutant containing a novel structural extension: 1H nuclear magnetic resonance studies.

Calbindin D9k is a small, well-studied calcium-binding protein consisting of two helix-loop-helix motifs called EF-hands. The P43MG2 mutant is one of a series of mutants designed to sequentially lengthen the largely unstructured tether region between the two EF-hands (F36-S44). A lower calcium affinity for P43MG was expected on the basis of simple entropic arguments. However, this is not the case and P43MG (-97 kJ.mol-1) has a stronger calcium affinity than P43M (-93 kJ.mol-1), P43G (-95 kJ.mol-1) and even wild-type protein (-96 kJ.mol-1). An NMR study was initiated to probe the structural basis for these calcium-binding results. The 1H NMR assignments and 3JHNH alpha values of the calcium-free and calcium-bound form of P43MG calbindin D9k mutant are compared with those of P43G. These comparisons reveal that little structure is formed in the tether regions of P43MG(apo), P43G(apo) and P43G(Ca) but a helical turn (S38-K41) appears to stabilize this part of the protein structure for P43MG(Ca). Several characteristic NOEs obtained from 2D and 3D NMR experiments support this novel helix. A similar, short helix exists in the crystal structure of calcium-bound wild-type calbindin D9k-but this is the first observation in solution for wild-type calbindin D9k or any of its mutants.

Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k.

The three-dimensional structures of the magnesium- and manganese-bound forms of calbindin D9k were determined to 1.6 A and 1.9 A resolution, respectively, using X-ray crystallography. These two structures are nearly identical but deviate significantly from both the calcium bound form and the metal ion-free (apo) form. The largest structural differences are seen in the C-terminal EF-hand, and involve changes in both metal ion coordination and helix packing. The N-terminal calcium binding site is not occupied by any metal ion in the magnesium and manganese structures, and shows little structural deviation from the apo and calcium bound forms. 1H-NMR and UV spectroscopic studies at physiological ion concentrations show that the C-terminal site of the protein is significantly populated by magnesium at resting cell calcium levels, and that there is a negative allosteric interaction between magnesium and calcium binding. Calcium binding was found to occur with positive cooperativity at physiological magnesium concentration.

Mastoparan binding induces a structural change affecting both the N-terminal and C-terminal domains of calmodulin. A 113Cd-NMR study.

113Cd-NMR studies of solutions of cadmium-loaded calmodulin (Cd4CaM) and the tetradecapeptide mastoparan in different ratios show that mastoparan binds to Cd4CaM with high affinity. The off-rate of protein- bound mastoparan is found to be 40 s-1 or less. The binding of one molecule of mastoparan to Cd4CaM is observed to affect all four metal-binding sites, indicating that both the N-terminal and C-terminal globular domains of the protein undergo conformational changes.

Peptidyl-prolyl cis-trans isomerase activity as studied by dynamic proton NMR spectroscopy.

Recently the identity of the peptidyl-prolyl cis-trans isomerase (PPIase), which accelerates the cis/trans isomerization of prolyl peptide bonds and cyclophilin, the binding protein for the immunosuppressive drug Cyclosporin A (CsA), was discovered. The PPIase catalysis toward the substrate Suc-Ala-Phe-Pro-Phe-pNA has been studied by 1H NMR spectroscopy. Using the bandshape analysis technique the rate of interconversion between the cis and trans isomers of the substrate could be measured in the presence of PPIase and under equilibrium conditions. The acceleration is inhibited by equimolar amounts of CsA. The results provide evidence that the PPIase catalysis is more complex than a simple exchange between two states.

Peptidyl-prolyl cis-trans isomerase does not affect the Pro-43 cis-trans isomerization rate in folded calbindin D9k.

The calcium-binding protein calbindin D9k has previously been shown to exist in two folded forms only differing in the proline cis-trans isomerism of the Gly-42-Pro-43 amide bond. This bond is located in a flexible loop connecting the two EF-hand Ca2+ sites. Calbindin D9k therefore constitutes a unique test case for investigating if the recently discovered enzyme peptidyl-prolyl cis-trans isomerase (PPIase) can affect the cis-trans exchange rate in a folded protein. The 1H NMR saturation transfer technique has been used to measure the rate of interconversion between the cis and trans forms of calbindin in the presence of PPIase (PPIase:calbindin concentration ratio 1:10) at 35 degrees C. No rate enhancement could be detected.