Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy

Prediction of the functional effect of novel SLC25A13 variants using a S. cerevisiae model of AGC2 deficiency

AGC2, a member of the mitochondrial carrier protein family, is as an aspartate-glutamate carrier and is important for urea synthesis and the maintenance of the malate-aspartate shuttle. Mutations in SLC25A13, the gene encoding AGC2, result in two age dependent disorders: neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) and type II citrullinemia (CTLN2). The clinical features of CTLN2 are very similar to those of other urea cycle disorders making a clear diagnosis difficult. Analysis of the SLC25A13 gene sequence can provide a definitive diagnosis, however the predictive value of DNA sequencing requires that the disease association of variants be characterized. We utilized the yeast Saccharomyces cerevisiae lacking AGC1 as a model system to study the effect on the function of AGC2 variants and confirmed that this system is capable of distinguishing between AGC2 variants with normal (p.Pro632Leu) or impaired function (p.Gly437Glu, p.Gly531Asp, p.Thr546Met, p.Leu598Arg and p.Glu601Lys). Three novel AGC2 genetic variants, p.Met1? (c.2T>C), p.Pro502Leu (c.1505C>T), and p.Arg605Gln (c.1814G>A) were investigated and our analysis revealed that p.Pro502Leu and p.Arg605Gln substitutions in the AGC2 protein were without effect and these variants were fully functional. The p.Met1? mutant is capable of expressing a truncated p.Met1_Phe34del AGC2 variant, however this protein is not functional due to disruptions in a calcium binding EF hand as well as incorrect intracellular localization. Our study demonstrates that the characterization of AGC2 expressed in yeast cells is a powerful technique to investigate AGC2 variants, and this analysis should aid in establishing the disease association of novel variants.

An in-cell NMR study of monitoring stress-induced increase of cytosolic Ca2+ concentration in HeLa cells

Recent developments in in-cell NMR techniques have allowed us to study proteins in detail inside living eukaryotic cells. The lifetime of in-cell NMR samples is however much shorter than that in culture media, presumably because of various stresses as well as the nutrient depletion in the anaerobic environment within the NMR tube. It is well known that Ca(2+)-bursts occur in HeLa cells under various stresses, hence the cytosolic Ca(2+) concentration can be regarded as a good indicator of the healthiness of cells in NMR tubes. In this study, aiming at monitoring the states of proteins resulting from the change of cytosolic Ca(2+) concentration during experiments, human calbindin D9k (P47M+C80) was used as the model protein and cultured HeLa cells as host cells. Time-resolved measurements of 2D (1)H-(15)N SOFAST-HMQC experiments of calbindin D9k (P47M+C80) in HeLa cells showed time-dependent changes in the cross-peak patterns in the spectra. Comparison with in vitro assignments revealed that calbindin D9k (P47M+C80) is initially in the Mg(2+)-bound state, and then gradually converted to the Ca(2+)-bound state. This conversion process initiates after NMR sample preparation. These results showed, for the first time, that cells inside the NMR tube were stressed, presumably because of cell precipitation, the lack of oxygen and nutrients, etc., thereby releasing Ca(2+) into cytosol during the measurements. The results demonstrated that in-cell NMR can monitor the state transitions of stimulated cells through the observation of proteins involved in the intracellular signalling systems. Our method provides a very useful tool for in situ monitoring of the "healthiness" of the cells in various in-cell NMR studies.

Two functional S100A4 monomers are necessary for regulating nonmuscle myosin-IIA and HCT116 cell invasion

S100A4, a member of the Ca(2+)-activated S100 protein family, regulates the motility and invasiveness of cancer cells. Moreover, high S100A4 expression levels correlate with poor patient survival in several cancers. Although biochemical, biophysical, and structural data indicate that S100A4 is a noncovalent dimer, it is unknown if two functional S100A4 monomers are required for the productive recognition of protein targets and the promotion of cell invasion. To address this question, we created covalently linked S100A4 dimers using a glycine rich flexible linker. The single-chain S100A4 (sc-S100A4) proteins exhibited wild-type affinities for calcium and nonmuscle myosin-IIA, retained the ability to regulate nonmuscle myosin-IIA assembly, and promoted tumor cell invasion when expressed in S100A4-deficient colon carcinoma cells. Mutation of the two calcium-binding EF-hands in one monomer, while leaving the other monomer intact, caused a 30-60-fold reduction in binding affinity for nonmuscle myosin-IIA concomitant with a weakened ability to regulate the monomer-polymer equilibrium of nonmuscle myosin-IIA. Moreover, sc-S100A4 proteins with one monomer deficient in calcium responsiveness did not support S100A4-mediated colon carcinoma cell invasion. Cross-linking and titration data indicate that the S100A4 dimer binds a single myosin-IIA target peptide. These data are consistent with a model in which a single peptide forms interactions in the vicinity of the canonical target binding cleft of each monomer in such a manner that both target binding sites are required for the efficient interaction with myosin-IIA.

Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k

The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S(2) order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data.

13C direct detected COCO-TOCSY: a tool for sequence specific assignment and structure determination in protonless NMR experiments

A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in (13)C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles phi as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D(9K), a 75 amino acid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49(3)J(C')(C') values were measured and related to backbone phi angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, (4)J(CC) and (5)J(CC), could be measured. This constitutes an unprecedented case for proteins of medium and small size.

Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks

Accurate predictions of metal-binding sites in proteins by using sequence as the only source of information can significantly help in the prediction of protein structure and function, genome annotation, and in the experimental determination of protein structure. Here, we introduce a method for identifying histidines and cysteines that participate in binding of several transition metals and iron complexes. The method predicts histidines as being in either of two states (free or metal bound) and cysteines in either of three states (free, metal bound, or in disulfide bridges). The method uses only sequence information by utilizing position-specific evolutionary profiles as well as more global descriptors such as protein length and amino acid composition. Our solution is based on a two-stage machine-learning approach. The first stage consists of a support vector machine trained to locally classify the binding state of single histidines and cysteines. The second stage consists of a bidirectional recurrent neural network trained to refine local predictions by taking into account dependencies among residues within the same protein. A simple finite state automaton is employed as a postprocessing in the second stage in order to enforce an even number of disulfide-bonded cysteines. We predict histidines and cysteines in transition-metal-binding sites at 73% precision and 61% recall. We observe significant differences in performance depending on the ligand (histidine or cysteine) and on the metal bound. We also predict cysteines participating in disulfide bridges at 86% precision and 87% recall. Results are compared to those that would be obtained by using expert information as represented by PROSITE motifs and, for disulfide bonds, to state-of-the-art methods.

Uncovering the Unfoldome: Enriching Cell Extracts for Unstructured Proteins by Acid Treatment

A method to enrich cell extracts in totally unfolded proteins was investigated. A literature search revealed that 14 of 29 proteins isolated by their failure to precipitate during perchloric acid (PCA) or trichloroacetic acid (TCA) treatment where also shown experimentally to be totally disordered. A near 100 000-fold reduction in yield was observed after 5% or 9% PCA treatment of total soluble E. coli protein. Despite this huge reduction, 158 and 142 spots were observed from the 5% and the 9% treated samples, respectively, on silver-stained 2-D SDS-PAGE gels loaded with 10 microg of protein. Treatment with 1% PCA was less selective with more visible spots and a greater than 3-fold higher yield. A substantial yield of unprecipitated protein was obtained after 3% TCA treatment, suggesting that the common use of TCA precipitation prior to 2-D gel analysis may result in loss of unstructured protein due to their failure to precipitate. Our preliminary analysis suggests that treating total protein extracts with 3-5% PCA and determining the identities of soluble proteins could be the starting point for uncovering unfoldomes (the complement of unstructured proteins in a given proteome). The 100 000-fold reduction in yield and concomitant reduction in number of proteins achieved by 5% PCA treatment produced a fraction suitable for analysis in its entirety using standard proteomic techniques. In this way, large numbers of totally unstructured proteins could be identified with minimal effort.

Unmasking the annexin I interaction from the structure of Apo-S100A11

S100A11 is a homodimeric EF-hand calcium binding protein that undergoes a calcium-induced conformational change and interacts with the phospholipid binding protein annexin I to coordinate membrane association. In this work, the solution structure of apo-S100A11 has been determined by NMR spectroscopy to uncover the details of its calcium-induced structural change. Apo-S100A11 forms a tight globular structure having a near antiparallel orientation of helices III and IV in calcium binding site II. Further, helices I and IV, and I and I', form a more closed arrangement than observed in other apo-S100 proteins. This helix arrangement in apo-S100A11 partially buries residues in helices I (P3, E11, A15), III (V55, R58, M59), and IV (A86, C87, S90) and the linker (A45, F46), which are required for interaction with annexin I in the calcium-bound state. In apo-S100A11, this results in a "masked" binding surface that prevents annexin I binding but is uncovered upon calcium binding.

A fast and simple method to calculate protonation states in proteins

A simple model for electrostatic interactions in proteins, based on a distance and position dependent screening of the electrostatic potential, is presented. It is applied in conjunction with a Monte Carlo algorithm to calculate pK(alpha) values of ionizable groups in proteins. The purpose is to furnish a simple, fast, and sufficiently accurate model to be incorporated into molecular dynamic simulations. This will allow for dynamic protonation calculations and for coupling between changes in structure and protonation state during the simulation. The best method of calculating protonation states available today is based on solving the linearized Poisson-Boltzmann equation on a finite difference grid. However, this model consumes far too much computer time to be a practical alternative. Tests are reported for fixed structures on bacteriorhodopsin, lysozyme, myoglobin, and calbindin. The studies include comparisons with Poisson-Boltzmann calculations with dielectric constants 4 and 20 inside the protein, a model with uniform dielectric constant 80 and distance-dependent dielectric models. The accuracy is comparable to that of Poisson-Boltzmann calculations with dielectric constant 20, and it is considerably better than that with epsilon = 4. The time to calculate the protonation at one pH value is at least 100 times less than that of a Poisson-Boltzmann calculation. Proteins 1999;36:474-483.

Molecular modeling of single polypeptide chain of calcium-binding protein p26olf from dimeric S100B(betabeta)

P26olf from olfactory tissue of frog, which may be involved in olfactory transduction or adaptation, is a Ca2+-binding protein with 217 amino acids. The p26olf molecule contains two homologous parts consisting of the N-terminal half with amino acids 1-109 and the C-terminal half with amino acids 110-217. Each half resembles S100 protein with about 100 amino acids and contains two helix-loop-helix Ca2+-binding structural motifs known as EF-hands: a normal EF-hand at the C-terminus and a pseudo EF-hand at the N-terminus. Multiple alignment of the two S100-like domains of p26olf with 18 S100 proteins indicated that the C-terminal putative EF-hand of each domain contains a four-residue insertion when compared with the typical EF-hand motifs in the S100 protein, while the N-terminal EF-hand is homologous to its pseudo EF-hand. We constructed a three-dimensional model of the p26olf molecule based on results of the multiple alignment and NMR structures of dimeric S100B(betabeta) in the Ca2+-free state. The predicted structure of the p26olf single polypeptide chain satisfactorily adopts a folding pattern remarkably similar to dimeric S100B(betabeta). Each domain of p26olf consists of a unicornate-type four-helix bundle and they interact with each other in an antiparallel manner forming an X-type four-helix bundle between the two domains. The two S100-like domains of p26olf are linked by a loop with no steric hindrance, suggesting that this loop might play an important role in the function of p26olf. The circular dichroism spectral data support the predicted structure of p26olf and indicate that Ca2+-dependent conformational changes occur. Since the C-terminal putative EF-hand of each domain fully keeps the helix-loop-helix motif having a longer Ca2+-binding loop, regardless of the four-residue insertion, we propose that it is a new, novel EF-hand, although it is unclear whether this EF-hand binds Ca2+. P26olf is a new member of the S100 protein family.

EF-hands at atomic resolution: the structure of human psoriasin (S100A7) solved by MAD phasing

BACKGROUND

The S100 family consists of small acidic proteins, belonging to the EF-hand class of calcium-binding proteins. They are primarily regulatory proteins, involved in cell growth, cell structure regulation and signal transduction. Psoriasin (S100A7) is an 11.7 kDa protein that is highly upregulated in the epidermis of patients suffering from the chronic skin disease psoriasis. Although its exact function is not known, psoriasin is believed to participate in the biochemical response which follows transient changes in the cellular Ca2+ concentration.

RESULTS

The three-dimensional structure of holmium-substituted psoriasin has been determined by multiple anomalous wavelength dispersion (MAD) phasing and refined to atomic resolution (1.05 A). The structure represents the most accurately determined structure of a calcium-binding protein. Although the overall structure of psoriasin is similar to those of other S100 proteins, several important differences exist, mainly in the N-terminal EF-hand motif that contains a distorted loop and lacks a crucial calcium-binding residue. It is these minor differences that may account for the different specificities among members of this family.

CONCLUSIONS

The structure of human psoriasin reveals that this protein, in contrast to other S100 proteins with known structure, is not likely to strongly bind more than one calcium ion per monomer. The present study contradicts the idea that calcium binding induces large changes in conformation, as suggested by previously determined structures of apo forms of S100 proteins. The substitution of Ca2+ ions in EF-hands by lanthanide ions may provide a general vehicle for structure determination of S100 proteins by means of MAD phasing.

1H NMR assignments of apo calcyclin and comparative structural analysis with calbindin D9k and S100 beta

The homodimeric S100 protein calcyclin has been studied in the apo state by two-dimensional 1H NMR spectroscopy. Using a combination of scalar correlation and NOE experiments, sequence-specific 1H NMR assignments were obtained for all but one backbone and > 90% of the side-chain resonances. To our knowledge, the 2 x 90 residue (20 kDa) calcyclin dimer is the largest protein system for which such complete assignments have been made by purely homonuclear methods. Sequential and medium-range NOEs and slowly exchanging backbone amide protons identified directly the four helices and the short antiparallel beta-type interaction between the two binding loops that comprise each subunit of the dimer. Further analysis of NOEs enabled the unambiguous assignment of 556 intrasubunit distance constraints, 24 intrasubunit hydrogen bonding constraints, and 2 x 26 intersubunit distance constraints. The conformation of the monomer subunit was refined by distance geometry and restrained molecular dynamics calculations using the intrasubunit constraints only. Calculation of the dimer structure starting from this conformational ensemble has been reported elsewhere. The extent of structural homology among the apo calcyclin subunit, the monomer subunit of apo S100 beta, and monomeric apo calbindin D9k has been examined in detail by comparing 1H NMR chemical shifts and secondary structures. This analysis was extended to a comprehensive comparison of the three-dimensional structures of the calcyclin monomer subunit and calbindin D9k, which revealed greater similarity in the packing of their hydrophobic cores than was anticipated previously. Together, these results support the hypothesis that all members of the S100 family have similar core structures and similar modes of dimerization. Analysis of the amphiphilicity of Helix IV is used to explain why calbindin D9k is monomeric, but full-length S100 proteins form homodimers.

The solution structure of the bovine S100B protein dimer in the calcium-free state

BACKGROUND

S100B (S100beta) is a member of the S100 family of small calcium-binding proteins: members of this family contain two helix-loop-helix calcium-binding motifs and interact with a wide range of proteins involved mainly in the cytoskeleton and cell proliferation. S100B is a neurite-extension factor and levels of S100B are elevated in the brains of patients with Alzheimer's disease or Down's syndrome: the pattern of S100B overexpression in Alzheimer's disease correlates with the pattern of neuritic-plaque formation. Identification of a growing class of S100 proteins and the likely neurochemical importance of S100B make the determination of the structure of S100B of interest.

RESULTS

We have used NMR to determine the structure of the reduced S100B homodimer in the absence of calcium. Each monomer consists of a four-helix bundle, arranged in the dimer in an antiparallel fashion. The fourth helix of each monomer runs close to the equivalent helix of the other monomer for almost its full length, extending the hydrophobic core through the interface. The N-terminal, but not the C-terminal, calcium-binding loop is similar to the equivalent loop in the monomeric S100 protein calbindin and is in a conformation ready to bind calcium.

CONCLUSIONS

The novel dimer structure reported previously for calcyclin (S100A6) is the common fold for the dimeric S100B proteins. Calcium binding to the C-terminal calcium-binding loop would be expected to require a conformational change, which might provide a signal for activation. The structure suggests regions of the molecule likely to be involved in interactions with effector molecules.

1H, 13C and 15N NMR assignments and solution secondary structure of rat Apo-S100 beta

The 1H, 13C and 15N NMR assignments of the backbone and side-chain resonances of rat S100 beta were made at pH 6.5 and 37 degrees C using heteronuclear multidimensional NMR spectroscopy. Analysis of the NOE correlations, together with amide exchange rate and 1H alpha, 13C alpha and 13C beta chemical shift data, provided extensive secondary structural information. Thus, the secondary structure of S100 beta was determined to comprise four helices (Leu3-Ser18, helix I; Lys29-Leu40, helix II; Gln50-Glu62, helix III; and Phe70-Ala83, helix IV), four loops (Gly19-His25, loop I; Ser41-Glu49, loop II; Asp63-Gly66, loop III; and Cys84-Glu91, loop IV) and two beta-strands (Lys26-Lys28, beta-strand I and Glu67-Asp69, beta-strand II). The beta-strands were found to align in an antiparallel manner to form a very small beta-sheet. This secondary structure is consistent with predictions that S100 beta contains two 'helix-loop-helix' Ca(2+)-binding motifs known as EF-hands. The alignment of the beta-sheet, which brings the two EF-hand domains of S100 beta into close proximity, is similar to that of several other Ca(2+)-ion-binding proteins.

Determination of the solution structure of Apo calbindin D9k by NMR spectroscopy

The three-dimensional structure of apo calbindin D9k has been determined using constraints generated from nuclear magnetic resonance spectroscopy. The family of solution structures was calculated using a combination of distance geometry, restrained molecular dynamics, and hybrid relaxation matrix analysis of the nuclear Overhauser effect (NOE) cross-peak intensities. Errors and inconsistencies in the input constraints were identified using complete relaxation matrix analyses based on the results of preliminary structure calculations. The final input data consisted of 994 NOE distance constraints and 122 dihedral constraints, aided by the stereospecific assignment of the resonances from 21 beta-methylene groups and seven isopropyl groups of leucine and valine residues. The resulting family of 33 structures contain no violation of the distance constraints greater than 0.17 A or of the dihedral angle constraints greater than 10 degrees. The structures consist of a well-defined, antiparallel four-helix bundle, with a short anti-parallel beta-interaction between the two unoccupied calcium-binding loops. The root-mean-square deviation from the mean structure of the backbone heavy-atoms for the well-defined helical residues is 0.55 A. The remainder of the ion-binding loops, the linker loop connecting the two sub-domains of the protein, and the N and C termini exhibit considerable disorder between different structures in the ensemble. A comparison with the structure of the (Ca2+)2 state indicates that the largest changes associated with ion-binding occur in the middle of helix IV and in the packing of helix III onto the remainder of the protein. The change in conformation of these helices is associated with a subtle reorganization of many residues in the hydrophobic core, including some side-chains that are up to 15 A from the ion-binding site.

Nuclear magnetic resonance assignments and secondary structure of bovine S100 beta protein

S100 beta is a neurite extension factor and has been implicated in Alzheimer's disease and Down's syndrome. It belongs to a group of low molecular weight calcium-binding proteins containing the helix-loop-helix calcium binding motif. The structure of only one S100 protein, calbindin D9k, which has the lowest sequence similarity to the other members of the S100 group has been determined. We report the NMR assignments and secondary structure of calcium-free S100 beta. The secondary structure is similar to that of calbindin D9k, determined using NMR, except that there is clear evidence for an additional well ordered 5-residue alpha-helix in S100 beta.

The S100 protein family: history, function, and expression

The S100 family of calcium binding proteins contains approximately 16 members each of which exhibits a unique pattern of tissue/cell type specific expression. Although the distribution of these proteins is not restricted to the nervous system, the implication of several members of this family in nervous system development, function, and disease has sparked new interest in these proteins. We now know that the original two members of this family, S100A1 and S100B, can regulate a diverse group of cellular functions including cell-cell communication, cell growth, cell structure, energy metabolism, contraction and intracellular signal transduction. Although some members of the family may function extracellularly, most appear to function as intracellular calcium-modulated proteins and couple extracellular stimuli to cellular responses via interaction with other cellular proteins called target proteins. Interaction of these proteins with target proteins appear to involve cysteine residues (one in S100A1 and two in S100B), as well as a stretch of 13 amino acids, in the middle of the molecule called the linker region, which connects the two EF-hand calcium binding domains. In addition to the amino acid sequence and secondary structures of these proteins, the structures of the genes encoding these proteins are highly conserved. Studies on the expression of these proteins have demonstrated that a complex mixture of transcriptional and postranscriptional mechanisms regulate S100 expression. Further analysis of the function and expression of these proteins in both nervous and nonnervous tissues will provide important information regarding the role of altered S100 expression in nervous system development, function and disease.

Quantification of the calcium-induced secondary structural changes in the regulatory domain of troponin-C

The backbone resonance assignments have been completed for the apo (1H and 15N) and calcium-loaded (1H, 15N, and 13C) regulatory N-domain of chicken skeletal troponin-C (1-90), using multidimensional homonuclear and heteronuclear NMR spectroscopy. The chemical-shift information, along with detailed NOE analysis and 3JHNH alpha coupling constants, permitted the determination and quantification of the Ca(2+)-induced secondary structural change in the N-domain of TnC. For both structures, 5 helices and 2 short beta-strands were found, as was observed in the apo N-domain of the crystal structure of whole TnC (Herzberg O, James MNG, 1988, J Mol Biol 203:761-779). The NMR solution structure of the apo form is indistinguishable from the crystal structure, whereas some structural differences are evident when comparing the 2Ca2+ state solution structure with the apo one. The major conformational change observed is the straightening of helix-B upon Ca2+ binding. The possible importance and role of this conformational change is explored. Previous CD studies on the regulatory domain of TnC showed a significant Ca(2+)-induced increase in negative ellipticity, suggesting a significant increase in helical content upon Ca2+ binding. The present study shows that there is virtually no change in alpha-helical content associated with the transition from apo to the 2Ca2+ state of the N-domain of TnC. Therefore, the Ca(2+)-induced increase in ellipticity observed by CD does not relate to a change in helical content, but more likely to changes in spatial orientation of helices.

Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2

The POU DNA-binding motif defines a conserved family of eukaryotic transcription factors involved in regulation of gene expression. This bipartite motif consists of an N-terminal POU-specific domain (POUs), a flexible linker, and a C-terminal POU-specific homeodomain (POUHD). Here we describe the solution structure of a POU-specific homeodomain. An NMR model is obtained from Oct-2, a human B-cell specific transcription factor which participates in the regulation of immunoglobulin genes. A fragment of Oct-2 containing POUHD and an adjoining linker was expressed in Escherichia coli and characterized by three-dimensional nuclear magnetic resonance (3D-NMR) spectroscopy. Complete 1H and 15N resonance assignment of the POUHD moiety is presented. The POUHD solution structure, as calculated by distance geometry and simulated annealing (DG/SA), is similar to that of canonical homeodomains. A salient difference between solution and crystal structures is observed in the C-terminal segment of alpha-helix 3 (the HTH recognition helix), which is not well ordered in solution. Because this segment presumably folds upon specific DNA binding, its flexibility in solution may reduce the intrinsic DNA affinity of POUHD in the absence of POUs.

Molecular tuning of ion binding to calcium signaling proteins

Intracellular calcium plays an essential role in the transduction of most hormonal, neuronal, visual, and muscle stimuli. (Recent reviews include Putney, 1993; Berridge, 1993a,b; Tsunoda, 1993; Gnegy, 1993; Bachset al.1992; Hanson & Schulman, 1992; Villereal & Byron, 1992; Premack & Gardner, 1992; Meanset al.1991).

Signal transduction versus buffering activity in Ca(2+)-binding proteins

The three-dimensional structure of calbindin D9k in the absence of Ca2+ has been determined using NMR spectroscopy in solution, allowing the first direct analysis of the consequences of Ca2+ binding for a member of the calmodulin superfamily of proteins. The overall response in calbindin D9k is much attenuated relative to the current model for calmodulin and troponin C. These results demonstrate a novel mechanism for modulating the conformational response to Ca(2+)-binding in calmodulin superfamily proteins and provide insights into how their Ca(2+)-binding domains can be fine-tuned to remain essentially intact or respond strongly to ion binding, in relation to their functional requirements.

Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation

The backbone dynamics of apo- and (Cd2+)1-calbindin D9k have been characterized by 15N nuclear magnetic resonance spectroscopy. Spin-lattice and spin-spin relaxation rate constants and steady-state [1H]-15N nuclear Overhauser effects were measured at a magnetic field strength of 11.74 T by two-dimensional, proton-detected heteronuclear NMR experiments using 15N-enriched samples. The relaxation parameters were analyzed using a model-free formalism that characterizes the dynamics of the N-H bond vectors in terms of generalized order parameters and effective correlation times. The data for the apo and (Cd2+)1 states were compared to those for the (Ca2+)2 state [Kördel, J., Skelton, N. J., Akke, M., Palmer, A. G., & Chazin, W. J. (1992) Biochemistry 31, 4856-4866] to ascertain the effects on ion ligation on the backbone dynamics of calbindin D9k. The two binding loops respond differently to ligation by metal ions: high-frequency (10(9)-10(12) s-1) fluctuations of the N-terminal ion-binding loop are not affected by ion binding, whereas residues G57, D58, G59, and E60 in the C-terminal ion-binding loop have significantly lower order parameters in the apo state than in the metal-bound states. The dynamical responses of the four helices to binding of ions are much smaller than that for the C-terminal binding loop, with the strongest effect on helix III, which is located between the linker loop and binding site II. Significant fluctuations on slower time scales also were detected in the unoccupied N-terminal ion-binding loop of the apo and (Cd2+)1 states; the apparent rates were greater for the (Cd2+)1 state. These results on the dynamical response to ion binding in calbindin D9k provide insights into the molecular details of the binding process and qualitative evidence for entropic contributions to the cooperative phenomenon of calcium binding for the pathway in which the ion binds first in the C-terminal site.

Metal ion-dependent modulation of the dynamics of a designed protein

The peptide alpha 4 is a designed four-helix bundle that contains a highly simplified hydrophobic core composed exclusively of leucine residues; its tertiary structure is therefore largely dictated by hydrophobic forces. This small protein adopts a structure with properties intermediate between those of the native and molten globule states of proteins: it is compact, globular, and has very stable helices, but its apolar side chains are mobile and not as well packed as in many natural proteins. To induce a more native-like state, two Zn(2+)-binding sites were introduced into the protein, thereby replacing some of the non-specific hydrophobic interactions with more geometrically restrictive metal-ligand interactions. In the metal-bound state, this protein has properties that approach those of native proteins. Thus, hydrophobic interactions alone are sufficient to drive polypeptide chain folding nearly to completion, but specific interactions are required for a unique structure.

Rapid purification and direct microassay of calbindin9kDa utilizing its solubility in perchloric acid

The 9 kDa calcium-binding protein, calbindin9kDa, was found to be soluble in 7% (v/v) perchloric acid. Calbindin9kDa was easily purified from rat duodenum in 1 day with perchloric acid precipitation followed by reverse-phase h.p.l.c. The yield was 21.4 +/- 2.3 nmol/g wet weight of tissue (mean +/- S.E.M.; n = 3) from normally fed 7-8-week-old rats (approx. 70% recovery). The purification was also effective with rabbit duodenum calbindin9kDa, but not with various other EF-hand calcium-binding proteins tested in the rat. Several criteria (h.p.l.c., u.v. spectrum, denaturing two-dimensional PAGE, N-terminal sequencing) indicated that the rat calbindin9kDa was purified to homogeneity and was not affected by proteolysis. High-affinity calcium-binding properties were retained and no evidence of isoforms or charge modification was observed. Residue 59, identified as Asn (not Asp as previously reported), was fully amidated. When adopted as a microassay with isocratic h.p.l.c., the perchloric acid procedure enabled rapid (less than 6 min) and direct (peptide bond absorbance) quantification of less than 1 pmol of calbindin9kDa. This new approach to purification and assay will be of particular utility for investigations of calbindin9kDa in previously intractable low-abundance sources (e.g. cultured cells).

1H-NMR resonance assignments, secondary structure, and global fold of the TR1C fragment of turkey skeletal troponin C in the calcium-free state

The TR1C fragment of turkey skeletal muscle TnC (residues 12-87) comprises the two regulatory calcium binding sites of the protein. Complete assignments of the 1H-NMR resonances of the backbone and amino acid side chains of this domain in the absence of metal ions have been obtained using 2D 1H-NMR techniques. Sequential (i,i+1) and short-range (i,i+3) NOE connectivities define two helix-loop-helix calcium binding motifs, and long-range NOE connectivities indicate a short two-stranded beta-sheet formed between the two calcium binding loops. The two calcium binding sites are different in secondary structure. In terms of helix length, site II conforms to a standard "EF-hand" motif with the first helix ending one residue before the first calcium ligand and the second helix starting one residue after the beta-sheet. In site I, the first helix ends three residues before the first calcium ligand, and the second helix starts three residues after the beta-sheet. A number of long-range NOE connectivities between the helices define their relative orientation and indicate formation of a hydrophobic core between helices A, B, and D. The secondary structure and global fold of the TR1C fragment in solution in the calcium-free state are therefore very similar to those of the corresponding region in the crystal structure of turkey skeletal TnC [Herzberg, O., & James, M.N.G. (1988) J. Mol. Biol. 203, 761-779].

Protein metal-binding sites

Metal ions have a role in a variety of important functions in proteins including protein folding, assembly, stability, conformational change, and catalysis. The presence or absence of a given metal ion is crucial to the conformation or activity of over one third of all proteins. Recent developments have been made in the understanding and design of metal-binding sites in proteins, an important and rapidly advancing area of protein engineering.

Backbone dynamics of calcium-loaded calbindin D9k studied by two-dimensional proton-detected 15N NMR spectroscopy

Backbone dynamics of calcium-loaded calbindin D9k have been investigated by two-dimensional proton-detected heteronuclear nuclear magnetic resonance spectroscopy, using a uniformly 15N enriched protein sample. Spin-lattice relaxation rate constants, spin-spin relaxation rate constants, and steady-state [1H]-15N nuclear Overhauser effects were determined for 71 of the 72 backbone amide 15N nuclei. The relaxation parameters were analyzed using a model-free formalism that incorporates the overall rotational correlation time of the molecule, and a generalized order parameter (S2) and an effective internal correlation time for each amide group. Calbindin D9k contains two helix-loop-helix motifs joined by a linker loop at one end of the protein and a beta-type interaction between the two calcium-binding loops at the other end. The amplitude of motions for the calcium-binding loops and the helices are similar, as judged from the average S2 values of 0.83 +/- 0.05 and 0.85 +/- 0.04, respectively. The linker region joining the two calcium-binding subdomains of the molecule has a significantly higher flexibility, as indicated by a substantially lower average S2 value of 0.59 +/- 0.23. For residues in the linker loop and at the C-terminus, the order parameter is further decomposed into separate order parameters for motional processes on two distinct time scales. The effective correlation times are significantly longer for helices I and IV than for helices II and III or for the calcium-binding loops. Residue by residue comparisons reveal correlations of the order parameters with both the crystallographic B-factors and amide proton exchange rates, despite vast differences in the time scales to which these properties are sensitive. The order parameters are also utilized to distinguish regions of the NMR-derived three-dimensional structure of calbindin D9k that are poorly defined due to inherently high flexibility, from poorly defined regions with average flexibility but a low density of structural constraints.