Prokaryotic calcium-binding protein of the calmodulin superfamily. Calcium binding to a Saccharopolyspora erythraea 20 kDa protein

FtsA-FtsZ interaction in Vibrio cholerae causes conformational change of FtsA resulting in inhibition of ATP hydrolysis and polymerization

Proper interaction between the divisome proteins FtsA and FtsZ is important for the bacterial cell division which is not well characterized till date. In this study, the objective was to understand the mechanism of FtsA-FtsZ interaction using full-length recombinant proteins. We cloned, over-expressed, purified and subsequently characterized FtsA of Vibrio cholerae (VcFtsA). We found that VcFtsA polymerization assembly was dependent on Ca²⁺ ions, which is unique among FtsA proteins reported until now. VcFtsA also showed ATPase activity and its assembly was ATP dependent. Binding parameters of the interaction between the two full-length proteins, VcFtsA, and VcFtsZ determined by fluorescence spectrophotometry yielded a K_d value of around 38 μM. The K_d value of the interaction was 3 μM when VcFtsA was in ATP bound state. We found that VcFtsZ after interacting with VcFtsA causes a change of secondary structure in the later one leading to loss of its ability to hydrolyze ATP, subsequently halting the VcFtsA polymerization. On the other hand, a double-mutant of VcFtsA (VcFtsA-D242E,R300E), that does not bind to VcFtsZ, polymerized in the presence of VcFtsZ. Though FtsA proteins among different organisms show 70-80% homology in their sequences, assembly of VcFtsA showed a difference in its regulatory processes.

Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding

Protein folding can begin co-translationally. Due to the difference in timescale between folding and synthesis, co-translational folding is thought to occur at equilibrium for fast-folding domains. In this scenario, the folding kinetics of stalled ribosome-bound nascent chains should match the folding of nascent chains in real time. To test if this assumption is true, we compare the folding of a ribosome-bound, multi-domain calcium-binding protein stalled at different points in translation with the nascent chain as is it being synthesized in real-time, via optical tweezers. On stalled ribosomes, a misfolded state forms rapidly (1.5 s). However, during translation, this state is only attained after a long delay (63 s), indicating that, unexpectedly, the growing polypeptide is not equilibrated with its ensemble of accessible conformations. Slow equilibration on the ribosome can delay premature folding until adequate sequence is available and/or allow time for chaperone binding, thus promoting productive folding.

Co-translational protein folding is thought to occur at equilibrium for fast-folding domains. Here authors use optical tweezers to show that the folding kinetics of stalled ribosome-bound nascent chains do not match the folding of nascent chains in real time.

Calcium binding proteins and calcium signaling in prokaryotes

With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding β-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.

Use of (113)Cd NMR to probe the native metal binding sites in metalloproteins: an overview

Our laboratories have actively published in this area for several years and the objective of this chapter is to present as comprehensive an overview as possible. Following a brief review of the basic principles associated with (113)Cd NMR methods, we will present the results from a thorough literature search for (113)Cd chemical shifts from metalloproteins. The updated (113)Cd chemical shift figure in this chapter will further illustrate the excellent correlation of the (113)Cd chemical shift with the nature of the coordinating ligands (N, O, S) and coordination number/geometry, reaffirming how this method can be used not only to identify the nature of the protein ligands in uncharacterized cases but also the dynamics at the metal binding site. Specific examples will be drawn from studies on alkaline phosphatase, Ca(2+) binding proteins, and metallothioneins.In the case of Escherichia coli alkaline phosphatase, a dimeric zinc metalloenzyme where a total of six metal ions (three per monomer) are involved directly or indirectly in providing the enzyme with maximal catalytic activity and structural stability, (113)Cd NMR, in conjunction with (13)C and (31)P NMR methods, were instrumental in separating out the function of each class of metal binding sites. Perhaps most importantly, these studies revealed the chemical basis for negative cooperativity that had been reported for this enzyme under metal deficient conditions. Also noteworthy was the fact that these NMR studies preceded the availability of the X-ray crystal structure.In the case of the calcium binding proteins, we will focus on two proteins: calbindin D(9k) and calmodulin. For calbindin D(9k) and its mutants, (113)Cd NMR has been useful both to follow actual changes in the metal binding sites and the cooperativity in the metal binding. Ligand binding to calmodulin has been studied extensively with (113)Cd NMR showing that the metal binding sites are not directly involved in the ligand binding. The (113)Cd chemical shifts are, however, exquisitely sensitive to minute changes in the metal ion environment.In the case of metallothionein, we will reflect upon how (113)Cd substitution and the establishment of specific Cd to Cys residue connectivity by proton-detected heteronuclear (1)H-(113)Cd multiple-quantum coherence methods (HMQC) was essential for the initial establishment of the 3D structure of metallothioneins, a protein family deficient in the regular secondary structural elements of α-helix and β-sheet and the first native protein identified with bound Cd. The (113)Cd NMR studies also enabled the characterization of the affinity of the individual sites for (113)Cd and, in competition experiments, for other divalent metal ions: Zn, Cu, and Hg.

Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium binding protein

The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal α-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.

Two-component signaling systems and cell cycle control in Caulobacter crescentus

Recent work on the regulation ofprokaryotic growth and development by two-component systems (TCS) has revealed unsuspected levels of complexity. In the dimorphic freshwater bacterium Caulobacter crescentus, TCS provide stringent temporal and spatial control of cellular development and cell-cycle progression. While the environmental signals modulating TCS regulatory networks are largely unknown, the components of the network and their interactions with each other are increasingly well-defined. Here, we present an overview of TCS regulation of cell-cycle control in C. crescentus.

Crystallization and preliminary X-ray diffraction studies of the calcium-binding protein CalD from Streptomyces coelicolor

Calcium ions play an important regulatory role in eukaryotes. However, the regulatory roles of Ca(2+) in prokaryotes are poorly understood. CalD, an 18 kDa calcium-binding protein from the model actinomycete Streptomyces coelicolor A3(2), was purified and crystallized for structure determination by X-ray crystallography. Crystals of CalD that were suitable for X-ray diffraction were obtained using the hanging-drop vapour-diffusion method and diffraction data were collected in-house to 1.56 A resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 32.9, b = 51.0, c = 87.0 A, alpha = beta = gamma = 90.0 degrees . There is one protein molecule per asymmetric unit.

NMR solution structure of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea

The structure of calerythrin, a prokaryotic 20 kDa calcium-binding protein has been determined by solution NMR spectroscopy. Distance, dihedral angle, J coupling, secondary chemical shift, residual dipolar coupling and radius of gyration restraints reveal four EF-hand motifs arranged in a compact globular structure. A tight turn in the middle of the amino acid sequence brings the two halves, each comprising a pair of EF-hands, close together. The structural similarity between calerythrin and the eukaryotic sarcoplasmic calcium-binding proteins is notable.

The functions of Ca(2+) in bacteria: a role for EF-hand proteins?

In bacteria, Ca(2+) is implicated in a wide variety of cellular processes, including the cell cycle and cell division. Dedicated influx and efflux systems tightly control the low cytoplasmic Ca(2+) levels in prokaryotes. Additionally, the growing number of proteins containing various Ca(2+)-binding motifs supports the importance of Ca(2+), which controls various protein functions by affecting protein stability, enzymatic activity or signal transduction. The existence of calmodulin-like proteins (containing EF-hand motifs) in bacteria is a long-standing hypothesis. Analysis of the prokaryotic protein sequences available in the databases has revealed the presence of several calmodulin-like proteins containing two or more authentic EF-hand motifs, suggesting that calmodulin-like proteins could be involved in Ca(2+) regulation in bacteria.

Characterization of apo and partially saturated states of calerythrin, an EF-hand protein from S. erythraea: a molten globule when deprived of Ca(2+)

Calerythrin, a four-EF-hand calcium-binding protein from Saccharopolyspora erythraea, exists in an equilibrium between ordered and less ordered states with slow exchange kinetics when deprived of Ca(2+) and at low temperatures, as observed by NMR. As the temperature is raised, signal dispersion in NMR spectra reduces, and intensity of near-UV CD bands decreases. Yet far-UV CD spectra indicate only a small decrease in the amount of secondary structure, and SAXS data show that no significant change occurs in the overall size and shape of the protein. Thus, at elevated temperatures, the equilibrium is shifted toward a state with characteristics of a molten globule. The fully structured state is reached by Ca(2+)-titration. Calcium first binds cooperatively to the C-terminal sites 3 and 4 and then to the N-terminal site 1, which is paired with an atypical, nonbinding site 2. EF-hand 2 still folds together with the C-terminal half of the protein, as deduced from the order of appearance of backbone amide cross peaks in the NMR spectra of partially Ca(2+)-saturated states.

NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea

Calerythrin is a 20 kDa calcium-binding protein isolated from gram-positive bacterium Saccharopolyspora erythraea. Based on amino acid sequence homology, it has been suggested that calerythrin belongs to the family of invertebrate sarcoplasmic EF-hand calcium-binding proteins (SCPs), and therefore it is expected to function as a calcium buffer. NMR spectroscopy was used to obtain structural information on the protein in solution. Backbone and side chain 1H, 13C, and 15N assignments were obtained from triple resonance experiments HNCACB, HN(CO)CACB, HNCO, CC(CO)NH, and [15N]-edited TOCSY, and HCCH-TOCSY. Secondary structure was determined by using secondary chemical shifts and characteristic NOEs. In addition, backbone N-H residual dipolar couplings were measured from a spin-state selective [1H, 15N] correlation spectrum acquired from a sample dissolved in a dilute liquid crystal. Four EF-hand motifs with characteristic helix-loop-helix patterns were observed. Three of these are typical calcium-binding EF-hands, whereas site 2 is an atypical nonbinding site. The global fold of calerythrin was assessed by dipolar couplings. Measured dipolar couplings were compared with values calculated from four crystal structures of proteins with sequence homology to calerythrin. These data allowed us to recognize an overall similarity between the folds of calerythrin and sarcoplasmic calcium-binding proteins from the sandworm Nereis diversicolor and the amphioxus Branchiostoma lanceolatum.

Lethal factor active-site mutations affect catalytic activity in vitro

The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093-1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase.

Isolated calcium-binding loops of EF-hand proteins can dimerize to form a native-like structure

Helix-loop-helix fragments of EF-hand proteins are known to dimerize in solution, re-producing the characteristic structure of native protein domains [Shaw, G.S., Hodges, R.S., & Sykes, B. D. (1990) Science 249, 280-283]. In this paper we present evidence that isolated calcium-binding loops can also dimerize, when saturated with lanthanide ions, interacting with each other in a similar way as do loops in intact proteins. A synthetic analogue of calcium binding loop III of calmodulin, AcDKDGDGYISAAE-NH2, has been studied by 1H NMR spectroscopy. For the La(3+)-saturated peptide, concentration dependent broadenings and shifts of certain signals have been observed indicating dimerization process of intermediate rate on the NMR time scale. Analysis of signal shape and position of the Tyr7 ring protons as a function of concentration makes it possible to determine the association and dissociation rate constants of the process for various temperatures within the range of 10-80 degrees C. The dimerization constant changes according to van't Hoff relationship with delta S = 233 J/mol.K and delta H = 62 kJ/mol. A distance of 11.4 +/- 0.4 A between the ions coordinated by dimer molecules has been determined by measurements of Tb(3+)-->Ho3+ luminescence energy transfer. This value suggests that the dimer structure is similar to that of two-loop structural elements in native EF-hand proteins. From a thermodynamic cycle it can be shown that La3+ ion binding to the peptide dimers must be highly cooperative. Therefore, cooperativity of ion binding to domains of EF-hand proteins is, at least partly, due to local interactions between binding loops.

Quantitative measurements of the cooperativity in an EF-hand protein with sequential calcium binding

Positive cooperativity, defined as an enhancement of the ligand affinity at one site as a consequence of binding the same type of ligand at another site, is a free energy coupling between binding sites. It can be present both in systems with sites having identical ligand affinities and in systems where the binding sites have different affinities. When the sites have widely different affinities such that they are filled with ligand in a sequential manner, it is often difficult to quantify or even detect the positive cooperativity, if it occurs. This study presents verification and quantitative measurements of the free energy coupling between the two calcium binding sites in a mutant form of calbindin D9k. Wild-type calbindin D9k binds two calcium ions with similar affinities and positive cooperativity--the free energy coupling, delta delta G, is around -8 kJ.mol-1 (Linse S, et al., 1991, Biochemistry 30: 154-162). The mutant, with the substitution Asn 56-->Ala, binds calcium in a sequential manner. In the present work we have taken advantage of the variations among different metal ions in terms of their preferences for the two binding sites in calbindin D9k. Combined studies of the binding of Ca2+, Cd2+, and La3+ have allowed us to conclude that in this mutant delta delta G < -6.4 kJ.mol-1, and that Cd2+ and La3+ also bind to this protein with positive cooperativity. The results justify the use of the (Ca2+)1 state of the Asn 56-->Ala mutant, as well as the (Cd2+)1 state of the wild type, as models for the half-saturated states along the two pathways of cooperative Ca2+ binding in calbindin D9k.