Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

Neoadjuvant chemotherapy reduces the levels of HMGB1 and E-cadherin in patients with breast cancer

This study investigated the changes in serum tumor marker levels in patients with breast cancer (BC) after neoadjuvant chemotherapy (NACT) and their potential as prognostic factors in NACT. A total of 134 consecutive patients with BC treated at our hospital between January 2019 and December 2021 were retrospectively analyzed. Patients were treated with NACT based on the docetaxel, epirubicin, and cyclophosphamide (TEC) regimen and assessed for marker levels, T cell subsets, and therapeutic outcomes. Receiver operating characteristic (ROC) curves were constructed to evaluate the predictive performance of the markers. Outcome assessments showed that NACT effectively reduced the tumor size, leading to increased complete remission, partial remission, stable disease, and significantly reduced disease progression. Improved immune function has also been observed after NACT. The levels of two (E-cadherin and HMGB1) out of five markers (CA153, CK19, CEA, E-cadherin, and HMGB1) were significantly reduced after NACT before surgery compared with those at admission, suggesting that NACT modulates the levels of biomarkers. ROC analysis revealed that the area under the curve (AUC) of HMGB1 and E-cadherin combination was 0.87 for discrimination of therapeutic response with a sensitivity and specificity of 91.3% and 88.4%, respectively. Serum tumor marker levels were reduced after NACT in patients with BC. The reduction was most prominent for HMGB1, followed by E-cadherin. These biomarkers can be used to predict the therapeutic response to NACT with an AUC of 0.87, thus offering a new tool to monitor treatment progress in NACT for patients with BC.

Conserved properties of individual Ca2+-binding sites in calmodulin

Calmodulin (CaM) is a Ca(2+)-sensing protein that is highly conserved and ubiquitous in eukaryotes. In humans it is a locus of life-threatening cardiomyopathies. The primary function of CaM is to transduce Ca(2+) concentration into cellular signals by binding to a wide range of target proteins in a Ca(2+)-dependent manner. We do not fully understand how CaM performs its role as a high-fidelity signal transducer for more than 300 target proteins, but diversity among its four Ca(2+)-binding sites, called EF-hands, may contribute to CaM's functional versatility. We therefore looked at the conservation of CaM sequences over deep evolutionary time, focusing primarily on the four EF-hand motifs. Expanding on previous work, we found that CaM evolves slowly but that its evolutionary rate is substantially faster in fungi. We also found that the four EF-hands have distinguishing biophysical and structural properties that span eukaryotes. These results suggest that all eukaryotes require CaM to decode Ca(2+) signals using four specialized EF-hands, each with specific, conserved traits. In addition, we provide an extensive map of sites associated with target proteins and with human disease and correlate these with evolutionary sequence diversity. Our comprehensive evolutionary analysis provides a basis for understanding the sequence space associated with CaM function and should help guide future work on the relationship between structure, function, and disease.

Metal-binding properties of human centrin-2 determined by micro-electrospray ionization mass spectrometry and UV spectroscopy

We analyzed the metal-binding properties of human centrin-2 (HsCen-2) and followed the changes in HsCen-2 structure upon metal-binding using micro-electrospray ionization mass spectrometry (muESI-MS). Apo-HsCen-2 is mostly monomeric. The ESI spectra of HsCen-2 show two charge-state distributions, representing two conformations of the protein. HsCen-2 binds four moles calcium/mol protein: one mol of calcium with high affinity, one additional mol of calcium with lower affinity, and two moles of calcium at low affinity sites. HsCen-2 binds four moles of magnesium/mol protein. The conformation giving the lower charge-state HsCen-2 by ESI, binds calcium and magnesium more readily than does the higher charge-state HsCen-2. Both conformations of HsCen-2 bind calcium more readily than magnesium. Calcium was more effective in displacing magnesium bound to HsCen-2 than vice versa. Binding of a peptide from a known binding partner, the xeroderma pigmentosum complementation group protein C (XPC), to apo-HsCen-2, occurs in the presence or the absence of calcium. Near and far-UV CD spectra of HsCen-2 show little difference with addition of calcium or magnesium. Minor changes in secondary structure are noted. Melting curves derived from temperature dependence of molar ellipticity at 222 nm for HsCen-2 show that calcium increases protein stability whereas magnesium does not. Delta 25 HsCen-2 behaves similarly to HsCen-2. We conclude that HsCen-2 binds calcium and magnesium and that calcium modulates HsCen-2 structure and function by increasing its stability without undergoing significant changes in secondary or tertiary structure.

Calcium Homeostasis in Human Placenta: Role of Calcium‐Handling Proteins

The human placenta is a transitory organ, representing during pregnancy the unique connection between the mother and her fetus. The syncytiotrophoblast represents the specialized unit in the placenta that is directly involved in fetal nutrition, mainly involving essential nutrients, such as lipids, amino acids, and calcium. This ion is of particular interest since it is actively transported by the placenta throughout pregnancy and is associated with many roles during intrauterine life. At term, the human fetus has accumulated about 25-30 g of calcium. This transfer allows adequate fetal growth and development, since calcium is vital for fetal skeleton mineralization and many cellular functions, such as signal transduction, neurotransmitter release, and cellular growth. Thus, there are many proteins involved in calcium homeostasis in the human placenta.

Diversification and Independent Evolution of Troponin C Genes in Insects

Troponin C (TpnC), the calcium-binding subunit of the troponin regulatory complex in the muscle thin filament, is encoded by multiple genes in insects. To understand how TpnC genes have evolved, we characterized the gene number and structure in a number of insect species. The TpnC gene complement is five genes in Drosophilidae as previously reported for D. melanogaster. Gene structures are almost identical in D. pseudoobscura, D. suboboscura, and D. virilis. Developmental patterns of expression are also conserved in Drosophila subobscura and D. virilis. Similar, but not completely equivalent, TpnC gene repertoires have been identified in the Anopheles gambiae and Apis mellifera genomes. Insect TpnC sequences can be divided into three groups, allowing a systematic classification of newly identified genes. The pattern of expression of the Apis mellifera genes essentially agrees with the pattern in Drosophilidae, providing further functional support to the classification. A model for the evolution of the TpnC genes is proposed including the most likely pathway of insect TpnC diversification. Our results suggest that the rapid increase in number and sequence specialization of the adult Type III isoforms can be correlated with the evolution of the holometabolous mode of development and the acquisition of asynchronous indirect flight muscle function in insects. This evolutionarily specialization has probably been achieved independently in different insect orders.

Thermodynamic analysis of calcium and magnesium binding to calmodulin

To elucidate some aspects still debated concerning the interaction of Ca2+ and Mg2+ with CaM, the thermodynamic binding parameters of Ca2+-CaM and Mg2+-CaM complexes were characterized by flow dialysis and isothermal microcalorimetry under different experimental conditions. In particular, the enthalpy and entropy changes associated with Ca2+ and Mg2+ binding to their sites were determined, allowing a better understanding of the mechanism underlying cation-CaM interactions. Ca2+-CaM interaction follows an enthalpy-entropy compensation relationship, suggesting that CaM explores a subspace of isoenergetical conformations which is modified by Ca2+ binding. This Ca2+-induced change in CaM dynamics is proposed to play a key role in CaM function, i.e. in its interaction with and/or activation of target proteins. Furthermore, data show that Mg2+ does not act as a direct competitor for Ca2+ binding on the four main Ca2+ binding sites, but rather as an allosteric effector. This implies that the four main Mg2+ binding sites are distinct from the EF-hand Ca2+ binding sites. Finally, Ca2+ is shown to interact with auxiliary binding sites on CaM. These weak affinity sites were thermodynamically characterized. The results presented here challenge the current accepted view of CaM ion binding.

The amino acid sequence of the light chain of Acanthamoeba myosin IC

The amino acid sequence of the light chain of Acanthamoeba myosin IC deduced from the cDNA sequence comprises 149 amino acids with a calculated molecular weight of 16,739. All but the 3 N-terminal residues were also determined by amino acid sequencing of the purified protein, which also showed the N-terminus to be blocked. Phylogenetic analysis shows Acanthamoeba myosin IC light chain to be more similar to the calmodulin subfamily of EF-hand calcium-modulated proteins than to the myosin II essential light chain or regulatory light chain subfamilies. In pairwise comparisons, the myosin IC light chain sequence is most similar to sequences of calmodulins (approximately 50% identical) and a squid calcium-binding protein (approximately 43% identical); the sequence is approximately 37% identical to the calcium-binding essential light chain of Physarum myosin II and approximately 30% identical to the essential light chain of Acanthamoeba myosin II, and the essential light chain and regulatory light chain of Dictyostelium myosin II. The sequence predicts four helix-loop-helix domains with possible calcium-binding sites in domains I and III, suggesting that calcium may affect the activity of this unconventional myosin. This is the first report of the sequence of an unconventional myosin light chain other than calmodulin.

Kinetic tuning of the EF-hand calcium binding motif: the gateway residue independently adjusts (i) barrier height and (ii) equilibrium

In EF-hand calcium binding sites of known structure, the side chain provided by the ninth EF-loop position lies at the entrance of the shortest pathway connecting the metal binding cavity to solvent. The location of this residue suggests that it could serve as a "gateway", providing steric and electrostatic control over the kinetics of Ca2+ binding and dissociation. To test this hypothesis, the present study has engineered the putative gateway side chain of a model EF-hand site and determined the resulting effects on metal ion affinity and dissociation kinetics. The model site chosen was that of the Escherichia coli galactose binding protein (GBP), in which the putative gateway is a Gln side chain. Nine engineered GBP molecules were generated and isolated, each exhibiting native-like activity and global conformation. Two control substitutions at the fourth EF-loop position, a noncoordinating surface residue, had no significant effect on either the equilibrium or the kinetics of the model site. The remaining seven proteins, which possessed unique substitutions at the ninth EF-loop position (Glu, Asn, Asp, Thr, Ser, Gly, Ala), in each case significantly altered the affinity or dissociation kinetics of the site for Tb3+, used as a probe metal ion. Neutral side chains at the gateway position yielded a 590-fold range of Tb3+ dissociation kinetics but only a 3-fold range of Tb3+ affinities, indicating that the size or polarity of these substitutions alters the transition state barrier for metal binding and release without substantially shifting the equilibrium. In contrast, acidic side chains yielded as much as a 34-fold decrease in the Tb3+ off-rate and a 33-fold increase in Tb3+ affinity, suggesting that a negative charge at the gateway position increases the equilibrium stability of the bound metal ion and thereby slows metal release. Thus, kinetic tuning by the gateway side chain exhibits both transition state and ground state tuning mechanisms. In natural EF-hand sequences, different gateway side chains are used by slow buffering sites and rapid signaling sites, providing evidence that the gateway position is an important physiological determinant of metal binding kinetics.

Molecular evolution of the Ca(2+)-binding photoproteins of the Hydrozoa

Alignment of the primary structures of the hydrozoan photoproteins, aequorin, mitrocomin, clytin and obelin showed very strong amino acid sequence identities. The Ca(2+)-binding sites of the proteins were found to be highly conserved. The Ca(2+)-binding sites were also homologous to the Ca(2+)-binding sites of other Ca(2+)-binding proteins. However, aequorin, mitrocomin, clytin and obelin differed from other Ca(2+)-binding proteins in that they contained a relatively large number of cysteine, tryptophan, histidine, proline and tyrosine residues, suggesting that these residues may have evolved as part of the light-emitting mechanism. Construction of a phylogenetic tree showed that aequorin, mitrocomin, clytin and obelin form a closely related group of proteins.

Dance of the dimers

The structure of the apo form of calcyclin, a member of the S100 family of calcium-binding proteins, reveals a novel dimer fold that may reflect the presence of a new interface for target protein recognition.

A novel EF-hand Ca(2+)-binding protein from abdominal muscle of crustaceans with similarity to calcyphosine from dog thyroidea

The amino acid sequence of a novel EF-hand Ca(2+)-binding protein from the abdominal muscle of the crayfish, Orconectes limosus, has been elucidated by tandem mass spectrometry and automated Edman degradation. The name CCBP-23 (23-kDa crustacean Ca(2+)-binding protein) is proposed. The protein can also exist as a disulfide-linked homodimer. The sequence of the monomeric form spans 200 residues with an acetylated N-terminal Ser and reveals four EF-hand domains. The 174-mass-unit difference between the calculated average molecular mass of 22,669.6 Da deduced from the sequence and the obtained electrospray ionization mass spectroscopy (ESI-MS) mass of 22,844 Da has not yet been explained. Partial sequence analysis (137 residues) of CCBP-23 from the lobster, Homarus americanus, showed a sequence identity of 74% with the crayfish protein. Homology searches revealed a 44% sequence identity of CCBP-23 from crayfish to calcyphosine, a Ca(2+)-binding protein from dog thyroidea (Lefort et al., 1989). Although CCBP-23 also shows a 44% identity to R2D5 antigen (Nemoto et al., 1993), we believe that both proteins represent two distinct subgroups within the family of EF-hand proteins.

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).

In vitro aging of calmodulin generates isoaspartate at multiple Asn-Gly and Asp-Gly sites in calcium-binding domains II, III, and IV

We have determined the major sites responsible for isoaspartate formation during in vitro aging of bovine brain calmodulin under mild conditions. Protein L-isoaspartyl methyltransferase (EC 2.1.1.77) was used to quantify isoaspartate by the transfer of methyl-3H from S-adenosyl-L-[methyl-3H]methionine to the isoaspartyl (alpha-carboxyl) side chain. More than 1.2 mol of methyl-acceptor sites per mol of calmodulin accumulated during a 2-week incubation without calcium at pH 7.4, 37 degrees C. Analysis of proteolytic peptides of aged calmodulin revealed that > 95% of the methylation capacity is restricted to residues in the four calcium-binding domains, which are predicted to be highly flexible in the absence of calcium. We estimate that domains III, IV, and II accumulated 0.72, 0.60, and 0.13 mol of isoaspartate per mol of calmodulin, respectively. The Asn-97-Gly-98 sequence (domain III) is the greatest contributor to isoaspartate formation. Other major sites of isoaspartate formation are Asp-131-Gly-132 and Asp-133-Gly-134 in domain IV, and Asn-60-Gly-61 in domain II. Significant isoaspartate formation was also localized to Asp-20, Asp-22, and/or Asp-24 in domain I, to Asp-56 and/or Asp-58 in domain II, and to Asp-93 and/or Asp-95 in domain III. All of these residues are calcium ligands in the highly conserved EF-hand calcium-binding motif. Thus, other EF-hand proteins may also be subject to isoaspartate formation at these ligands. The results support the idea that isoaspartate formation in structured proteins is strongly influenced by both the C-flanking residue and by local flexibility.

Evolution of EF-hand calcium-modulated proteins. V. The genes encoding EF-hand proteins are not clustered in mammalian genomes

The chromosomal assignments of genes belonging to the EF-hand family which have a common origin are compiled in this article. So far data are available from 27 human gene loci belonging to 6 subfamilies and 8 murine loci belonging to 4 subfamilies. Chromosomal localization has been obtained by somatic-cell hybrid analysis using the Southern blot technique or PCR amplification, metaphase spread in situ hybridization, or isolation of the particular genes from chromosome-specific libraries. Except for genes of the S-100 alpha proteins which are grouped on human chromosome 1q12-25 and mouse chromosome 3, no linkage has been found for genes encoding EF-hand proteins, indicating absence of selective pressure for maintaining chromosomal clustering. Six of these genes map to known syntenic groups conserved in the human and mouse genomes. This suggests that chromosomal translocations occurred before divergence of these species. The possible significance of chromosomal positioning with respect to nearby located known genes and genetic disease loci is discussed.

Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins

In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.