Hsiau-Wei Lee

Structural analysis, identification, and design of calcium-binding sites in proteins

Assigning proteins with functions based on the 3‐D structure requires high‐speed techniques to make a systematic survey of protein structures. Calcium regulates many biological systems by binding numerous proteins in different biological environments. Despite the great diversity in the composition of ligand residues and bond angles and lengths of calcium‐binding sites, our structural analysis of 11 calcium‐binding sites in different classes of proteins has shown that common local structural parameters can be used to identify and design calcium‐binding proteins. Natural calcium‐binding sites in both EF‐hand proteins and non‐EF‐hand proteins can be described with the smallest deviation from the geometry of an ideal pentagonal bipyramid. Further, two different magnesium‐binding sites in parvalbumin and calbindinD9K can also be identified using an octahedral geometry. Using the established method, we have designed de novo calcium‐binding sites into the scaffold of non‐calcium‐binding proteins CD2 and Rop. Our results suggest that it is possible to identify calcium‐ and magnesium‐binding sites in proteins and design de novo metal‐binding sites. Proteins 2002;47:344–356.

Prediction of EF‐hand calcium‐binding proteins and analysis of bacterial EF‐hand proteins

The EF‐hand protein with a helix–loop–helix Ca2+ binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca2+ in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF‐hand and EF‐like Ca2+‐binding proteins. The canonical EF‐hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of the conserved sequence of both the N‐ and C‐terminal EF‐hands within S100 and S100‐like proteins, a new signature profile has been established to allow for the identification of pseudo EF‐hand and S100 proteins from genomic information. The new patterns have a positive predictive value of 99% and a sensitivity of 96% for pseudo EF‐hands. Furthermore, using the developed patterns, we have identified zero pseudo EF‐hand motif and 467 canonical EF‐hand Ca2+ binding motifs with diverse cellular functions in the bacteria genome. The prediction results imply that pseudo EF‐hand motifs are phylogenetically younger than canonical EF‐hand motifs. Our prediction of Ca2+ binding motifs provides not only an insight into the role of Ca2+ and Ca2+‐binding proteins in bacterial systems, but also a way to explore and define the role of Ca2+ in other biological systems (calciomics). Proteins 2006.

Identification and Dissection of Ca2+-binding Sites in the Extracellular Domain of Ca2+-sensing Receptor

Ca2+-sensing receptors (CaSRs) represent a class of receptors that respond to changes in the extracellular Ca2+ concentration ([Ca2+]o) and activate multiple signaling pathways. A major barrier to advancing our understanding of the role of Ca2+ in regulating CaSRs is the lack of adequate information about their Ca2+-binding locations, which is largely hindered by the lack of a solved three-dimensional structure and rapid off rates due to low Ca2+-binding affinities. In this paper, we have reported the identification of three potential Ca2+-binding sites in a modeled CaSR structure using computational algorithms based on the geometric description and surface electrostatic potentials. Mutation of the predicted ligand residues in the full-length CaSR caused abnormal responses to [Ca2+]o, similar to those observed with naturally occurring activating or inactivating mutations of the CaR, supporting the essential role of these predicted Ca2+-binding sites in the sensing capability of the CaSR. In addition, to probe the intrinsic Ca2+-binding properties of the predicted sequences, we engineered two predicted continuous Ca2+-binding sequences individually into a scaffold protein provided by a non-Ca2+-binding protein, CD2. We report herein the estimation of the metal-binding affinities of these predicted sites in the CaSR by monitoring aromatic-sensitized Tb3+ fluorescence energy transfer. Removing the predicted Ca2+-binding ligands resulted in the loss of or significantly weakened cation binding. The potential Ca2+-binding residues were shown to be involved in Ca2+/Ln3+ binding by high resolution NMR and site-directed mutagenesis, further validating our prediction of Ca2+-binding sites within the extracellular domain of the CaSR.

Identification of the Calmodulin Binding Domain of Connexin 43

Calmodulin (CaM) has been implicated in mediating the Ca2+-dependent regulation of gap junctions. This report identifies a CaM-binding motif comprising residues 136–158 in the intracellular loop of Cx43. A 23-mer peptide encompassing this CaM-binding motif was shown to bind Ca2+-CaM with 1:1 stoichiometry by using various biophysical approaches, including surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and NMR. Far UV circular dichroism studies indicated that the Cx43-derived peptide increased its α-helical contents on CaM binding. Fluorescence and NMR studies revealed conformational changes of both the peptide and CaM following formation of the CaM-peptide complex. The apparent dissociation constant of the peptide binding to CaM in physiologic K+ is in the range of 0.7–1 μm. Upon binding of the peptide to CaM, the apparent Kd of Ca2+ for CaM decreased from 2.9 ± 0.1 to 1.6 ± 0.1 μm, and the Hill coefficient nH increased from 2.1 ± 0.1 to 3.3 ± 0.5. Transient expression in HeLa cells of two different mutant Cx43-EYFP constructs without the putative Cx43 CaM-binding site eliminated the Ca2+-dependent inhibition of Cx43 gap junction permeability, confirming that residues 136–158 in the intracellular loop of Cx43 contain the CaM-binding site that mediates the Ca2+-dependent regulation of Cx43 gap junctions. Our results provide the first direct evidence that CaM binds to a specific region of the ubiquitous gap junction protein Cx43 in a Ca2+-dependent manner, providing a molecular basis for the well characterized Ca2+-dependent inhibition of Cx43-containing gap junctions.

Structural biology of the cell adhesion protein CD2: alternatively folded states and structure-function relation.

Cluster of differentiation 2 (CD2) is a cell surface glycoprotein expressed on most human T cells and natural killer (NK) cells and plays an important role in mediating cell adhesion in both T-lymphocytes and in signal transduction. The understanding of the biochemical basis of molecular recognition by the cell adhesion molecule CD2 has been advanced greatly through the determination of structures and the dynamic properties of the complexes and their individual components and through site-directed mutagenesis. A number of general principles can be derived from the structural and functional studies of the extracellular domains of CD2 and CD58 and their complex. Significant electrostatic interactions within the protein-protein interfaces contribute directly to the formation of macromolecular complexes of CD2 and CD58. Also, residues located on the protein-protein interface demonstrate a certain degree of conformational change upon the formation of a complex. Structural analysis of CD2 has revealed that this adhesion molecule exhibits strong conformational flexibility with a partial non-native helical conformation at high temperatures and in the presence of an organic solvent. In addition, it can be converted into a domain swapped dimer, or trimer and tetramer through hinge deletion. Thus, the conformational status of the adhesive proteins contributes to the regulation of cell adhesion and the folding of CD2.

Identification of a Ca2+-Binding Domain in the Rubella Virus Nonstructural Protease

ABSTRACT The rubella virus (RUB) nonstructural protein (NS) open reading frame (ORF) encodes a polypeptide precursor that is proteolytically self cleaved into two replicase components involved in viral RNA replication. A putative EF-hand Ca2+-binding motif that was conserved across different genotypes of RUB was predicted within the nonstructural protease that cleaves the precursor by using bioinformatics tools. To probe the metal-binding properties of this motif, we used an established grafting approach and engineered the 12-residue Ca2+-coordinating loop into a non-Ca2+-binding scaffold protein, CD2. The grafted EF-loop bound to Ca2+ and its trivalent analogs Tb3+ and La3+ with Kds of 214, 47, and 14 μM, respectively. Mutations (D1210A and D1217A) of two of the potential Ca2+-coordinating ligands in the EF-loop led to the elimination of Tb3+ binding. Inductive coupled plasma mass spectrometry was used to confirm the presence of Ca2+ ([Ca2+]/[protein] = 0.7 ± 0.2) in an NS protease minimal metal-binding domain, RUBCa, that spans the EF-hand motif. Conformational studies on RUBCa revealed that Ca2+ binding induced local conformational changes and increased thermal stability (ΔTm = 4.1°C). The infectivity of an RUB infectious cDNA clone containing the mutations D1210A/D1217A was decreased by ∼20-fold in comparison to the wild-type (wt) clone, and these mutations rapidly reverted to the wt sequence. The NS protease containing these mutations was less efficient at precursor cleavage than the wt NS protease at 35°C, and the mutant NS protease was temperature sensitive at 39°C, confirming that the Ca2+-binding loop played a structural role in the NS protease and was specifically required for optimal stability under physiological conditions.

Isolated EF-loop III of calmodulin in a scaffold protein remains unpaired in solution using pulsed-field-gradient NMR spectroscopy.

Calmodulin (CaM) is a trigger calcium-dependent protein that regulates many biological processes. We have successfully engineered a series of model proteins, each containing a single EF-hand loop but with increasing numbers of Gly residues linking the EF-hand loop to a scaffold protein, cluster of differentiation 2 (CD2), to obtain the site-specific calcium-binding ability of a protein with EF-hand motifs without the interference of cooperativity. Loop III of calmodulin with two Gly linkers in CD2 (CaM-CD2-III-5G) has metal affinities with K(d) values of 1.86 x 10(-4) and 5.8 x 10(-5) M for calcium and lanthanum, respectively. The oligomeric states of the CD2 variants were examined by pulsed-field-gradient nuclear magnetic resonance (PFG NMR). The diffusion coefficient values of CD2 variants are about 11.1 x 10(-7) cm(2)/s both in the presence and absence of metal ions, which are the same as that of wild-type CD2. This suggests that the isolated EF-loop III of calmodulin inserted in the scaffold protein is able to bind calcium and lanthanum as a monomer, which is in contrast to the previous observation of the EF-hand motif. Our results imply that additional factors that reside outside of the EF-loop III may contribute to the pairing of EF-hand motifs of calmodulin. This result is of interest as it opens up the way for studying the ion-binding properties of isolated EF-hands, which in turn can answer important questions about the properties of EF-hands, the large and important group of calcium-binding signaling proteins.

Design, synthesis, and characterization of a calcium-sensitive near infrared dye.

Intracellular calcium concentration in biological cells varies from 0.1 to 10 muM depending upon cell signaling and disease states. A direct estimate of calcium concentration in cell tissues within this range is possible with a novel calcium-selective reagent 15C5-774. The molecule of 15C5-774 consists of a near-infrared (NIR) chromophore (lambda(max)=774 nm) and a metal complexing moiety of benzo-15-crown-5. The reagent shows a strong calcium binding affinity in a 1:1 ratio and metal selectivity in the order Ca(2+)>Mg(2+)>Sr(2+) approximately K(+) approximately Na(+)>Zn(2+)>Li(+). The high sensitivity is achieved by conducting absorption measurements in the NIR region where background interference from the biological matrix is low.

Identifying and Designing of Calcium Binding Sites in Proteins by Computational Algorithm

Our studies for the identification of the natural calcium binding sites with both classic and pseudo EF-hand motifs in three EF-hand proteins have shown that natural calcium binding sites can be accurately relocated with Dezymer using a set of geometric descriptions of an ideal pentagonal bipyramid. The success of each constructed site can be ranked by the relative U(p) values. The searched native-like sites in three EF-hand proteins have the smallest deviation from the target geometry. Our work indicates that a useful method for searching calcium-binding sites in proteins has been established. It is possible to use established parameters to design novel calcium binding proteins.

Rational design of a protein that binds integrin α(v)β(3) outside the ligand binding site

Integrin αvβ3 expression is altered in various diseases and has been proposed as a drug target. Here we use a rational design approach to develop a therapeutic protein, which we call ProAgio, that binds to integrin αvβ3 outside the classical ligand-binding site. We show ProAgio induces apoptosis of integrin αvβ3-expressing cells by recruiting and activating caspase 8 to the cytoplasmic domain of integrin αvβ3. ProAgio also has anti-angiogenic activity and strongly inhibits growth of tumour xenografts, but does not affect the established vasculature. Toxicity analyses demonstrate that ProAgio is not toxic to mice. Our study reports a new integrin-targeting agent with a unique mechanism of action, and provides a template for the development of integrin-targeting therapeutics.