Binding studies of a triple-helical peptide model of macrophage scavenger receptor to tetraplex nucleic acids

Synthesis and biological applications of collagen-model triple-helical peptides

Triple-helical peptides (THPs) have been utilized as collagen models since the 1960s. The original focus for THP-based research was to unravel the structural determinants of collagen. In the last two decades, virtually all aspects of collagen structural biochemistry have been explored with THP models. More specifically, secondary amino acid analogs have been incorporated into THPs to more fully understand the forces that stabilize triple-helical structure. Heterotrimeric THPs have been utilized to better appreciate the contributions of chain sequence diversity on collagen function. The role of collagen as a cell signaling protein has been dissected using THPs that represent ligands for specific receptors. The mechanisms of collagenolysis have been investigated using THP substrates and inhibitors. Finally, THPs have been developed for biomaterial applications. These aspects of THP-based research are overviewed herein.

Modified low density lipoproteins binding requires a lysine cluster region in the murine macrophage scavenger receptor class A type II

Atherosclerosis is a consequence of lipid deposition and foam cell formation in the arterial wall. Macrophage scavenger receptor A II is involved in the uptake of modified low density lipoproteins. It contains an extracellular conserved lysine cluster which has been proposed to form a positively charged groove that interacts with acetylated low density lipoproteins (AcLDL). This study evaluated the role of the murine SRA-II and a lysine mutated SRA-II on AcLDL uptake. Fluorescence labeled AcLDL uptake was quantified using a Laser Scan Cytometer. A significant increase in fluorescence uptake was found in the cells transfected with SRA-II versus those with empty vector. Cells expressing the lysine mutated SRA-II also demonstrated a significant decrease in their uptake of AcLDL. This data supports the concept that the conserved lysine cluster in murine SRA-II is the binding region for AcLDL or contributes to the trimeric structure of SRA-II necessary for AcLDL binding.

The many roles of the class A macrophage scavenger receptor

The class A macrophage scavenger receptor (SR-A) is the prototypic example of a group of plasma membrane receptors collectively known as scavenger receptors. SR-A displays the ability to bind and endocytose large quantities of modified lipoprotein. Hence, it is thought to be one of the main receptors involved in mediating lipid influx into macrophages (Mphi), which promotes their conversion into foam cells that are abundant in the atherosclerotic lesion. However, as a result of increased interest and research effort and through the development of specific reagents and animal models, it is now appreciated to be multifunctional. These roles include Mphi growth and maintenance, adhesion to the substratum, cell-cell interactions, phagocytosis, and host defense. In this review, we attempt to summarize the evidence and argue that these kinds of activities underlie the biological versatility of Mphi.

G-quadruplex DNA structures--variations on a theme

To be functional, nucleic acids need to adopt particular three-dimensional structures. For a long time DNA was regarded as a rigid and passive molecule with the sole purpose to store genetic information, but experimental data has now accumulated that indicates the full dynamic repertoire of this macromolecule. During the last decade, four-stranded DNA structures known as G-quadruplexes, or DNA tetraplexes, have emerged as a three-dimensional structure of special interest. Motifs for the formation of G-quadruplex DNA structures are widely dispersed in eukaryotic genomes, and are abundant in regions of biological significance, for example, at telomeres, in the promoters of many important genes, and at recombination hotspots, to name but a few in man. Here I explore the plethora of G-quadruplex DNA structures, and discuss their possible biological functions as well as the proteins that interact with them.

Hydrolysis of triple-helical collagen peptide models by matrix metalloproteinases

The matrix metalloproteinase (MMP) family has been implicated in the process of a variety of diseases such as arthritis, atherosclerosis, and tumor cell metastasis. To study the mechanisms of MMP action on collagenous substrates, we have constructed homotrimeric triple-helical peptide (THP) models of the collagenase cleavage sites in types I and II collagen. The THPs incorporate either the alpha1(I)772-786 or the alpha1(II)772-783 sequence. The alpha1(I)772-786 and alpha1(II)772-783 THPs were hydrolyzed by MMP-1 at the Gly-Ile and Gly-Leu bonds, respectively, analogous to the bonds cleaved in corresponding native collagens. Thus, the THPs contained all necessary information to direct MMP-1 binding and proteolysis. Subsequent investigations using the alpha1(I)772-786 THP showed hydrolysis by MMP-2, MMP-13, and a COOH-terminal domain-deleted MMP-1 (MMP-1(Delta(243-450))) but not by MMP-3 or a COOH-terminal domain-deleted MMP-3 (MMP-3(Delta(248-460))). Kinetic analyses showed a k(cat)/K(m) value of 1,808 s(-1) m(-1) for MMP-1 hydrolysis of alpha1(I)772-786 THP, approximately 10-fold lower than for type I collagen. The effect is caused primarily by relative K(m) values. MMP-2 and MMP-13 cleaved the THP more rapidly than MMP-1, but MMP-2 cleavage occurred at distinct multiple sites. Comparison of MMP-1 and MMP-1(Delta(243-450)) hydrolysis of alpha1(I)772-786 THP showed that both can cleave a triple-helical substrate with a slightly higher K(m) value for MMP-1(Delta(243-450)). We propose that the COOH-terminal domain of MMPs is necessary for orienting whole, native collagen molecules but may not be necessary for binding to and cleaving a THP. This proposal is consistent with the large distance between the MMP-1 catalytic and COOH-terminal domains observed by three-dimensional structural analysis and supports previous suggestions that the features of the catalytic domain contribute significantly toward enzyme specificity.

Molecular modeling of the collagen-like tail of asymmetric acetylcholinesterase

The asymmetric form of acetylcholinesterase comprises three catalytic tetramers attached to ColQ, a collagen-like tail responsible for the anchorage of the enzyme to the synaptic basal lamina. ColQ is composed of an N-terminal domain which interacts with the catalytic subunits of the enzyme, a central collagen-like domain and a C-terminal globular domain. In particular, the collagen-like domain of ColQ contains two heparin-binding domains which interact with heparan sulfate proteoglycans in the basal lamina. A three-dimensional model of the collagen-like domain of the tail of asymmetric acetylcholinesterase was constructed. The model presents an undulated shape that results from the presence of a substitution and an insertion in the Gly-X-Y repeating pattern, as well as from low imino-acid regions. Moreover, this model permits the analysis of interactions between the heparin-binding domains of ColQ and heparin, and could also prove useful in the prediction of interaction domains with other putative basal lamina receptors.

Oligonucleotide aggregates bind to the macrophage scavenger receptor

We have prepared a model receptor containing a Lys cluster (320-340) in the collagen-like domain of the bovine macrophage scavenger receptor, and have shown that it has a similar binding specificity to the native scavenger receptor. The native scavenger receptor is reported to bind the quadruplex structure of nucleotides. In this study, we analyzed the model receptor binding of nucleotides with various structures, random, parallel or antiparallel quadruplex and aggregate forms. This was carried out by direct binding assays using labeled oligonucleotides or surface plasmon resonance, and by an inhibition assay using Chinese hamster ovary (CHO) cells expressing the scavenger receptor. The results showed that the nucleotides forming the quadruplex structure did not exhibit any binding. Only the aggregate forms of the nucleotide could bind to the model receptor. They also inhibited the degradation of acetylated low density lipoprotein by CHO cells expressing the native scavenger receptor, whereas nucleotides that did not bind to the model receptor had no effect on cellular acetylated low density lipoprotein degradation. Our results suggest that the quadruplex structure is not essential but may be required for the formation of the nucleotide aggregates, which can interact with the scavenger receptor.

Dissection of the class A scavenger receptor by peptide engineering

The construction of portions of a protein provides information about its functional mechanisms. Peptide engineering is a recently developed technique to construct a small tertiary structure or a portion of a protein, and allows expansion to applications for bio- and physicochemistries. In this article, we focus on the class A scavenger receptor, which plays a key role in atherogenesis, and may be involved in other pathogenic processes. The receptor is mainly composed of simple tertiary structures, such as collagen and alpha-helical coiled coil structures, which have different functions. We constructed both the collagen-like and alpha-helical coiled coil domains by peptide engineering, and analysed the structure-function relationships of the receptor. Understanding the mechanisms of their functions at the amino acid level should help us to mimic the functional domains and to create de novo designed proteins with new functions.

Scavenger receptors: diverse activities and promiscuous binding of polyanionic ligands

Scavenger receptors are a diverse family of proteins that share a common property--the binding of modified lipoprotein--but they have recently been shown to recognise a diverse range of ligands. Understanding the molecular interaction of receptor-ligand binding should provide insight into how scavenger receptors contribute to important biological processes.

Functional changes in scavenger receptor binding conformation are induced by charge mutants spanning the entire collagen domain

Macrophage scavenger receptors are trimeric integral membrane proteins that bind a diverse array of negatively charged ligands. They have been shown to play a role in the pathogenesis of atherosclerosis and in host responses to microbial infections. Earlier mutational studies demonstrated that the distal segment of the collagen domain of the receptor was critically important for high affinity ligand binding activity. In this study, mutations spanning the entire collagen domain were generated and binding was assayed in transfected cells, as well as in assays employing a secreted, receptor fusion protein. Many of the distal, positively charged C-terminal residues in the type II collagen domain of the receptor, previously reported to be essential for binding at 37 degreesC, were found not to be critical for binding at 4 degreesC. Conversely, more proximally charged residues of the collagen receptor that have not been previously mutated were shown to have substantial effects on binding that were also temperature-dependent. These data suggest that scavenger receptor ligand recognition depends on more complex conformational interactions, involving charged residues throughout the entire collagen domain, than was previously recognized.

Progress in developments of triplex-based strategies

Recognition of B-DNA by oligonucleotides that form triple helices is a unique method to specifically recognize sequences of double-stranded DNA. Recently, some significant limitations of the triple-based applications have been overcome. Stable intermolecular triplexes can be formed under physiologic conditions. Binding affinities of modified oligonucleotides to their target sequence due to Hoogsteen or reverse Hoogsteen hydrogen bonding interactions are now in the range of those obtained for duplex formation via Watson-Crick hydrogen bonding interactions even if the kinetics may be quite different. Progress has been made toward developing general procedures to determine the molecular mechanisms of action of triplex-forming oligonucleotides (TFO) administered to cultured cells to provide a rational proof-of-concept for antigene strategies. The antigene strategy has reached a point where TFOs can be used to interfere with several biologic progresses (replication, transcription, recombination, repair) in relevant systems both in vitro and ex vivo.

Binding of fluorescence- and gold-labeled oligodeoxyribonucleotides to cytoplasmic intermediate filaments in epithelial and fibroblast cells

Previously, in vitro experiments have demonstrated the capacity of intermediate filaments (IFs) to associate with polyanionic compounds, including nucleic acids. To prove that this activity is also shown by IFs in quasi-intact cells, digitonin-permeabilized epithelial PtK2 and mouse fibroblast cells were treated with FITC-labeled, single-stranded oligodeoxyribonucleotides and analyzed, after indirect decoration of their IF systems with TRITC-conjugated antibodies, by fluorescence microscopy. While cytokeratin IFs exhibited a strong affinity for and exact codistribution with oligo(dG)25, vimentin IFs were less active in binding this oligonucleotide. Other oligonucleotides, like oligo(dT)25, oligo[d(GT)12G] and oligo[d(G3T2A)4G], were bound to IFs with lower efficiency. In general, the introduction of dA residues into oligo(dG)n or oligo(dGT)n tracts reduced the IF-binding potential of the nucleic acids. This, however, increased significantly upon reduction of the ionic strength to half physiological, indicating a strong electrostatic binding component. The binding reaction was often obscured by simultaneous association of the oligonucleotides with cellular membranes mostly in the perinuclear region, an activity that was largely abolished by prior cell extraction with nonionic detergent. Strongly IF-binding oligonucleotides also disassembled microtubules, presumably via their interaction with microtubule-associated proteins, but left microfilaments intact. In PtK2 cells, oligo(dG)25-loaded IFs were frequently seen coaligned with microfilaments and to cross-bridge stress fibers with the formation of rope ladder-like configurations. Employing microinjection and confocal laser scanning microscopy, association of IFs with oligonucleotides could also be visualized in intact cells. In accord with these fluorescence microscopic data, transmission electron microscopy of permeabilized cells treated with gold-conjugated oligonucleotides revealed decoration of IFs and membrane systems with gold particles, whereby in PtK2 cells these structures showed a distinctly heavier labeling than in fibroblasts. These results demonstrate that in animal cells IFs are able to bind nucleic acids and, very likely, also nucleoprotein particles and suggest that this capacity is exploited by the cells for transient storage and, in cooperation with microtubules and microfilaments, controlled transport of such material in the cytoplasm.

The collagen triple-helix structure

Recent advances, principally through the study of peptide models, have led to an enhanced understanding of the structure and function of the collagen triple helix. In particular, the first crystal structure has clearly shown the highly ordered hydration network critical for stabilizing both the molecular conformation and the interactions between triple helices. The sequence dependent nature of the conformational features is also under active investigation by NMR and other techniques. The triple-helix motif has now been identified in proteins other than collagens, and it has been established as being important in many specific biological interactions as well as being a structural element. The nature of recognition and the degree of specificity for interactions involving triple helices may differ from globular proteins. Triple-helix binding domains consist of linear sequences along the helix, making them amenable to characterization by simple model peptides. The application of structural techniques to such model peptides can serve to clarify the interactions involved in triple-helix recognition and binding and can help explain the varying impact of different structural alterations found in mutant collagens in diseased states.