Molecular dynamics insights into glycosaminoglycan effects on the extracellular domains of syndecan 2 and 4 dimers.

Protein structure prediction has matured over years, particularly those which use structure templates for building a model. It can build a model with correct overall conformation in cases where appropriate templates are available. Models with the correct topology can be practically useful for limited purposes that need residue-level accuracy, but further improvement of the models can allow the models to be used in tasks that need detailed structures, such as molecular replacement in X-ray crystallography or structure-based drug screening. Thus, model refinement is an important final step in protein structure prediction to bridge predictions to real-life applications. Model refinement is one of the categories in recent rounds of critical assessment of techniques in protein structure prediction (CASP) and has recently been drawing more attention due to its realized importance. Here we report our group's performance in the refinement category in CASP12. Our method is based on inexpensive short molecular dynamics (MD) simulations in implicit solvent. Our performance in CASP12 was among the top, which was consistent with the previous round, CASP11. Our method with short MD runs achieved comparable performance with other methods that used longer simulations. Detailed analyses found that improvements typically occurred in entire regions of a structure rather than only in flexible loop regions. The remaining challenge in the structure refinement includes large conformational refinement which involves substantial motions of secondary structure elements or domains.

Proteoglycans (PG) are crucial components of the cell surface and extracellular matrix, acting as critical effectors of cellular homeostasis and cancer pathogenesis. Betaglycan (BG) is a ubiquitously expressed transmembrane PG containing a core protein domain with glycosaminoglycan (GAG) attachment sites at S534/S545 residues on its extracellular domain, to which heparan sulfate (HS) and chondroitin sulfate (CS) chains are covalently attached. BG is commonly referred to as a “part-time proteoglycan” since BG can be expressed on the cell surface with or without GAG chain modifications. BG's ectodomain can also be shed (shed-BG) from the cell surface to release a soluble form. BG is an established co-receptor for the TGF-β superfamily that modulates signaling of TGF-β members both at the cell surface and via the shed form as has been previously reported in breast cancer. Although majority of the prior work has focused on BG's core protein interactions and functions, a thorough understanding of the effects of the BG GAG chains remains lacking. We find in preliminary studies, elevated shed-BG in the ascites fluid of ovarian cancer (OVCA) patients compared to circulating levels in healthy individuals. Interestingly, analysis of the GAG chains on shed-BG from ascites fluid indicates majority of shed-BG in patient sample to be heavily modified with a higher degree of CS modification as compared to HS modifications on BG. Given the gap in knowledge on BG GAG chain functions and our observations in patients, I hypothesize that the GAG chains of BG may impact shedding and cell signaling that regulates ovarian cancer growth and metastasis. To examine the effect of GAG modifications on shedding of BG, we constructed point mutations at S534/S545 to abrogate GAG chain attachment sites on BG. These constructs were expressed in a panel of OVCA cell lines generating cell lines expressing either 1: Wild Type BG (BG-FL), 2: S534A (BG-CS), 3: S545A (BG-HS) or 4: S534A, S545A double mutant designated (∆GAG). Cellular expression of BG constructs confirmed the alterations in BG GAG chains. Evaluation of shedding of BG revealed a significant reduction in BG shedding from cells expressing unmodified BG (∆GAG) compared to cells expressing GAG modified BG despite no change in cell surface expression. To next evaluate the impact of expression of GAG modified BG on tumor cell biology, in vitro cell proliferation, cell invasion and migration assays were conducted. We find that both cell proliferation and invasion of BG-CS and BG-HS mutants were significantly lower as compared to BG-∆GAG mutant. These findings together suggest distinct roles for the different modified forms of BG in promoting BG shedding from the cell surface and tumor cell behavior. Additional data on the effect of BG chain modification on TGF-β, Wnt, and FGF2 signaling modulation will also be presented. Based on our findings we propose that the, GAG chains of BG regulate core protein shedding and growth factor signaling thereby impacting OVCA cell biology.

Expression of decorin using the vaccinia virus/T7 expression system resulted in secretion of two distinct glycoforms: a proteoglycan substituted with a single chondroitin sulfate chain and N-linked oligosaccharides and a core protein glycoform substituted with N-linked glycans but without a glycosaminoglycan chain. In this report, we have addressed two distinct questions. What is the rate-limiting step in glycosaminoglycan synthesis? Is glycosylation with either N-linked oligosaccharides or glycosaminoglycan required for secretion of decorin? N-terminal sequencing of the core protein glycoform, the addition of benzyl-beta-d-xyloside, and a UDP-xylose: core protein beta-d-xylosyltransferase activity assay show that xylosylation is a rate-limiting step in chondroitin sulfate biosynthesis. Decorin can be efficiently secreted with N-linked oligosaccharides alone or with a single chondroitin sulfate chain alone; however, there is severely impaired secretion of core protein devoid of any glycosylation. A decorin core protein mutant devoid of N-linked oligosaccharide attachment sites will not be secreted by Chinese hamster ovary cells deficient in xylosyltransferase or by parental Chinese hamster ovary wild type cells if the xylosyltransferase recognition sequence is disrupted. This finding suggests that quality control mechanisms sensitive to an absence of N-linked oligosaccharides can be abrogated by interaction of the core protein with the glycosaminoglycan synthetic machinery. We propose a model of regulation of decorin secretion that has several components, including appropriate substitution with N-linked oligosaccharides and factors involved in glycosaminoglycan synthesis.

Proteoglycans (PGs) are complex glycoconjugates that are composed of a core protein and glycosaminoglycan (GAG) chains. The GAG chains are covalently bound to the serine residue of the core protein via a common core tetrasaccharide (glucuronic acid-galactose-galactose-xylose) as the linkage region. The endo-type glycosidases were investigated with the aim of performing enzymatic synthesis of PG. It is known that many glycosidases catalyze a transglycosylation reaction as a re-verse reaction in addition to their main hydrolysis reaction. Therefore, the transglycosylation mechanism of testicular hyaluronidase, which is an endo-β-N-acetylhexosaminidase, was investi-gated. It was found that disaccharides are successively released from the nonreducing terminal of a donor hyaluronic acid (HA) and rapidly transferred to the nonreducing terminal of an acceptor HA. It was also found that testicular hyaluronidase also acted on chondroitin (Ch), chondroitin 4-sulfate (Ch4S), chondroitin 6-sulfate (Ch6S), and other GAGs as well as HA. Therefore, by repeating the transglycosylation using suitable combinations of Ch, Ch4S, Ch6S, and other GAGs as acceptors and donors, it was possible to custom synthesize GAGs. It is likely that application of this system would facilitate artificial reconstruction of GAG moieties of PG. Subsequently, we found that an endo-β-xylosidase activity was present in rabbit liver. This enzyme specifically hydrolyzed the xylose-serine linkage between the core protein and GAG chains of PG, thereby allowing intact GAGs to be obtained. At present, we are studying the enzymatic transfer of the reconstructed GAG chains to the core protein using the transglycosylation activity of this enzyme.

Proteoglycans consist of a core protein and an associated glycosaminoglycan (GAG) chain of heparan sulfate, chondroitin sulfate, dermatan sulfate or keratan sulfate, which are attached to a serine residue. The core proteins of cell surface proteoglycans may be transmembrane, e.g., syndecan, or GPI-anchored, e.g., glypican. Many different cell surface and matrix proteoglycan core proteins are expressed in the mammary gland and in mammary cells in culture. The level of expression of these core proteins, the structure of their GAG chains, and their degradation are regulated by many of the effectors that control the development and function of the mammary gland. Regulatory proteins of the mammary gland that bind GAG include many growth factors and morphogens (fibroblast growth factors, hepatocyte growth factor/scatter factor, members of the midkine family, wnts), matrix proteins (collagen, fibronectin, and laminin), enzymes (lipoprotein lipase) and microbial surface proteins. Structural diversity within GAG chains ensures that each protein-GAG interaction is as specific as necessary and a number of sequences of saccharides that recognize individual proteins have been elucidated. The GAG-protein interactions serve to regulate the signal output of growth factor receptor tyrosine kinase and hence cell fate as well as the storage and diffusion of extracellular protein effectors. In addition, GAGs clearly coordinate stromal and epithelial development, and they are active participants in mediating cell-cell and cell-matrix interactions. Since a single proteoglycan, even if it carries a single GAG chain, can bind multiple proteins, proteoglycans are also likely to act as multireceptors which promote the integration of cellular signals.

Effect of glypican-1 covalently attached chains on turkey myogenic satellite cell proliferation, differentiation, and fibroblast growth factor 2 responsiveness

Reactive oxygen species (ROS) overproduction and oxidative stress are increasingly being implicated in the extracellular matrix (ECM) degradation associated with chronic inflammatory conditions, such as periodontal diseases. The present study investigated the effects of ROS exposure on the proteoglycans of gingival tissues, utilizing an in vitro model system comprised of supra-physiological oxidant concentrations, to ascertain whether gingival proteoglycan modification and degradation by ROS contributed to the underlying mechanisms of ECM destruction during active gingivitis. Proteoglycans were purified from ovine gingival tissues and exposed to increasing H2O2 concentrations or a hydroxyl radical (·OH) flux for 1 h or 24 h, and ROS effects on proteoglycan core proteins and sulfated glycosaminoglycan (GAG) chains were assessed. ROS were capable of degrading gingival proteoglycans, with ·OH species inducing greater degradative effects than H2O2 alone. Degradative effects were particularly manifested as amino acid modification, core protein cleavage, and GAG chain depolymerization. Proteoglycan core proteins were more susceptible to degradation than GAG chains with H2O2 alone, although core proteins and GAG chains were both extensively degraded by ·OH species. Proteoglycan exposure to ·OH species for 24 h induced significant core protein amino acid modification, with decreases in glutamate, proline, isoleucine, and leucine; and concomitant increases in serine, glycine, and alanine residues. As clinical reports have previously highlighted proteoglycan core protein degradation during chronic gingivitis, whereas their sulfated GAG chains remain relatively intact, these findings potentially provide further evidence to implicate ROS in the pathogenesis of active gingivitis, complementing the enzymic mechanisms of periodontal tissue destruction already established.

Two small interstitial dermatan sulfate-containing proteoglycans, biglycan and decorin, are present in extracellular matrices of skin, tendon, ligament, and cartilage. We investigated the effects of biglycan and decorin on the inhibition of alpha-thrombin by the serine proteinase inhibitor heparin cofactor II. In solution, heparin cofactor II inhibition of thrombin is accelerated by intact biglycan or decorin and by the dermatan sulfate-containing glycosaminoglycan (GAG) chains prepared from the proteoglycans, while core protein from cartilage biglycan had no effect. L-Iduronic acid-rich skin decorin and GAG chains had a greater accelerating effect than proteoglycan and GAG chains from cartilage that had lower L-iduronic acid content. Treatment of skin decorin and GAG chains with chondroitinase ABC totally eliminated the ability of these compounds to accelerate thrombin inhibition by heparin cofactor II suggesting that dermatan sulfate was responsible for this action. Both biglycan and decorin bound to type V collagen in a saturable and specific manner. Biglycan, decorin, and core protein from biglycan competed for decorin binding to the type V collagen, while only the intact proteoglycans competed for biglycan binding. When bound to type V collagen, both biglycan and decorin accelerated the heparin cofactor II/thrombin inhibition reaction as efficiently as the proteoglycans in solution. Our results demonstrate that heparin cofactor II in the presence of biglycan or decorin bound to type V collagen provides a "thromboresistant surface," further suggesting a physiological function for these proteins in regulating the extravascular activities of thrombin.

Syndecan-4 is a cell membrane proteoglycan composed of a transmembrane core protein and substituted glycosaminoglycan (GAG) and N-linked glycosylated (N-glycosylated) chains. The core protein has three domains: extracellular, transmembrane and cytoplasmic domains. The GAG and N-glycosylated chains and the cytoplasmic domain of syndecan-4, especially the amino acids: Ser(178) and Tyr(187) are critical in regulation of turkey satellite cell growth and development. How these processes are regulated is still unknown. The objective of the current study was to determine whether the syndecan-4 GAG and N-glycosylated chains and the cytoplasmic domain functions through modulating focal adhesion formation and apoptosis. Twelve mutant clones were generated: a truncated syndecan-4 without the cytoplasmic domain with or without GAG and N-glycosylated chains, and Ser(178) and Tyr(187) mutants with or without GAG and N-glycosylated chains. The wild type syndecan-4 and all of the syndecan-4 mutants were transfected into turkey myogenic satellite cells after which cell apoptosis and focal adhesion formation were measured. Syndecan-4 increased cell membrane localization of β1 integrin and the activity of focal adhesion kinase (FAK) whereas the cytoplasmic domain mutation decreased the phosphorylation of FAK. However, syndecan-4 and syndecan-4 mutants did not influence cell apoptosis. They also had no effect on vinculin or paxillin-containing focal adhesion formation. These results suggested that the syndecan-4 cytoplasmic domain plays an important role in regulating FAK activity and β1 integrin cell membrane localization but not cell apoptosis and vinculin or paxillin-containing focal adhesion formation.

Structure, Metabolism, and Tissue Roles of Chondroitin Sulfate Proteoglycans

The structural characteristics of proteoglycans produced by seminiferous peritubular cells and by Sertoli cells are defined. Peritubular cells secrete two proteoglycans designated PC I and PC II. PC I is a high molecular mass protein containing chondroitin glycosaminoglycan (GAG) chains (maximum 70 kDa). PC II has a protein core of 45 kDa and also contains chondroitin GAG chains (maximum 70 kDa). Preliminary results imply that PC II may be a degraded or processed form of PC I. A cellular proteoglycan associated with the peritubular cells is described which has properties similar to those of PC I. Sertoli cells secrete two different proteoglycans, designated SC I and SC II. SC I is a large protein containing both chondroitin (maximum 62 kDa) and heparin (maximum 15 kDa) GAG chains. Results obtained suggest that this novel proteoglycan contains both chondroitin and heparin GAG chains bound to the same core protein. SC II has a 50-kDa protein core and contains chondroitin (maximum 25 kDa) GAG chains. A proteoglycan obtained from extracts of Sertoli cells is described which contains heparin (maximum 48 kDa) GAG chains. In addition, Sertoli cells secrete a sulfoprotein, SC III, which is not a proteoglycan. SC III has properties similar to those of a major Sertoli cell-secreted protein previously defined as a dimeric acidic glycoprotein. The stimulation by follicle-stimulating hormone of the incorporation of [35S]SO2(-4) into moieties secreted by Sertoli cells is shown to represent an increased production or sulfation of SC III (i.e. dimeric acidic glycoprotein), and not an increased production or sulfation of proteoglycans. Results are discussed in relation to the possible functions of proteoglycans in the seminiferous tubule.

Among the four members of the syndecan family there exists a high level of divergence in the ectodomain core protein sequence. This has led to speculation that these core proteins bear important functional domains. However, there is little information regarding these functions, and thus far, the biological activity of syndecans has been attributed largely to their heparan sulfate chains. We have previously demonstrated that cell surface syndecan-1 inhibits invasion of tumor cells into three-dimensional gels composed of type I collagen. Inhibition of invasion is dependent on the syndecan heparan sulfate chains, but a role for the syndecan-1 ectodomain core protein was also indicated. To more closely examine this possibility and to map the regions of the ectodomain essential for syndecan-1-mediated inhibition of invasion, a panel of syndecan-1 mutational constructs was generated, and each construct was transfected individually into myeloma tumor cells. The anti-invasive effect of syndecan-1 is dramatically reduced by deletion of an ectodomain region close to the plasma membrane. Further mutational analysis identified a stretch of 5 hydrophobic amino acids, AVAAV (amino acids 222-226), critical for syndecan-1-mediated inhibition of cell invasion. This invasion regulatory domain is 26 amino acids from the start of the transmembrane domain. Importantly, this domain is functionally specific because its mutation does not affect syndecan-1-mediated cell binding to collagen, syndecan-1-mediated cell spreading, or targeting of syndecan-1 to specific cell surface domains. This invasion regulatory domain may play an important role in inhibiting tumor cell invasion, thus explaining the observed loss of syndecan-1 in some highly invasive cancers.

Proteoglycans (PGs), a class of carbohydrate-modified proteins, are present in essentially all metazoan organisms investigated to date. PGs are composed of glycosaminoglycan (GAG) chains attached to various core proteins and are important for embryogenesis and normal homeostasis. PGs exert many of their functions via their GAG chains and understanding the details of GAG-ligand interactions has been an essential part of PG research. Although PGs are also involved in many diseases, the number of GAG-related drugs used in the clinic is yet very limited, indicating a lack of detailed structure-function understanding. Structural analysis of PGs has traditionally been obtained by first separating the GAG chains from the core proteins, after which the two components are analyzed separately. While this strategy greatly facilitates the analysis, it precludes site-specific information and introduces either a “GAG” or a “core protein” perspective on the data interpretation. Mass-spectrometric (MS) glycoproteomic approaches have recently been introduced, providing site-specific information on PGs. Such methods have revealed a previously unknown structural complexity of the GAG linkage regions and resulted in identification of several novel CSPGs and HSPGs in humans and in model organisms, thereby expanding our view on PG complexity. In light of these findings, we discuss here if the use of such MS-based techniques, in combination with various functional assays, can also be used to expand our functional understanding of PGs. We have also summarized the site-specific information of all human PGs known to date, providing a theoretical framework for future studies on site-specific functional analysis of PGs in human pathophysiology.

Decorin, the main proteoglycan in skin, has a small size with a core protein of ∼ 40kDa and one chondroitin sulfate/dermatan sulfate glycosaminoglycan (GAG) chain. The main function of decorin is to regulate the collagen matrix assembly. Decorin is distributed along collagen fibrils with the core protein and the decorin GAG chain controls the distance between the collagen fibrils. Reducing the length of the decorin GAG chain reduces the distance between the collagen fibrils. Age-related changes in decorin are apparent in the GAG chain in respect to the molecular size and sulfate position but not in the core protein. Structural changes in the decorin GAG chain may be involved in changes in collagen matrix assembly during the aging process.

We have previously reported that liver sinusoidal endothelial cells (LSECs) are responsible for the clearance of monocyte chondroitin sulfate proteoglycan serglycin from the circulation (Øynebråten et al.(2000) J. Leukocyte Biol. 67; 183-188). The aim of the present study was to investigate the kinetics of degradation of endocytosed serglycin in primary cultures of LSECs. The final degradation products of serglycin labelled biosynthetically in the glycosaminoglycan (GAG) chains with [3H] in the acetyl groups of N-acetyl galactosamine residues, [14C] in the pyranose rings, or [35S] in the sulfate groups were identified as[3H]-acetate, [14C]-lactate and [35S]-sulfate. Comparison of the rate of release of degradation products from the cells after endocytosis of serglycin labelled chemically with 125I in the tyrosine residues, or biosynthetically with [35S] or [3H] in the sulfate or acetyl groups, respectively, showed that 125I appeared more rapidly in the medium than [35S]-sulfate and [3H]-acetate. Judging from the speed of appearance of free 125I both intracellularly and in the medium, the core protein is degraded considerably more rapidly than the GAG chains. Desulfation of the GAG chains starts after the GAG chains are released from the core protein. Generation of lactate and acetate as the final products from degradation of the carbon skeleton of the GAG chains indicates that catabolism of endocytosed macromolecules in LSECs proceeds anaerobically.