iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC.

Protein hydroxylation is a posttranslational modification (PTM), in which a CH group in Pro (P) or Lys (K) residue has been converted into a COH group, or a hydroxyl group (-OH) is converted into an organic compound. Closely associated with cellular signaling activities, this type of PTM is also involved in some major diseases, such as stomach cancer and lung cancer. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of P or K, which ones can be hydroxylated, and which ones cannot? With the explosive growth of protein sequences in the post-genomic age, the problem has become even more urgent. To address such a problem, we have developed a predictor called iHyd-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition (PseAAC) and introducing the "Random Forest" algorithm to operate the calculation. Rigorous jackknife tests indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for iHyd-PseCp has been established at http://www.jci-bioinfo.cn/iHyd-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

Effect of 3D chondrocyte culturing conditions on the formation of extracellular matrix in cartilage tissue-engineering constructs.

We studied biochemical, morphological, and histological parameters of the extracellular matrix in scaffold-free tissue engineering chondrotransplants prepared from chondrocytes isolated from knee joint cartilage biopsy specimens of Haflinger horses (age 3.5-14 years) and in transplants prepared on the basis of commercial matrixes of Ethisorb® and Chondro-Gide(®). A total of 50 tissue-engineering constructs were designed and analyzed. Passage 2 cells populations were used. Mechanical stimulation during culturing of scaffold-free constructs considerably activated synthesis of the basic components of the cartilage matrix (proteoglycan concentration was 35% of the content in the native tissue, and the content of collagen-specific amino acids hydroxyproline and hydroxylysine attained 29.3 and 12.7%, respectively). The architecture of these cartilage constructs was morphologically and histologically similar to the native cartilage tissue. Insufficient support of the chondrogenesis by scaffold-based chondrotransplants and no differences between these constructs by the studied parameters were noted despite different chemical nature and structure of these scaffolds.

Effects of fish collagen peptides on collagen post-translational modifications and mineralization in an osteoblastic cell culture system.

Collagen is one of the most widely used biomaterials for tissue engineering and regenerative medicine. Fish collagen peptides (FCP) have been used as a dietary supplement, but their effects on the cellular function are still poorly understood. The objective of this study was to investigate the effects of FCP on collagen synthesis, quality and mineralization using an osteoblastic MC3T3-E1 cell culture system. Cells treated with FCP significantly upregulated the gene expression of several collagen modifying enzymes and more collagen was deposited in the cultures. Collagen in the treated group showed a greater extent of lysine hydroxylation, higher levels of hydroxylysine-aldehyde derived cross-links and accelerated cross-link maturation compared with the untreated group. Furthermore, the treated group showed accelerated matrix mineralization. These results indicate that FCP exerts a positive effect on osteoblastic cells in terms of collagen synthesis, quality and mineralization, thereby suggesting the potential utility of FCP for bone tissue engineering.

Prediction and analysis of protein hydroxyproline and hydroxylysine.

BACKGROUND: Hydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we developed a novel sequence-based method for identifying the two main types of hydroxylation sites--hydroxyproline and hydroxylysine. First, feature selection was made on three kinds of features consisting of amino acid indices (AAindex) which includes various physicochemical properties and biochemical properties of amino acids, Position-Specific Scoring Matrices (PSSM) which represent evolution information of amino acids and structural disorder of amino acids in the sliding window with length of 13 amino acids, then the prediction model were built using incremental feature selection method. As a result, the prediction accuracies are 76.0% and 82.1%, evaluated by jackknife cross-validation on the hydroxyproline dataset and hydroxylysine dataset, respectively. Feature analysis suggested that physicochemical properties and biochemical properties and evolution information of amino acids contribute much to the identification of the protein hydroxylation sites, while structural disorder had little relation to protein hydroxylation. It was also found that the amino acid adjacent to the hydroxylation site tends to exert more influence than other sites on hydroxylation determination. CONCLUSIONS/SIGNIFICANCE: These findings may provide useful insights for exploiting the mechanisms of hydroxylation.

Characterization of a complex glycoprotein whose variable metabolic clearance in humans is dependent on terminal N-acetylglucosamine content.

Glycoproteins can be cleared from circulation if they carry oligosaccharide structures that are recognized by specific receptors. High-mannose type and asialo complex oligosaccharides are cleared by the mannose and asialoglycoprotein receptors, respectively. This paper presents the protein and terminal saccharide characterization for nine batches of a glycoprotein developed for pharmaceutical use. Each of these batches was evaluated in human pharmacokinetic (PK) studies, and had similar terminal elimination half-lives, but the initial clearance of this glycoprotein varied between batches. The protein is lenercept, an immunoadhesin comprising the Fc domain of human IgG1 and two tumor necrosis factor (TNF) binding domains derived from the extracellular portion of the TNFR1(p55). Lenercept is manufactured in Chinese hamster ovary (CHO) cells and is extensively N-glycosylated but is devoid of high-mannose glycans. The pharmacokinetic variability between these lots only correlated with terminal N-acetylglucosamine and not with terminal galactose, sialic acid or any polypeptide related parameter. The data emphasize the need for appropriate analytical methods for the characterization of glycoproteins, especially those designed for long half-lives, and show that assessment of the content of all three terminal saccharides is sufficient to ensure consistency of their PK performance properties.

Melanoma cell CD44 interaction with the alpha 1(IV)1263-1277 region from basement membrane collagen is modulated by ligand glycosylation.

Invasion of the basement membrane is believed to be a critical step in the metastatic process. Melanoma cells have been shown previously to bind distinct triple-helical regions within basement membrane (type IV) collagen. Additionally, tumor cell binding sites within type IV collagen contain glycosylated hydroxylysine residues. In the present study, we have utilized triple-helical models of the type IV collagen alpha1(IV)1263-1277 sequence to (a) determine the melanoma cell receptor for this ligand and (b) analyze the results of single-site glycosylation on melanoma cell recognition. Receptor identification was achieved by a combination of methods, including (a) cell adhesion and spreading assays using triple-helical alpha1(IV)1263-1277 and an Asp(1266)Abu variant, (b) inhibition of cell adhesion and spreading assays, and (c) triple-helical alpha1(IV)1263-1277 affinity chromatography with whole cell lysates and glycosaminoglycans. Triple-helical alpha1(IV)1263-1277 was bound by melanoma cell CD44/chondroitin sulfate proteoglycan receptors and not by the collagen-binding integrins or melanoma-associated proteoglycan. Melanoma cell adhesion to and spreading on the triple-helical alpha1(IV)1263-1277 sequence was then compared for glycosylated (replacement of Lys(1265) with Hyl(O-beta-d-galactopyranosyl)) versus non-glycosylated ligand. Glycosylation was found to strongly modulate both activities, as adhesion and spreading were dramatically decreased due to the presence of galactose. CD44/chondroitin sulfate proteoglycan did not bind to glycosylated alpha1(IV)1263-1277. Overall, this study (a) is the first demonstration of the prophylactic effects of glycosylation on tumor cell interaction with the basement membrane, (b) provides a rare example of an apparent unfavorable interaction between carbohydrates, and (c) suggests that sugars may mask "cryptic sites" accessible to tumor cells with cell surface or secreted glycosidase activities.

The third activity for lysyl hydroxylase 3: galactosylation of hydroxylysyl residues in collagens in vitro.

Lysyl hydroxylase (LH, EC 1.14.11.4), galactosyltransferase (EC 2.4.1.50) and glucosyltransferase (EC 2.4.1.66) are enzymes involved in posttranslational modifications of collagens. They sequentially modify lysyl residues in specific positions to hydroxylysyl, galactosylhydroxylysyl and glucosylgalactosyl hydroxylysyl residues. These structures are unique to collagens and essential for their functional activity. Lysines and hydroxylysines form collagen cross-links. Hydroxylysine derived cross-links, usually as glycosylated forms, occur especially in weight-bearing and mineralized tissues. The detailed functions of the hydroxylysyl and hydroxylysyl linked carbohydrate structures are not known, however. Hydroxylysine linked carbohydrates are found mainly in collagens, but recent reports indicate that these structures are also present and probably have an important function in other proteins. Earlier we have shown that human LH3, but not isoforms LH1, LH2a and LH2b, possesses both LH and glucosyltransferase activity (J. Biol. Chem. 275 (2000) 36158). In this paper we demonstrate that galactosyltransferase activity is also associated with the same gene product, thus indicating that one gene product can catalyze all three consecutive steps in hydroxylysine linked carbohydrate formation. In vitro mutagenesis experiments indicate that Cys(144) and aspartates in positions 187-191 of LH3 are important for the galactosyltransferase activity. Our results suggest that manipulation of the gene for LH3 can be used to selectively alter the glycosylation and hydroxylation reactions, and provides a new tool to clarify the functions of the unique hydroxylysine linked carbohydrates in collagens and other proteins.

Different pattern of collagen cross-links in two sclerotic skin diseases: lipodermatosclerosis and circumscribed scleroderma.

Changes in the process of cross-linking of collagen molecules are associated with defects in the biomechanical stability of the extracellular matrix. Fibrosis of skin is characterized by an increase in pyridinolines, which are hydroxylysine aldehyde derived cross-links usually absent in healthy skin. In this study, we analyzed cross-links in lipodermatosclerosis and localized scleroderma to address the question whether all the mature cross-links currently characterized are increased in fibrosis in addition to the increase in pyridinolines. As psoralen plus ultraviolet A treatment leads to clinical improvement of fibrotic plaques in localized scleroderma we analyzed the cross-link content in lesional skin after bath psoralen plus ultraviolet A therapy. In skin from patients with localized scleroderma an increase in the total number of mature cross-links was found to be due to an increase in both pyridinolines and dehydro-histidinohydroxymerodesmosine. The concentration of histidinohydroxylysinonorleucine was unchanged. By contrast, the total number of mature cross-links was decreased in lipodermatosclerosis. This decrease was caused by a decrease of lysine aldehyde derived cross-links (dehydro-histidinohydroxymerodesmosine and histidinohydroxylysinonorleucine), whereas the concentration of pyridinolines increased. A decrease in the content of pyridinolines after bath psoralen plus ultraviolet A treatment was found in six out of nine patients with localized scleroderma, which might reflect a remodeling of the extracellular matrix. Our data provide evidence that sclerosis of skin is associated with either an increase in the number of cross-links per molecule of collagen or a change in the molecular nature of the cross-links formed.

Adenoviral gene transfer restores lysyl hydroxylase activity in type VI Ehlers-Danlos syndrome.

Type VI Ehlers-Danlos syndrome is a disease characterized by disturbed lysine hydroxylation of collagen. The disease is caused by mutations in lysyl hydroxylase 1 gene and it affects several organs including the cardiovascular system, the joint and musculoskeletal system, and the skin. The skin of type VI Ehlers-Danlos syndrome patients is hyperelastic, scars easily, and heals slowly and poorly. We hypothesized that providing functional lysyl hydroxylase 1 gene to the fibroblasts in and around wounds in these patients would improve healing. In this study we tested the feasibility of transfer of the lysyl hydroxylase 1 gene into fibroblasts derived from rats and a type VI Ehlers-Danlos syndrome patient (in vitro) and into rat skin (in vivo). We first cloned human lysyl hydroxylase 1 cDNA into a recombinant adenoviral vector (Ad5RSV-LH). Transfection of human type VI Ehlers-Danlos syndrome fibroblasts (about 20% of normal lysyl hydroxylase 1 activity) with the vector increased lysyl hydroxylase 1 activity in these cells to near or greater levels than that of wild type, unaffected fibroblasts. The adenoviral vector successfully transfected rat fibroblasts producing both beta-galactosidase and lysyl hydroxylase 1 gene activity. We next expanded our studies to a rodent model. Intradermal injections of the vector to the abdominal skin of rats produced lysyl hydroxylase 1 mRNA and elevated lysyl hydroxylase 1 activity, in vivo. These data suggest the feasibility of gene replacement therapy to modify skin wound healing in type VI Ehlers-Danlos syndrome patients.

Sibs affected with both Ehlers-Danlos syndrome type IV and cystic fibrosis.

We report on the unprecedented combination of two recessively inherited disorders, the kyphoscoliosis type of Ehlers-Danlos syndrome (EDS type VI) and cystic fibrosis (CF), in two sibs born to consanguineous Turkish parents. Because of failure to thrive and bronchitis CF was diagnosed in the index patient early whereas EDS VI was recognized only very late. Both patients had marked muscular hypotonia at birth, delayed gross motor development, progressive kyphoscoliosis, joint dislocations, Marfanoid habitus, hypertrophic and atrophic scars, and osteopenia. EDS VI was proven by collagen studies and the pathognomonic pattern of urinary pyridinolines. Because the genes coding for the two disorders are located on different chromosomes and a chromosomal rearrangement was excluded, we conclude that their combination is a chance association. The cardiopulmonary impairment common to both diseases makes the prognosis dismal.

Altered x-ray diffraction pattern is accompanied by a change in the mode of cross-link formation in lipodermatosclerosis.

We studied the molecular packing of collagen fibrils by x-ray diffraction in skin specimens of patients with lipodermatosclerosis and in controls. A difference in the tilt angles of the collagen molecules relative to the fiber axis is suggested by a D-stagger that is 1 nm larger in sclerotic skin than in normal skin. In parallel, the collagen cross-links in the skin specimens were analyzed, and a marked increase of both hydroxylysylpyridinoline and lysylpyridinoline, the trivalent mature cross-links characteristic of skeletal tissues, was found. The content of hydroxylysylpyridinoline and lysylpyridinoline was higher in the deep layer of the affected dermis than in the superficial dermis. This increase was always accompanied by an increase in the hydroxylysylpyridinoline/lysylpyridinoline ratio, suggesting that hydroxylysylpyridinoline is a sclerosis-associated cross-link. In addition, lysyl hydroxylation was increased in affected skin, and this increase was apparently restricted to the collagen telopeptides, which are crucial anchoring structures for lysyl dependent cross-links.

Composition and posttranslational modification of individual collagen chains from osteosarcomas and osteofibrous dysplasias.

The composition of collagen was analyzed and the degree of lysyl hydroxylation of individual collagen chains was determined in four osteosarcomas and two osteofibrous dysplasias. In addition, the tumor proliferation (number of mitoses, proliferating-nuclear-antigen-positive cells, MIB) as well as the response to chemotherapy (morphological regression grade) were checked. All tumors contained a high proportion of collagen III and, in all but one osteosarcoma, pepsin-extracted collagens I and III were overmodified. Furthermore, the proportion of diglycosides in collagen I was about four times higher than in controls. The collagen composition and modification resembled those of bones at early stages of human development. One osteosarcoma and both osteofibrous dysplasias were in the normal range of lysyl hydroxylation. There was no correlation between the collagen properties and the histopathological marker of tumor proliferation.

Amino acid analysis of collagen hydrolysates by reverse-phase high-performance liquid chromatography of 9-fluorenylmethyl chloroformate derivatives.

A recently described procedure for amino acid analyses has been modified and adapted for use in quantitating the unique mixture of products commonly found in hydrolysates of the collagens. The method involves precolumn derivatization of hydrolysates with 9-fluorenylmethyl chloroformate (FMOC-CL), chromatographic separation of the derivatives and excess reagent on a reverse-phase column, and quantitation based on the fluorescent properties of the derivatives. The method takes advantage of the ease with which stable derivatives are formed with the FMOC reagent. Using a ternary gradient system, a complete amino acid analysis with good resolution of all components can be performed within 35 min. The sensitivity of the method is comparable to levels attained by other derivatives and the fluorescence response of each derivative is linear over the total range of 1-800 pmol. Given these parameters, the method allows complete amino acid analyses to be performed on 100 ng of collagen corresponding to a single picomole of a collagen chain (Mr 100,000).

Keratoconus: I. Biochemical studies.

The present study analyses collagenous and non-collagenous components from age-matched normal and keratoconus corneas. Intact keratoconus corneas showed decreased collagen, total protein, and hydroxylysine levels, with normal reducible collagen cross-linking. Non-collagenous fractions were isolated from corneas with a 4 M guanidine procedure. As demonstrated by PAGE-silver stain, the keratoconus cornea guanidine extracts had a 75 kDa band that was absent in normal cornea guanidine extracts. In addition, there was a markedly increased level of protein, uronic acid and neutral hexose in keratoconus extracts as compared with controls. Our Western blot studies showed increased affinity for the castor-bean agglutinin (RCA120, specific for terminal galactose) in the keratoconus extracts as compared with normals. These data suggest the presence of an abnormal noncollagenous component in keratoconus corneas.

Collagen glycosylation in human granulation tissue and scar.

Some biochemical characteristics of collagen extracted from granulation tissue were studied and compared with those of normal skin and scar. By using electrophoretic techniques the type III collagen content was confirmed to be significantly greater in granulation tissue and lower in scar with respect to normal skin. The chromatographic determination of hydroxylysine (Hyl) glycosides in collagen extracted from granulation tissue showed a significant increase in both the degree of Hyl glycosylation and in the di-/monoglycoside ratio, while both parameters turned out to be lower in scar. These data suggest that the degree of Hyl glycosylation and the di-/monoglycoside ratio could represent an index of the degree of collagen fiber maturation.

Further studies of a putative cross-linking amino acid (3-deoxypyridinoline) in skin from patients with abdominal aortic aneurysms.

A recent report claimed that an amine in human skin (believed to be pyridinoline) was deficient in specimens from patients with abdominal aortic aneurysms (AAA). Further studies suggest that this work was erroneous in two respects. First, the amine has been isolated and partially characterized; the major component of the peak of interest is a deoxyanalogue of pyridinoline. It may be a collagen cross-link of some biologic importance, because it is not detectable in skin from a patient with Marfan's syndrome. Second, further studies in an additional 19 patients with AAA and an additional 13 controls suggest that this amine is abnormally abundant in skin from patients with AAA. This difference cannot be accounted for by any potential source of artifact that has been traceable. The effects of age, diabetes, sex, race, site of biopsy, and source of specimen (autopsy versus surgery) have been studied; none of these variables can account for the high ratio of pyridinolines to hydroxylysine found in skin from patients with AAA.

Measurement of changes in amino acids related to total collagen in fibrotic human liver.

In the liver, total collagen accumulation during the fibrotic or cirrhotic process was measured using a methodology based on the determination of collagen amino acids in liver biopsies from adults with alcoholic liver diseases or children with biliary atresia. The results obtained with this methodology were compared to histopathological findings. Thus, it was shown that generally the severity of hepatic injury was dependent on collagen accumulation. In biliary atresia, collagen accumulation increased with the children's age despite reconstructive surgery and restoration of biliary flow.