A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum

Menéndez‐Arias, Luis; Gómez-Gutiérrez, Julián; García-Ferrández, Miguel; García‐Tejedor, Álvaro J.; Morán, Federico

doi:10.1093/bioinformatics/4.4.479

Cited by 19 publications

(18 citation statements)

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“…Standard conditions were 25 mM Na 3 PO 4 , 150 mM NaCl, pH 6.0, using a 0.2-cm path length cuvette and with a water bath at 10°C. Then the spectra were analyzed using the Menendez-Arias program (23).…”

Section: Determination Of the Native Molecular Size By Electrophoresimentioning

confidence: 99%

Self-assembly and Supramolecular Organization of EMILIN

Mongiat¹,

Mungiguerra²,

Bot³

et al. 2000

Journal of Biological Chemistry

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The primary structure of human Elastin microfibril interface-located protein (EMILIN), an elastic fiber-associated glycoprotein, consists of a globular C1q domain (gC1q) at the C terminus, a short collagenous stalk, a long region with a high potential for forming coiled-coil ␣ helices, and a cysteine-rich N-terminal sequence. It is not known whether the EMILIN gC1q domain is involved in the assembly process and in the supramolecular organization as shown for the similar domain of collagen X. By employing the yeast two-hybrid system the EMILIN gC1q domains interacted with themselves, proving for the first time that this interaction occurs in vivo. The gC1q domain formed oligomers running as trimers in native gels that were less stable than the comparable trimers of the collagen X gC1q domain since they did not withstand heating. The collagenous domain was trypsin-resistant and migrated at a size corresponding to a triple helix under native conditions. In reducing agarose gels, EMILIN also migrated as a trimer, whereas under non-reducing conditions it formed polymers of many millions of daltons. A truncated fragment lacking gC1q and collagenous domains assembled to a much lesser extent, thus deducing that the C-terminal domain(s) are essential for the formation of trimers that finally assemble into large EMILIN multimers.Elastin microfibril interface-located protein (EMILIN) belongs to the C1q/TNF 1 superfamily of proteins (1) and is a considerable component of the elastic fiber system. Elastic fibers confer the properties of resiliency and elastic recoil to connective tissues and are secreted in the extracellular matrix (ECM) of many tissues in various forms. In the elastic ligaments they are deposited as solid branching and unbranching fine and thick rod-like fibers, in the blood vessels as concentric sheets of lamellae, in the elastic cartilages as a three-dimensional meshwork of fine fibrils, and in skin and lung as a combination of these (2). As previously studied in the chick model, the major characteristics of EMILIN, first extracted by means of denaturating and reducing agents, are as follows. It is preferentially extracted from tissues using buffers containing guanidine HCl and reducing agents; it forms a fibrillar network in the ECM of in vitro grown smooth muscle cells and fibroblasts and in the ECM of several tissues including blood vessels, skin, heart, lung, kidney, and cornea; it codistributes with elastin in most sites (3-7); it is a component of elastic fibers being mainly localized at the interface between amorphous elastin and the surrounding microfibrils (8); finally and more important for the functional significance of EMILIN, the process of in vitro elastin deposition was perturbed by the addition of anti-EMILIN antibodies to the culture medium suggesting that this protein plays a leading role during the elastic fiber formation process (8).Recently, the primary structure of the human EMILIN has been elucidated (1). The mature form of this multimodular protein consists of 996 amino acids and d...

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Section: Determination Of the Native Molecular Size By Electrophoresimentioning

confidence: 99%

Self-assembly and Supramolecular Organization of EMILIN

Mongiat¹,

Mungiguerra²,

Bot³

et al. 2000

Journal of Biological Chemistry

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“…7) exhibited a classic ␤-sheet CD spectrum with a minimum at 217 nm. The evaluation of the content in ␤-sheet conformation for the peptide using the Menendez-Arias program (27) gives a value higher than 70%, therefore confirming that also the EMILIN gC1q-like domain fits very well with the structure determined for ACRP-30/AdipoQ (50). Cell adhesion to fibronectin was high and comparable for all cell lines with a cell binding of about 90%, the EMILIN gC1q-like domain promoted a high level of adhesion of SK-UT-1 cells, whereas HT1080 were negative, and SK-LMS-1 bound with a low percentage (Fig.…”

Section: Purification and Peptide Sequences Of Chick Emilin-amentioning

confidence: 99%

EMILIN, a Component of the Elastic Fiber and a New Member of the C1q/Tumor Necrosis Factor Superfamily of Proteins

Doliana

Mongiat

Bucciotti

et al. 1999

Journal of Biological Chemistry

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EMILIN (elastin microfibril interface located protein)is an extracellular matrix glycoprotein abundantly expressed in elastin-rich tissues such as blood vessels, skin, heart, and lung. It occurs associated with elastic fibers at the interface between amorphous elastin and microfibrils. Avian EMILIN was extracted from 19-dayold embryonic chick aortas and associated blood vessels and purified by ion-exchange chromatography and gel filtration. Tryptic peptides were generated from EMI-LIN and sequenced, and degenerate inosine-containing oligonucleotide primers were designed from some peptides. A set of primers allowed the amplification of a 360-base pair reverse transcription polymerase chain reaction product from chick aorta mRNA. A probe based on a human homologue selected by comparison of the chick sequence with EST data base was used to select overlapping clones from both human aorta and kidney cDNA libraries. Here we present the cDNA sequence of the entire coding region of human EMILIN encompassing an open reading frame of 1016 amino acid residues. There was a high degree of homology (76% identity and 88% similarity) between the chick C terminus and the human sequence as well as between the N terminus of the mature chick protein where 10 of 12 residues, as determined by N-terminal sequencing, were identical or similar to the deduced N terminus of human EMILIN. The domain organization of human EMILIN includes a C1q-like globular domain at the C terminus, a collagenous stalk, and a longer segment in which at least four heptad repeats and a leucine zipper can be identified with a high potential for forming coiled-coil ␣ helices. At the N terminus there is a cysteine-rich sequence stretch similar to a region of multimerin, a platelet and endothelial cell component, containing a partial epidermal growth factor-like motif. The native state of the recombinantly expressed EMILIN C1q-like domain to be used in cell adhesion was determined by CD spectra analysis, which indicated a high value of ␤-sheet conformation. The EMILIN C1q-like domain promoted a high cell adhesion of the leiomyosarcoma cell line SK-UT-1, whereas the fibrosarcoma cell line HT1080 was negative.

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“…The melting curve was analyzed according to [18]. Spectra were analyzed using the program of Menendez-Arias et al [19]. Isothermal unfolding of TTF-1HD was achieved by adding increasing volumes of 8 M urea up to a final volume of 500 ~1.…”

Section: Circular Dichroism Andbuorescence Studiesmentioning

confidence: 99%

Analysis of the conformation and stability of rat TTF‐1 homeodomain by circular dichroism

et al. 1994

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The conformational stability of TTF-IHD has been determined by CD-monitored thermal denaturation and isothermal urea unfolding studies. The Gibbs free energy of stabilization found are 1.44 and 1.26 kcal.mol-', respectively. TTF-1HD exhibits a T, of 42°C and a AC, of 80 cal.mol-' K-' indicating that TTF-IHD, when free in solution, is a mobile flexible segment folded into loose helices. Such a flexibility would be relevant for the DNA-binding function of this homeodomain. In fact, a small reduction of the a-helical content of TTF-1HD significally modifies its DNA-binding activity.

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A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum

Cited by 19 publications

References 0 publications

Self-assembly and Supramolecular Organization of EMILIN

Self-assembly and Supramolecular Organization of EMILIN

EMILIN, a Component of the Elastic Fiber and a New Member of the C1q/Tumor Necrosis Factor Superfamily of Proteins

Analysis of the conformation and stability of rat TTF‐1 homeodomain by circular dichroism

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