STRUCTURAL CHARACTERISATION OF 5-HYDROXYTRYPTAMINE2A RECEPTOR IN HOMO SAPIENS BY IN - SILICO METHOD

Objective: Structural characterization of 5-hydroxytryptamine (5-HT)2A receptor in homo sapiens using in silico method.Methods: In silico approach has particularly providing a realistic representation needed to understand the fundamental molecular structure of a serotonin receptor. The structure has been generated using Swiss model, Modeller 9.14, Phyre2, and Geno three-dimensional, which was visualized using PyMol, and validated by Procheck and ERRAT analysis along with the values of different secondary structures mapping to diverse sections of the Ramachandran plot.Results: We compared all different models. Further structural analysis suggested that the structure of 5-HT2A is a monomer with 18 alpha helices, seven beta sheets, and one disulfide bridge. There is no signal peptide region in the protein sequence. The structure contains mostly polar and aromatic amino acid as suggested by using hydropathy plot. However, in both partitioning systems bilayer to water and water to bilayer, there are some hydropathy predicted segments, which are also transmembrane segments. Finally, the pore features, including diameter profile, size, and shape, were determined by porewalker, and the shape of the pore was found to be UDSD.Conclusion: This study suggested that 5-HT2A receptor interaction with its natural ligand serotonin and other inhibitor compounds would further additional information about G protein-coupled receptors. The 5-HT2A receptor could be an important target for therapeutics development.

Cloning, expression, and characterization of the trout cardiac Na+/Ca2+exchanger

Isoform 1 of the cardiac Na+/Ca2+exchanger (NCX1) is an important regulator of cytosolic Ca2+ concentration in contraction and relaxation. Studies with trout heart sarcolemmal vesicles have shown NCX to have a high level of activity at 7°C, and this unique property is likely due to differences in protein structure. In this study, we describe the cloning of an NCX (NCX-TR1) from a Lambda ZAP II cDNA library constructed from rainbow trout ( Oncorhynchus mykiss) heart RNA. The NCX-TR1 cDNA has an open reading frame that codes for a protein of 968 amino acids with a deduced molecular mass of 108 kDa. A hydropathy plot indicates the protein contains 12 hydrophobic segments (of which the first is predicted to be a cleaved leader peptide) and a large cytoplasmic loop. By analogy to NCX1, NCX-TR1 is predicted to have nine transmembrane segments. The sequences demonstrated to be the exchanger inhibitory peptide site and the regulatory Ca2+ binding site in the cytoplasmic loop of mammalian NCX1 are almost completely conserved in NCX-TR1. NCX-TR1 cRNA was injected into Xenopus oocytes, and after 3–4 days currents were measured by the giant excised patch technique. NCX-TR1 currents measured at ∼23°C demonstrated Na+-dependent inactivation and Ca2+-dependent activation in a manner qualitatively similar to that for NCX1 currents.

Mapping B cell epitopes in Goodpasture's disease.

The target antigen of the pathogenic autoantibodies in Goodpasture's disease is the noncollagenous domain of the alpha 3 chain of type IV collagen. A panel of membrane-bound peptides was used to identify antibody-binding regions within the protein, and the significance of the binding by inhibition studies using soluble peptides, and by a structural analysis of the antigen, was confirmed. A total of 117 overlapping 12-mer peptides spanning the entire antigen was simultaneously synthesized as individual spots on a cellulose membrane. All nine patients' sera bound to the membrane, with a conserved pattern of peptides recognized by all sera. Inhibition studies were performed using a panel of overlapping 20-mer peptides, also spanning the entire antigen. Peptides from the regions that bound IgG were able to inhibit the binding of autoantibodies to native antigen. Predictions of the secondary structure of the noncollagenous domain of the alpha 3 chain of type IV collagen were performed by a conventional hydropathy plot and by multiple alignment of homologous alpha chains of type IV collagen and comparison with a structural data base. The core peptides binding and inhibiting Goodpasture's antibodies were predicted to be surface exposed and antigenic. Thus, the conformational epitope(s) of the Goodpasture antigen can be mapped using linear peptides.

Alternative splicing of ClC-6 (a member of the CIC chloride-channel family) transcripts generates three truncated isoforms one of which, ClC-6c, is kidney-specific

ClC-6 is a protein that structurally belongs to the family of ClC-type chloride channels. We now report the identification of three additional ClC-6 isoforms that are truncated because of alternative splicing. We have isolated, from human K562 cells, four types of ClC-6 cDNAs that encode four distinct ClC-6 protein isoforms. ClC-6a (869 amino acids) corresponds to the previously published ClC-6 protein [Brandt and Jentsch (1995) FEBS Lett. 377, 15–20] and it has a canonical ClC structure. However, ClC-6b (320 amino acids), ClC-6c (353 amino acids) and ClC-6d (308 amino acids) are truncated at their C-termini. Hydropathy-plot analysis indicates that the shortened isoforms contain maximally four (ClC-6b and -6d) or seven (ClC-6c) transmembrane domains. Sequence analysis of a human genomic ClC-6 fragment indicates that the cDNA variability arises from alternative splicing at two different positions: the first alternative site consists of an intron flanked by two alternative donor sites and two alternative acceptor sites, the second being due to an exon that is optionally included or excluded. Reverse-transcription-PCR analysis of ClC-6 expression in human cell lines and tissues shows that the majority (83%) of ClC-6 mRNAs consists of ClC-6a or ClC-6c messengers. Furthermore, in a mouse tissue panel, the ClC-6a mRNA has a relatively broad tissue expression pattern, since it could be detected in brain, kidney, testis, skeletal muscle, thymus and pancreas. In contrast, expression of ClC-6c is more restricted, since it was only detected in kidney.

Cloning and expression of a renal Na-Pi cotransport system from flounder

Starting with the recently published sequence of the rat renal Na-Pi cotransport system, we have cloned a corresponding cDNA from the kidney of winter flounder (Pseudopleuronectes americanus), designated flounder NaPi-II. Expression of the cognate in vitro transcribed RNA in Xenopus laevis oocytes stimulated Na-dependent Pi transport specifically and in a time- and dose-dependent manner. Apparent affinities of Na and Pi, as well as the pH dependency, were very similar to those found for the mammalian systems. The flounder NaPi-II cDNA is 2,424 base pairs long and encodes a protein of 637 amino acids. The hydropathy plot predicts eight transmembrane spanning domains. In these regions the flounder NaPi-II-deduced protein shows high homology (approximately 80%, identity, approximately 92% similarity) with the amino acid sequences reported for mammalian NaPi-II proteins. However, in the hydrophilic parts of flounder NaPi-II protein, only minimal similarity could be found between fish and mammalian systems (30% homology, 45% similarity). Northern blot analysis with flounder NaPi-II cDNA as a probe confirmed this finding: even under nonstringent washing conditions, no cross-hybridization with mRNA from rat renal cortex was observed. Interestingly, flounder intestine was found to contain high levels of mRNA corresponding to NaPi-II. Supplementary bands of 1.9 and 4.2 kb were observed on Northern blots of renal and intestinal tissue. The close functional relationship of the flounder NaPi-II protein with the previously described Na-Pi cotransport systems and the pronounced differences on the level of their primary structures provide the tools for detailed structure-function analysis of Na-Pi cotransport.

Sequence Analysis of the D1 and D2 Reaction Center Proteins of Photosystem II

A compilation of 38 sequences for the D1 and 15 sequences for the D 2 reaction center pro­teins of photosystem II is presented. The sequences have been compared and a similarity index that takes into account the degree of conservation and the quality of the changes in each posi­tion has been calculated. The similarity index is used to identify and describe functionally im­portant domains in the D1 / D2 heterodimer. Comparative hydropathy plot are presented for the aminoacid sidechains that constitute the binding domain of the tyrosine radicals, TyrZ and TyrD, in photosystem II. The structure around TyrZ is more hydrophilic than the structure around TyrD. The hydrophilic residues are clustered in the part of the binding pocket for TyrZ that is turned towards the lumenal side of the thylakoid membrane. Most prominent is the presence of two conserved carboxylic am inoacids, D1-Asp 170 and D1-Glu 189. Their respec­tive carboxyl-groups come close in space and are proposed to constitute a metal binding site together with D1-Gln 165. The distance between the proposed metal binding site and the cen­ter of the ring of TyrZ is approximately 7Å . The cavity that constitutes the binding site for TyrD is composed of residues from the D 2 protein. Its character is more hydrophobic than the TyrZ site and the environment around TyrD lacks the cluster of putative metal binding side­-chains.