Showing papers on "Protein primary structure published in 2017"

Amino Acids, Peptides, and Proteins

Abstract: The amino acid constituents are linked to each other in a linear sequence via substituted amide bonds. Unlike the glycosidic bonds in polysaccharides and phosphodiester bonds in nucleic acids, which are single bonds, the substituted amide linkage in proteins is a partial double bond, which further underscores the unique structural property of protein polymers. This chapter discusses both desirable and undesirable effects of food processing on proteins. It describes the effects of heat treatments on chemical changes in, and functional properties of proteins. The diverse biological functions of proteins can be categorized as enzyme catalysts, structural proteins, contractile proteins, electron transporters, ion pumps, hormones, transfer proteins, antibodies, storage proteins, and toxins. The primary structure of a protein refers to the linear sequence in which the constituent amino acids are covalently linked through amide bonds, also known as peptide bonds. Quaternary structure refers to the spatial arrangement of a protein when it contains more than one polypeptide chain.

Spontaneous H-2 mutants provide evidence that a copy mechanism analogous to gene conversion generates polymorphism in the major histocompatibility complex (protein sequence/restriction endonuclease analysis/genetic hypothesis)

Abstract: The analysis of H-2K products from sponta- neously generated major histocompatibility complex (MHC) mu- tants and of the primary structure of other class I antigens suggests the genetic hypothesis that diversity in the MHC results from a copy mechanism analogous to gene conversion. The hypothesis was tested by making precise structural predictions about three partially characterized MHC mutants (bml, bm3, and bm8). The predictions were based on consensus sequences among class I genes that differ from H-2Kb in the same region of the molecule as do the Kb mutants. In two cases (bm3 and bm8) we successfully predicted the correct amino acid substitution at positions known to be altered but for which the specific nature of the substitution had not been determined. In two additional cases (bml and bm8) we predicted and found both new mutation sites and the specific amino acid substitutions. The positions and identifications of the variant amino acids were determined by radiolabeled amino acid sequence analysis and DNA restriction endonuclease analysis. The interaction of MHC genes through a copy mechanism to generate diversity permits the introduction of multiple nucleotide base sub- stitutions into class I sequences by a single genetic event. Such a mechanism may account in part for the large structural divergence among alleles of MHC loci and the high degree of MHC poly-

3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy.

Abstract: Orchestration of the multiple enzymes engaged in O-mannose glycan synthesis provides a matriglycan on α-dystroglycan (α-DG) which attracts extracellular matrix (ECM) proteins such as laminin. Aberrant O-mannosylation of α-DG leads to severe congenital muscular dystrophies due to detachment of ECM proteins from the basal membrane. Phosphorylation at C6-position of O-mannose catalyzed by protein O-mannosyl kinase (POMK) is a crucial step in the biosynthetic pathway of O-mannose glycan. Several mis-sense mutations of the POMK catalytic domain are known to cause a severe congenital muscular dystrophy, Walker-Warburg syndrome. Due to the low sequence similarity with other typical kinases, structure-activity relationships of this enzyme remain unclear. Here, we report the crystal structures of the POMK catalytic domain in the absence and presence of an ATP analogue and O-mannosylated glycopeptide. The POMK catalytic domain shows a typical protein kinase fold consisting of N- and C-lobes. Mannose residue binds to POMK mainly via the hydroxyl group at C2-position, differentiating from other monosaccharide residues. Intriguingly, the two amino acid residues K92 and D228, interacting with the triphosphate group of ATP, are donated from atypical positions in the primary structure. Mutations in this protein causing muscular dystrophies can now be rationalized.

In silico analysis, structure modeling and phosphorylation site prediction of vitellogenin protein from Gibelion catla

Abstract: Vitellogenin is an egg yolk precursor protein expressed in the females of nearly all oviparous species including fish, amphibians, reptiles, birds, most invertebrates and monotremes .In the present study using bioinformatics tools and in silico modeling and analysis of Vitellogenin protein sequences of Gibelion catla was conducted. Primary structure prediction and physicochemical characterization were performed by computing theoretical isoelectric point (pI) 9.03, molecular weight 144862.03 Da, extinction co-efficient 78325, instability index 42.86 and aliphatic index 113.01. Grand Average of hydropathicity (GRAVY) was computed 0.212. Secondary structure assessment of Vitellogenin protein of carp Gibelion catla using GORIV reveals greater percentage of residues as alpha helix and random coils against the beta sheets. After performing homology modeling using Swiss model, a 3D structure of Vitellogenin of Gibelion catla have been predicted from its amino acid sequence. After the prediction structure has been validated through various validation tools. This homology modeling based structure will provide an insight to its functional aspects and further studies which are based on tertiary structure of protein.

Affinity labelling in situ of the bL12 protein on E. coli 70S ribosomes by means of a tRNA dialdehyde derivative.

Abstract: In this report, we have used periodate-oxidized tRNA (tRNAox) as an affinity laleling reagent to demonstrate that: (i) the bL12 protein contacts the CCA-arm of P-site bound tRNA on the Escherichia coli 70S ribosomes; (ii) the stoichiometry of labelling is one molecule of tRNAox bound to one polypeptide chain of endogenous bL12; (iii) cross-linking in situ of bL12 with tRNAox on the ribosomes provokes the loss of activity; (iv) intact tRNA protects bL12 in the 70S ribosomes against cross-linking with tRNAox; (v) both tRNAox and pyridoxal 5'-phosphate (PLP) compete for the same or for proximal cross-linking site(s) on bL12 inside the ribosome; (vi) the stoichiometry of cross-linking of PLP to the recombinant E. coli bL12 protein is one molecule of PLP covalently bound per polypeptide chain; (vii) the amino acid residue of recombinant bL12 cross-linked with PLP is Lys-65; (viii) Lys-65 of E. coli bL12 corresponds to Lys-53 of eL42 which was previously shown to cross-link with P-site bound tRNAox on human 80S ribosomes in situ; (ix) finally, E. coli bL12 and human eL42 proteins display significant primary structure similarities, which argues for evolutionary conservation of these two proteins located at the tRNA-CCA binding site on eubacterial and eukaryal ribosomes.

In silico characterization and molecular modelling of sodium-dependent serotonin transporter protein from homo sapiens

Abstract: Objective: The objective of our investigation is to apply computational tools for a protein sodium-dependent serotonin transporter (SERT). It plays a role in sudden infant death syndrome, aggressive behavior in Alzheimer disease, and depression-susceptibility. Although various conventional and experimental therapies have been directed for the treatment, still it needs attention for more effective treatments. Toward this pursuit, we performed in silico analysis of the protein using computational tools and servers. Methods: Homology modeling approach has been used to define the tertiary structure of the protein using SWISS-MODEL workspace. Modal validation was done to verify the generated modal. Furthermore, primary and secondary structural and functional analysis was performed to provide more perceptions into the selected protein. The protein disorder analysis was performed using PrDOS server. Results: The results of the primary structure analyses suggested that SERT is an acidic and hydrophobic protein in nature. It is structurally stable. The secondary structural analysis results revealed that random coils dominated among secondary structure elements. The homology modeling showed that the QMEAN score of the model was −5.17, and the sequence identity was 52%. Validation protein models using Rampage revealed that more that 95.9% residues were in favored regions. The protein disorder detected by PrDOS showed the total disorder amino acid residues were 89 (14.1%). Conclusion: The study provides valuable clues for initiation of experimental characterization of this protein and throws light on some novel insights into the structural features of sodium-dependent SERT protein from Homo sapiens . This will also helpful in conducting docking studies for the receptor protein against various drug molecules.

Predicting the effects of the single nucleotide polymorphism A122V on CXC chemokine receptor type 1 of Bos taurus (Artiodactyla: Bovidae) cattle by in silico analyses

Abstract: This study aimed to perform in silico analyses of the primary and secondary structures of the bovine chemokine receptor CXCR1, the non-polymorphic and A122V-harboring polymorphic proteins to predict differences. Two sequences of the CXCR1 protein of Bos taurus cattle were selected from the non-redundant protein sequence database UniProtKB/Swiss-Prot: a) a non-polymorphic sequence (A7KWG0), with alanine (A) at position 122, and b) a sequence harboring the causal polymorphism A122V with substitution by valine (V) at the same position. Protein primary and secondary structures were analyzed using the ProtParam program and Chou & Fasman Protein Secondary Structure Prediction CFSSP algorithm. No differences in physical or chemical parameters were predicted from the primary structure of the two bovine protein sequences. The presence of a helix domain situated between positions 100 and 150 was only found in the non-polymorphic CXCR1 protein. Amino acid residues with different biochemical features were detected at position 122 in the ruminant and human CXCR1 protein sequences, suggesting that this peptide seems to be highly polymorphic in vertebrates. Findings described herein predict differences in the secondary structure pattern of non-polymorphic and polymorphic A122V-harboring CXCR1 proteins using bioinformatics tools.

Cloning, analysis, and expression of murine perforin 1 cDNA, a component of cytolytic T-cell granules with homology to complement component C9 (cytotoxic lymphocyte/pore-forming proteins/cytotoxic mechanisms/primary structure)

Abstract: The nucleotide sequence coding for the cyto- toxic T-lymphocyte (CTL) protein perforin 1 (Pl) has been determined and the corresponding protein sequence has been derived. Murine CTL cDNA libraries contained in the vector Agtll were screened by using a monospecific antiserum to purified P1. Three recombinant phages were isolated and their cDNA inserts were sequenced. The derived protein sequence contains 554 amino acids and displays, as expected, consider- able homology with certain functional domains in the comple- ment components C9, C8a, C8fi, and C7. The identity of P1 cDNA clones was verified by prokaryotic expression and the reactivities of antisera produced to the expressed proteins. In addition, antisera were produced to two synthetic peptides located in the center and C-terminal portions of P1. All antisera reacted with purified Pl. In Northern blot analyses, P1 cDNA probes recognized a 2.9-kilobase mRNA only in CTL. Perforin mRNA was found in all cloned CTL and in all mixed lympho- cyte reactions that gave rise to cytotoxic cells. Perforin mRNA was also detected in virus-specific CTL that had been generated in vivo and isolated from liver tissue of mice infected with lymphocytic choriomeningitis virus. The cell-specific expres- sion of perforin is consistent with its postulated role in cytolysis. Cytotoxic T lymphocytes (CTL) are of primary importance

Antibody complementary determining region conformation fingerprint database

Abstract: The invention relates to an antibody complementary determining region conformation fingerprint database, and belongs to the field of bioinformatics. Each piece of antibody protein comprises four groups of data, including name, amino acid sequence, complementary determining region fragment range and full information conformation fingerprint, wherein the amino acid sequence and the complementary determining region fragment range are obtained from a protein knowledge database; the full information conformation fingerprint is processed in two types of situations: for antibody protein of a known three-dimensional structure, all structure data is obtained from the protein database and is shown by a protein folding shape code; and for the antibody protein of an unknown three-dimensional structure, the three-dimensional space conformation of the antibody complementary determining region is predicted to obtain a conformation spectral band. The database not only contains the primary structure and the regular secondary structure of an antibody protein sequence but also expands and covers an irregular tertiary structure. By use of the database, a similar score of the conformation fingerprint can be adopted to label antibody complementary determining region conformation features, and a new parameter is provided for the classification of the antibody complementary determining region.