swissmodel expasy database. Introduction. Aeromonas is a genus of Gram-negative, facultative anaerobic, rod-shaped bacteria that morphologically resemble ...
Putative lytic polysaccharide monooxygenase LPMO from
Aeromonas media Postgraduate studies program Faculty of pharmacy Beni-Suef University
By Anas badawy, Hesham Sassd, Shereen ELsherkawy, Marwa Oomer, Noha Khakid Supervisor Dr. Yasser Gaber
Abstract Homology modeling for NAGBP for finds the most appropriate template and best resolution for building model, we search for the first protein structure sequence in the cazy database (AA10 family) and get the amino acid sequences from NCBI data base in fasta format, then by using amino acid sequences we get the protein parameter such as number of amino acid and its molecular weight and theoretical PI, information about cysteine amino acid and disulfide bond prediction from DIANNA 1.1 web server, single peptide prediction using CBS database (signal 4.1 server ) and finally seeking for homology modeling via paste amino acid sequence by swissmodel expasy database Introduction Aeromonas is a genus of Gram-negative, facultative anaerobic, rod-shaped bacteria that morphologically resemble members of the family Enterobacteriaceae. Most of the 14 described species have been associated with human diseases. The most important pathogens are A. hydrophila, A. caviae, and A. veronii biovar sobria. The organisms are ubiquitous in fresh and brackish water. Aeromonas media colonies are dull, off-white in color and round while slightly raised with an entire margin. On the cellular level it is a gram-negative rod-shaped bacteria, 1 by 2 μm in size with rounded ends that are not grouped together in any particular way. There are no antimicrobial properties known at this time and while much is known about other species of this genus, there is little significance given to this particular one. However, a strain producing high levels of DOPA-melanin known as Aeromonas media WS has recently surfaced and potentially could be useful in bioinsecticides e found in iridescent bird plumage N-Acetylglucosamine (N-acetyl-D-glucosamine, or GlcNAc, or NAG) is a monosaccharide and a derivative of glucose. It is an amide between glucosamine and acetic acid. It has a molecular formula of C8H15NO6, a molar mass of 221.21 g/mol, and it is significant in several biological systems. It is part of a biopolymer in the bacterial cell wall, which is built from alternating units of GlcNAc and N-acetylmuramic acid (MurNAc), cross-linked with oligopeptides at the lactic acid residue of MurNAc. This layered structure is called peptidoglycan (formerly called murein). GlcNAc is the monomeric unit of the polymer chitin, which forms the outer coverings
of insects and crustaceans. It is the main component of the radulas of mollusks, the beaks of cephalopods, and a major component of the cell walls of most fungi. Polymerized with glucuronic acid, it forms hyaluronan.GlcNAc has been reported to be an inhibitor of elastase release from human polymorphonuclear leukocytes (range 8–17% inhibition), however this is much weaker than the inhibition seen with N-acetylgalactosamine (range 92– 100%) Medical usesIt has been proposed as a treatment for autoimmune diseases,and recent tests have claimed some success Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to study and process biological data
Method and data used We used some Bioinformatics Databases Online to get information about one member of chitinases enzymes -http://www.cazy.org/ -http://web.expasy.org/translate/ -http://web.expasy.org/protparam/ -http://clavius.bc.edu/~clotelab/DiANNA/ -http://www.cbs.dtu.dk/services/SignalP/ Auxiliary Activity Family 10 = AA10 lass of recently discovered enzymes that help degradation of chitin (sometimes cellulose) by monooxygenase Go to http://www.cazy.org, Search For AA10 Family, Choose one of 2989 record “ouer choice is Aeromonas media WS", Go to Genbaank accession “ NCBI “https://www.ncbi.nlm.nih.gov/protein/AHX63512.1, Enter FASTA formate
,copy
FASTA format and Past in http://web.expasy.org/protparam/ And take computer parameters “Number of amino acids: 474Molecular weight: 51169.76 Theoretical pI:5.48” go to http://clavius.bc.edu/~clotelab/DiANNA/ To detect Possibilities of Disulfide bonds in protein, Predict signal Peptide using http://www.cbs.dtu.dk/services/SignalP/ , Seeking for Homology Protein Modeling via Paste amino acid Sequence in http://swissmodel.expasy.org/interactive
Result and discussion
After using the previous method and data base there is a lot of information about protein structure obtain with each stage tell reach to the homology protein modeling and most appropriate template on the final stage Frist at cazy database where is the family AA10 and bacterial gene (Aeromonas media ws) gene bank : AHX63512.1
Amino acid sequence of protein obtained using NCBI data base.
Then from ExPasy
Top of Form Amino acid composition: Ala (A) 43 9.1% Arg (R) 11 2.3% Asn (N) 26 5.5% Asp (D) 25 5.3% Cys (C) 6 1.3% Gln (Q) 42 8.9% Glu (E) 18 3.8% Gly (G) 52 11.0% His (H) 10 2.1% Ile (I) 17 3.6% Leu (L) 35 7.4% Lys (K) 22 4.6% Met (M) 4 0.8% Phe (F) 14 3.0% Pro (P) 28 5.9% Ser (S) 28 5.9% Thr (T) 36 7.6% Trp (W) 12 2.5% Tyr (Y) 17 3.6% Val (V) 28 5.9% Pyl (O) 0 0.0% Sec (U) 0 0.0%
CSV format
(B) 0 0.0% (Z) 0 0.0% (X) 0 0.0% Bottom of Form Total number of negatively charged residues (Asp + Glu): 43 Total number of positively charged residues (Arg + Lys): 33 Atomic composition: Carbon C 2264 Hydrogen H 3459 Nitrogen N 629
Oxygen O Sulfur S
710 10
Formula: C2264H3459N629O710S10 Total number of atoms: 7072 Extinction coefficients: Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. Ext. coefficient 91705 Abs 0.1% (=1 g/l) 1.792, assuming all pairs of Cys residues form cystines Ext. coefficient 91330 Abs 0.1% (=1 g/l) 1.785, assuming all Cys residues are reduced Estimated half-life: The N-terminal of the sequence considered is M (Met). The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro). >20 hours (yeast, in vivo). >10 hours (Escherichia coli, in vivo). Instability index: The instability index (II) is computed to be 30.48 This classifies the protein as stable. Aliphatic index: 68.99 Grand average of hydropathicity (GRAVY): -0.497 And the detection for possibilities of disulfide bonds
Then the single peptide prediction using CBS show that
and finally Seeking for Homology Protein Modeling via Paste amino acid Sequence in http://swissmodel.expasy.org/interactive and find best resolution method
References Bioinformatics Data comes from http://www.cazy.org/ http://web.expasy.org/translate/ -http://web.expasy.org/protparam/ -http://clavius.bc.edu/~clotelab/DiANNA/ -http://www.cbs.dtu.dk/services/SignalP Homology Modeling Data from http://swissModel.expacy.org Other Data comes from https://en.wikipedia.org/wiki/Aeromonas_media https://microbewiki.kenyon.edu/index.php/Aeromonas_media https://en.wikipedia.org/wiki/N-Acetylglucosamine https://microbewiki.kenyon.edu/index.php/Aeromonas_media
