Method tothe haloacid dehalogenase-like hydrolase domain containing 2
Structural analysis
The structural information was obtained from the /Protein Data Bank website using the PDB accession code H2O4. 3D views of the structure were analyzed using MBT protein workshop and /KiNG, and the RCSB ligand explorer 2.0 provided animated views of the ligands, ligand-binding sites and their interactions.
Dali is a tool designed to find structurally similar, although may be functionally different, matches for a query protein. The Dali search was performed with a threshold of Z> 12 to include only the highly significant structural matches. The list of similar structures returned by the search was carefully analyzed by noting the sequence identity, which showed the sequence similarity of the result with the query. Besides the Z value and the sequence identity, the coverage of the results was also considered.
The significant matches were studied using the /PDB website and the structures were visually examined using PDB structure viewer. Their annotations from /SCOP or /CATH, if available, were noted. pYmol was then used to examine the superimposition of the similar structures with 2HO4.
For determining the conserved residues, a protein BLAST (blastp) search was used to obtain matches above 1e-63. A multiple sequence alignment of the proteins for the blast search was performed using clustalX from the DVD provided by the Biol3004 course coordinator.
Functional analysis
Internet research is a widely method to get millions pieces of work from people around the world. Before starting gather informations, we need to understand about protein and focus on main point of our protein.
Use search engine/AmiGo from the Gene Ontology database to define what its main function. Use the /Protein Data Bank to look at the sequence details and identifies number of domains in the structure, and ligands and prosthetic groups in the protein. Use the Mouse Genome Informatics to identifies all function and process of the protein. With MGI search engine, Mammalian homology Load also identify all species containing sequence of this protein. Use Genomics Institute of the Novartis Research Foundation search engine to define where about the protein sequence are mainly locate in the body. Use /STRING search using proteins sequence orthology information from the COG database, to predict protein's functional partners.
With the above understanding of the protein, we can search the literature and journal relate to our protein.
Evolutionary analysis
Nucleotide sequence was found from NCBI. Saved into FASTA format and BLAST searches with the whole nucleotide alignment was run for the human HDHD2 and also another for the first 100 nucleotides for checking of conserved sequences.
After BLAST results were obtained, used CLUSTALX to perform nucleotide alignment and top matches were used with CLUSTALX and PHYLIP to contruct phyologenetic trees for determination of conservation and to aid in study of function.
