HOPE is a mutational analysis tool that combines the information to give the effect of a certain mutation on the protein structure. It is an online web service where the user can submit a sequence and mutation. HOPE will show the outcome of that mutation in such a way that even those without a bioinformatics background can understand it.
The web server allows the user to submit a protein sequence (in fasta format or not) or an accession code of the protein of interest. In a next step the user can show the mutated residue with a simple mouse click. In the final step the user can simply click on one of the other 19 amino acid types that will become the mutant residue.
The Basic Local Alignment Search Tool is a well-known bioinformatics method to compare sequences. The BLAST algorithm is often utilized to search sequence databases for homologous sequences. HOPE uses BLAST to search with the submitted sequence in both the UniProt database and the PDB. The MRS web service is used to perform the BLAST search, where the low-complexity filter is switched off.
BLAST against UniProt
This BLAST search will result in the UniProt entry of the protein of interest. Every known protein has an entry of UniProt identified with an accession code. This accession code is saved to be able to access other servers/services later in the process.
BLAST against PDB
We perform this second BLAST search to find the 3D structure of the protein of interest, or a possible template for homology modeling. This file can simply be downloaded and used for further analysis. Sometimes a sequence does not have a 100% identical match this means that no structure was found for that protein. However, a homologous protein structure might be solved. When the amount of identity between the submitted sequence and PDB file exceeds the homology modeling threshold HOPE will build a model. When a structure or modeling template isn’t available we have to rely on other sources of information.
The program Yasara is used to build a homology model when possible. This program has an automatic modeling script that obtained very good results in the CASP8 competition.
Information from the 3D Structure
The protein structure of interest (downloaded or built by Yasara) is analyzed by a series of WHAT IF web services. These services can for example calculate residue accessibility, secondary structure, ligand contacts, metal contacts, ionic interactions, disulfide bonds, hydrogen bonds, etc. This information is collected and stored in HOPE’s database.
Information from UniProt
We access the UniProt XML-file of the protein of interest using the accession code as an identifier. In this file we find the sequence features; structural information that can be assigned to one or more residue(s).
Information from Reprof
Reproof is a secondary structure prediction program. HOPE uses it to take information about both secondary structure and solvent accessibility. HOPE will only use this when no other information source is available.
In this step, all collected information is combined into a report. The tree makes sure that the most reliable source of information is used, being information from the “real protein structure” followed by annotated information in UniProt followed by predictions by Reprof. The tree is divided in 5 branches
- Contacts like metal, DNA, hydrogen bonds, ionic interactions etc.
- Structural locations including motifs, domains, trans-membrane domains etc. The three checks whether the mutation is located in a part of the protein with an assigned name, and corresponding function;
- Non-structural features like post translational modifications
- Variations have information about known variants at that position. The tree checks whether a variation (either a SNP, mutagenesis site, splice variant etc) is known at this position
- Amino acid properties consist of size, charge, hydrophobicity. These features are used to determine the effect of the mutation in the other branches of the three.