4FSE , BACE1



Introduction


Alzheimer's disease is human brain disease that cause the problem of memory, ability to think, and ability to act. Alzheimer's disease is popularly known to occur when the plaques that is abnormal fragment of part of protein is made between nerve cells. Plaques are made by aggregation of protein fragments called Aß. Aß is chemically sticky and cumulates it to make plaques. Aß is cut two pieces of APP by BACE1. Therefore, inhibition of BACE1's function can prevent Alzheimer's disease through binding site blocking or find allosteric sites to change BACE1's conformation or functions.




Method



Step 1: Search PDB ID or Text.


To see the BACE1's function in dbALP, use PDB ID search or Text search.
PDB ID is 4SFE and Text, we used, is "Beta-secretase1" by compound field.


     


In case of "Text search", field selection first and type the text.



Step 2: Search list and Result page.



There are protein 4FSE's properties. Result page is shown by click PDB ID.




Result



The dbALP suggested 5 ligands and 56 binding sites of 4FSE.




DPSP score was calculated by correlation with ligand and pocket (see the tutorial page). Red color means a score over 0 and pocket volume is bigger than ligand volume, blue color means a score below 0 and ligand volume is bigger than pocket. Therefore, red positions are strong candidates. We can understand a similar pattern of ligand in 'Heatmap'. If ligand's structure or volume is similar to other ligands, position of pocket which combines with ligand seems to similar because DPSP score is defined by correlation with ligand and pocket. BACE1 protein has Z75, PP7, IH4, FMT, and BFX (ligand IDs defined in Protein Data Bank, PDB) as ligand candidates. These are red positions, so we can think these ligand candidates can function as inhibitor.





We calculated pocket and select 3 pockets (#17, #51, #39). The number 17 pocket is main pocket, the number 51 and 39 pockets are possible for allosteric sites with ligands, TLA (in pocket 51) and PCA (in pocket 39), respectively.





5P21, Ras oncogene protein

Introduction


Guanine nucleotide binding proteins (G protein) act as molecular switches on protein transport, signal transduction, and polypeptide elongation. Particularly, Ras protein has known as signal transduction family. 'On' state is complexed to GTP, 'Off' state is complexed to GDP. It is normally in the 'Off' state, with GDP bound in the site. Signaling is terminated when GTP is hydrolyzed to GDP. When the GDP is swapped for GTP, Ras protein becomes 'On' state. This, P21 ras oncogene, is believed to be included in a growth promoting signal transduction process. Ras protein is a middle complex of signaling pathway. And it is the most common oncogene in human cancer. 5P21 is suitable for this example because it is consist of chain A, and protein only structure without other molecule like DNA.



Method


Step1: Search by FASTA sequence data




Step2: Search list and Result page.

In the FASTA serach, Mathch rate is shown. It indicates percentage of comparison with input sequences and dbALP database sequences. 100% means that input sequences are included 100% in the dbALP database sequences.



Result



The dbALP found 6 ligands and 20 binding sites of 5P21.




Red color means a score over 0 and pocket volume is bigger than ligand volume, blue color means a score below 0 and ligand volume is bigger than pocket. Therefore, red positions are strong candidates. Then, compare GTP and GDP. GTP has more one phosphate than GDP, so the structure of GTP and GDP are very similar. As a result, distribution is also similar in the 'Heatmap'. This is strong point of our 'Heatmap' system. Ras protein has functions of combining with GTP or GDP. When it combines with GTP, Ras protein has 'ON' state function. But, when it has GDP, Ras protein has 'OFF' state function. In this case, the results are XY2, MG, GTP, GDP, and G3D. They are all of ligand of combining with Ras protein. 'Heatmap' shows quite high accuracy of ligand distribution.




Taken as a function of Ras protein, 5P21's ligand are organized as GTP and GDP. MG ion helps nucleotide binding. Therefore, we can select MG, GTP, GDP as candidates of Ras protein's ligand. Red color is representative of available pocket, blue color is representative of ligand positions, and yellow sphere is an overlap position of pocket and ligand. GDP's best score is 0.8, GTP's best score is 0.3. Available pocket is number 2 pocket. MG's best score is 0.4 at number 2 pocket. Mg also will has a role at a same pocket because it helps nucleotide binding. So MG's best score 0.6 at number 15 pocket is not valid. When compare experimental results, we can see that DPSP prediction is similar to experimental result. In the GDP and MG cases, pocket is almost same. GTP's case is little different but it is near position.



Conclusion


The dbALP is useful for prediction when a researcher did not know about binding sites of protein and ligand information when they are not speicialist for protein structures. Particularly, when you know about protein structure sequences, but don't know about ligand and pocket information, the dbALP can be used efficiently. Heatmap result is easy to know ligand and pocket's correlation. Also, annotation accuracy is good.