Databases Searched

Triples Database

Database of Interacting Proteins

YRC Two-Hybrid Analysis

Munich Information Center for Protein Sequences

Scop Superfamily

Yale Gerstein Lab

3Dpssm

What is There?

Introduction to this Page

The purpose of this webpage is to look at the unannotated gene YOL085C and see if I can characterize the protein that is coded by YOL085C. To accomplish this task I searched multiple databases that specialize in protein structures and interactions. Based on protein interactions, if any are found, I will make an attempt to deduce the protein's function by the types of proteins the databases associate with the YOL085C protein. At the end of this page I will look at the information that I have gathered and design a hypothetical experiment that could prove or disprove the possible function of unknown protein YOL085C.

Database Search Results

Triples Database

In my search (Click Here For My Results) of the Triples Database I discovered that the insertion of mTn into the YOL085C gene caused only a light to faint blue stain in the growth. A light staining indicates that the LacZ gene inserted into YOL085C was only lightly expressed and thus YOL085C is only lightly expressed. The YOL085C is localized in the "background" of the cell according to the data search. This means that there isn't a definite location of the YOL085C protein. There was a medium score for the disruption phenotype Ben10, which indicates that the YOL085C protein may be partially involved in microtubule dynamics.

Database of Interacting Proteins

The lower left node in the protein interaction chart is YOL085C. The other two proteins that it is most closely associated with are DPO4 (the node directly connected to it) and DNL4 (the node with the stronger interaction to DPO4). Both DPO4 and DNL4 are located in the nucleus and are involved in DNA synthesis. Since there is no real localization for the YOL085C protein, it is possible that it could be localized in the nucleus. Though since there are no other possible interactions given in this diagram and since the one interaction between YOL085C and DPO4 is weak, one cannot place much confidence in this finding. There is simply not adequate enough data to make a proper conclusion about the function of YOL085C protein.

YRC Two-Hybrid Analysis

The YRC Two-Hybrid Analysis did not offer any information on YOL085C interactions.

Munich Information Center for Protein Sequences

The MIPS database search yielded one protein interaction with YOL085Cp. My unknown protein interacted with POL4p, which is a DNA polymerase and is involved in DNA recombination/repair. This is a encouraging result since it reinforces the data that I found in the DIP database, because in my MIPS search I found a interaction with a different DNA polymerase protein.

Scop Superfamily

The Scop Superfamily yeilded no possible families that YOL085C might be catagorized under.

Yale Gerstein Lab

The Yale Gerstein lab yielded some very useful data. The most exciting information was that there was a 0.42 probability that the YOL085C protein is localized in the nucleus. The Gerstein Lab also concluded that the YOL085C protein is not an essential gene and that the protein's isoelectric point is 9.38.

3Dpssm

There were no significant protein matches found by 3Dpssm.

What is There?

The were was no information on YOL085C given by the WIT database.

Protein Interaction Files

There were no interactions between any protein and the YOL085C protein in any of the protein interaction files.

Benno Figure1 § Aging § Membrane § Degradation

Experimental Design

The most promising information that I have that can help to define the function of the YOL085C protein is that the YOL085C gene is most likely located in the nucleus. Additionally, YOL085C protein interacts with DNA polymerases DPO4, POL4 and possibly other proteins involved in the DNA recombination/repair process. This is an excellent place to start defining an unknown protein because I know with a fair amount of certainty where the YOL085C protein is located and with which process it is associated. The big obstacle now is how to definitively conclude the YOL085C protein function. Defining the function of a single protein using proteomic methods is very difficult because proteomic methods are designed to handle lots of throughput, not a single protein. The most specific single protein method that could be useful is attach a monoclonal tagged antibody that is specific for YOL085C and confirm where the protein is located in the cell. Any other proteomic methods of determination are not as helpful. A hypothetical method that I would try to develop for this purpose is an experiment that is similar to a 2D gel. I would try to isolate and precipitate a YOL085C protein while it was still in interaction with another protein. If I had a fluorescent tagged YOL085C protein and focused at the isoelecticpoints that YOL085C stopped I would analyze the proteins at the isoelectic points in close proximity to where YOL085C stopped. If there were any reoccurring proteins that were identified in the vicinity of YOL085C protein I could take that larger group of proteins and use higher throughput proteomic methods to better define the function of YOL085C.

Referecnces

SGD. 2002. http://genome-www.stanford.edu/Saccharomyces. Accessed 15 Nov 2002.

patoran@davidson.edu