The YmL28 protein has a length of 147 amino acids and a molecular weight of 17342 Da ( SwissProt ).  The protein assists the large ribosomal subunit in translation of RNA into proteins.  This protein has not been crystallized yet, and thus there is not a chime file showing the 3D structure of the protein.  When a BLAST search was performed, it was found that the most similar protein is the RGS4 protein from Rattus norvegicus which "regulates G protein signaling in the C. elegans nervous system and shares a conserved domain with many mammalian proteins" ( Koelle, et al, 1996 ).  An attempt in Swiss-Model to determine similar 3D structures showed that there were no documented proteins with a 3D stucture similar to MRPL28 with an E-value of <0.0001.  A PREDATOR search reveals that the protein is made up of  47.62% each of alpha-helices and random coils, and 4.76% extended strand ( PREDATOR Search ).  A hydropathy plot was then conducted, and it was found that the protein is largely hydrophilic, with a small hydrophobic region around amino acid numbers 15 through 23 and again from around amino acid numbers 35 through 50.  The amino acid sequence for the YmL28 protein is included below:

	MLAQTFKKPH RAVLEQVSGT TVFIRNKRTK SKSSLSPLAQ RVVTQLSVMS ASRKQPKLLK
	LAREDLIKHQ TIEKCWSIYQ QQQRERRNLQ LELQYKSIER SMNLLQELSP RLFEAANASE
	KGKRFPMEMK VPTDFPPNTL WHYNFRK
										(obtained from SwissProt)

Databases Searched

PREDATOR (results above)

PSIPRED v2.1 Protein Structure Prediction Server

3Dpssm

Sanger Institute pfam

Scop Superfamily

Protein Structure Initiative

Database of Interacting Proteins

What Is There?

Enzymes and Metabolic Pathways Database

Yale Gerstein Lab

Triples Database

PDF Protein Interaction Files

• Aging
• Degradation
• Membrane
• NB Figure 1
• NB Figure 2

Database Results

PSIPRED

• PSIPRED results show the predicted secondary structure for the protein. The results for the YmL28 protein show that the protein has several regions that have sequences consistent with coils (thin black lines), and more that are predicted to be helices (green cylinders), but relatively few strand regions (yellow arrows). These two regions predicted to fold into coils and helices are usually predicted with a fairly high confidence level (teal bars above predicted structure and sequences), but the regions that are predicted to be coils are significantly lower.
• The MEMSAT test was performed, but no related sequences were found.
• GenTHREADER Results show some results, but none are very significant. The highest confidence level for any possible match identified was "low," which was equated to 70%. The actual numerical probability of match for this lone PDB protein (1hs7A0) was 0.616. The 1hs7A0 protein is another protein from S. cerevisiae that is involved in endocytosis and exocytosis.

Prof

Prof again shows the predicted secondary structure for the protein. The Prof results show the same type of results that the PSIPRED showed, but used a different way to display them. The Prof results came in via an email that simply listed each amino acid, its predicted correlation in structure (helix/coil/strand), and the confidence level of the prediction. Again, the protein showed mainly coils and helices, but only a few small regions containing strands.

3Dpssm

The 3Dpssm Results for YmL28 show that the protein has no PROSITE motifs, but shows some alignment sequence with many proteins. However, the lowest PSSM E-value that is found for the protein is 3.39, which does not indicate statistical significance. However, many of the proteins that YmL28 resembles are alpha proteins, which could prove to be the basis for future studies. It is interesting to note that the weight for the two identified "functional keywords" is equal, and the two are "ribosomal protein" and "mitochondrion" domains, again consistent with what we already know from the literature.

Sanger Institue pfam

The pfam results show no matches for pfam, TIGR, and SMART for the YmL28 amino acid sequence.

SCOP Superfamily

SCOP Superfamily search produced a message saying, "Sorry, no significant hits" for YmL28.

Protein Structure Initiative

The Protein Structure Initiative is a database that "aims at determination of the 3D structure of all proteins." When searched, it is found that YmL28 has structural similarities with a vast number of proteins, probably due to the small sequence provided. However, the proteins vary so widely that no real conclusions can be drawn from this database.

Database of Interacting Proteins

This database did not contain any information about the YmL28 protein. However, many other ribosomal, mitochondrial proteins are present, including YmL27. This probably means that the information about the YmL28 protein has not been analyzed yet by this lab, but that it will be coming in the near future. Until then, it is very difficult to guess which proteins interact with YmL28.

What Is There?

This database lacked information about the YmL28 protein.

Enzymes and Metabolic Pathways Database

This database also lacked information about the YmL28 protein.

Yale Gerstein Lab

The Gerstein Lab database provided some already-known information, but it was helpful to get another hit for this protein (See the results here). It is shown that the YmL28 protein is probably located in the ribosome, which is consistent with previous knowledge. It is also shown that the protein is not a vital one, and that there are very few copies of the protein per cell. Protein chip data is not yet available for this protein.

Triples Database

This database contained no significant data about the YmL28 protein.

PDF Protein Interaction Files

These files contained no interactions for the YmL28 protein. MRPL28 (the YmL28 protein gene) and YDR462W (the YmL28 protein ORF) were also searched, but no results were found.

It would further the knowledge of the YmL28 protein to know if the ribosome in the mitochondrion would be functional with deletion and/or mutation of the YmL28 protein, and also to observe whole mitochondrial function analysis with wild-type and YmL28 deletion/mutant proteins. The question about ribosomal function could be answered by tagging a certain protein made by the mitochondrial ribosome with a radioactive or fluorescent marker, then letting the yeast grow on a medium and testing for the presence of the protein. The yeast could also be tested in an environment where the protein is needed for survival - if the yeast does not produce the protein, it cannot live. This could be done by identifying which vital proteins are made in the mitochondrial ribosome, then growing the yeast with different disruptions in the MRPL28 gene or the YmL28 protein in a medium that requires the previously identified vital proteins. The yeast that survive would show that the disruption would not be in a vital area to proper YmL28 function. The second question (about total mitochondrial function) could be best analyzed by putting the organism under extreme energy demands, then analyzing the growth rate, rate of division, and other metabolically-related processes for the yeast. A structure analysis could be done on the protein, and it would obviously help to have the protein crystallized. Because "only a minority of the MRPs that have been characterized show significant sequence similarities to known ribosomal proteins from other sources" ( Graack HR, et al, 1998 ), the crystallization of YmL28 would help us a great deal in learning more about the difference between Mitochondrial Ribosomal Proteins (MRP's, which include the YmL28 protein) and other ribosomal proteins. These important proteins are very far upstream in many cellular processes, and could have drastic effects on various cellular functions.

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Peter Lowry
pelowry@davidson.edu
Davidson College