Abstract Rough Draft and Continued Research 4/17/19

Rationale

The rationale behind today in lab was to create a project outline to help guide the rest of our research and to help us begin to prepare for our final presentations. In addition, when we were done with our presentation outline, we continued working on sequencing and protein folding in order to collect the necessary data.

Tools/Procedure

1. Presentation outline was submitted
2. MEME Motif was used to find repeating motifs in the TMPs of selected proteins from each usable cluster

Results

The results above were generated using the MEME software to find motifs. The logo above represents a motif that was found in all 43 selected TMPs suggesting an area of conservation. In addition, when searching for other common motifs 2 appeared with much less frequency but much more similarity, which will require further research. This motif shows that there is less similarity in the actual amino acid sequences, but the color coding suggests that structure is more likely to be conserved as many of the amino acids at a location are color-coded the same, suggesting that the amino acids will behave very similarly.

Conclusion

This motif demonstrates that there is at least one conserved motif for all of the randomly selected phage tested, answering our guiding question that, at least to a small degree, there are shared similarities between all TMPs.

Future Plans

In the future, we will continue to look for similarities and difference in the amino acid while continuing our folding of proteins to try to figure out if there are key conserved regions in TMPs. This motif needs to be further investigated, and I will see if I can find more motifs in all the proteins. I will also try to fold the amino acids found in just the motif to see if they are structurally similar to the sequences identified as the same motif.

04/17/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. The individual research was worked on.
2. two group members have started finding the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence
3. one group member began to use jmol and raptor x to start structure analysis
4. the abstract for the presentation was drafted
5. The group worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

abstract draft:

ATG, TTG and GTG are the three start codons that initiate gene translation in all bacteria. When ribosomes detects these start codons, they begin to synthesize proteins according to the sequence of the codons. Each start codons produce different amino acids, which interact differently with other amino acids to form different structure i.e. leads to a different function. Genes in arthrobacter phage genomes are used to explore whether this change is significant and affects the preference for the start codons in specific genes based on the change or lack thereof. The start codons for tape measure protein, major tail proteins, and minor tail proteins in the annotated genome of known sequenced arthrobacter phage were collected using DNA Master and the PhagesDB database to determine the start codons of the genes that produce these proteins. The gene length, genome length, cluster %GC, and direction of the genes were also recorded to determine possible factors that make one start codon preferable to another. i.e. ribosomal binding and initiation of translation, in the phage genome. Raptor X and Jmol are used to determine the most probable structure of the product protein based on the amino acid sequence. Protein models are produced for each type of protein using different start codons and the structures are then compared.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.

04/17/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. The individual research was worked on
2. the group members found the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence.
3. group made the project outline
4. The grouped worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

project outline:

Title:

Analysis of start codons and change in structure due to start codons in proteins from arthrobacter phages

Guiding Question:

Can a different start site affect the translation of the gene sequence? Will it change the structure of the product protein? If the structure does not change, is there a possible reason to prefer a certain start codon over another?

Abstract:

ATG, TTG and GTG are the three start codons that initiate gene translation. But there is no known correlation between the start codons and the genes. Is there a factor that makes one start site preferable to another?. To answer this question, the start codons for tape measure protein, major tail protein and minor tail proteins were collected to find possible correlations. To analyze the structure of the product protein, predicted models were produced for the same protein using different start codons to see if there was a significant change in structure due to the change in start codons.

List of tools used

Phages DB, DNA Master, raptor x and jmol

Introduction (Background Information)

The standard genetic code table has one start codon, ATG. Over the years, however, many studies have demonstrated that alternative start codons, such as GTG and TTG, could be utilized for translation initiation. In accord of ranking of the start codons, genes starting with ATG are, on average, expressed at significantly higher levels than genes that start with GTG, and the very few genes that contain the start TTG. This is generally the case for genes in other bacteria as well, with ATG being the predominant start codon.

The AUG starts are replaced by GUG and especially UUG significantly less frequently than expected under the neutral expectation derived from the frequencies of the respective nucleotide triplet substitutions in non-coding regions and in 4-fold degenerate sites. Thus, AUG is the optimal start start codon that is actively maintained sites

Types of Data Collected

All the start codons of sequenced and annotated phages

Predicted protein structure of tape measure proteins with different start codons

Results (to date)

All start codons have been determined for tape measure proteins and major tail proteins.

Structures are still to be modelled and collected.

Conclusions (if any have been drawn)

As data is still being collected, we do not have any conclusions as of now

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.