This is an assignment for proteomics course and I have done almost half of it but I need someone to help me complete it and since this report is based on student perspective there are not many instructions and my professor asked us to approach it with our own way. I have attached my incomplete report and the sample report that my professor provided.
In addition, these are my professor instructions:
[The objective of this task is use PyMOL molecular graphics to show how receptors bind small molecules. Some good choices are presented in the "Assignment 2 – GPCRs" tab. Each row contains a link for the 3D coordinate file in the Protein Data Bank and a PDF of the paper that describes it.
If you try to keep the figures to a minimum number, you will find they have the most information if you do it carefully. Also the fewer views figures you make, the fewer figures you have to annotate.
The written component of the report should state the paper you are citing and key findings from the structural analysis. What kind of approach was used (NMR, X-ray or Cryo-EM)? How did they obtain their pure protein (expression in E coli or another microorganism like the yeast, Pichia pastoris)? Why is the small molecule important In physiology or medicine? In terms of conveying the material in your report, pretend you were the author of the structure and you were making a presentation to your colleagues at a pharmaceutical about the importance knowing how that drug or compound bound the receptor. A sample report I made for the doxepin compound bound is found in its own tab.
Some people have ask me what I am looking for when grading. For the most part, it’s originality. You can copy my exact format of the doxepin report and you will likely get a C+ to a B. Perhaps, you’re are okay with that or you are at odds with what to do. Then, by all means do that. My sample report is not an example of perfection. There will be reports from some students in the class whose insights and efforts will be in ways I could have never imagined.
How you present your report depends on the following
(1) the paper and protein you picked. If the paper is short and not that informational, then tell me, and find another paper on PubMed that can provide some more insight. Investigation or going off on a tangent of your own that interests you is a good thing !
(2) Look at the paper and molecule and choose a few points that you really want to emphasize and then make your molecule figures to show it. I often write my figures first and then the text around them.
(3) You don’t have to use all of the structural insights revealed by the authors of the original paper. Just pick a few that you think are the most important and also that you feel comfortable explaining in your own words. To do this, I usually take a highlighter, real or virtual, and identify some key things in the paper.
(4) I showed some figures of doxepin and other molecules related to it and histamine, the parent. At the time of writing, I didn’t know anything about doxepin or histamine so a bit of investigation was required. An analysis of similar drugs may or may not be appropriate in your case
(5) take some time to do the report. It’s not something that can be done in one frenzied go a few days or the day before it’s due. It’s best to spend some time figuring out what you might want to say and show and then coming back and making some figures and then coming back again to write a little bit of intro text or results/comparison. Depending on how well you write, it may take a few drafts or a lot of drafts. I think I’m somewhere in between those extremes. If you have a proof reader, that’s great.
(6) When you have decided on how your report is going to go, it can be good to tell me why somewhere in the report. "This view of the molecule is important because…" or "The way this molecule binds drug X in my paper and drug Y in another paper was interesting to be because…". ]
please let me know if anyone can help me with this.