代做Coursework 3 (APH106) Applications of PyMOL帮做R编程

Coursework 3 (APH106)

Applications of PyMOL

Instructions: Please write down detailed steps of solving the following questions and use screenshots as evidence in a Word document. Convert Word into PDF format to avoid any error codes. You also need to save the PyMOL files for all questions and submit them together with your PDF document. Please name each of the PyMOL files with the corresponding numbers of questions.

1. Tyrosine kinases are enzymes that play a crucial role in cell signaling and regulation, particularly in the process of transferring phosphate groups from adenosine triphosphate (ATP) to tyrosine residues on proteins. This process is known as phosphorylation and is a key mechanism in cellular communication, growth, and differentiation. Try to select a tyrosine kinase and retrieve the structure through PDB, import it into PyMol, and display its amino acid sequence in the format of Residue Names. Label its first and last residue. Ensure that the labels are not obstructed. (Please also show the PDB code of the selected protein and the relevant PDB webpage) (20 marks)

2. Import protein 2M05 into PyMol.

(1) Color its Helix structure as red, Sheet structure as yellow, and Loop structure as green through its structure. (10 marks)

(2) Select the first ten residues from the beginning of the protein, represent them in STICK form, rename it as Segment1, and hide all other residues. (10 marks)

(3) For Segment1, select the residue at the beginning of the sequence, save it as Residue1, keep its STICK form, and display the other residues as SPHERE. (10 marks)

(4) For Residue1, calculate the distance between any two carbon atoms and then calculate the bond angle formed by any three carbon atoms. (10 marks)

3. Import protein 4AT3 into PyMol.

(1) Observe the protein structure, hide water in the view, find the small molecule represented in STICK form. and label its elements to provide its chemical formula. (20 marks)

(2) Show the polar forces between the small molecule displayed in the STICK mode and main chain of the protein. Label the amino acid sequences that interact with the small molecule. (20 marks)