Part A. Conceptual Questions

• Answer any of the following questions by Shuguang Zhang:

  • How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons)

  500g of beef will contain about 125g pf protein. All protein is made up of amino acid, therefore the mass of the amino acid is 125g.

  If we convert this to moles we get

  125g/100 g/mol =1.25 moles.

  inorder to get the number of amino acids, we multiply by the Avogadro’s constant

  6.022×1023 molecules/mol.

  which is

  1.25×6.022×1023 =7.53×1023  molecules

Part B: Protein Analysis and Visualization

In this part of the homework, you will be using online resources and 3D visualization software to answer questions about proteins.

1. Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions.

   • Briefly describe the protein you selected and why you selected it.

   Dendroatins is the most dominant snake veno toxin in black mambas which are native to Africa. Black mamba is the most venomous snake in Africa and dendrotoxins plays a major role becasue it a neurotixc. It is a Serine protease inhibitor homolog that selectively blocks voltage-gated potassium channels homooligomer Kv1.1/KCNA1 (EC50=0.6 nM) and Kv1.1-containing heterooligomer hence causes paralysis due to nerve blocakage

   

   • Identify the amino acid sequence of your protein.

   SGHLLLLLGLLTLWAELTPVSGAAKYCKLPLRIGPCKRKIPSFYYKWKAKQCLPFDYSGCGGNANRFKTIEECRRTCVG

   • How long is it? What is the most frequent amino acid? You can use this notebook to count most frequent amino acid - https://colab.research.google.com/drive/1vlAU_Y84lb04e4Nnaf1axU8nQA6_QBP1?usp=sharing

   79 amino acids

   Leucine “L” is the most common amino acid 12

   • How many protein sequence homologs are there for your protein?Hint: Use the pBLAST tool to search for homologs and ClustalOmega to align and visualize them. Tutorial Here

   100 homologs

   

   

   

   • Does your protein belong to any protein family?

   yes, Kunitz-type superfamily

   

   • Identify the structure page of your protein in RCSB

     • When was the structure solved? Is it a good quality structure? Good quality structure is the one with good resolution. Smaller the better (Resolution: 2.70 Å)

     1993

     • Are there any other molecules in the solved structure apart from protein?

     no, only the protein

     • Does your protein belong to any structure classification family?

     Kunitz-type serine protease inhibitor homolog dendrotoxin K (Fragment)

   • Open the structure of your protein in any 3D molecule visualization software:

     • PyMol Tutorial Here (hint: ChatGPT is good at PyMol commands)
     • Visualize the protein as "cartoon", "ribbon" and "ball and stick".
     • Color the protein by secondary structure. Does it have more helices or sheets?
     • Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?
     • Visualize the surface of the protein. Does it have any "holes" (aka binding pockets)?