Part A. Conceptual Questions

• Answer any of the following questions by Shuguang Zhang:

  • Why there are only 20 natural amino acids?

  The standard genetic code consists of nucleotide triplets (codons) that encode amino acids. The 64 possible codons efficiently map to 20 amino acids, with built-in redundancy (multiple codons encoding the same amino acid) which helps minimize the impact of mutations.

  Adding more than 20 amino acids would require significant changes to cellular translation machinery (tRNAs, ribosomes, etc.), a path that evolution has not generally favored.

  It is also due to biochemical simplicity and efficiency. Cells synthesize and degrade these 20 amino acids efficiently, without excessive metabolic cost. Also, having a fixed set ensures reliable folding and interactions in proteins.

  • Where did amino acids come from before enzymes that make them, and before life started?

  It has been studied that amino acids can form through natural chemical processes that do not involve enzyme mediation. For example, one hypothesis is that amino acids were formed in hydrothermal vents in ocean caves. These vents emit hot, mineral-rich fluids that could have driven the formation of organic molecules.

  • Why many amyloid diseases form b-sheet?

  β-sheet structures dominate amyloid diseases because they form highly stable, self-propagating aggregates that resist degradation and can induce more misfolding. This stability, while useful in some biological functions (like silk and bacterial biofilms), becomes pathological when unchecked.

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.

Maltoporin is a transmembrane protein found in the outer membrane of E. coli. It is responsible for the transport of sugars such as maltose and maltodextrine. It is coded by the LamB gene. This protein is relevant since it is also a receptor for the Lambda phage; this phage has been widely studied because it can be used to introduce genes into the bacteria. I chose this protein because I was researching about the different membrane proteins of E. coli that are used as receptors for phage invasion. This protein has been highly described and is well characterized.

The amino acido sequence for this protein is 446aa. The amino acid chain for the LamB gene is the following:

<aside> 🧬

MMITLRKLPLAVAVAAGVMSAQAMAVDFHGYARSGIGWTGSGGEQQCFQTTGAQSKYRLGNECETYAELKLGQEVWKEGDKSFYFDTNVAYSVAQQNDWEATDPAFREANVQGKNLIEWLPGSTIWAGKRFYQRHDVHMIDFYYWDISGPGAGLENIDVGFGKLSLAATRSSEAGGSSSFASNNIYDYTNETANDVFDVRLAQMEINPGGTLELGVDYGRANLRDNYRLVDGASKDGWLFTAEHTQSVLKGFNKFVVQYATDSMTSQGKGLSQGSGVAFDNEKFAYNINNNGHMLRILDHGAISMGDNWDMMYVGMYQDINWDNDNGTKWWTVGIRPMYKWTPIMSTVMEIGYDNVESQRTGDKNNQYKITLAQQWQAGDSIWSRPAIRVFATYAKWDEKWGYDYTGNADNNANFGKAVPADFNGGSFGRGDSDEWTFGAQMEIWW

</aside>

Protein sequence homologs:

To find the homologs I used the pBLAST tool. This resulted in finding that LamB protein has many homologs since this is a protein that is shared within the Enterobacteriaceae family.

I chose Enterobacteriaceae, Shigella dysenteriae and Escherichia albertii to compare the sequences and they showed a 100% coincidence.

• 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)
  • Are there any other molecules in the solved structure apart from protein?
  • Does your protein belong to any structure classification family?

Structure of the protein in

This structure has been solved in 1987 and has a resolution of 2.40Å

This protein belongs to the Porin family, specifically to those that are specific to sugars. Its structure classification is that of a beta-barrel protein; it folds a trimeric beta-barrel structure.

• 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)?