ACTIVITY NO.

4
Proteomics: Exploring Protein Structure Using Online Database

Learning Goals:
1. Visualize the structure of a given molecule using RCSB Protein Data Bank (PDB)
resources.
2. Explore the structure to understand its structure function relationships.

Background:
Proteomics is an emerging area of systems biology that allows simultaneous study of
thousands of proteins expressed in cells, tissues, or whole organisms. Bioinformatics, the
discipline of biology that employs computerized search algorithms and extensive databases of
biological information to investigate biological processes and relationships, has grown
exponentially in the past decade. Genomics continues to be the best-known and most data-rich
area of bioinformatics; the Human Genome Project, as well as the sequencing of genomes from
many other species, has amassed genetic data from laboratories around the world. These data
are available in public databases such as the National Center for Biotechnology Information and
RCSB Protein Data Bank. Many genomics-oriented educational activities have been developed
to allow students to use genomic data repositories to study biological questions.

Table 1. Names and web address of sites for protein and genome databases.
Website Web Address
National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov
Mascot Proteomic Search Engine http://www.matrixscience.com/
UniProt Proteomic Database http://www.uniprot.org
Protein Data Bank (PDB) https://www.rcsb.org/

In addition to genomics, proteomics is a growing discipline of bioinformatics. Like the

extensive databases of nucleotide sequences, there are also databases containing amino acid
sequences of proteins isolated from species as diverse as bacteria and humans. These
databases allow for the discovery and analysis of protein properties in a manner analogous to
nucleotides. Thus, proteomics is the area of bioinformatics that makes use of these amino acid
sequence databases and allows examination of all the proteins expressed by a cell, tissue, or
organism.
Why put such emphasis on proteins? Proteins are almost exclusively responsible for
cellular function and metabolism, as well as for much of cellular structure. Therefore, proteins
determine the phenotype of the cell and the organism. Being able to identify and examine the
proteins present in cells or tissues, and compare protein expression among groups, can provide
important information concerning an organism's physiology, health, or evolutionary history. Thus,
proteomics has been the recent focus of much research and technology development, and the
field will grow in importance as scientists explore the links among genes, protein expression, and
biological function.
Instructions

I. Part A. Use the tools in the PDB to examine the structures mentioned below and answer the
assessment questions. Navigate into the Protein Data Bank and search for the proteins
corresponding to the following PDB codes:

1. 6PHJ
2. 4INS
3. 7CM4
4. 6VXX
5. 3V81
6. 3U71

Read/review the page and answer the following questions based on the descriptions provided:
1. What is the source (organism) of the molecule in the structure?
2. Name the authors who solved the structure of this protein?
3. Explore the 3-D structure of this protein by clicking on 3D View Tab and make sure that
you toggle on the JSmol viewer under the image as shown in the following figures:
4. View the polymer chains shown to contain helical ribbons (in magenta), arrows (in golden
yellow) and coil-like regions (white/grey). Mouse-over the structure by moving the cursor.
Based on the 3-D model that you see, describe the overall composition of each protein
molecule – how many and what chains are present in the structure. Also describe the structure
of each protein molecule in terms of the helical, arrow-like (beta-sheet) or coiled regions in
each chain.
Part B
1. Bring up the Protein Data Bank website and look up entry 4HFH.

Ligand-gated ion channels are multi-protein complexes and have a characteristic number of
individual proteins in the complex. Look at the structure of 4HFH, press the Subunit button to the
right, and determine the number of distinct proteins in the complex.

a. What type of complex is 4HFH? (dimer, trimer, tetramer, pentamer)

b. The bottom half of 4HFH consists entirely of right-handed α-helices. Of what type of secondary
structure does the top half primarily consist of?

(left-handed alpha-helices, more right-handed alpha-helices, beta-sheets, random coils)

2. Bring up the Protein Data Bank website and look up entry 2RH1.

Look at the part of the structure 2RH1 with no β-sheet. There are a number of long α-helices
oriented in a generally parallel direction. Counting only the full-length helices, how many
transmembrane helices does entry 2RH1 have? (Counting helices is sometimes difficult. Rotate
the structure by clicking and moving the mouse to get a different, perhaps better view of the
various helices).

II. Exploring Ramachandran Plots

Compare the Ramachandran plots below to answer the questions. *Please see attached
document on Ramachandran Plots.

A. 1ZEN vs. 1B57

The PDB contains numerous entries for the protein 1,6-bisphosphate aldolase. Two of the entries
are 1ZEN and 1B57. The Ramachandran plots for both are shown below. Which entry appears to
be a better model for the structure of the protein?
Ramachandran plot for 1ZEN
Ramachandran plot for 1B57
B. Structures of hemoglobin
Three entries for hemoglobin are 2HHB, 3HHB, and 4HHB. Ramachandran plots for all three are
shown below. Which is the least satisfactory model for the protein's structure?

Ramachandran plot for 2HHB

Ramachandran plot for 3HHB
Ramachandran plot for 4HHB
 ACTIVITY NO. 4

Proteomics: Exploring Protein Structure Using Online Database

NAME: ______________________________ DATE: _______________________

CHM/CHEM: _______ SECTION: ________ SCORE: _____________________
I. Part A.
PDB Code Name of Protein Author/s Structural Features

6PHJ

4INS

7CM4

6VXX

3V81

3U71

Part B
Questions Answer
1. a. What type of complex is 4HFH?
b. What type of secondary structure does the top half primarily consist of?
2. How many transmembrane helices does entry 2RH1 have?

II. Comparing Ramachandran Plots

A. 1ZEN vs. 1B57
Which entry appears to be a better model for the structure of the protein 1ZEN and 1B57? Why?
____________________________________________________________________________
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B. Structures of hemoglobin
Which is the least satisfactory model for the protein's structure of hemoglobin: 2HHB, 3HHB, and
4HHB? Why?
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