7.2 Applications and skills
7.2.3 Bioinformatics and protein structure
- Bioinformatics is an interdisciplinary field that uses tools from computer science, mathematics and engineering to analyse genome and proteome sequencing data.
- There are many ways that researchers use bioinformatics in their research.
- Applications such as BLAST (Basic Logical Alignment Search Tool) allow for sequences from different species to be ‘aligned’ to look for similarities and evolutionary relationships.
- A useful application of bioinformatics for students is molecular visualisation software.
Skill: Using molecular visualisation software
- Go to the RCSB Protein Data Bank website: www.rcsb.org
- This site is designed for experienced users – in order to search directly for specific molecules, you need to know their ID number in the database.
- A way to get around this is to use the education tools features on the website.
- On the top tool bar, choose ‘Molecule of the month’ from the drop-down menu under the heading ‘Learn’. This will open a new window.
- Use the search box to look for the molecule you would like to see.
- A page with information about the molecule of your choice will appear. Look for links to the database entries.
- This will open a page with a 3D viewer. You can manipulate the molecule with your mouse and change the settings to obtain different points of view.
- Use the software to observe the structures from the list below:
Pay attention to the …
… characteristic branched shape
Eukaryotic (80S) ribosomes
… arrangement of subunits
Levels of protein structure
- The product of translation is a polypeptide. The sequence and number of amino acids in the polypeptide is the primary structure of the protein.
- Proteins are not functional in their primary structure. After translation, polypeptides fold into three-dimensional (functional) proteins.
- The secondary structure results from hydrogen bonding between the carboxyl and amino groups of different amino acids of a polypeptide.
- The main shapes of proteins at this stage of folding are alpha helices and beta pleated sheets.
- Further folding results in the tertiary structure. A protein is functional at this level of organisation.
- The tertiary structure is stabilised by interactions between R-groups of different amino acids. There are four types of interaction possible:
- Many proteins are made of more than one polypeptide subunit. These proteins have a quaternary structure.
Figure 7.2.3h – Molecular model showing quaternary structure of ATP synthase. Subunits are shown in different colours.
Source: RCSB Protein Data Bank
Nature of Science
Developments in scientific research follow improvements in computing. Bioinformatics has enabled scientists to locate genes within genomes and identify conserved sequences.
Watch how proteins take shape in this video produced using molecular visualisation software.