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.

Figure 7.2.3a – Amino acid alignment of histone proteins in different speciesFigure 7.2.3a – Amino acid alignment of histone proteins in different species

Source: Wikipedia

  • 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.

Figure 7.2.3b – Choose ‘Molecule of the month’Figure 7.2.3b – Choose ‘Molecule of the month’

  • 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.

Figure 7.2.3c – Look for links to 3D viewerFigure 7.2.3c – Look for links to 3D viewer

  • 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.

Figure 7.2.3d – Manipulate the image using your mouseFigure 7.2.3d – Manipulate the image using your mouse

  • Use the software to observe the structures from the list below:

Structure

Pay attention to the …

Nucleosome

… association between protein and DNA

tRNA

… characteristic branched shape

Eukaryotic (80S) ribosomes

… arrangement of subunits

Levels of protein structure

Figure 7.2.3e – Primary structureFigure 7.2.3e – Primary structure

  • 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.

Figure 7.2.3f – Secondary structureFigure 7.2.3f – Secondary structure

  • Further folding results in the tertiary structure. A protein is functional at this level of organisation.

Figure 7.2.3g – Tertiary structureFigure 7.2.3g – Tertiary structure

Source: plantcellbiology.masters.grkrag.org

  • The tertiary structure is stabilised by interactions between R-groups of different amino acids. There are four types of interaction possible:
    • ionic bonds between charged R-groups
    • hydrogen bonds between polar R-groups
    • hydrophobic interactions between non-polar R-groups
    • di-sulphide bridges between sulphur-containing R-groups.
  • 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.Figure 7.2.3h – Molecular model showing quaternary structure of ATP synthase. Subunits are shown in different colours.

Source: RCSB Protein Data Bank

  • Proteins with quaternary structure may also have non-polypeptide components, called prosthetic groups.
  • These proteins are called conjugated proteins.
  • An example is hemoglobin, which is composed of four polypeptides and four non-protein heme co-factors.

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.

Try it!

Use the RCSB database to observe some proteins that you have learned about in the course 2.2.4. Can you relate the protein’s function to its structures?

Figure 7.2.3i – Four levels of protein structure in hemoglobinFigure 7.2.3i – Four levels of protein structure in hemoglobin
Source: Cambridge Biology for the IB Diploma, 1st edition

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