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The amino acid sequences (primary structures) of the protein are shown in the Sequence viewer. Each letter represents an individual amino acid (e.g. s = serine; t = threonine, i = isoleucine, etc.). Identify the primary structure of the . |
Secondary structure
In the cartoon representation, you are able to see structures of . The folded protein structures of alpha helices, beta pleated sheets, and random coils are represented in the 3D Structure below. You can click and drag the protein to rotate it.
Identify alpha helices, beta-pleated sheets, and random coils in the .
Copy the gene for translation by our bioinformatics tool
Click/tap copy text to take the DNA sequence from for translation.
Translate the gene
Bioinformatics tools can quickly perform this task. You will use the translate tool to quickly process your coding DNA sequence into a translated amino acid sequence. Use the tool below to translate the copied nucleotide sequence to a protein primary structure. Paste the sequence into the sequence box and click/tap TRANSLATE.
Protein Sequence
Compare your protein sequence with the primary structure in the table at the top of the page. What do you notice?
Mutate the gene
Paste the same sequence into the sequence box. Delete 1, 2 or 3 nucleotides and click/tap TRANSLATE to generate a mutant primary structure.
Protein Sequence
Compare your mutant protein sequence with your original protein sequence. What do you notice?
Compare the original and mutant gene sequences
Your coding DNA consists of the start codon, the stop codon and all of the nucleotides between. Each codon in your coding DNA will be transcribed into mRNA and translated into a sequence of amino acids.
Original Sequence
Mutant Sequence
Every second codon First stop codon
Identify the impact of your mutation: compare the codons in your original and mutant gene
Use AI to fold your mutant protein
Recent advances in artificial intelligence have allowed scientists to use computers to simulate protein folding in order to determine what a protein’s 3D structure might look like without needing to make observations of real proteins. AlphaFold is a tool that uses machine learning algorithms to perform high accuracy predictions about what a protein’s 3D structure might look like using only an amino acid sequence as an input. Copy the amino acid sequence from your mutant amino acid translation.
Navigate to this page: AlphaFold Server.
How does your mutation impact the 3D structure of your ?
Atomic Structure
Amino acid chains fold into tertiary structures that have 3D shapes. These shapes are closely related to how they function and interact with systems within organisms. Historically, 3D protein structures have been empirically determined using powerful tools and techniques including X-ray crystallography and electron microscopy. In the atomic structure model, every atom in each amino acid is shown. Carbon, Oxygen, Nitrogen, and Hydrogen are represented in this view.
Suggest which elements are represented by the grey, blue, red, and yellow atoms.
Space fill structure
The properties of amino acids determines how they arrange themselves and interact with one another. In this representation, the space taken up by each amino acid is represented by spheres. In addition, each amino acid is coloured by its hydrophobicity and charge:
- ● Hydrophobic
- Hydrophilic
- ● Negatively charged (Asp, Glu)
- ● Positively charged (Arg, Lys)
- ●
Where are the hydrophilic and hydrophobic amino acids mainly located – inside or outside the protein? Why do you think that might occur? Where are the positively and negatively charged amino acids located in relation to one another? Why might this be the case?
Active site
Select residues in the primary structure by clicking or tapping the single letter code to highlight any part of the protein with green spheres.
Where is the sequence located in the 3D structure? How might PBP function be affected if some of the amino acids are changed?
Compare your mutant with the original protein
Return to AlphaFold Server and download and/or screenshot your model. Upload and view the mutant protein.
Mutant protein
Original protein
Upload PDB or ZIP file
AlphaFold Image
How might the mutation impact the ability of to do their job? How might the mutation impact the ability of this protein to do its job?