The artwork for August in our 2020 PDBe calendar is inspired by the cell’s protein making machines called ribosomes. Ribosomes are highly complex and crucial structures in the cell that fulfil the vital role of protein synthesis.
The cell’s protein factory
Each cell in our body contains around 10 billion proteins to enable us to think, move, eat, play and do much more. Making them efficiently is the work of these macromolecular machines called ribosomes, that are found in all living cells across all species, from bacteria to humans.
Ribosomal complex structure
Looking at a ribosome, it appears to be a tangled mishmash of proteins and RNA molecules, however it is in fact stitched together with immaculate precision.
The two subunits of the ribosome assembled together with the small and large subunits shown as ribbons in grey and teal, respectively (PDB entry 6KE0)
Cryo-electron microscopy and X-ray crystallography have revealed that the ribosome is made of two subunits: the small and large subunits. Each of these subunits form an intricate mesh of several RNA molecules with tens of different proteins. In 2000, structural biologists Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath resolved the first atomic-resolution crystal structures of the ribosome. In 2009, the Nobel Prize in Chemistry was awarded to these three researchers for their studies of the structure and function of the ribosome which is a testament to the importance of the ribosome.
Protein synthesis
Synthesis of new proteins starts in the nucleus, where ribosomes get their instruction to begin the process. Sections of DNA (genes), encoding a specific protein, are copied over to messenger RNA (mRNA) strands in a process called transcription.
After the transcription of DNA to mRNA is complete, the next process is translation - where these mRNAs are read to make proteins. Each mRNA dictates the order in which amino acids should be added to the protein chain as it is being synthesised. If DNA is the blueprint, then ribosomes are the masons - they build the protein using amino acids as the ‘bricks’.
To build proteins, the two ribosomal subunits, small and large, assemble together to form the complete ribosome. It has binding sites for mRNA and transfer RNA (tRNA) molecules. The large subunit sits on top of the small subunit, with the mRNA template sandwiched in between the two. Once fully assembled, the ribosome begins its protein making process.
Making protein
Driving along the mRNA, the ribosome reads a set of three-nucleotide sequences on the mRNA called codon that encodes a specific amino acid. The tRNA brings these amino acids, protein’s building blocks, to the ribosome. Each tRNA molecule has two distinct ends or sites, one to bind a specific amino acid, and another to bind the corresponding mRNA codon. During translation, these tRNAs carry amino acids to the ribosome and join with their complementary codons on the mRNA. These are subsequently translated to the correct amino acids in the new protein chain.
The assembled amino acids are stitched together with the help of rRNA (ribosomal RNA) molecules that guide the process of making the new protein chain. By repeating this process for each amino acid the whole protein is constructed in a process called elongation. The growing protein chain only stops when it encounters a stop codon on mRNA. This signals the end of the polypeptide chain during translation. Once the amino acids are formed correctly, the newly synthesised protein chain is either transported to the cytoplasm or the golgi apparatus, in prokaryotes or eukaryotes, respectively.
Below is a video from YourGenome that explains this process
More than a protein factory
The faithful and rapid translation of the genetic information is critically important to produce functional proteins for cells’ viability. The rate of protein production has to be fast and highly accurate to respond in a timely fashion to changes in the environment. The astounding accuracy of the ribosome machinery has an error rate of one in 1000–10,000 amino acids. A single ribosome in a eukaryotic cell can add 2 amino acids to a protein chain every second, however, in prokaryotes, ribosomes can work even faster, by adding about 20 amino acids to a polypeptide every second. Ribosomes consume a large amount of energy to synthesise proteins and make up a significant amount of the cell’s mass, with much of the cell’s metabolism devoted to making ribosomal proteins and RNAs.
Targeting bacterial ribosomes
Ribosomes are found in all life forms and are essential for protein synthesis, making them a desirable drug target. Most clinically used antibiotics target ribosomes and inhibit the process of protein synthesis by interfering in mRNA translation or by blocking the formation of peptide bonds.
Bacterial ribosomes are one of the major targets for antibiotics. These antibiotics prevent the bacteria from synthesising its own proteins due to the inhibition of its ribosome that eventually kills the bacteria. The development of such antibiotics has been possible due to differences between the bacterial and eukaryotic ribosomes. They differ not only in their size but also in sequence and structure, allowing the antibiotics to kill only the bacteria by inhibiting its ribosomes, while leaving human ribosomes unaffected.
In the PDB, structures of many antibiotics in complex with ribosomes are available. These structures, resolved to atomic level resolution, allow us to better understand their mechanism of action.
Life saving antibiotics
Antibiotics such as neomycin, gentamicin and streptomycin, belong to aminoglycosides group which are widely used to treat severe infections of the abdomen and urinary tract. These inhibit the small ribosomal subunit including tetracyclines that block the binding of tRNAs.
Another widely prescribed antibiotic, erythromycin belongs to a class of natural products. It has two effects on translation, first, preventing elongation of the polypeptide chain and second inhibiting the formation of the large ribosomal subunit.
The figure below shows a number of antibiotics that target the bacterial ribosome at different sites on the large (cyan grey) and the small (yellow) ribosomal subunit.
This image is taken from The bacterial ribosome as a target for antibiotics. Nat Rev Microbiol 3, 870–881 (2005). https://doi.org/10.1038/nrmicro1265
Inhibiting the eukaryotic ribosome
Some antibiotics like geneticin, also called G418, inhibit the elongation step in both prokaryotic and eukaryotic ribosomes. Ricin, a lectin (a carbohydrate-binding protein) produced in the seeds of the castor oil plant, is a highly potent toxin. Just a few grains of purified ricin powder can kill an adult human. It inhibits elongation by enzymatically modifying rRNA of the eukaryotic large ribosomal subunit. Another known inhibitor of eukaryotic translation is cycloheximide, that is commonly used in laboratories to inhibit protein synthesis.
Cancer therapeutics
Ribosome biogenesis, a process of making ribosomes, has recently emerged as an effective target in cancer therapy. Several compounds inhibiting ribosome production or function, preferentially killing cancer cells, have entered clinical trials. Recent research indicates that cells express heterogeneous populations of ribosomes and that the composition of ribosomes may play a key role in tumorigenesis, exposing novel therapeutic opportunities.
About the image
The two artworks, the ceramic sculpture (left) and silk batik piece (right), were created by Sheen Gahlaut and Marie Bischofs, 13-year-old students from The Perse School and Impington Village College, respectively. Both the artists took inspiration from the complexes of proteins and nucleic acids in the PDB database, with their artworks based on the process of protein synthesis and ribosomes.
Deepti Gupta
