Protein Synthesis

Proteins

Proteins are complex molecules that are made up of smaller building blocks, amino acids. They are incredibly diverse in both structure and function and play vital roles in all living organisms. Proteins play structural roles, serve as catalysts for chemical reactions, and function as receptors, transporters, and genetic regulators.

Protein Synthesis

Protein synthesis occurs on macromolecular machines called ribosomes. This process is called translation because the genetic information in a messenger RNA (mRNA) transcript is translated into a sequence of amino acids. Translation begins when the ribosome binds an mRNA molecule and recognizes a “start” sequence of nucleotides. The ribosome then moves along the mRNA, reading its sequence and adding corresponding amino acids to the growing polypeptide chain. It continues until it recognizes a “stop” sequence, causing it to release the polypeptide (Vázquez-Laslop and Mankin, 2018). Learn more about ribosomes.

Initiation

During prokaryotic initiation, the ribosome prepares itself for the elongation cycle by completing three tasks:
1. Recruiting an mRNA molecule
2. Placing the mRNA start codon in the P-site of the small subunit (SSU)
3. Binding the large subunit (LSU) to the SSU to form a 70S complex

These tasks are aided by three initiation factors (IFs), called IF1, IF2, and IF3. When initiation begins, the two ribosomal subunits are not bound to each other. To prevent them from prematurely associating, IF3 binds to the SSU. After this has been completed, the SSU proceeds to recruit an mRNA molecule. Most prokaryotic mRNAs contain a special Shine-Dalgarno sequence that is complementary to the 3’ end of the rRNA on the SSU. They subsequently interact to place the start codon in the P-site and allow the association of the initiator tRNA (Rodnina, 2018). After the mRNA molecule is properly positioned, IF1 and IF2 bind to the SSU. The association of the IFs induces a conformation change in the SSU, allowing the LSU to bind to it and form a 70S ribosomal complex (Arnez and Wilson, 2016).

Elongation

During elongation, amino acids are added to the nascent polypeptide chain. The elongation phase is perhaps the most important to understanding antibiotic action because it is targeted by several classes of FDA approved drugs such as the tetracyclines, oxazolidinones, lincosamides, macrolides, and aminoglycosides (Arnez and Wilson, 2016). The elongation process entails repetitive cycles of three steps:
1. Decoding mRNA sequences and pairing them with complementary tRNAs
2. Forming peptide bonds between amino acids
3. Translocating the tRNAs as the ribosome moves

In protein synthesis, the ribosome selects tRNAs that are complementary to mRNA codons in a process known as decoding. This is a significant step in translation because it ensures that the correct amino acid is added to the polypeptide chain. If the decoding process fails and the wrong tRNA pairs with an mRNA codon, an incorrect amino acid will be inserted into the protein, possibly impacting its structure and function. To prevent decoding errors, the ribosome monitors the correct Watson-Crick geometry of the codon-anticodon interactions in the “decoding center” in the A-site. Three rRNA bases in the SSU, A1492, A1493, and G530, discriminate between correct or incorrect tRNAs (Demeshkina et al., 2012). Recognition of a correct codon-anticodon interaction causes large-scale conformational changes, which allow for the accommodation of the tRNA into the A-site (Rodnina, 2018).

Figure 1. A ribbon representation of the decoding center. The tRNA anticodon (shown in red) matches up with the mRNA codon (shown in yellow) via hydrogen bonding (shown in cyan). These interactions are monitored by the SSU bases A1492, A1493, and G530 (PDB ID: 4v5c, Voorhees et al., 2009).

After a tRNA is delivered to the ribosome via elongation factor Tu (EF-Tu) and decoding occurs, a peptide bond is formed between the amino acid attached to the A-site tRNA and the nascent polypeptide chain attached to the P-site tRNA. Once the A-site tRNA is accommodated and positioned, conformational changes occur in the peptidyl transferase center. These changes expose the amino acid attached to the A-site tRNA. A peptide bond forms between the A-site amino acid and the nascent polypeptide chain (Rodnina, 2018). As a result, the polypeptide grows by one amino acid and moves through the ribosomal exit tunnel as it increases in length (Jha and Komar, 2011).

After peptide bond formation, the translocation step begins which prepares the ribosome for the next round of elongation. In translocation, the mRNA and tRNAs shift to vacate the A-site. First, the mRNA shifts towards the E-site by exactly one codon, placing a new codon in the A-site. Second, the tRNAs shift towards the E-site. As a result, the tRNA occupying the P-site moves to the E-site, and the tRNA from the A-site moves to the P-site. As a result, the A-site becomes vacant of a tRNA molecule. Translocation of the mRNA and tRNAs is aided by elongation factor G (EF-G) which directs and accelerates the process (Arnez and Wilson, 2016).

Figure 2. Steps of elongation in bacterial protein synthesis. The structure shown on the left (PDB ID: 4v5g, Schmeing et al., 2009) illustrates a new tRNA being delivered by EF-Tu (light gray). The center structure (PDB ID: 4v5d, Voorhees et al., 2009) shows three tRNA molecules bound within the ribosome as peptide transfer occurs. The structure on the right (PDB ID: 4v5f, Gao et al., 2009) shows EF-G (dark gray) aiding translocation of the tRNAs.

Termination

In the termination phase, the ribosome encounters a stop codon and ceases elongation. The large and small ribosomal subunits are then separated to prepare for a new round of translation (Arnez and Wilson, 2016). Termination involves two key steps:
1. Recognition of a stop codon in the mRNA molecule
2. Separation of the ribosomal subunits

Termination begins when class I release factors bound in the A-site recognize a stop codon in the mRNA. This signals to the ribosome that no more amino acids should be added to the polypeptide chain. The release factors trigger the hydrolysis of the P-site tRNA which releases the polypeptide from the ribosome. Following this, EF-G and ribosome recycling factors bind to the ribosomal subunits which subsequently separate them. IF3 then binds to the 30S subunit, preventing reassociation of the two subunits. This step also provides a link from the last step (i.e., termination) back to the first step (i.e., initiation) (Rodnina, 2018).

Protein Synthesis as a Target for Antibiotics

Protein synthesis or translation is a dynamic biological process with three major phases: initiation, elongation, and termination/recycling (Rodnina, 2018). Although these steps are fairly similar in prokaryotes and eukaryotes, there are some key differences. For example, eukaryotic ribosomes are larger and more complex. They consist of a 60S large subunit and a 40S small subunit which form an 80S ribosome (Myasnikov et al., 2009). Structural differences like these allow the ribosome to serve as a target for drug action in prokaryotes. Many antibiotic classes target bacterial ribosomes to disrupt translation via a few different mechanisms (Hong et al., 2014). Some examples of these antibacterial drug classes are listed in Table 1 (Arnez and Wilson, 2016, and CARD 2017).

Table 1: Classes of antibiotics that target ribosomes and disrupt protein synthesis.
* These drugs are currently used as US FDA approved antibiotics. #These drugs have been withdrawn by the US FDA.

References

Arenz, S., Wilson, D. N. (2016). Bacterial protein synthesis as a target for antibiotic inhibition. Cold Spring Harbor Perspectives in Medicine, 6(9), a025361. https://doi.org/10.1101/cshperspect.a025361

Beyer, D., Pepper, K. (1998) The streptogramin antibiotics: update on their mechanism of action. Expert Opin Investig Drugs. 7(4):591-9. https://doi.org/10.1517/13543784.7.4.591

Borovinskaya, M. A., Pai, R. D., Zhang, W., Schuwirth, B. S., Holton, J. M., Hirokawa, G., Kaji, H., Kaji, A., Cate, J. H. (2007) Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol. 14(8):727-32. https://doi.org/10.1038/nsmb1271

Demeshkina, N., Jenner, L., Westhof, E., Yusupov, M., Yusupova, G. (2012). A new understanding of the decoding principle on the ribosome. Nature, 484(7393), 256–259. https://doi.org/10.1038/nature10913

Gao, Y. G., Selmer, M., Dunham, C. M., Weixlbaumer, A., Kelley, A. C., Ramakrishnan, V. (2009). The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science, 326(5953), 694–699. https://doi.org/10.1126/science.1179709 PDB ID: 4v5f

Jha, S., Komar, A. A. (2011). Birth, life and death of nascent polypeptide chains. Biotechnology Journal, 6(6), 623–640. https://doi.org/10.1002/biot.201000327

Jia, B., Raphenya, A. R., Alcock, B., Waglechner, N., Guo, P., Tsang, K. K., Lago, B. A., Dave, B. M., Pereira, S., Sharma, A. N., Doshi, S., Courtot, M., Lo, R., Williams, L. E., Frye, J. G., Elsayegh, T., Sardar, D. Westman, E. L., Pawlowski, A. C., Johnson, T. A., Brinkman, F. S., Wright, G. D., McArthur, A. G. (2017) CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research 45, D566-573. https://doi.org/10.1093/nar/gkw1004

Myasnikov, A. G., Simonetti, A., Marzi, S., Klaholz, B. P. (2009). Structure-function insights into prokaryotic and eukaryotic translation initiation. Current Opinion in Structural Biology, 19(3), 300–309. https://doi.org/10.1016/j.sbi.2009.04.010

Rodnina M. V. (2018). Translation in prokaryotes. Cold Spring Harbor perspectives in biology, 10(9), a032664. https://doi.org/10.1101/cshperspect.a032664

Schmeing, T. M., Voorhees, R. M., Kelley, A. C., Gao, Y. G., Murphy, F. V., Weir, J. R., Ramakrishnan, V. (2009). The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science (New York, N.Y.), 326(5953), 688–694. https://doi.org/10.1126/science.1179700 PDB ID: 4v5g

Vázquez-Laslop, N., Mankin, A. S. (2018). How macrolide antibiotics work. Trends in Biochemical Sciences, 43(9), 668–684. https://doi.org/10.1016/j.tibs.2018.06.011

Voorhees, R. M., Weixlbaumer, A., Loakes, D., Kelley, A. C., Ramakrishnan, V. (2009). Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nature Structural & Molecular Biology, 16(5), 528–533. https://doi.org/10.1038/nsmb.1577 PDB ID: 4v5c, 4v5d

March 2025, Steven Arnold; Reviewed by Drs. Albert Berghuis and Tolou Golkar
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/prot-syn