Structural View of Biology
Protein Synthesis
The major molecules of protein synthesis, from DNA to RNA to ribosomes to folded proteins, are available in the PDB archive. Proteins are built in several steps in all living organisms. The blueprint for each protein is stored in the genome, encoded in strands of DNA. This information is transcribed into an RNA copy, which is then used to construct the protein chain. After the chain is synthesized, it may be modified with special chemical groups, chaperoned into its proper folded shape, and ultimately destroyed when it is not needed any longer.
Translation
Proteins are built by ribosomes, based on the genetic information carried by RNA strands. Ribosomes read the sequence of nucleotides in RNA strands and use it to link together the amino acids in proteins. This requires the cooperation of many molecules, including transfer RNA molecules that match up the proper amino acids with the proper set of RNA nucleotides, and a host of protein factors that get the process started, add energy at each step, and determine when to finish.
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Aminoacyl-tRNA Synthetases
When a ribosome pairs a "CGC" tRNA with "GCG" codon, it expects to find an alanine carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins.
Read MoreDiscussed Structures
aspartyl-tRNA synthetase
isoleucyl-tRNA synthetase
valyl-tRNA synthetase
glutamyl-tRNA synthetase
phenylalanyl-tRNA synthetase
threonyl-tRNA synthetase -
Elongation Factors
At first glance, we might think that cells are primarily protein synthesis factories. Over half of the molecular machinery in a typical bacterial cell is dedicated to building new proteins. These include the DNA and messenger RNA, which provide the instructions, transfer RNA, which performs the translation of this information, and ribosomes, which do the major construction work. Protein synthesis also requires a flurry of protein factors to orchestrate each step. These include initiation factors that get it all started, release factors that finish each chain, and elongation factors that assist the many steps between the beginning and the end.
Read MoreDiscussed Structures
tRNA and EF-Tu
EF-Tu and EF-Ts
EF-G -
Ribosomal Subunits
Protein synthesis is the major task performed by living cells. For instance, roughly one third of the molecules in a typical bacterial cell are dedicated to this central task. Protein synthesis is a complex process involving many molecular machines. You can look at many of these molecules in the PDB, including DNA, DNA polymerases, and RNA polymerases; a host of repressors, DNA repair enzymes, topoisomerases, and histones; tRNA and acyl-tRNA synthetases; and molecular chaperones. This month, for the first time, you can also look at the factory of protein synthesis in atomic detail.
Read MoreDiscussed Structures
ribosome large subunit
ribosome small subunit
ribosome small subunit -
Ribosome
Ribosomes are one of the wonders of the cellular world, and one of the many wonders you can explore yourself at the RCSB PDB. In 2000, structural biologists Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath made the first structures of ribosomal subunits available in the PDB, and in 2009, they each received the Nobel Prize for this work. Structures are also available for many of the other players in protein synthesis, including transfer RNA and elongation factors. Building on these structures, there are now hundreds of structures of entire ribosomes in the PDB, revealing the atomic details of many important steps in protein synthesis.
Read MoreDiscussed Structures
ribosome and Shine-Delgarno sequence
ribosome and EF-Tu
ribosome peptide transfer
ribosome and EF-G
ribosome and RF1 -
Riboswitches
Why use two or more molecules when one will do? In our own cells, protein synthesis is controlled by thousands of regulatory proteins, which work together to decide when a particular protein will be made. Bacteria are masters of economy, however, and in some cases, they have figured out a way for messenger RNA to control itself, without the need for help by proteins.
Read MoreDiscussed Structures
guanine riboswitch
metal-sensing riboswitch
c-di-GMP riboswitch
riboswitch and ribozyme -
Small Interfering RNA (siRNA)
Double-stranded RNA is often a sign of trouble. Our transfer RNA and ribosomes do contain little hairpins that are double-stranded, but most of the free forms of RNA, messenger RNA molecules in particular, are single strands. Many viruses, however, form long stretches of double-stranded RNA as they replicate their genomes. When our cells find double-stranded RNA, it is often a sign of an infection, and they mount a vigorous response that often leads to death of the entire cell. However, plant and animal cells also have a more targeted defense that attacks the viral RNA directly, termed RNA interference.
Read MoreDiscussed Structures
Dicer
argonaute
tombusvirus p19 -
Transfer RNA
Since the process of DNA-directed protein synthesis was discovered, scientists and philosophers have searched, more or less seriously, for a relationship between the triplet nucleic acid codons and the chemical nature of the amino acids. These attempts have been uniformly unsuccessful, but remain an occasional topic of speculation because of their possible insights into the origins of life. There does not appear to be a specific interaction between the codons and the amino acids themselves. Instead, the match is made by transfer RNA, the Rosetta Stone that translates the nucleotide language of codons into the amino acid language of proteins. This translation is physical and direct: at one end of each tRNA is an anticodon that recognizes the genetic code, and at the other end is the appropriate amino acid for that code.
Read MoreDiscussed Structures
phenylalanyl tRNA
tRNA and EF-Tu -
Transfer-Messenger RNA
Damaged messenger RNA poses a double danger to cells. If a messenger RNA is truncated, it will be missing its stop codon, so it will encode a faulty, truncated protein. Also, ribosomes get stalled at the end of these truncated messages and are unable to release the mRNA and move on to the next protein synthesis job. Bacteria possess an ingenious molecular method for solving both of these problems at the same time, that destroys the faulty protein and releases the ribosome all at once.
Read MoreDiscussed Structures
tmRNA and SmpB
Ribosome with tmRNA, tRNA and EF-G
Ribosome with tmRNA, tRNA and EF-G
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