The Protein Printer

Ribosomes are molecular machines programmed by genetic blueprints, which make proteins by linking amino acids together into linear chains that fold into sequence-dependent shapes. LMU biochemist Roland Beckmann studies how they do it.

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High-resolution imaging and structural analysis of nanomachines such as ribosomes requires high-performance computers. Roland Beckmann (left) in the data center. Photo: Jan Greune

Roland Beckmann is a basic researcher – in two senses. He studies fundamental biochemical processes that take place in all cell types, and he analyzes the molecular complexes that carry them out in the finest possible detail. When he talks about his findings, he transports the listener into a world where minuscule biological machines form nanoscale production lines that turn out intricately structured macromolecules to order. Their products are in turn responsible for the assembly, packaging and dispatch of myriads of other molecules. These processes are the very stuff of life.

Beckmann, Professor of Biochemistry at LMU‘s Gene Center, specializes in the investigation of ribosomes, which textbooks refer to as ‘the sites of protein synthesis’ in cells. This is true as far as it goes, but researchers continue to discover new aspects of the regulation and dynamics of the process, and many of the structural details remain unknown. One thing is clear – protein production in cells is mass production. A single yeast cell may contain up to 200,000 ribosomes, a human liver cell may have up to a million. When one considers that an adult human is made up of over a billion cells, the magnitude of the task of the protein-synthesizing machinery, and its indispensability at every second of our existence, begins to dawn on us. “Ribosomal assembly-lines are constantly on the go,” says Beckmann.

How then do cells set about making proteins, the instructions for which are stored in their genetic material? This is the question at the heart of Beckmann’s research. As a biochemist, he develops new analytical techniques with which to measure, perturb, monitor and model gene regulatory processes. The goal is to understand biological systems in all their complexity, in particular the dense networks of intermolecular communications that keep cells alive, each one representing a metastable system held together by sensors, signals and interactions. A typical human cell is made up of a surface membrane, and so-called organelles including the nucleus, membrane-bounded compartments and macromolecular complexes, which carry out specific and vital tasks. The nucleus harbors the genetic material – double-stranded DNA packaged into DNA-protein complexes – and controls all cellular functions; mitochondria provide energy, lysosomes dispose of proteins, and ribosomes synthesize proteins.

Deciphering the book of genes

Researchers basically understand how ribosomes use the information encoded in the DNA of the ‘genome’ to build thousands of different proteins. The genome can be thought of as a collection of blueprints for building the organism. These only make sense if they can be accessed, read and the instructions they contain used to direct the construction of the molecules they specify. Ribosomes are responsible for implementing these plans, which are encoded in defined sequences of DNA subunits called bases. Programmed by the genetic text, ribosomes assemble all the proteins – enzymes that catalyze chemical reactions, components of the cell’s internal skeleton, antibodies that recognize pathogens – the organism needs for its growth and survival. And since a protein’s function is largely dependent on its shape, ribosomes can be thought of as 3-D printers.

The details of the process are rather more complicated. The base sequence specifying the structure of a given protein is first copied from the appropriate segment of the coding strand of the double-stranded DNA into messenger RNA (mRNA) molecules, which are single-stranded. Ribosomes themselves comprise several ‘ribosomal RNAs’ and 50-80 proteins and consist of two subunits. The mRNA is fed into the smaller subunit – rather like threading a bicycle chain onto a sprocket wheel – and its base sequence is decoded. The code is both clever and efficient. It is read successively in non-overlapping sets of three bases (known as triplets or codons), and the specific combination of bases in a triplet tells the ribosome which amino acid should be inserted at that position in the protein chain. As DNA and RNA sequences contain four different types of bases, 4×4×4 or 64 different combinations are possible. However, since only 20 distinct amino acids are found in proteins, most amino acids are encoded by more than one codon, while four triplets serve as punctuation signals. Thus the ribosome proceeds from the start signal to a stop signal, reading the code in threes, and capturing and linking up amino acids in the specified sequence.

Proteins can comprise up to several thousand amino acid subunits, and the growing chain is fed into a 10-nanometer (10-8 cm) long exit tunnel in the large subunit of the ribosome, emerging either as an already three-dimensionally folded molecule or as a randomly coiled chain, depending on the protein concerned. “It is a fascinating fact that all organisms, from microbes to humans, possess these machines,” says Beckmann. “All living things use basically the same genetic language and the same type of code, which implies that the triplet code was established early in evolution. Over time, however, the ribosomes became more and more complex.”

Structural biologists have long known that all ribosomes consist of a large and a small subunit, though these differ somewhat in structure between lower (prokaryotic) and higher (eukaryotic) organisms. But the rapid progress made in analyzing their structures in the past two decades is largely due to the advent of cryo-electron microscopy. “Technology is crucial for us,” Beckmann remarks. He became acquainted with the method when he was a postdoc in Günter Blobel’s laboratory at Rockefeller University in New York City, although he learned about it not from Blobel (who went on to win a Nobel Prize) but from Joachim Frank, who pioneered the technique and was using it to analyze molecular structures in the state capital, Albany. “Cryo-electron microscopy was a new frontier at the time,” Beckmann says, but it would become the basis of his own area of research.