Protein synthesis and chance: A 'stochastic' model of protein synthesis

January 29, 2014
Credit: Duncan Hull

In the process of protein synthesis there is a "stochastic" component, i.e., involving random chance, which influences the time the process takes. This aspect has been investigated by two research scientists at the International School for Advanced Studies (SISSA) in Trieste.

Gene expression (the functional activation of genes within a cell) is a crucial process for life. An important step in this process is protein synthesis, whereby the single , the "" that make up the strand of protein, are strung together like beads on a necklace. Even though this mechanism had previously been described in detail, some "stochastic" aspects had been neglected: in the chain of events that characterizes protein synthesis there is a certain random component that influences the time it takes for the protein to be assembled. A research team at SISSA has investigated this aspect and described the process of protein translation by using a mathematical model. The study has just been published in the scientific journal Physical Review E.

In mathematics, a stochastic system refers to a process that is subject to random changes, which fluctuate, however, around an average value. For the sake of simplicity, the system can be described considering only the average value, i.e., in a "deterministic" manner, where, given the conditions, the variable can assume only a single definite value. In actual fact, however - and this is true for many biological processes – the "cloud of values" that a variable can assume when the process is repeated over time can affect the efficiency of the process.

A group of scientists at SISSA has analyzed the stochastic nature of the protein translation process, testing it with computer simulations. "We considered a specific aspect of translation: the distribution of binding times (BT) that is the time needed for tRNA (a molecule capable of transporting amino acids) to carry the proper amino acid to the 'matrix' (mRNA) which 'prints' the proteins according to a specific code", explains Pierangelo Lombardo, who carried out the research together with Luca Caniparoli – both from SISSA. "This time interval is not always the same, but it varies in a more or less random manner".

"Imagine you know there is an average BT value, for example 1, which can be used conventionally when describing the system. In actual fact, however, each time we observe the process the value may be 1.1, 0.9, 0.7, 1.3 and so on. The value assumed each time by the BT changes in a stochastic, though not completely random, manner because it distributes into a cloud with a specific shape around the mean", continues Lombardo. "The shape of this cloud is not indifferent, as it has an effect on the time needed for process of protein synthesis. What we found in our study is that the BT fluctuates more (i.e., the cloud is more spread out) than previously thought and consequently so does the time needed for ".

"Observations like this extend our knowledge on protein synthesis processes", he concludes. "Knowing how translation times decrease and increase may also be useful to understand under which conditions these mechanism can fail".

Gene expression consists in building proteins (or other macromolecules) starting from the genetic information contained in the DNA. The process occurs inside the cells. The original matrix of proteins are genes, small parts of DNA contained in the cell nucleus. The sequence of elements (nucleotides) making up the DNA contains the information needed for building proteins.

Simplifying the process greatly, we can say that first a sort of carbon copy is made of the sequences encoded in the gene. This first step is called "transcription": a portion of DNA is copied into a small RNA molecule, termed mRNA or messenger RNA. This portion travels to the parts of the cell where the second step, translation (or ), takes place with the help of structures called ribosomes which "read" the mRNA sequence and collect the material needed to build the protein.

Proteins, in fact, are made up of long chains of amino acids, the tiny building blocks normally found dissolved in the cytoplasmic fluid. Some small RNA molecules, called tRNA and different from mRNA, bind specifically to amino acids giving rise to tRNA-amino acid complexes. These complexes then go and interlock, like the teeth of a zipper, with the chain of mRNA, one after the other into the proper sequence of amino acids, which bind to each other to form the strand of protein.

Explore further: To live and learn: Making memories has to be a speedy business

More information: "Nonequilibrium stochastic model for tRNA binding time statistics." Luca Caniparoli, Pierangelo Lombardo. Volume 89 " Issue 1 Phys. Rev. E 89, 012712 (2014). DOI: 10.1103/PhysRevE.89.012712

Related Stories

Study shows stressed-out cells halt protein synthesis

January 9, 2013

(—Cells experience stress in multiple ways. Temperature shifts, mis-folded proteins and oxidative damage can all cause cellular stress. But whatever the form of the stress, all cells quickly stop making proteins ...

Study reveals key step in protein synthesis

June 27, 2013

Scientists at the University of California, Santa Cruz, have trapped the ribosome, a protein-building molecular machine essential to all life, in a key transitional state that has long eluded researchers. Now, for the first ...

'Rhythm' of protein folding encoded in RNA, biologists find

January 31, 2013

(—Multiple RNA sequences can code for the same amino acid, but differences in their respective "optimality" slow or accelerate protein translation. Stanford biologists find optimal and non-optimal codons are consistently ...

A protein complex for the long haul

November 18, 2013

A multiprotein complex called TREX plays a key role in expression of the genetic information. Moreover, as a new study demonstrates – the longer the gene, the greater the need for TREX function.

Biologists simulate a cell in action

July 2, 2013

( —The inner workings of a cell involve hundreds of thousands of discrete molecules, engaged in a repeating cycle of interactions that sustain life.

Recommended for you

Researchers discover new rules for quasicrystals

October 25, 2016

Crystals are defined by their repeating, symmetrical patterns and long-range order. Unlike amorphous materials, in which atoms are randomly packed together, the atoms in a crystal are arranged in a predictable way. Quasicrystals ...

Making silicon-germanium core fibers a reality

October 25, 2016

Glass fibres do everything from connecting us to the internet to enabling keyhole surgery by delivering light through medical devices such as endoscopes. But as versatile as today's fiber optics are, scientists around the ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.