Free-energy dissipation constraints on the accuracy of enzymatic selections

Structural insights into translational fidelity

The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.

Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites

An information analysis of the 5' (donor) and 3' (acceptor) sequences spanning the ends of nearly 1800 human introns has provided evidence for structural features of splice sites that bear upon spliceosome evolution and function: (1) 82% of the sequence information (i.e. sequence conservation) at donor junctions and 97% of the sequence information at acceptor junctions is confined to the introns, allowing codon choices throughout exons to be largely unrestricted. The distribution of information at intron-exon junctions is also described in detail and compared with footprints. (2) Acceptor sites are found to possess enough information to be located in the transcribed portion of the human genome, whereas donor sites possess about one bit less than the information needed to locate them independently. This difference suggests that acceptor sites are located first in humans and, having been located, reduce by a factor of two the number of alternative sites available as donors. Direct experimental evidence exists to support this conclusion. (3) The sequences of donor and acceptor splice sites exhibit a striking similarity. This suggests that the two junctions derive from a common ancestor and that during evolution the information of both sites shifted onto the intron. If so, the protein and RNA components that are found in contemporary spliceosomes, and which are responsible for recognizing donor and acceptor sequences, should also be related. This conclusion is supported by the common structures found in different parts of the spliceosome.

Differential pattern of misreading induced by streptomycin in vitro

A simplified, plasmid-directed coupled system was used to study the effect of streptomycin on the accuracy of natural messenger translation in vitro. The interaction of six different codons with their cognate tRNAs and 18 non-cognate tRNAs was analysed in the presence and absence of the antibiotic. Streptomycin appeared to modify, to a varying extent, the frequency of errors in codon-anticodon recognition. From this observation, some rules for mistranslation were inferred.

Free energy and time economy for the mutual selection of monomers in biosynthesis, primarily protein synthesis

The starting point of this work is the fact that the correction of errors in biosynthesis must be paid for by an increased dissipation (free energy loss) or a time delay. Further, a low accuracy is wasteful in this respect as the cell then produces a number of non-functioning products with a significant "production cost". One can then look for the situations of best "economy" for the selection processes. This is particularly obvious in reciprocal selections, where in some cases a substrate A shall be selected but discriminated against a competitor B, and in other cases, the opposite is true, B shall be selected with A as a competitor. It can be expected only in certain symmetric situations that these reciprocal selections are made in an equal way. Because one substrate shall be selected more often or it may be more relevant for the product, it may occur in higher concentrations and/or be selected more accurately (at a higher cost). The opposite selection may then be less accurate. The work studies various aspects of this.

Theoretical modelling of protein synthesis

This article provides an overview of the use of mathematical and computer modelling in furthering the understanding of protein synthesis. In particular, we discuss issues such as the nature of the rate limiting step(s), error rates, tRNA-codon adaptation, codon bias, attenuation control, and problems of selection and error corrections, focussing on their theoretical treatment.

Constraints on the accuracy of messenger RNA movement

Theoretical as well as experimental studies of translational accuracy have most often been concerned with the selection of aminoacyl-tRNA by codon-programmed ribosomes. The selection of the successive codons on the mRNA has received much less attention, probably because it represents both conceptually and experimentally, a much more demanding physical problem. Nevertheless, it would seem that errors in the selection of the codon are potentially much more destructive than errors in selection of aminoacyl-tRNA species. This can be appreciated from the following.

Logical elements in living cells

Recognition processes with enhanced accuracy (as performed by structures like enzymes or ribosomes) are investigated using elementary ideas of statistical mechanics and related concepts of thermodynamics. The analysis starts from a formal definition of recognition and provides a correspondence with appropriate physical properties of the macromolecular logical elements. Transitions of the recognizing system between different modifications are a necessary feature of a more exacting recognition process. Rearrangement steps provide the process with higher accuracy by performing two physical operations: (1) rearranging the phase space of the system so that the "correct" states be better separated from the "wrong" states and the probability of occupation of the "correct" states be enhanced, (2) directing the process toward the more favourable modifications thus formed. Both operations are related to changes in the physical properties of the recognizing system. These changes can be expressed as differences of macromolecular Gibbs energy levels; if ligand binding or release participate in a step, directivity of the step depends also on the actual chemical potentials of the ligands in solution. The two operations just mentioned resemble two basic operations known to be necessary in electronic digital networks: directivity of control and signal standardization. An analysis of the entire reaction catalysed by a macromolecular logical element takes into account the requirements imposed by the logical functions as well as the need that the chemical potential of the product be not restricted to very low values. To satisfy these conditions, the reaction must be supported by a so-called non-specific reaction, usually implemented by the cleavage reaction of a nucleoside triphosphate.

Costs of accuracy determined by a maximal growth rate constraint

The present study is best understood as an extension and critique of two schools of thought. The first is that of Malloe and his students, among whom we number ourselves. It is to Maaloe that we are indebted for the idea that logarithmically growing bacteria assemble and use tibosomes in amounts that are optimally adjusted to yield the maximal growth rates supported by different media. Her, we begin our analysis by applying this optimization priciple to all the components of a logarithmically growing system. Our objective is to use the growth optimization constraint as a tool to explore the physiological limits on the accuracy of gene expression. This brings us to our second source of inspiration, which is Orgel's (1963) conception of a problem that Ninio (1982) has referred to as the ‘great error loop’.

Free energy cost and accuracy in branched selection processes of biosynthesis

Selection in biochemical synthesis processes is a very important task: processes as protein or nucleic acid synthesis must be very accurate although the cell abounds with closely related molecules which, intuitively, should be difficult to distinguish. The mechanisms of selection and the underlying processes have been extensively studied in the last years, and the ideas have been developed into mathematical models to visualize the potentials of recognition and error correction. There are several aspects on this, the main aspect of the present work being the important fact that the cell must pay for the increased accuracy in terms of available free energy: processes are driven from equilibrium, and do away with appreciable dissipation.

Information-theoretic significance of Gibbs energy supply to editing mechanisms

If a branched multistep editing mechanism is implemented by an enzyme with a single site for the specific substrates, there is no reason to believe that the number of testing steps is fixed and cannot be controlled by some external factors. The paper considers the mechanisms of single- or multistep editing done in response to various factors, particularly to the value of displacement from the reaction equilibrium. To avoid a complicated analysis of a fully specified case, which would be likely to obscure the general significant features, the operating modes of those mechanisms are estimated using the method of minimizing associated information gains. It turns out that sufficiently far from equilibrium the variable mechanisms can essentially operate just as well as the fixed multistep mechanisms.