tRNA acceptor stem and anticodon bases form independent codes related to protein folding

Abstract

Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3′ acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each sidechain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for β-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or β-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.genetic code | aminoacyl-tRNA synthetases | urzymes | multivariate regression | protein folding T he genetic code is implemented by two distinct superfamilies of protein-RNA complexes between an aminoacyl-tRNA synthetase (aaRS) from one of two classes (1, 2) and its cognate tRNA. These recognition complexes effect the transfer of activated amino acids to the correct tRNA molecule, producing aminoacyl-tRNAs needed for protein synthesis by the ribosome. Errors in charging are rare (3, 4), and it is generally agreed that the low frequency of mischarging is based on synthetase recognition of specific identity elements in tRNA molecules (5). Many investigators (6-8) have observed that the codon table tends to reduce deleterious effects of point mutations (9) by assuring that they do minimal violence to the physical requirements of protein folding. One earlier study (10) identified a nonrandom tendency for hydrophilic side-chains to be coded by an A as the second codon base, hinting at more extensive relationships between the code and factors that direct protein folding.tRNA identity elements (5, 11) map to both the anticodon and acceptor stem at opposite ends of the L-shaped tRNA molecule and are distinct from binding determinants for elongation factorTu in the T-stem (12). Invariant cores of both classes of aaRS, termed urzymes (from the prefix ur-= primitive), lack anticodon-binding domains and cannot recognize the anticodon. However, they catalyze amino acid activation and acyl transfer with K M values approaching those of contemporary aaRS, consistent with their participation in early protein synthesis (13-16). The implied ability of ancestral aaRS to recognize tRNA acceptor stems, but not anticodons, is consistent with the suggestion that the earliest proteins were coded no...

Temperature dependence of amino acid hydrophobicities

“…Our recent reanalysis indicates that two separate codes, for amino acid size and hydrophobicity, appear to be embedded in tRNA sequences, with size encoded in the acceptor stem and hydrophobicity embedded in the anticodon (16). One aim of the present work was to determine whether these relationships are likely to have been maintained at elevated temperatures.…”

“…Thus, a pyrimidine at the second codon position signals amino acids whose average hydrophobicity is much greater than those coded by a purine at the same position (2,3). The values reported here allow a more detailed analysis, described in a companion paper (16), which reveals that two separate codes for amino acid size and hydrophobicity appear to be embedded in different parts of their tRNA sequences, with size (represented by vapor-to-cyclohexane equilibria) encoded in the acceptor stem, and hydrophobicity (represented by water-to-cyclohexane equilibria) embedded in the anticodon. Would one expect these relationships to be maintained at elevated temperatures?…”

tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

“…11 Class II amino acids occur significantly more frequently at the surfaces of proteins, whereas Class I amino acids occur more frequently in their cores.…”

“…10 The use of partition coefficients, rather than solubilities, avoids anomalies arising from idiosyncratic properties of the solid state. 8,10 In two recent papers 11,12 we described a procedure for estimating the distribution of amino acids between the surfaces and cores of folded proteins, based on these experimental transfer free energies. Previous quantitative relationships between polarity and folding fell short of accounting for the surface-to-core distributions observed for different amino acids in folded proteins.…”

Amino acid physical chemistry furnishes a two-dimensional basis set for computational structural biology

“…Recent work on aminoacyl-tRNA synthetase recognition elements in tRNA highlighted the possibility that experimental transfer free energies from water to cyclohexane and vapor to cyclohexane-closely related to side chain hydrophobicity and sizefor side chain mimics furnish an improved basis set to account for the accessible surface areas in folded proteins of 18 of the 20 amino acids [1,2]. Cysteine and proline are outliers, presumably because their roles in metal binding and in turns, respectively, produce large deviations in their expected distributions in folded proteins.…”