Analysis of the code relating sequence to conformation in globular proteins. Theory and application of expected information

1. An information theory analysis of the folding of a globular protein is proposed. 2. The folding is seen as a transfer of information between two messages, the primary sequence and the biologically active conformation. 3. It is shown how the information transferred was estimated by inspection of proteins of known primary sequence and conformation. 4. In this estimation, concerted use of subjective (Bayesian) probabilities leads to a more robust approach which can be employed whether the number of proteins of known sequence and conformation is large or small. 5. Further, it is demonstrated that the problem then becomes a very simple algebraic formulation for information estimates. 6. Finally, it is shown how this process of information theory analysis can be reversed to predict the conformation of a protein by using its primary sequence and the above information estimates obtained from other proteins. 7. The present paper provides the theoretical basis for the derivation and application of a stereochemical alphabet (Robson & Pain, 1974a,c), and for an investigation of the effects of residues on the conformations of their neighbours (Robson & Pain, 1974b).     

Differential localisation of tyrosinated, detyrosinated, and acetylated alpha-tubulins in neurites and growth cones of dorsal root ganglion neurons

The comparative distribution of tyrosinated, detyrosinated, and acetylated alpha-tubulins was examined in neurites of rat dorsal root ganglion neurones in culture using immunofluorescence microscopy. Phase contrast observations of single neurones revealed that the neurites were actively motile, and rhodamine phalloidin staining of actin filaments showed the extent of lamellopodia and microspike projections from the growth cones. From double-labelling experiments using antibodies against tyrosinated, detryrosinated, or acetylated alpha-tubulin, it was found that the three different isoforms were differentially localised in neurites and growth cones. Detyrosinated and acetylated forms of alpha-tubulin were in the main restricted to the neurites extending no further than the base of the growth cones. Tyrosinated alpha-tubulin was, however, distributed throughout the body of the growth cone and into the base of some microspikes. Following treatment with taxol to promote microtubule assembly, detyrosinated and acetylated alpha-tubulins were found to be colocalised with tyrosinated alpha-tubulins throughout the growth cones of all cells examined. These results would be consistent with axonal transport of tyrosinated alpha-tubulin followed by assembly in the growth cone and subsequent detyrosination and acetylation. In addition the presence of unmodified alpha-tubulin in the growth cone may be necessary for the provision of labile microtubules for growth cone motility and extension.     

Phylogenetic relations between microbats, megabats and primates (Mammalia: Chiroptera and Primates)

We examine the paraphylectic hypothesis of bat origins, both in the light of previous discussions, and in the light of new evidence from our analyses of neurological traits and wing morphology. Megabats share with primates a variety of complex details in the organization of neural pathways that have not been found in any other mammalian group, particularly not in microbats. The features previously used to link microbats and megabats have been examined and found to be questionable bases for support of a monophyletic origin. In particular, morphological analyses of the musculoskeletal adaptations associated with the flight apparatus are consistent with two separate origins of the mammalian wing. Taken together, these analyses suggest that megabats evolved from an early branch of the primate lineage. This branch was comprised of moderate-sized, phytophagous gliders, of which the other living descendants are the dermopterans. Microbats, in contrast, probably evolved much earlier from small, agile insectivores whose forelimbs had long metacarpals in relation to their phalanges.     

Efficiency in evolutionary games: Darwin, Nash and the secret handshake

This paper considers any evolutionary game possessing several evolutionarily stable strategies, or ESSs, with differing payoffs. A mutant is introduced which will "destroy" any ESS which yields a lower payoff than another. This mutant possesses a costless signal and also conditions on the presence of this signal in each opponent. The mutant then can protect itself against a population playing an inefficient ESS by matching this against these non-signalers. At the same time, the mutants can achieve the more efficient ESS against the signaling mutant population itself. This construction is illustrated by means of the simplest possible example, a co-ordination game. The one-shot prisoner's dilemma is used to illustrate how a superior outcome which is not induced by an ESS may be temporarily but not permanently attained. In the case of the repeated prisoner's dilemma, the present argument seems to render the "evolution of co-operation" ultimately inevitable.     

Genetic and transgenic evidence that phytochromes A and B act to modulate the gravitropic orientation of Arabidopsis thaliana hypocotyls

Hypocotyls of Arabidopsis thaliana exhibit negative gravitropism in the dark, growing against the gravity vector. The direction of growth is randomized in red light (R). In single mutants lacking either phytochrome A or B randomization of hypocotyl orientation in R is retained. However, a double mutant lacks this response, indicating that either phytochrome A or B is capable of inducing randomization and phytochrome A and B are the only phytochromes involved in this process. The induction of randomization was confirmed using lines that express to different levels PHYA and PHYB cDNAs. Overexpression of PHYA cDNAs induced randomization of hypocotyl orientation in the dark. Dark randomization was also seen in the phyB-1 mutant but not in two other phyB alleles, suggesting that dark randomization in the phyB-1 line may be due to a second mutation. When germination was induced by gibberellin, rather than exposure to brief white light, randomization in the dark associated with phytochrome A overproduction was not observed but was retained in the phyB-1 mutant. Overexpression of PHYB cDNAs induced a light-dependent randomization of hypocotyl orientation that responded to R:far-red light ratio. We conclude that the default situation in Arabidopsis hypocotyls is, therefore, negative gravitropism, and either phytochrome A or phytochrome B can mediate randomization.     

Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals

alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical to recognition of and binding to target proteinases, is highly divergent within and among species. This appears to be a consequence of accelerated rates of evolution that may have been driven by positive Darwinian selection. In order to examine this and other features of alpha 1-PI evolution in more detail, we have isolated and sequenced cDNAs representing alpha 1- PI mRNAs of the mouse species Mus saxicola and Mus minutoides and have compared these with a number of other mammalian alpha 1-PI mRNAs. Relative to other mammalian mRNAs, the extent of nonsynonymous substitution is generally high throughout the alpha 1-PI mRNA molecule, indicating greater overall rates of amino acid substitution. Within and among mouse species, the 5'-half of the mRNA, but not the 3'-half, has been homogenized by concerted evolution. Finally, the reactive center is under diversifying or positive Darwinian selection in murid rodents (rats, mice) and guinea pigs yet is under purifying selection in primates and artiodactyls. The significance of these findings to alpha 1-PI function and the possible selective forces driving evolution of serpins in general are discussed.