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At least 487 records · Page 27Linked to original sources
PubMed1991

Characterization and evolutionary aspects of a transcript encoding a neuropeptide precursor of Lymnaea neurons, VD1 and RPD2.

We isolated and characterized a cDNA clone encoding the major prohormone of VD1 and RPD2, two electrotonically coupled identified neurons in the central nervous system of the freshwater snail, Lymnaea stagnalis. The VD1/RPD2 prohormone may be cleaved to generate a set of 4 different neuropeptides, called epsilon, delta, alpha 1 and beta peptides, as well as a single aspartate. Since VD1 and RPD2 probably are involved in O2 perception and modulation of cardio-respiratory functions, it is thought that the neuropeptides synthesized and released by these neurons coordinate the adaptive physiological and behavioural processes that occur in response to changes in O2 availability. Comparison of the Lymnaea VD1/RPD2 precursor with two related precursors, prohormones R15-1 and R15-2, identified from neuron R15 in the marine mollusc Aplysia californica revealed a similar pattern of organization of the preprohormones. The overall homology is rather low, however, detailed comparisons show a highly differential pattern of conservation of peptide regions on the precursors.

Amino Acid Sequence↗
PubMed2005

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses.

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Base Composition↗
PubMed2005

Downhill protein folding: evolution meets physics.

Proteins can be redesigned to fold downhill on a free energy surface characterized by only a few coordinates, confirming a principal prediction of the 'energy-landscape' model. Nonetheless, natural proteins have small but significant barriers. Spectroscopy and kinetics reveal potential biological causes for activation barriers during protein folding: evolution against protein aggregation and for protein function.

Animals↗
PubMed2001

Molecular mechanism of stop codon recognition by eRF1: a wobble hypothesis for peptide anticodons.

We propose that the amino acid residues 57/58 and 60/61 of eukaryotic release factors (eRF1s) (counted from the N-terminal Met of human eRF1) are responsible for stop codon recognition in protein synthesis. The proposal is based on amino acid exchanges in these positions in the eRF1s of two ciliates that reassigned one or two stop codons to sense codons in evolution and on the crystal structure of human eRF1. The proposed mechanism of stop codon recognition assumes that the amino acid residues 57/58 interact with the second and the residues 60/61 with the third position of a stop codon. The fact that conventional eRF1s recognize all three stop codons but not the codon for tryptophan is attributed to the flexibility of the helix containing these residues. We suggest that the helix is able to assume a partly relaxed or tight conformation depending on the stop codon recognized. The restricted codon recognition observed in organisms with unconventional eRF1s is attributed mainly to the loss of flexibility of the helix due to exchanged amino acids.

Amino Acid Sequence↗
PubMed2002

Molecular evolution from abiotic scratch.

Recent papers on the emerging new theory of protein evolution are reviewed. Reconstruction of codon chronology, analysis of loop fold structure of proteins, and quantitative correspondence between optimal DNA ring closure size and protein domain size allow to outline specific stages in early protein evolution, each with its own size range.

Amino Acid Sequence↗
PubMed1988

The use of Markov chain models in studying the evolution of the proteins.

In a recent paper Giulio & Caldararo (1987) used a Markov chain model to study the evolution of proteins. Unfortunately, their use of a first-order Markov chain model at the amino acid level is incorrect. The model has to be applied at the codon level [Jorre & Curnow (1975a)] followed by amalgamation of the codon states corresponding to each amino acid and of the three codons specifying termination. The model is correctly applied in this paper. The results obtained do not differ substantially from those obtained by Giulio & Caldararo (1987). The interpretation of the results as supporting the neutralist view of protein evolution is criticized.

Amino Acids↗