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M Ycas

Publications and source records attributed to M Ycas.

At least 19 recordsLinked to original sources
PubMed1999

Codons and hypercycles.

Several hypotheses on the origin of codon assignments imply that the present protein synthesizing machinery was already in place when the assignments were made. These are examined by computer modeling. The results do not suggest that assignments were optimized for resistance to reading and mutation errors, nor that the assignments are random. It is improbable that the number of species of amino acids increased in the course of evolution. An originally ambiguous dictionary is likely to have been subject to error catastrophe and is improbable. A relation between amino acid properties and their codons exists, and suggests that the codon assignments were established at the time of origin of the hypercycle, i.e. a system of aminoacyl synthetases which attaches amino acids to tRNA, and before the present protein synthesizing machinery was in place. The origin of a hypercycle is only possible if the system began with components which were catalytically active even when they did not form a self-replicating system. A model of such a system is proposed.

Amino Acids↗
PubMed1990

Computing tertiary structures of proteins.

Using only data on sequence, a method of computing a low-resolution tertiary structure of a protein is described. The steps are: (a) Estimate the distances of individual residues from the centroid of the molecule, using data on hydrophobicity and additional geometrical constraints. (b) Using these distances, construct a two-valued matrix whose elements, the distances between residues, are greater or less than R, the radius of the molecule. (c) Optimize to obtain a three-dimensional structure. This procedure requires modest computing facilities and is applicable to proteins with 164 residues and presumably more. It produces structures with r (correlation between inter-residue distances in the computed and native structures) between 0.5 and 0.7. Furthermore, correct inference of two or three long-range contacts suffices to yield structures with r values of 0.8-0.9. Because segments forming parallel or antiparallel folding structures intersect the radius vector at similar angles, from centroidal point distances it is possible to infer some of these long-range contacts by an elaboration of the procedure used to construct the input matrix. A criterion is also described which can be used to determine the quality of a proposed input matrix even when the native structure is not known.

Amino Acid Sequence↗
PubMed1976

The error catastrophe hypothesis and aging.

A theory of the propagation of errors in the system of enzymes translating genetic information into proteins developed earlier is extended to include errors at the transcription level. The theory is compared to other statistical theories. The properties are defined of the protein synthesizing machineries, especially those of the erroneous enzymes, which give catastrophe, stable self-replication containing errors, recovery from errors, etc. Experimental data are analyzed in light of the theory to determine the validity of the error catastrophe hypothesis of aging.

Aging↗
PubMed1976

On certain homologies between proteins.

Using, in part, comparisons between reconstructed ancestral sequences, homologies are suggested between certain proteins. Genetically related groups seem to be: 1. pancreatic and bacterial nucleases, 2. lysozymes and subtilisins, 3. c type cytochromes, ferredoxins and rubredoxins, 4. b type cytochromes, myoglobins and hemoglobins, catalase, and glutamic dehydrogenase. These homologies suggest that a given ancestral sequence can evolve into quite different tertiary structures.

Amino Acid Sequence↗
PubMed1976

Origin of periodic proteins.

Certain proteins, of which collagen is the best known example, have an approximately periodic sequence of amino acids. Evidence is available that the nucleic acid templates of at least some of these proteins have a large amount of internal self-complementarity. It is difficult to explain the origin of such proteins from nonperiodic proteins by accumulation of single amino acid replacements. A saltatory origin is suggested; the process would be a repetitive replication of a small nucleic acid segment. Internal self-complementarity occurs because the repeating segment incorporates sequences from both strands of DNA. The same process could produce RNA with a large amount of internal self-complementarity; tRNA may be an example.

Amino Acid Sequence↗
PubMed1969

Albert Tyler.

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Biology↗