Margaret O. Dayhoff

Establishing homologies in protein sequences.

Computer-based statistical techniques used to determine homologies between proteins occurring in different species are reviewed. The technique is based on comparison of two protein sequences, either by relating all segments of a given length in one sequence to all segments of the second or by finding the best alignment of the two sequences. Approaches discussed include selection using printed tabulations, identification of very similar sequences, and computer searches of a database. The use of the SEARCH, RELATE, and ALIGN programs (Dayhoff, 1979) is explained; sample data are presented in graphs, diagrams, and tables and the construction of scoring matrices is considered.

Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences

The structure of present-day ferredoxin, with its simple, inorganic active site and its functions basic to photon-energy utilization, suggests the incorporation of its prototype into metabolism very early during biochemical evolution, even before complex proteins and the complete modern genetic code existed. The information in the amino acid sequence of ferredoxin enables us to propose a detailed reconstruction of its evolutionary history. Ferredoxin has evolved by doubling a shorter protein, which may have contained only eight of the simplest amino acids. This shorter ancestor in turn developed from a repeating sequence of the amino acids alanine, aspartic acid or proline, serine, and glycine. We explain the persistence of living relics of this primordial structure by invoking a conservative principle in evolutionary biochemistry: The processes of natural selection severely inhibit any change a well-adapted system on which several other essential components depend.

The occurrence in proteins of the tripeptides Asn-X-Ser and Asn-X-Thr and of bound carbohydrate☆

Abstract The 101 occurrences of the tripeptides Asn-X-Ser and Asn-X-Thr in the available protein sequence data are tabulated; carbohydrate is found, attached to the asparagine, in not more than 20 of the 101 tripeptides. A statistical analysis of the data from all completely sequenced proteins shows that the observed frequency of occurrence of the two kinds of tripeptides is only about 65% of the expected. This lowered frequency is evidence for a newly postulated kind of limitation—which we call a “restricted sequence”—imposed by natural selection on the primary structure of proteins.

Venus: Atmospheric Evolution

Because of the high temperatures prevailing in the lower atmosphere of Venus, its chemistry is dominated by the tendency toward thermodynamic equilibrium. From the atomic composition deduced spectroscopically, the thermodynamic equilibrium composition of the atmosphere of Venus is computed, and the following conclusions drawn. (i) There can be no free carbon, hydrocarbons, formaldehyde, or any other organic molecule present in more than trace amounts. (ii) The original atomic composition of the atmosphere must have included much larger quantities of hydrogen and a carbon/oxygen ratio ≤ 0.5. (This ratio is now almost precisely 0.5.) (iii) The present atomic proportions of the atmosphere of Venus are so unique that an evolutionary mechanism involving two independent processes seems necessary, as follows. Water, originally present in large quantities, has been photodissociated in the upper atmosphere, and the resulting atomic hydrogen has been lost in space. The resulting excess oxygen has been very effectively bound to the surface materials. (iv) There must be some weathering process, for example, violent wind erosion, to disturb and expose a sufficient quantity of reduced surface material to react with the oxygen produced by photodissociation.

ukaryotes versus Prokaryotes: An Estimate of Evolutionary Distance

The divergence of nucleated organisms and bacteria was 2.6 times more remote in evolution than the divergences of the nucleated organisms into sparate kingdoms, as evidenced by genetic changes in cytochrome c and transfer RNA. The development of the genetic code through the differentiation of transfer RNAs for different amino acids was still more remote in evolution. The overall states of transfer RNA evolution in bacteria and nucleated organisms were comparable.

MASSPEC: A computer program for complete sequence analysis of large proteins from mass spectrometry data of a single sample

Abstract A new method is suggested here for determining the amino acid sequence of proteins from the mass spectrum of a single solution. A computer simulation of the reconstruction of the sequence from ideal mass-spectrometer data is presented. The method requires first the random fragmentation of a protein, as by partial acid hydrolysis. Volatile derivatives of the fragments, still mixed together, must next be made. The mass measurements are performed on the mixture of volatile derivatives. All the required chemical treatments would be simple and of such nature that the whole analysis, beginning with a sample of purified protein and ending with the computer printout of the amino acid sequences, could be made rapidly. The required amount of volatile derivative protein sample is expected to be very small, of the order of 1 mg. This should make feasible various experiments, for example with single organisms which are impossible at present.