The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

/pdf/gapped-blast-and-psi-blast-a-new-generation-of-protein-2ybl67x5yx.pdf

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

CHAPTER 24 – Evolution of Protein Molecules

A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized least-squares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3 +/- 11.7, 13.3 +/- 1.5, 10.9 +/- 1.2, 3.7 +/- 0.6, and 2.7 +/- 0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the pipedal creature Australopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a proto-chimpanzee after the former had developed bipedalism.

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.

Solvent content of protein crystals.

Peptidoglycan types of bacterial cell walls and their taxonomic implications.

The structure of normal adult human hemoglobins

Of two closely related species of geese, one, the greylag goose, lives in the Indian plains all year round, while the other, the bar-headed goose, lives at the Tibetan lakes and migrates across the Himalayas to winter in India. Another species, the Andean goose, lives in the High Andes all year round. Possession of a Hb with high oxygen affinity helps to adapt bar-headed and Andean geese to high altitudes. The Hb amino acid sequences of the bar-headed and the greylag geese differ by four substitutions, of which only one is unique among bird sequences: Pro-119 alpha (H2)----Ala. Perutz proposed that the two-carbon gap left by this substitution at the alpha 1 beta 1 contact raises the oxygen affinity, because it relaxes the tension in the deoxy or T structure [Perutz, M. F. (1983) Mol. Biol. Evol. 1, 1-28]. It was later found that the Hb of the Andean goose has a gap in the same position, due to the complementary substitution Leu-55 beta (D6)----Ser. We have tested Perutz's hypothesis by introducing each of these substitutions into human globin synthesized in Escherichia coli. The reconstituted Hbs combine cooperatively with oxygen. Their oxygen affinities exceed that of normal human Hb by an even larger factor than that found between the high-flying geese and the greylag goose. The mutant Hb Met-55 beta (D6)----Ser was crystallized. Its structure is the same as that of HbA, except in the immediate environment of the gap left by the substitution of the serine for the methionine side chain, which evidently causes the increased oxygen affinity of this Hb.

https://www.pnas.org/content/pnas/88/15/6519.full.pdf

Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering.

Virusproteine, IV. Die Konstitution des Hüllproteins des Phagen fd

The complete amino acid sequence of the basic nuclear protein of bull spermatozoa.

Partial amino acid sequences of six major subunits of bovine β-crystallin have been determined by automatic liquid-phase Edman degradation and the dansyl-Edman procedure, complemented by amino acid analyses of peptides. The results show that, including the previously established βBp sequence [H. P. C. Driessen et al. (1981) Eur. J. Biochem. 121, 83–91], there exist at least seven primary gene products in bovine β-crystallin, which exhibit 40% or more sequence homology. Two of the gene products are completely identical except for the presence in one of them of 17 additional residues at the N terminus, possibly caused by differential splicing of the same primary RNA transcript. The rate of evolutionary change of the β chains (4% sequence change per 100 × 106 years) is about equally slow as that of α-crystallin, and the gene duplications giving rise to the different chains must have occurred very early in vertebrate evolution. The β chains can be divided into two groups, according to sequence homology and presence of deletions/insertions and C-terminal extension, on which basis a new, rational nomenclature for the β subunits is introduced. The N-terminal extensions of all β chains are very different in length and sequence, even between homologous β chains in different species. Possible explanations for this finding are discussed.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1984.tb08029.x

Gerhard Braunitzer

Papers

The structure of normal adult human hemoglobins

Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering.

Virusproteine, IV. Die Konstitution des Hüllproteins des Phagen fd

The complete amino acid sequence of the basic nuclear protein of bull spermatozoa.

Homology between the primary structures of the major bovine beta-crystallin chains.