A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: “once a gap, always a gap”. The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods.

Progressive sequence alignment as a prerequisite to correct phylogenetic trees.

http://aracnologia.macn.gov.ar/st/biblio/de%20Pinna%201991%20homology%20in%20the%20cladistic%20paradigm.pdf

Concepts and tests of homology in the cladistic paradigm

Multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence-structure relationships. Until recently, it has been impractical to apply dynamic programming, the most widely accepted method for producing pairwise alignments, to comparisons of more than three sequences. We describe the design and application of a tool for multiple alignment of amino acid sequences that implements a new algorithm that greatly reduces the computational demands of dynamic programming. This tool is able to align in reasonable time as many as eight sequences the length of an average protein.

https://www.pnas.org/content/pnas/86/12/4412.full.pdf

A tool for multiple sequence alignment

The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit.

From the Publisher:
Computational methods are increasingly used in conjunction with organic, inorganic, medicinal, biological, physical, and analytical chemistry and research as well as in biotechnology, materials science, and physics. Individuals in these fields must understand and stay current with recent developments in the field. This series brings together leading authorities in the field of computer-aided molecular research. Volume 11 explores computer-aided ligand design and modeling of biomolecules.

Reviews in Computational Chemistry

SUMMARY The insulin-like growth factors and hystricomorph insulins have been modelled by interactive computer graphics on the assumption that their sequence homology to insulin implies that they will have a similar tertiary structure. These studies suggest that, although the insulin-related molecules can adopt the insulin fold, they are unlikely to form hexamers and if they form dimers they will be of reduced stability. The non-suppressibility of insulin-like growth factors by anti-insulin antibodies is explained in terms of differences of surface residues in the region A8–A10 and B1–B5. Receptor affinity of insulins and insulin-like growth factors for insulin receptors is explicable in terms of a receptor-binding site in the vicinity of B25 Phe on the insulin surface. An equivalent region around B25 Tyr of insulin-like growth factors may be responsible for their binding to type 1 receptors, although binding type 2 receptors must involve a different surface region not shared by insulin.

The conformation of insulin-like growth factors: relationships with insulins.

The fact that biological information is stored in the form of DNA has led some molecular biologists and biophysicists to the view that evolutionary history will be most evident in DNA sequences. This view is attractive, for there is a redundancy in the genetic code, and the number of base changes is a sensitive indicator of evolutionary distances between closely related gene sequences. However, selective pressures in evolution will be mainly on the functions of the proteins as manifested in the whole organism. These are dependent on certain critical amino acids, such as those that constitute catalytic groups or substrate binding sites, and on the maintenance of a stable three-dimensional structure. The invariant functionally impor­ tant amino acids may comprise a very small percentage of the total. Furthermore, because many differing amino acid sequences are able to attain the same three-dimensional arrangement of the polypeptide main­ chain, we may conclude that there may be little restraint on amino acid sequences over long periods of time. Variations of the DNA sequences will be even more extensive as a result of codon redundancy, so that there may be little statistically significant resemblance to an ancestral gene sequence. Thus it is in tertiary structures that the most distant relationships between proteins may be evident. For these reasons this review is unashamedly concerned with tertiary structures in the evolution of proteins. We begin with a discussion of tech­ niques for comparing the relatedness of protein structures, with particular

Evolution and the tertiary structure of proteins

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The conformation of insulin-like growth factors: relationships with insulins.

Evolution and the tertiary structure of proteins