Lois T. Hunt

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.

A surprising new protein superfamily containing ovalbumin, antithrombin-III, and alpha1-proteinase inhibitor

Abstract A distant relationship between chicken ovalbumin and two human plasma protease inhibitors was revealed by computer analyses. We propose a new protein superfamily containing at least three families: ovalbumin (and probably gene X and gene Y proteins), antithrombin-III, and alpha 1 -proteinase inhibitor. Although these families may have diverged from a common ancestor more than 500 million years ago, they may still share similarity in gene structure as well as in protein sequence.

Amino-terminal sequence identity of ubiquitin and the nonhistone component of nuclear protein A24

Abstract The amino-terminal 37 residues of bovine and human ubiquitin and of the nonhistone component from bovine nuclear protein A24 are identical. The probability that the two proteins are unrelated is infinitesimal. That they share such a highly conserved sequence indicates that they perform a cell function of basic importance and have a common evolutionary origin. They may even be products of the same gene. We make several suggestions concerning their structural and functional relationships based on a correlation of existing information.

Evolution of protein complexity : the blue copper-containing oxidases and related proteins

SummaryThe blue copper proteins and their relatives have been compared by sequence alignments, by comparison of three-dimensional structures, and by construction of phylogenetic trees. The group contains proteins varying in size from 100 residues to over 2,300 residues in a single chain, containing from zero to nine copper atoms, and with a broad variation in function ranging from electron carrier proteins and oxidases to the blood coagulation factors V and VIII. Difference matrices show the sequence difference to be over 90% for many pairs in the group, yet alignment scores and other evidence suggest that they all evolved from a common ancestor. We have attempted to delineate how this evolution took place and in particular to define the mechanisms by which these proteins acquired an ever-increasing complexity in structure and function. We find evidence for six such mechanisms in this group of proteins: domain enlargement, in which a single domain increases in size from about 100 residues up to 210; domain duplication, which allows for a size increase from about 170 to about 1,000 residues; segment elongation, in which a small segment undergoes multiple successive duplications that can increase the chain size 50-fold; domain recruitment, in which a domain coded elsewhere in the genome is added on to the peptide chain; subunit formation, to form multisubunit proteins; and glycosylation, which in some cases doubles the size of the protein molecule. Size increase allows for the evolution of new catalytic properties, in particular the oxidase function, and for the formation of coagulation factors with multiple interaction sites and regulatory properties. The blood coagulation system is examined as an example in which a system of interacting proteins evolved by successive duplications of larger parts of the genome. The evolution of size, functionality, and diversity is compared with the general question of increase in size and complexity in biology.

Mutation data matrix and its uses.

Publisher Summary This chapter describes the mutation data matrix (MDM) and its application for comparing protein sequences. Basic to all sequence comparison is the concept of an alignment that defines the relationship between sequences on a residue-by-residue basis. Sequence comparison methods use a scoring matrix that assigns a value to each possible pair of aligned amino acids. One of the most widely used similarity measures is the mutation data matrix (MDM) developed by Dayhoff and colleagues. The first MDM, published in 1968, was derived from over 400 accepted point mutations between present-day sequences and inferred ancestral sequences. Within the Markovian model, the MDM is derived from a transition probability matrix in which each matrix element gives the probability that amino acid A will be replaced by amino acid B in one unit of evolutionary change. The diagonal elements give the probabilities that the amino acids will remain unchanged. The probability of an amino acid being replaced is estimated as its relative mutability, which is calculated as the ratio of the number of observed changes of an amino acid to its total exposure to change.

Sequence similarity between cholera toxin and glycoprotein hormones: Implications for structure activity relationship and mechanism of action

Abstract The B chain of cholera toxin and the β subunits of thyrotropin, luteinizing hormone, human chorionic gonadotropin, and follicle-stimulating hormone are shown to have a region of sequence analogy believed to correlate with their ability to bind to receptors on cell membranes. A possible sequence analogy is also defined in the α subunits of these glycoprotein hormones and a region of the cholera toxin A 1 chain believed to be responsible for adenylate cyclase activation.

Epidermal growth factor: Internal duplication and probable relationship to pancreatic secretory trypsin inhibitor

Abstract The sequence of the first half of epidermal growth factor is related to that of the second half, indicating a gene elongation through duplication; it is also similar to that of pancreatic secretory trypsin inhibitor, which suggests a common evolutionary origin for these two proteins. Statistical evaluation shows that it is very unlikely that either similarity in sequence could have occurred by chance. The two proteins may also be functionally related, as each forms a complex with an arginine esterase.

New perspectives on bacterial ferredoxin evolution

SummaryRecent evidence indicates that a gene transposition event occurred during the evolution of the bacterial ferredoxins subsequent to the ancestral intrasequence gene duplication. In light of this new information, the relationships among the bacterial ferredoxins were reexamined and an evolutionary tree consistent with this new understanding was derived. The bacterial ferredoxins can be divided into several groups based on their sequence properties; these include the clostridial-type ferredoxins, theAzotobacter-type ferredoxins, and a group containing the ferredoxins from the anaerobic, green, and purple sulfur bacteria. Based on sequence comparison, it was concluded that the amino-terminal domain of theAzotobacter-type ferredoxins, which contains the novel 3Fe∶3S cluster binding site, is homologous with the carboxyl-terminal domain of the ferredoxins from the anaerobic photosynthetic bacteria.A number of ferredoxin sequences do not fit into any of the groups described above. Based on sequence properties, these sequences can be separated into three groups: a group containingMethanosarcina barkeri ferredoxin andDesulfovibrio desulfuricans ferredoxin II, a group containingDesulfovibrio gigas ferredoxin andClostridium thermoaceticum ferredoxin, and a group containingDesulfovibrio africanus ferredoxin I andBacillus stearothermophilus ferredoxin. The last two groups differ from all of the other bacterial ferredoxins in that they bind only one Fe∶S cluster per polypeptide, whereas the others bind two. Sequence examination indicates that the second binding site has been either partially or completely lost from these ferredoxins.Methanosarcina barkeri ferredoxin andDesulfovibrio desulfuricans ferredoxin II are of interest because, of all the ferredoxins whose sequences are presently known, they show the strongest evidence of internal gene duplication. However, the derived evolutionary tree indicates that they diverged from theAzotobacter-type ferredoxins well after the ancestral internal gene duplication. This apparent discrepancy is explained by postulating a duplication of one halfchain sequence and a deletion of the other halfchain. TheClostridium thermoaceticum andBacillus stearothermophilus groups diverged from this line and subsequently lost one of the Fe∶S binding sites.It has recently become apparent that gene duplication is ubiquitous among the ferredoxins. Several organisms are now known to have a variety of ferredoxins with widely divergent properties. Unfortunately, in only one case are the sequences of more than one ferredoxin from the same organism known. Thus, although the major features of the bacterial ferredoxin tree are now understood, a complete bacterial phylogeny cannot be inferred until more sequence information is available.

Cystatin domains in alpha-2-HS-glycoprotein and fetuin

We have found that chain A of alpha‐2‐HS‐glycoprotein contains two cystatin domains that show closest similarity to those of kininogen. Most likely, the two proteins diverged after the primary duplication of a single cystatin domain as the two cystatin domains of alpha‐2‐HS‐glycoprotein are more similar, especially in disulfide bonding, to the corresponding domains of kininogen than to each other. We also propose that the carboxyl‐terminal (non‐cystatin) parts of kininogen and alpha‐2‐HS‐glycoprotein contain homologous segments. We suggest that alpha‐2‐HS‐glycoprotein may act as an inhibitor of the cysteine proteinases responsible for bone resorption. We have also found that fetuin is closely related to alpha‐2‐HS‐glycoprotein.

Von Willebrand factor shares a distinctive cysteine-rich domain with thrombospondin and procollagen

The identification of common domains among different proteins is of great interest at present. We have found that a cysteine-rich domain in thrombospondin, also present in types I and III procollagen alpha 1 chains, is related to two internally homologous domains in von Willebrand factor. In the four proteins these domains are similar in length (64-74 residues) and have nine invariant cysteines, some of which form intramolecular disulfide bonds. The structural and functional similarities of this domain in the four kinds of proteins, and its correspondence in procollagen to an exon, support our hypothesis of a common origin for the domain.