Christoph de Haën

“Homology” in proteins and nucleic acids: A terminology muddle and a way out of it

“Homology” has the precise meaning in biology of “having a common evolutionary origin,” but it also carries the loose meaning of “possessing similarity or being matched.” Its rampant use in the loose sense is clogging the literature on protein and nucleic acid sequence comparisons with muddy writing and, in some cases, muddy thinking In its precise biological meaning, “homology” is a concept of quality. The word asserts a type of relationship between two or more things. Thus, amino acid or nucleotide sequences are either homologous or they are not. They cannot exhibit a particular “level of homology” or “percent homology.” Instead, two sequences possess a certain level of similarity. Similarity is thus a quantitative property. Homologous proteins or nucleic acid segments can range from highly similar to not recognizably similar (where similarity has disappeared through divergent evolution). If using “homology” loosely did not interfere with our thinking about evolutionary relationships, the way in which we use the term would be a rather unimportant semantic issue. The fact is, however, that loose usage in sequence comparison papers often makes it difficult to know the authors intent and can lead to confusion for the reader (and even for the author). There are three common situations in which hazards arise by using “homology” to mean similarity. The first case is the most obvious offense but perhaps the least troublesome. Here an author identifies sequence similarities (calling them homologies) but claims that the sequences being compared are not evolutionarily related. Some awkward moments occur in such a paper, since the author claims both homology (i.e., similarity) and nonhomology (i.e., lack of a common ancestor). Nonetheless, the author’s ideas are likely to be clear since arguments against common ancestry are presented explicitly. A second case is one in which an author points out similarities (again called homologies) but does not address the issue of evolutionary origins. The reader, seeing the term “homology,” may infer that the author is postulating coancestry when that is not the authors intent. The final case occurs most frequently and is the most subtle and therefore most troublesome. Here, similarities (called homologies) are used to support a hypothesis of evolutionary homology. In this case, the two meanings of homology seem to overlap, and it is almost inevitable that the thinking of author and reader alike will be intrusively distorted as follows. Similarity is relatively straightforward to document. In comparing sequences, a similarity can take the form of a numerical score (O/o amino acid or nucleotide positional identity, in the simplest approach) or of a probability associated with such a score. In comparisons of three-dimensional structures, a typical numerical description is root-mean-square positional deviation between compared atomic positions. A similarity, then, can become a fully documented, simple fact. On the other hand, a common evolutionary origin must usually remain a hypothesis, supported by a set of arguments that might include sequence or three-dimensional similarity. Not all similarity connotes homology but that can be easily overlooked if similarities are called homologies. Thus, in this third case, we can deceive ourselves into thinking we have proved something substantial (evolutionary homology) when, in actuality, we have merely established a simple fact (a similarity, mislabeled as homology). Homology among similar structures is a hypothesis that may be correct or mistaken, but a similarity itself is a fact, however it is interpreted. We believe that the concepts of evolutionary homology and sequence or three-dimensional similarity can be kept distinct only if they are referred to with different words. We therefore offer the following recommendations: *Sequence similarities (or other types of similarity) should simply be called similarities. They should be documented by appropriate statistical analysis. In writing about sequence similarities the following sorts of terms might be used: a level or degree of similarity; an alignment with optimized similarity; the % positional identity in an alignment; the probability associated with an alignment. *Homology should mean “possessing a common evolutionary origin” and in the vast majority of reports should have no other meaning. Evidence for evolutionary homology should be explicitly laid out, making it clear that the proposed relationship is based on the level of observed similarity, the statistical significance of the similarity, and possibly other lines of reasoning. One could argue that the meaning of the term “homology” is itself evolving. But if that evolution is toward vagueness and if it results in making our scientific discourse unclear, surely we should intervene. With a collective decision to mend our ways, proper usage would soon become fashionable and therefore easy. We believe that we and our scientific heirs would benefit significantly.

The phylogeny of trypsin-related serine proteases and their zymogens. New methods for the investigation of distant evolutionary relationships

Abstract The sequence of all presently known trypsin-related serine proteases and their zymogens of animal and bacterial origin were optimally aligned on the basis of three different scoring schemes for amino acid comparisons. Sequence homology was found to extend into the activation peptides. The gaps resulting from the alignment of the sequences of the active enzymes formed the basis for a new procedure based on position and number of gaps, which allowed the correct topology of the evolutionary relationship of thrombin and the pancreatic enzymes trypsin, chymotrypsin and elastase to be determined. The procedure was applied in an analogous manner to changes in disulfide bridges as well as to a selected set of amino acid positions. Evolutionary distances between proteins were estimated by minimum, base differences as well as according to the stochastic model of evolution . These distances were used successfully to find the best topology of evolutionary relationships. The fact that the branch lengths in evolutionary trees were less affected by the number of sequences considered when evolutionary distances between contemporary sequences were measured in minimum base differences than when measured according to the stochastic model of evolution, suggested in our specific case, that minimum base differences yielded estimates of evolutionary distance closer to reality than the stochastic model of evolution. All these techniques combined yielded the following picture for the evolution of the four protease families. Prothrombin and the zymogens of the pancreatic serine proteases had a common ancestor with tryptic specificity. After the initial divergence, the gene for trypsinogen duplicated. Evidence was found that the duplicated gene underwent drastic changes for a short period of time to become eventually the common ancestor of chymotrypsin and elastase. The phylogenetic tree elaborated for these enzyme families and the methods introduced to determine its topology, should readily allow determination of the attachment site of branches leading to newly sequenced serine proteases, provided their amino acid sequence can be aligned fairly unambiguously. In addition, the consequences of the alignment of the different serine proteases for the relationship of zymogen to enzyme are discussed.

[8] The translational friction coefficient of proteins

Publisher Summary This chapter discusses the translational friction coefficient of proteins. It presents a semiempirical method for calculating the geometrical arrangement of subunits in oligomeric proteins. It also presents a method to calculate friction coefficients of proteins from atomic coordinates. In the chapter, the theory by which friction properties of objects can be calculated is discussed and the mechanics of such calculations are illustrated. The method for finding the principle axes of translation of a particle is provided in the chapter. Using the rigorous theory on protein atoms alone yields friction coefficients that are less than the observed values. Calculations based on the complete test sphere shell gives values greater than observed for proteins. Placing test spheres only on charged groups and computing the friction coefficients based on these test spheres and surface protein atoms yield values essentially in agreement with experimental values. Considering that a rigorous theory has been used and that charged groups are recognized to be hydrated, it appears legitimate to equate test spheres in this case with water of hydration. Thus, the frictional behavior of proteins is determined by several factors: overall dimensions, rugosity of the surface, and the hydration of charged groups on the surface.

The non-stoichiometric floating receptor model for hormone sensitive adenylyl cyclase.

Based on a large body of circumstantial evidence, the non-stoichiometric floating receptor model for hormone sensitive adenylyl cyclase is proposed. It is thought to be the most economical model able to rationalize the available data. According to this model, the adenylyl cyclase system consists of two protein components: receptors and enzymatic units, each capable of assuming two conformations. Hormones activate adenylyl cyclase by association with receptors, which then have an increased affinity for the enzymatic units in the catalytically active conformation. There is no fixed stoichiometric relationship between the number of enzymatic units and the number of hormone receptors in a cell, but they only form 1:1 complexes with each other. Hormone receptors are assumed to be capable of lateral diffusion in the membrane. The model is also formulated in physico-chemical terms in order to elucidate the consequences. The non-stoichiometric floating receptor model (1) underscores the absence of homotropic allosterism with respect to hormonal activation. (2) It explains, at least qualitatively, the differing maximal effects of various hormones. (3) It gives a clue to the effect of hormone combinations, describing them as being competitive in origin, rather than caused by positive or negative heterotropic allosterism. (4) It explains how one system can be responsive to many agents. (5) It explains both the easy ontogenetic as well as phylogenetic adaptation of the adenylyl cyclase system. (6) It suggests a basic structural similarity of all receptors for hormones affecting adenylyl cyclase. Finally, the model constitutes a suitable working hypothesis for further experimentation and suggests new approaches.

The low Reynolds number translational friction of ellipsoids, cylinders, dumbbells, and hollow spherical caps. Numerical testing of the validity of the modified Oseen tensor in computing the friction of objects modeled as beads on a shell

A method is presented by which low Reynolds number translational friction coefficients of objects of arbitrary shape can be computed. Each object was modeled by a shell of small beads describing the surface of the object, and translational friction coefficients were computed using the modified Oseen tensor of Rotne and Prager [J. Chem. Phys. 50, 4831 (1969)]. The bead size, and therefore their number, was varied, and translational friction coefficients were extrapolated to zero bead size. The accuracy of the method in predicting translational friction coefficients was established by comparison to cases for which exact solutions are known. This leads to the conjecture that the method is exact in the limit of infinitesimal bead size. Finally, shell model calculations on cylinders were shown to agree closely with experimentally determined settling rates.

The evolutionary origin of proinsulin: Amino acid sequence homology with the trypsin-related serine proteases detected and evaluated by new statistical methods

Abstract Proinsulins and pancreatic serine proteases were analyzed for possible amino acid sequence similarity, using an adapted version of the nucleotide sequence alignment technique of Sankoff (1972). The technique allowed us to determine simultaneously the statistical significance of both the sequence alignment and the number of gaps necessary to achieve that alignment. In the course of this work, it was realized that a rigorous analysis required non-parametric statistics. For the B-chain (amino-terminal) of insulin a highly significant gap-free sequence alignment with the serine proteases was found. For the A-chain (carboxy-terminal) of insulin a sequence alignment of modest statistical significance with two gaps could be obtained, while the search for a corresponding alignment for the C-peptide remained unsuccessful. Presumably the rapid evolution of the C-peptide has obscured its origin. Reconstruction of ancestral sequences was of no help. In contrast to the amino acid sequences, three-dimensional structures of the two protein families are quite different. Considering current histophysiological understanding of ontogeny and phylogeny of exocrine and endocrine pancreas, the observed sequence similarity of proinsulins and serine proteases was interpreted to mean that the two protein families have diverged from a common genetic ancestor. Moreoever, from the organismic distribution of these proteins it was concluded that at least one serine protease existed first, and that proinsulin was generated after duplication of a serine protease gene and subsequent drastic modification, such as a large deletion. Thus proinsulin, basically an anabolic hormone, is derived from a serine protease, an enzyme involved in digestion. This constitutes a refinement of a similar proposal by Steiner et al . (1973). The emergence of proinsulin seems to have occurred after coelenterates diverged, and possibly before most other major animal phyla diverged from the line leading to vertebrates, i.e. 520 to 700 million years ago. The evolution of proinsulin seems to have paralleled the evolution of endocrine cells. Homology of the secreted products of endocrine and exocrine cells was most readily reconciled with a common embryological and phylogenetic origin of the two cell types, as considered by Pictet & Rutter (1972).

Creeping flow translational resistance of rigid assemblies of spheres

The creeping flow translational resistance of dimers and tetrahedral tetramers was measured using spheres glued to each other. The results for the dimer were in excellent agreement with exact theory. Computations based on the modified Oseen tensor differed in the case of the tetramer by 9% from the observed value. Dramatically improved results were obtained by modeling the objects as shells of spherical beads and extrapolation to an infinite number of beads of infinitesimal size. The calculations were extended to other rigid assemblies of spheres.

Dynamic aspects of insulin action: synchronization of oscillatory glycolysis in isolated perifused rat fat cells by insulin and hydrogen peroxide.

Glucose oxidation to CO2 was investigated in isolated perifused rat epididymal fat cells. Insulin stimulated rates of oxidation up to 30-fold. Multiple pulses of insulin or prolonged perifusion with the hormone led to a time-dependent desensitization of the cells. The action of insulin could be mimicked by H2O2. Reversal of H2O2 effects was associated with a damped oscillation of large initial amplitude. Initiation of perifusion with insulin induced rates of glucose oxidation that oscillated around a mean elevated rate with an amplitude of about +/- 4% of the mean, significantly larger than the measurement error. Basal rates did not show clear oscillations. The oscillations after insulin had a statistically significant period of around 14 min. The results were the same with C1- or C6-labeled glucose and occurred in the presence of both 0.275 and 5.5 mM glucose in the perifusion medium. The oscillations were interpreted as the result of insulin- or H2O2-induced synchronization of oscillatory glycolysis by individual fat cells. The similarity of the observed oscillatory period with the period of oscillatory insulin secretion by pancreatic beta cells suggests that oscillatory glycolysis may constitute the internal pacemaker for the latter process.

On the mechanisms of inhibition of insulin action by small-molecular-weight trypsin inhibitors.

Evidence from a number of laboratories has suggested that the mechanism of insulin action involves the release of an intracellular mediator polypeptide from the plasma membrane. It has been proposed that activation of a protease with trypsin-like specificity is involved in release of the putative mediator. In an effort to assess the potential role of such a protease in intact cells, the present study tested the effects of a variety of low-mol-wt protease inhibitors on insulins metabolic action in isolated rat epididymal fat cells. The protease inhibitors studied included paminobenzamidine, benzamidine, phenylguanidine, diisopropylflubrophosphate, leupeptin, and the competitive substrate N-α-tosyl-L-arginine methylester. Leupeptin was devoid of activity. Most of the other inhibitors used were able to interfere with insulin-stimulated metabolism if used in sufficiently high concentrations, concentrations considerably higher than those required for inhibition of known proteases or inhibition of intracellular processes in a previously described system which involves a trypsin-like enzyme. Moreover, they displayed various activities unrelated to protease inhibition that could explain their effects on insulin action better than protease inhibition. While none of the data on individual inhibitors were by themselves convincing enough to either confirm or reject the hypothesis concerning the involvement of a protease with trypsin-like specificity in insulin action, taken together our results do weaken the hypothesis considerably and in particular render the involvement of an extracellular trypsin-like enzyme improbable.

[12-Homoarginine]glucagon: synthesis and observations on conformation, biological activity, and copper-mediated peptide cleavage.

Specific modification of the single lysine residue (Lys-12) in glucagon with O-methylisourea has been effected by blocking the reactivity of the amino terminal histidine with copper, providing a method for obtaining [12-homoarginine]glucagon. It was found that as a side reaction, under the conditions of the modification reaction, Cu(II) catalyzed cleavage of the polypeptide chain between Asp-9 and Tyr-10, and between Lys-12 and Tyr-13. This observation may be of value for development of a sequence-specific peptide cleavage procedure. The dilute solution conformations of glucagon and [12-homoarginine]-glucagon were compared by circular dichroism, fluorescence, phosphorescence, energy transfer, and optical detection of magnetic resonance. The results indicate that conversion of Lys-12 to homoarginine does not alter the helix content the side chain conformation in the vicinity of the tyrosine and tryptophan residues, or the relative distances and orientations between these residues. However, the modification reduces the hormone potency towards activation of lipolysis in isolated rat epididymal fat cells by a factor of seven. We attribute the loss of potency to an interference with a specific interaction between the lysine residue and the fat cell hormone receptor, and not to a change in the solution conformation of the hormone.