Twenty thousand ORFan microbial protein families for the biologist?

The genomes of most newly sequenced organisms contain a significant fraction of ORFs (open reading frames) that match no other sequence in the databases. We refer to these singleton ORFs as sequence ORFans. Because little can be learned about ORFans by homology, the origin and functions of ORFans remain a mystery. However, in this era of full genome sequencing, it seems that ORFans have been underemphasized. In this minireview, we draw attention to the increasing number of ORFans and to the consequences of this growth to biological research in the postgenomic era.     

Can correlated mutations in protein domain families be used for protein design?

Evidence from diverse studies, such as protein design experiments and analysis of the emergence of drug resistance in human immunodeficiency virus 1 (HIV-1), indicates that protein function can be diminished or altered by mutations at positions distant from the classic 'functional' site. Furthermore, results from correlation analysis of the ligand-binding domain of nuclear receptors suggest that mutation events at positions distributed throughout a protein domain may be involved in functional diversification during the evolution of homologous domain families. This review explores potential applications for a protein design procedure based on correlated substitutions.     

Cardiovascular pressure-flow relationships: what should be taught?

Cardiovascular physiology reflects the interrelations of flow, pressure, and resistance. Undergraduate students are often confused by the complexity of the system. This symposium presents a sequential presentation of the underlying concepts, building on analogies, past experience, and conceptual models to allow students to develop a physiologically appropriate understanding of cardiovascular physiology.     

Pulmonary and renal pressure-flow relationships: what should be taught?

This article is from a symposium presented at the annual meeting of the Human Anatomy and Physiology Society (HAPS) on June 11, 2000. The presentation was funded under the auspices of a National Science Foundation Course, Curriculum, and Laboratory Improvement Program entitled "Development of Active Learning Materials for Physiology and Functional Anatomy: A Cooperative HAPS-APS Initiative." This symposium was part of the first module to be developed on "gradients and conductances: what flows where and why?" This presentation was designed to model the usefulness of the general model of gradients and conductances in the physiology and pathophysiology of the respiratory and renal systems. Thirteen different examples of pressure-flow-resistance and concentration-flux relationships are introduced; several ideas for active-learning activities and simple figures appropriate for undergraduate physiology classes are included. The symposium assumes that undergraduate students have already learned about diffusion, osmosis, and the basic principles of cardiovascular physiology. The presentation was designed to follow a symposium entitled: "Cardiovascular pressure-flow relationships: what should be taught?"     

Nonvesicular sterol transport: two protein families and a sterol sensor?

Sterols, essential components of eukaryotic membranes, are actively transported between cellular membranes. Although it is known that both vesicular and non-vesicular means are used to move sterols, the molecules and molecular mechanisms involved have yet to be identified. Recent studies point to a key role for oxysterol binding protein (OSBP) and its related proteins (ORPs) in nonvesicular sterol transport. Here, evidence that OSBP and ORPs are bona fide sterol carriers is discussed. In addition, I hypothesize that ATPases associated with various cellular activities regulate the recycling of soluble lipid carriers and that the Niemann Pick C1 protein facilitates the delivery of sterols from endosomal membranes to ORPs and/or the ensuing membrane dissociation of ORPs.     

DWARF – a data warehouse system for analyzing protein families

Background  

The emerging field of integrative bioinformatics provides the tools to organize and systematically analyze vast amounts of highly diverse biological data and thus allows to gain a novel understanding of complex biological systems. The data warehouse DWARF applies integrative bioinformatics approaches to the analysis of large protein families.     

Rapid search for tertiary fragments reveals protein sequence–structure relationships

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure.     

Evolution of protein families: is it possible to distinguish between domains of life?

Understanding evolutionary relationships between species can shed new light into the rooting of the tree of life and the origin of eukaryotes, thus, resulting in a long standing interest in accurately assessing evolutionary parameters at time scales on the order of a billion of years. Prior work suggests large variability in molecular substitution rates, however, we still do not know whether such variability is due to species-specific trends at a genomic scale, or whether it can be attributed to the fluctuations inherent in any stochastic process. Here, we study the statistical properties of gene and protein-family sizes in order to quantify the long time scale evolutionary differences and similarities across species. We first determine the protein families of 209 species of bacteria and 20 species of archaea. We find that we are unable to reject the null hypothesis that the protein-family sizes of these species are drawn from the same distribution. In addition, we find that for species classified in the same phylogenetic branch or in the same lifestyle group, family size distributions are not significantly more similar than for species in different branches. These two findings can be accounted for in terms of a dynamical birth, death, and innovation model that assumes identical protein-family evolutionary rates for all species. Our theoretical and empirical results thus strongly suggest that the variability empirically observed in protein-family size distributions is compatible with the expected stochastic fluctuations for an evolutionary process with identical genomic evolutionary rates. Our findings hold special importance for the plausibility of some theories of the origin of eukaryotes which require drastic changes in evolutionary rates for some period during the last 2 billion years.     

Is a multivariate consensus representation of genetic relationships among populations always meaningful?

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis.     

Intramolecular isopeptide bonds: protein crosslinks built for stress?

The recent discovery of intramolecular isopeptide bonds formed between lysine and asparagine residues in certain bacterial cell-surface proteins represents a new component in nature's toolbox for stabilising proteins. Although isopeptide bonds are well known as intermolecular crosslinks in processes such as ubiquitylation, these intramolecular isopeptide bonds form autocatalytically during protein folding, as the reacting groups are brought together in a hydrophobic environment. First identified in the Ig-like pilin subunits of Gram-positive bacterial pili, these internal crosslinks provide stabilisation against chemical, thermal and mechanical stress and provide new opportunities for applications in biotechnology. The crucial role of structural biology and mass spectrometry in their discovery and characterisation raises the likelihood that further novel post-translational modifications resulting from intramolecular reactions in proteins await discovery.     

Brain death: a durable consensus?

Is it even conceivable that this global consensus [on the whole-brain definition of death] could, in time, be regarded as a very temporary and makeshift expedient, a momentary substitute for a resolution of some profoundly difficult issues which for a time, perhaps a brief time, fit with both the technical capacities and the legal needs of those who endorsed it? And that in the long run it could linger as a footnote, or perhaps a chapter heading, in the long history of man's conceptions of life and death? This suggestion is so far from conventional wisdom today that one who espouses it risks being regarded as a crank. Nevertheless, I believe that the argument in its favor, while not conclusive, is much stronger than the argument against it (and in favor of the prevailing consensus). I will state the argument briefly, with particular reference to the landmark report in 1982 in Washington of the President's Commission for the Study of Ethical Problems in Medicine, and will situate the argument in the context of trends in contemporary bioethics. I do not expect to win over, in this one pass, those who have been convinced of the validity of the conventional view. I do hope, however, to re-open the issue; in particular, to provide reasons to regard the issue as far from settled.     

Metabolic scaling: consensus or controversy?

Background  

The relationship between body mass (M) and standard metabolic rate (B) among living organisms remains controversial, though it is widely accepted that in many cases B is approximately proportional to the three-quarters power of M.     

PHOG-BLAST – a new generation tool for fast similarity search of protein families

Background  

The need to compare protein profiles frequently arises in various protein research areas: comparison of protein families, domain searches, resolution of orthology and paralogy. The existing fast algorithms can only compare a protein sequence with a protein sequence and a profile with a sequence. Algorithms to compare profiles use dynamic programming and complex scoring functions.     

What should the Z-score of native protein structures be?

The Z-score of a protein is defined as the energy separation between the native fold and the average of an ensemble of misfolds in the units of the standard deviation of the ensemble. The Z-score is often used as a way of testing the knowledge-based potentials for their ability to recognize the native fold from other alternatives. However, it is not known what range of values the Z-scores should have if one had a correct potential. Here, we offer an estimate of Z-scores extracted from calorimetric measurements of proteins. The energies obtained from these experimental data are compared with those from computer simulations of a lattice model protein. It is suggested that the Z-scores calculated from different knowledge-based potentials are generally too small in comparison with the experimental values.     

Functional redundancy and compensation among members of gap junction protein families?

Gap junctions are intercellular conduits for small molecules made up by protein subunits called connexins. A large number of connexin genes were found in mouse and man, and most cell types express several connexins, lending support to the view that redundancy and compensation among family members exist. This review gives an overview of the current knowledge on redundancy and functional compensation - or lack thereof. It takes into account the different properties of connexin subunits which comprise gap junctional intercellular channels, but also the compatibility of connexins in gap junctions. Most insight has been gained by the investigation of mice deficient for one or more connexins and transgenic mice with functional replacement of one connexin gene by another. Most single deficient mice show phenotypical alterations limited to critical developmental time points or to specific organs and tissues, while mice doubly deficient for connexins expressed in the same cell type usually show more severe phenotypical alterations. Replacement of a connexin by another connexin in some cases gave rise to rescue of phenotypical alterations of connexin deficiencies, which were restricted to specific tissues. In many tissues, connexin substitution did not restore phenotypical alterations of connexin deficiencies, indicating that connexins are specialized in function. In some cases, fatal consequences arose from the replacement. The current consensus gained from such studies is that redundancy and compensation among connexins exists at least to a limited extent. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics.     

Diatoms and biomonitoring: should cell size be accounted for?

Despite the fact that biovolume calculation is a common procedure in most phytoplankton and periphyton studies, diatom community analyses are usually based on relative abundance data. In a biomonitoring context, a community metric that accounts for cell size could be of interest due to the potential differences that might exist in nutrient uptake between large and small-sized species. This paper addresses the question of whether diatom community analysis should be based on relative abundance, biovolume or cell surface. The results show that although community structure expressed as relative proportion of taxa varied according to the metric used, the ordinations conducted with each metric were similar. The explained percentage of species variance was slightly higher with the relative abundance metric compared to the metrics based on relative biovolume or cell surface area. Partial CCAs showed that each water chemistry variable generally explained a higher portion of species variance when the relative abundance was used. The analyses conducted with two size groups (small and large taxa) expressed as relative abundance and relative biovolume showed similar results. Moreover, our data showed that there is no significant relationship between diatom size and total phosphorus. According to these results, it seems that relative abundance would be the most appropriate metric to use for biomonitoring purposes. The biovolume and cell surface area calculations added substantially to the total analysis time due to the numerous measurements required, but did not improve the variance explained in community structure, and site ordinations were not significantly different. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.