Comparative molecular dynamics—Similar folds and similar motions?

Proteins possessing the same fold may undergo similar motions, particularly if these motions involve large conformational transitions. The increasing amounts of structural data provide a useful starting point with which to test this hypothesis. We have performed a total of 0.29 micros of molecular dynamics across a series of proteins within the same fold family (periplasmic binding proteinlike) in order to address to what extent similarity of motion exists. Analysis of the local conformational space on these timescales (10-20 ns) revealed that the behavior of the proteins could be readily distinguished between an apo-state and a ligand-bound state. Moreover, analysis of the root-mean-square fluctuations reveals that the presence of the ligand exerts a stabilizing effect on the protein, with similar motions occurring, but with reduced magnitude. Furthermore, the conformational space in the presence of the ligand appears to be dictated by sequence but not by the type of ligand present. In contrast, apo-simulations showed considerable overlap of conformational space across the fold as a result of their ability to undergo larger fluctuations. Indeed, we observed several transitions from different simulations between states corresponding to the closed-cleft and open-cleft forms of the fold, with the predominant motions being conserved across the different proteins. Thus, large-scale conformational changes do indeed appear to be conserved across this fold architecture, but smaller conformational motions appear to reflect the differences in sequence and local fold.     

Plant and animal transglutaminases: do similar functions imply similar structures?

In plants the post-translational modification of proteins by polyamines catalysed by transglutaminases has been studied since 1987; it was identified by the production of glutamyl-polyamine derivatives, biochemical features, recognition by animal antibodies and modification of typical animal substrates. Transglutaminases are widespread in all plant organs and cell compartments studied until now, chloroplast being the most studied. Substrates are: photosynthetic complexes and Rubisco in chloroplasts, cytoskeleton and cell wall proteins. Roles either specific of plants or in common with animals are related to photosynthesis, fertilisation, stresses, senescence and programmed cell death, showing that the catalytic function is conserved across the kingdoms. AtPng1p, the first plant transglutaminase sequenced shows undetectable sequence homology to the animal enzymes, except for the catalytic triad. It is, however, endowed with a calcium-dependent activity that allowed us to build a three-dimensional model adopting as a template the animal tranglutaminase 2.     

Do mandibular cross‐sectional properties and dental microwear give similar dietary signals?

Previous animal experimental work evaluating the effects of dietary consistency on mastication was generally limited to studies of either mandibular structure or rates and types of tooth wear. Control groups fed hard diets (HD) consistently exhibited increased cortical remodeling and/or bone strength when compared to groups fed soft diets (SD). Results of tooth-wear studies showed faster rates of tooth wear in HD animals. This study evaluates the effects of dietary differences on both mandibular structural morphology and postcanine dental microwear in the same animals. We examined mandibles and dentitions from eight miniature swine, raised from 4 weeks to 9 months of age on HD and SD (n = 4, each group). Mandibular structural properties were calculated from peripheral quantitative computed tomography slices at the dp3-dp4 and dp4-M1 junctions. Dental microwear analysis was performed on mandibular lingual crushing facets of dp4 and M1, using photomicrographs of high-resolution casts taken at 500x magnification in a scanning electron microscope. Our results suggest that between the dp3-dp4 contact, HD animals have mandibles that are stronger and more rigid mediolaterally than SD animals. At the dp4-M1 contact, HD animals have mandibles that are stronger and more rigid mediolaterally, dorsoventrally, and in torsion than SD animals. Dental microwear results indicate that SD pigs have higher incidences of pitting and more overall microwear features on their premolars than do HD pigs, yet there are no significant differences in molar microwear morphology between the dietary groups. Near-significant correlations exist between pit size and dorsoventral bending strength, but only for HD pigs. These results suggest that dietary consistency significantly affects both mandibular structure and dental microwear, yet direct correlations between the two are complicated by a number of factors.     

Do variables that affect similar bistable apparent-movement displays result in similar changes in perception?

Two bistable apparent-movement displays (i.e. ones that generate two qualitatively different kinds of movement percepts under different conditions) were compared. They were designed to be as similar as possible spatially, and were studied with identical stimulus manipulations to see whether changes in balance between their bistable percepts would be similar. Results show that the two displays had different response characteristics to the same stimulus manipulations. Two models of motion perception that have previously predicted at least one kind of bistable apparent motion were considered in terms of how well they address the current data. As yet, neither model has been shown to predict the motion states and bistable behavior of the two displays studied here. It is concluded that results of the type described here (specifically, differences in the psychophysical functions yielded by two structurally similar but qualitatively different bistable displays) present a challenge for theories of motion perception.     

Do proteins with similar folds have similar transition state structures? A diffuse transition state of the 169 residue apoflavodoxin

Apoflavodoxin from Anabaena PCC 7119 is a 169 residue globular protein of known structure and energetics. Here, we present a comprehensive Phi-value analysis to characterize the structure of its transition state. A total of 34 non-disruptive mutations are made throughout the structure and a range of Phi-values from zero to one are observed. In addition, a small set of eight aliphatic small-to-large mutations have been introduced in the hydrophobic core of the protein and they have been analyzed to investigate the feasibility of stabilizing the unfolding transition state by creating new non-native interactions. We find that the transition state of apoflavodoxin (so far the largest protein subjected to Phi-analysis) is diffuse and that it can be stabilized by unspecific hydrophobic interactions that can speed up the folding reaction. The data gathered on the apoflavodoxin transition state are compared with results from experimental studies in other proteins to revisit the relationship between the native state topology and transition state structure.     

Do climatically similar regions contain similar alien floras? A comparison between the mediterranean areas of central Chile and California

Aim Taxonomic comparisons of alien floras across climatically similar regions have been proposed as a powerful approach for increasing our understanding of plant invasions across scales. However, detailed comparisons between the alien biotas of climatically similar regions are scarce. This study aims to compare the taxonomic patterns of alien species richness in mediterranean‐type climate areas of central Chile and California, in order to better understand how climatically similar regions converge or diverge in terms of their alien flora. Location Central Chile and California, United States. Methods We compared the alien floras of the state of California in the United States and central Chile, considering within‐region variation and taxonomic composition up to the species level. To test for within‐region variation, administrative units and counties were grouped within seven latitudinal bands for each region. We tested for differences in the relative contributions of the various origins of the naturalized species to each region. We used a family naturalization index to establish which families had relatively higher numbers of naturalized species in each region. We evaluated the similarity, using cluster analyses with Jaccard’s similarity index, of alien taxa between regions and latitudinal bands using presence–absence matrices at the species, genus and family levels. We used principal components analysis to determine the presence of a compositional gradient including all latitudinal bands. Results We recorded 1212 alien plant species in California and 593 in central Chile, of which 491 are shared between the two regions. These figures include 25 species that are native to California and 37 that are native to Chile. A comparison between the alien floras of central Chile and California reveals three major trends: (1) higher naturalized species diversity for California than for Chile, at all taxonomic levels; (2) differences in the proportion of species according to origin, with America, Africa, Asia and Australia providing a larger number of species in California than in Chile; (3) segregation between regions in terms of taxonomic composition of their alien flora, and a rather weak differentiation within regions; and (4) a trend towards higher similarity between the alien floras of latitudinal bands associated with higher levels of human disturbances. Main conclusions The alien floras of central Chile and California are significantly different, but this difference diminishes in highly disturbed areas. Thus, the current high levels of species movement caused by globalization, together with increasing levels of anthropogenic disturbances, should reduce the differentiation of the alien floras in these regions, increasing overall biotic homogenization.     

Comparison of inhibitory activity of isomeric triazolopyridine derivatives towards adenosine receptor subtypes or do similar structures reveal similar bioactivities?

The synthesis of an array of 8-amino-2-aryl-[1,2,4]triazolo[1,5-a]pyridine-6-carboxyl amide derivatives is described for the first time. A subset of 20 derivatives were compared to their isomeric 5-amino-2-aryl-[1,2,4]triazolo[1,5-a]pyridine-7-carboxyl amide counterparts with regard to their potential to inhibit the human adenosine 2a (hA2a) receptor and their selectivity against the human adenosine 1 (hA1) receptor. Based on the analysis of H-bond donor/acceptor capabilities of the isomeric triazolopyridine pairs it can be concluded that the H-bond donor strength of the free amino functionality is the main determinant for hA2a inhibitory activity and hA1 selectivity.     

How similar are daily and seasonal biological clocks?

Daily and seasonal timing systems in insects have usually been supposed to share similar mechanisms, because both rely in large measure on information from the daily light-dark cycle: daily clocks can ensure that activity coincides with the appropriate time of day, and seasonal time is indicated most reliably by daylength. However, several lines of evidence suggest that the systems are different. For example, receptor features, photosensitive pigments, clocks, and the effectors that mediate responses to information derived from the clock may have different daily, seasonal and general functions and properties, and several different systems are known. There are many different additional elements in the seasonal response. Therefore, these responses may not rely on similar timing mechanisms, despite the long-standing belief that the seasonal clock has circadian components. Such a difference would be consistent with the fact that temporal responses serve a very wide range of purposes, meeting many different ecological needs on different time frames. Consequently, understanding the seasonal relevance of the photoperiodic responses is more important than revealing any possible involvement with circadian systems.     

Nuclear and mitochondrial DNA repair: similar pathways?

Mitochondrial DNA (mtDNA) alterations are implicated in a broad range of human diseases and alterations of the mitochondrial genome are assumed to be a result of its high susceptibility to oxidative damage and its limited DNA repair compared to nuclear DNA (nDNA). Characterization of DNA repair mechanisms has generally focused on these processes in nDNA but increasing interest and research effort have contributed to our knowledge of the mechanisms underlying DNA repair in mitochondria. In this review, we make comparisons between nDNA and mtDNA repair pathways and propose a model for how these pathways interact in mitochondria.     

How do biological systems discriminate among physically similar ions?

This paper reviews the history of understanding how biological systems can discriminate so strikingly among physically similar ions, especially alkali cations. Appreciation of qualitative regularities ("permitted sequences") and quantitative regularities ("selectivity isotherms") in ion selectivity grew first from studies of ion exchangers and glass electrodes, then of biological systems such as enzymes and cell membranes, and most recently of lipid bilayers doped with model pores and carriers. Discrimination of ions depends on both electrostatic and steric forces. "Black-box" studies on intact biological membranes have in some cases yielded molecular clues to the structure of the actual biological pores and carriers. Major current problems involve the extraction of these molecules; how to do it, what to do when it is achieved, and how (and if) it is relevant to the central problems of membrane function. Further advances are expected soon from studies of rate barriers within membranes, of voltage-dependent ("excitable") conducting channels, and of increasingly complex model systems and biological membranes.     

Wild type and <Emphasis Type="Italic">H43Y</Emphasis> variant of human <Emphasis Type="Italic">TRIM5α</Emphasis> show similar anti-human immunodeficiency virus type 1 activity both in vivo and in vitro

Polymorphisms in human genes have been shown to affect the rate of disease progression to acquired immune deficiency syndrome in human immunodeficiency virus type 1 (HIV-1)-infected individuals. Recently, tripartite motif 5α (TRIM5α) was identified as a factor that confers resistance to HIV-1 infection in Old World monkey cells. Subsequently, Sawyer et al. (Curr Biol 16:95–100, 2006) reported a single nucleotide polymorphism (H43Y) in the human TRIM5α gene and TRIM5α protein with 43Y was found to lose its ability to restrict HIV-1. In the present study, we reevaluated effects of this allele on in vitro anti-HIV-1 activity as well as on HIV-1 disease progression in European and Asian cohorts of HIV-1-infected individuals. Our epidemiological and molecular biological findings clearly indicate H43Y has a very minor effect on anti-HIV-1 activity of TRIM5α, suggesting that this allele is immaterial, at least in HIV-1-infected Europeans and Asians.     

Description of a new species of Distenia (Coleoptera,Disteniidae, Disteniini) from Southeastern China,with?records and diagnoses of similar species

A new species, Distenia orientalis sp. n. is described from Southeastern China. It was misidentified as Distenia gracilis (Blessig, 1872) but can be separated from the latter by the color of antennae and legs, structure differences on scape, maxillary palp, pronotum, tibiae, punctures on elytra, etc. Three related species are carefully diagnosed and treated.     

Are in vivo and in situ brain tissues mechanically similar?

Brain tissue mechanical properties have been well-characterized in vitro, and were found to be inhomogeneous, nonlinear anisotropic and influenced by neurological development and postmortem time interval prior to testing. However, brain in vivo is a vascularized tissue, and there is a paucity of information regarding the effect of perfusion on brain mechanical properties. Furthermore, mechanical properties are often extracted from preconditioned tissue, and it remains unclear if these properties are representative of non-preconditioned tissue. We present non-preconditioned (NPC) and preconditioned (PC) relaxation responses of porcine brain (N = 10) obtained in vivo, in situ and in vitro, at anterior, mid and posterior regions of the cerebral cortex during 4mm indentations at either 3 or 1 mm/s. Material property characteristics showed no dependency on the site tested, thus revealing that cortical gray matter on the parietal and frontal lobes can be considered homogenous. In most cases, preconditioning decreased the shear moduli, with a more pronounced effect in the dead (in situ and in vitro) brain. For most conditions, it was found that only the long-term time constant of relaxation (tau > 20 s) significantly decreased from in vivo to in situ modes (p < 0.02), and perfusion had no effect on any other property. These findings support the concept that perfusion does not affect the stiffness of living cortical tissue.