Structure and functions of the prokaryotic elongation factor G

Structural and functional data on elongation factor G (EF-G) are reviewed with regard to nucleotide exchange, GTP hydrolysis, mechanism of action of fusidic acid, and functional roles of the EF-G structural domains in translocation. Biochemical data are correlated with structural dynamics of the EF-G molecule on interaction with various ligands. Data on EF-Tu are also considered, as EF-G and EF-Tu share certain structural and functional features.     

Structure and Functions of the Prokaryotic Elongation Factor G

Structural and functional data on elongation factor G (EF-G) are reviewed with regard to nucleotide exchange, GTP hydrolysis, mechanism of action of fusidic acid, and functional roles of the EF-G structural domains in translocation. Biochemical data are correlated with structural dynamics of the EF-G molecule on interaction with various ligands. Data on EF-Tu are also considered, as EF-G and EF-Tu share certain structural and functional features.     

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach

MOTIVATION: Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner. RESULTS: We have systematically analyzed svNTXs and classified them using structure-function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community. AVAILABILITY: We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/).     

Cross-polarized reflected light measurement of fast optical responses associated with neural activation

We developed an optical probe for cross-polarized reflected light measurements and investigated optical signals associated with electrophysiological activation in isolated lobster nerves. The cross-polarized baseline light intensity (structural signal) and the amplitude of the transient response to stimulation (functional signal) measured in reflected mode were dependent on the orientation of the nerve axis relative to the polarization plane of incident light. The maximum structural signal and functional response amplitude were observed at 45 degrees , and the ratio of functional to structural signals was approximately constant across orientations. Functional responses were measured in single trials in both transmitted and reflected geometries and responses had similar waveforms. Both structural and functional signals were an order of magnitude smaller in reflected than in transmitted light measurements, but functional responses had similar signal/noise ratios. We propose a theoretical model based on geometrical optics that is consistent with experimental results. In the model, the cross-polarized structural signal results from light reflection from axonal fibers and the transient functional response arises from axonal swelling associated with neural activation. Polarization-sensitive reflected light measurements could greatly enhance in vivo imaging of neural activation since cross-polarized responses are much larger than scattering signals now employed for dynamic functional neuroimaging.     

Functional fingerprints of folds: evidence for correlated structure-function evolution

Using structural similarity clustering of protein domains: protein domain universe graph (PDUG), and a hierarchical functional annotation: gene ontology (GO) as two evolutionary lenses, we find that each structural cluster (domain fold) exhibits a distribution of functions that is unique to it. These functional distributions are functional fingerprints that are specific to characteristic structural clusters and vary from cluster to cluster. Furthermore, as structural similarity threshold for domain clustering in the PDUG is relaxed we observe an influx of earlier-diverged domains into clusters. These domains join clusters without destroying the functional fingerprint. These results can be understood in light of a divergent evolution scenario that posits correlated divergence of structural and functional traits in protein domains from one or few progenitors.     

Motifs in brain networks

Complex brains have evolved a highly efficient network architecture whose structural connectivity is capable of generating a large repertoire of functional states. We detect characteristic network building blocks (structural and functional motifs) in neuroanatomical data sets and identify a small set of structural motifs that occur in significantly increased numbers. Our analysis suggests the hypothesis that brain networks maximize both the number and the diversity of functional motifs, while the repertoire of structural motifs remains small. Using functional motif number as a cost function in an optimization algorithm, we obtain network topologies that resemble real brain networks across a broad spectrum of structural measures, including small-world attributes. These results are consistent with the hypothesis that highly evolved neural architectures are organized to maximize functional repertoires and to support highly efficient integration of information.     

Massive structural redundancies in species composition patterns of floodplain forest moths

Terrestrial arthropod communities usually consist of very large species numbers. Data from experiments or long time‐series would be required to ascertain the functional significance of individual species. Both are largely unavailable for species‐rich natural communities. Recognising structural redundancies in species composition allows for an alternative approach to address how strong functional redundancy might be in natural assemblages, if structural and functional redundancies are related to each other. Determining structural redundancies is a regular topic in aquatic ecology, but has rarely been applied to terrestrial communities. We explored the extent of structural redundancy in species‐rich terrestrial insect assemblages and whether structural redundancies are contingent to species abundances or functional group affiliations. We used the BVSTEP algorithm to determine structural redundancies in a large data set of moth species (32 181 individuals; 448 species) that had been sampled with light‐traps in three different floodplain forests in eastern Austria. We partitioned the moth species into 12 functional types based on larval host‐plant affiliations to test if moth species included in reduced subsets represent functional groups in the same proportions as they occur in the entire fauna. We observed far more massive structural redundancies in moth assemblages than previously found in aquatic communities. Subsets containing only 8–15 species (1.8–3.3% of all recorded species) were still highly representative for the overall data. Subsets selected by the BVSTEP procedure performed better than equally small subsets that were defined solely by species abundances or by functional group affiliations. Effective ‘surrogate’ subsets contained only 6–9 of the 12 functional moth types. High abundance only loosely corresponded with the frequency at which a moth species was included in the subsets. Thus, certain uncommon species contribute importantly to species composition patterns. Our results show unexpectedly extensive structural redundancies in complex floodplain forest moth communities, which may also indicate strong functional redundancies.     

The role of scaffold attachment regions in the structural and functional organization of plant chromatin

Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended to different plant species and indicate that SARs are involved in the structural and functional organization of the plant genome, as is the case for other eukaryotes. One type of SAR seems to delimit structural chromatin loops and may also border functional units of gene expression and DNA replication. Another group of SARs map close to regulatory elements and may be directly involved in gene expression. In this overview, we summarize the structural and functional properties of plant SARs in comparison with those of SARs from animals and yeast.     

Arm lengths and arm reaches: some interrelationships of structural and functional body dimensions

Structural measurements of the human body have for the most part been of little practical use as indicators of such functional body dimensions as arm reaches. These dimensions, which define the area around the body to which a person can reach given certain specified conditions and constraints are often critical for the design and layout of workspaces. However, they are relatively difficult and time-consuming to obtain, usually requiring specially constructed measuring systems for each differing design situation, as well as resurveys for each physically distinct population. An alternate approach, described here, investigates the interrelationships between these two classes of measurements with the aim of predicting functional reaches from structural body dimensions. In the present study traditional structural measurements and 117 functional arm reaches were obtained on 100 subjects. Correlations between the two types of measures are reported. Regression equations are presented which can predict functional arm reaches from two structural body dimensions on anthropometrically differing populations under a fixed set of workspace conditions.     

Evolution of function in protein superfamilies, from a structural perspective

The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. Combining sequence and structure information to identify relatives, the majority of superfamilies display variation in enzyme function, with 25 % of superfamilies in the PDB having members of different enzyme types. We determined the extent of functional similarity at different levels of sequence identity for 486,000 homologous pairs (enzyme/enzyme and enzyme/non-enzyme), with structural and sequence relatives included. For single and multi-domain proteins, variation in EC number is rare above 40 % sequence identity, and above 30 %, the first three digits may be predicted with an accuracy of at least 90 %. For more distantly related proteins sharing less than 30 % sequence identity, functional variation is significant, and below this threshold, structural data are essential for understanding the molecular basis of observed functional differences. To explore the mechanisms for generating functional diversity during evolution, we have studied in detail 31 diverse structural enzyme superfamilies for which structural data are available. A large number of variations and peculiarities are observed, at the atomic level through to gross structural rearrangements. Almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a superfamily, whilst the reaction chemistry is maintained. In many superfamilies, the position of catalytic residues may vary despite playing equivalent functional roles in related proteins. The implications of functional diversity within supefamilies for the structural genomics projects are discussed. More detailed information on these superfamilies is available at http://www.biochem.ucl.ac.uk/bsm/FAM-EC/.     

Structural and Functional Alterations in Right Dorsomedial Prefrontal and Left Insular Cortex Co-Localize in Adolescents with Aggressive Behaviour: An ALE Meta-Analysis

Recent neuroimaging work has suggested that aggressive behaviour (AB) is associated with structural and functional brain abnormalities in processes subserving emotion processing and regulation. However, most neuroimaging studies on AB to date only contain relatively small sample sizes. To objectively investigate the consistency of previous structural and functional research in adolescent AB, we performed a systematic literature review and two coordinate-based activation likelihood estimation meta-analyses on eight VBM and nine functional neuroimaging studies in a total of 783 participants (408 [224AB/184 controls] and 375 [215 AB/160 controls] for structural and functional analysis respectively). We found 19 structural and eight functional foci of significant alterations in adolescents with AB, mainly located within the emotion processing and regulation network (including orbitofrontal, dorsomedial prefrontal and limbic cortex). A subsequent conjunction analysis revealed that functional and structural alterations co-localize in right dorsomedial prefrontal cortex and left insula. Our results are in line with meta-analytic work as well as structural, functional and connectivity findings to date, all of which make a strong point for the involvement of a network of brain areas responsible for emotion processing and regulation, which is disrupted in AB. Increased knowledge about the behavioural and neuronal underpinnings of AB is crucial for the development of novel and implementation of existing treatment strategies. Longitudinal research studies will have to show whether the observed alterations are a result or primary cause of the phenotypic characteristics in AB.     

Structural and taxonomic diversity predict above-ground biomass better than functional measures of maximum height in mixed-species forests

Aims: Mixed-species forests are known to be highly productive systems because of their high species diversity, including taxonomic diversity (species richness) and structural diversity. Recent empirical evidence also points to plant maximum height, as a functional trait that potentially drives forest above-ground biomass (AGB). However, the interrelations between these biotic variables are complex, and it is not always predictable if structural diversity attributes or functional metrics of plant maximum height would act as the most important determinant of stand biomass. Here we evaluated the relative importance of structural diversity attributes and functional metrics of plant maximum height (Hmax) in predicting and mediating AGB response to variation in species richness in mixed-species forests, while also accounting for fine-scale environmental variation. Location: Northern Benin. Methods: We used forest inventory data from mixed-species stands of native and exotic species. We quantified structural diversity as coefficient of variation of tree diameter at breast height (CVdbh) and of height (CVHt). For plant Hmax, we computed three metrics: functional range (FRHmax), functional divergence (FDHmax) and community-weighted mean (CWMHmax). We used topographical variables such as elevation and slope to account for possible environmental effects. Simple and multiple mixed-effects models, and structural equation models were performed to assess the direct and indirect links of AGB with species richness through structural diversity attributes and functional metrics of plant Hmax. Results: Species richness and CVdbh were positively related to AGB, while functional metrics of plant Hmax were not. Structural equation models revealed that species richness influenced AGB indirectly via CVdbh, which alone strongly promoted AGB. Elevation only had a positive direct effect on AGB. While increasing species richness enhanced CVdbh and functional measures of plant Hmax, there was no support for the latter mediating the effects of species richness on AGB. Conclusion: Structural diversity has a significant advantage in predicting and mediating the positive effect of species richness on AGB more so than functional measures of plant Hmax. We argue that structural diversity acts as a mechanism for the species richness–AGB relationship, and that maintaining high structural diversity would enhance biomass in mixed-species forests.     

Computational analysis of functional connectivity between areas of primate cerebral cortex

Recent analyses of association fibre networks in the primate cerebral cortex have revealed a small number of densely intra-connected and hierarchically organized structural systems. Corresponding analyses of data on functional connectivity are required to establish the significance of these structural systems. We therefore built up a relational database by systematically collating published data on the spread of activity after strychnine-induced disinhibition in the macaque cerebral cortex in vivo. After mapping these data to two different parcellation schemes, we used three independent methods of analysis which demonstrate that the cortical network of functional interactions is not homogeneous, but shows a clear segregation into functional assemblies of mutually interacting areas. The assemblies suggest a principal division of the cortex into visual, somatomotor and orbito-temporo-insular systems, while motor and somatosensory areas are inseparably interrelated. These results are largely compatible with corresponding analyses of structural data of mammalian cerebral cortex, and deliver the first functional evidence for 'small-world' architecture of primate cerebral cortex.     

Identification of homology in protein structure classification.

Structural biology and structural genomics are expected to produce many three-dimensional protein structures in the near future. Each new structure raises questions about its function and evolution. Correct functional and evolutionary classification of a new structure is difficult for distantly related proteins and error-prone using simple statistical scores based on sequence or structure similarity. Here we present an accurate numerical method for the identification of evolutionary relationships (homology). The method is based on the principle that natural selection maintains structural and functional continuity within a diverging protein family. The problem of different rates of structural divergence between different families is solved by first using structural similarities to produce a global map of folds in protein space and then further subdividing fold neighborhoods into superfamilies based on functional similarities. In a validation test against a classification by human experts (SCOP), 77% of homologous pairs were identified with 92% reliability. The method is fully automated, allowing fast, self-consistent and complete classification of large numbers of protein structures. In particular, the discrimination between analogy and homology of close structural neighbors will lead to functional predictions while avoiding overprediction.     

Inhibitors of protein and RNA synthesis block structural changes that accompany long-term heterosynaptic plasticity in Aplysia.

Synaptic connections between the sensory and motor neurons of Aplysia in culture undergo long-term facilitation in response to serotonin (5-HT) and long-term depression in response to FMRFamide. These long-term functional changes are dependent on the synthesis of macromolecules during the period in which the transmitter is applied and are accompanied by structural changes. There is an increase and a decrease, respectively, in the number of sensory neuron varicosities in response to 5-HT and FMRFamide. To determine whether macromolecular synthesis is also required for the structural changes, we examined in parallel the effects of inhibitors of protein (anisomycin) or RNA (actinomycin D) synthesis on the structural and functional changes. We have found that anisomycin and actinomycin D block both the enduring alterations in varicosity number and the long-lasting changes in synaptic potential. These results indicate that macromolecular synthesis is required for expression of the long-lasting structural changes in the sensory cells and that this synthesis is correlated with the long-term functional modulation of sensorimotor synapses.     

Exploring overlapping functional units with various structure in protein interaction networks

Revealing functional units in protein-protein interaction (PPI) networks are important for understanding cellular functional organization. Current algorithms for identifying functional units mainly focus on cohesive protein complexes which have more internal interactions than external interactions. Most of these approaches do not handle overlaps among complexes since they usually allow a protein to belong to only one complex. Moreover, recent studies have shown that other non-cohesive structural functional units beyond complexes also exist in PPI networks. Thus previous algorithms that just focus on non-overlapping cohesive complexes are not able to present the biological reality fully. Here, we develop a new regularized sparse random graph model (RSRGM) to explore overlapping and various structural functional units in PPI networks. RSRGM is principally dominated by two model parameters. One is used to define the functional units as groups of proteins that have similar patterns of connections to others, which allows RSRGM to detect non-cohesive structural functional units. The other one is used to represent the degree of proteins belonging to the units, which supports a protein belonging to more than one revealed unit. We also propose a regularizer to control the smoothness between the estimators of these two parameters. Experimental results on four S. cerevisiae PPI networks show that the performance of RSRGM on detecting cohesive complexes and overlapping complexes is superior to that of previous competing algorithms. Moreover, RSRGM has the ability to discover biological significant functional units besides complexes.     

The functional approach in biology

The concepts of structural and functional approaches are analysed. The existence of a logical limit to the domain of applicability of the structural approach is indicated. Some sources of possible failure of the structural method in biology are pointed out. Two fundamental characteristics of biological systems, inductive development and inductive functioning. necessitating the functional approach, are discussed.     

The development of the thoracic duct lymphangions in the prenatal period of human ontogeny]

This paper concerns structural and functional organization of the human lymphatic system during the prenatal period. For the first time the data is presented on the development of thoracic duct based on the concept of lymphangion as a structural and functional unit of a lymphatic vessel. The formation of the duct is considered in connection with structural changes of its wall and variants of duct roots fusion. The following stages are distinguished in the development of the thoracic duct: valval segment stage, protolymphangion, and lymphangion.     

Molecular mechanisms coordinating functional and morphological plasticity at the synapse: Role of GluA2/N-cadherin interaction-mediated actin signaling in mGluR-dependent LTD

Long-lasting synaptic plasticity involves changes in both synaptic morphology and electrical signaling (here referred to as structural and functional plasticity). Recent studies have revealed a myriad of molecules and signaling processes that are critical for each of these two forms of plasticity, but whether and how they are mechanistically linked to achieve coordinated changes remain controversial.It is well accepted that functional plasticity at the excitatory synapse is dependent upon the activities of glutamate receptors. While the activation of NMDARs (N-methyl-D-aspartic acid receptors) and/or mGluRs (metabotropic glutamate receptors) is required for the induction of many forms of plasticity, AMPARs (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptors), the principal mediators of fast excitatory synaptic transmission, are the ultimate targets of modifications that express functional plasticity. Investigations exploring structural plasticity have been mainly focused on the small membranous protrusions on the dendrites called spines. The morphological regulation of these spines is mediated by the reorganization of the actin cytoskeleton, the predominant structural component of the synapse. In this regard, the Rho family of GTPases, particularly Rac1, RhoA and Cdc42, is found to be the central regulator of spine actin and structural plasticity of the synapse.It is thought that the collaborative interaction between functional and structural factors underlies the sustained or permanent nature of long-lasting synaptic plasticity such as long-term potentiation (LTP) and long-term depression (LTD), the most extensively studied forms of synaptic plasticity widely regarded as cellular mechanisms for learning and memory. However, data specifically pertaining to whether and how these two distinct components are linked at the molecular level remain sparse. In this regard, we have identified a number of synaptic proteins that are involved in both structural and functional changes during mGluR-dependent LTD (mGluR-LTD). Among these are the GluA2 (formerly called GluR2) subunit of AMPARs, Rac1 and Rac1-activated kinases. We have discovered that these proteins interact and reciprocally regulate each other, which led us to hypothesize that the GluA2–Rac1 interaction may serve as a coordinator between functional and morphological plasticity. In this review, we will briefly discuss the available evidence to support such a hypothesis.     

Plant functional types and climate at the global scale

Abstract. Globally applicable sets of terrestrial plant functional types (PFTs) have been identified as a major need in the development of dynamic global vegetation models for use with global atmospheric models. Global sets of PFTs should represent the world's most important plant types; characterize them through their functional behavior; and provide complete, geographically representative coverage of the world's land areas. Three main schools of thought on PFTs have emerged: (1) a physiological focus on internal function, especially at the level of basic metabolism; (2) an ecological focus on function in relation to plant form and environmental conditions; and (3) a geophysical focus on how plant functions affect the adjacent atmosphere. A structural approach based on pheno-physiognomy permits ready identification of relatively familiar, recognizable plant types. Many of the criteria cited by other approaches also are intimately related to structure and its seasonal changes. An earlier global system of structural-functional PFTs and their climatic relations has been improved, including addition of less well-known plant types, and is briefly described. A more strictly ‘functional’ approach is proposed, in which major aspects of plant function, initially metabolism and water balance, are used to classify functional types and suggest how these are constrained by climate. Such functional considerations, however, are closely linked to structural manifestations - but also require other functional criteria for more completely functional classifications. A recent global model of potential natural vegetation types suggested ca. 15 major plant types as necessary to cover the world's main terrestrial vegetation patterns. These essential types correspond well with a first-cut set of structural types implied by metabolic considerations.