Considerations on the possible structrual basis of neuronal integrated functions

Different types of dendro-dendritic and dendro-somatic contacts in several species are described. They are classified in five varieties: (a) parallel dendro-dendritic contacts; (b) crossed dendro-dendritic contacts; (c) perisomatic interdendritic contacts; (d) perivascular interdendritic contacts; (e) dendro-somatic contacts. It is hypothetically postulated, in agreement with other authors, that the structurally differentiated interdendritic and dendro-somatic contacts could act as functional junctions for the electrotonic spread of stimuli between neighbour neuronal elements.     

Dynamics underlying synaptic gain between pairs of cortical pyramidal neurons

Changes in connectivity between pairs of neurons can serve as a substrate for information storage and for experience-dependent changes in neuronal circuitry. Early in development, synaptic contacts form and break, but how these dynamics influence the connectivity between pairs of neurons is not known. Here we used time-lapse imaging to examine the synaptic interactions between pairs of cultured cortical pyramidal neurons, and found that the axon-dendrite contacts between each neuronal pair were composed of both a relatively stable and a more labile population. Under basal conditions, loss and gain of contacts within this labile population was well balanced and there was little net change in connectivity. Selectively increasing the levels of activated CaMKII in the postsynaptic neuron increased connectivity between pairs of neurons by increasing the rate of gain of new contacts without affecting the probability of contact loss, or the proportion of stable and labile contacts, and this increase required Calcium/calmodulin binding to CaMKII. Our data suggest that activating CaMKII can increase synaptic connectivity through a CaM-dependent increase in contact formation, followed by stabilization of a constant fraction of new contacts.     

GABA-immunohistochemistry as a label for identifying types of local interneurons and their synaptic contacts in the antennal lobes of the American cockroach

Summary Synaptic contacts between GABA-immunoreactive neurons, antennal receptor fibers and non-GABA-immunoreactive neurons in the glomerular neuropil of the antennal lobes have been identified by means of a combination of (i) immunohistochemical labeling and (ii) labeling of afferent fibers of the antenna by experimentally induced degeneration. Characteristic contacts of these neurons are: a) Serially arranged polysynaptic contacts between degenerated antennal fibers, GABA-immunoreactive neurons and non-GABA-immunoreactive neurons. b) Monosynaptic contacts between degenerated antennal fibers and non-GABA-immunoreactive neurons. c) Reciprocal synaptic contacts between immunostained and non-stained neurons and synaptic contacts between individual GABA-immunoreactive neurons. d) Synaptic output contacts of GABA-immunoreactive neurons with degenerated antennal fibers.GABA-immunoreactive neuron profiles in the glomeruli are assigned to multiglomerular local interneurons (Distler 1989a); non-immunolabeled profiles may be assigned to projection neurons and other not yet identified interneurons.     

GABA-immunohistochemistry as a label for identifying types of local interneurons and their synaptic contacts in the antennal lobes of the American cockroach

Synaptic contacts between GABA-immunoreactive neurons, antennal receptor fibers and non-GABA-immunoreactive neurons in the glomerular neuropil of the antennal lobes have been identified by means of a combination of (i) immunohistochemical labeling and (ii) labeling of afferent fibers of the antenna by experimentally induced degeneration. Characteristic contacts of these neurons are: a) Serially arranged polysynaptic contacts between degenerated antennal fibers, GABA-immunoreactive neurons and non-GABA-immunoreactive neurons. b) Monosynaptic contacts between degenerated antennal fibers and non-GABA-immunoreactive neurons. c) Reciprocal synaptic contacts between immunostained and non-stained neurons and synaptic contacts between individual GABA-immunoreactive neurons. d) Synaptic output contacts of GABA-immunoreactive neurons with degenerated antennal fibers. GABA-immunoreactive neuron profiles in the glomeruli are assigned to multiglomerular local interneurons (Distler 1989a); non-immunolabeled profiles may be assigned to projection neurons and other not yet identified interneurons.     

Role of medium- and long-range interactions to the stability of the mutants of T4 lysozyme

Inter-residue interactions play an important role to the folding and stability of protein molecules. In this work, we analyze the role of medium- and long-range interactions to the stability of T4 lysozyme mutants. We found that, in buried mutations, the increase in long-range contacts upon mutations destabilizes the protein, whereas, in surface mutations, the increase in long-range contacts increases the stability, indicating the importance of surrounding polar residues to the stability of surface mutations. Further, the increase in medium-range contacts decreases the stability of buried and surface mutations and a direct relationship is observed between the increase of medium-range contacts and increase in stability for partially buried/exposed mutations. Moreover, the relationship between amino acid properties and stability of T4 lysozyme mutants at positions Ile3, Phe53, and Leu99 showed that the effect of medium- and long-range contacts is less for buried mutations and the inter-residue contacts have significant correlation with the stability of partially buried mutations.     

Specialized contacts between sarcolemma and sarcoplasmic reticulum at the ends of muscle fibers in the diaphragm of the rat

Summary An electron-microscopic study of the myotendinous portion of the diaphragm in the Wistar rat has shown that at the ends of muscle fibers, longitudinally oriented invaginations and peripheral furrows of the sarcolemma establish specialized contacts with individual sacs of the sarcoplasmic reticulum. The construction of these terminal contacts is similar to that of contacts between sarcolemmic T-tubules and terminal cisternae of the sarcoplasmic reticulum, characterized by formation of triads. The contact zones of the sac membrane are undulated and bound to the adjoining sarcolemma via electron-dense profiles of varying forms. Frequently, the terminal contacts and triads are located at the same level within the muscle fiber, at the borderline between A- and I-bands of the sarcomeres. At the ends of muscle fibers combined contacts between peripheral furrows of the sarcolemma, terminal cisternae of the sarcoplasmic reticulum, and T-tubules of the triads are also disclosed. The implications of the terminal contacts for muscle contraction are discussed.     

Protein secondary structure assignment through Voronoï tessellation

We present a new automatic algorithm, named VoTAP (Vo ronoï T essellation A ssignment P rocedure), which assigns secondary structures of a polypeptide chain using the list of α‐carbon coordinates. This program uses three‐dimensional Voronoï tessellation. This geometrical tool associates with each amino acid a Voronoï polyhedron, the faces of which unambiguously define contacts between residues. Thanks to the face area, for the contacts close together along the primary structure (low‐order contacts) a distinction is made between strong and normal ones. This new definition yields new contact matrices, which are analyzed and used to assign secondary structures. This assignment is performed in two stages. The first one uses contacts between residues close together along the primary structure and is based on data collected on a bank of 282 well‐refined nonredundant structures. In this bank, associations were made between the prints defined by these low‐order contacts and the assignments performed by different automatic methods. The second step focuses on the strand assignment and uses contacts between distant residues. Comparison with several other automatic assignment methods are presented, and the influence of resolution on the assignment is investigated. Proteins 2004. © 2004 Wiley‐Liss, Inc.     

Protein contacts, inter-residue interactions and side-chain modelling

Three-dimensional structures of proteins are the support of their biological functions. Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-Calpha distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria. First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted. Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues. Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SCCOMP) on the distribution of contacts. The prediction rates of these different methods are quite similar. However, using a distance criterion between side chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed. Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviours distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease.     

Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins

Proteins from thermophilic organisms exhibit high thermal stability, but have structures that are very similar to their mesophilic homologues. In order to gain insight into the basis of thermostability, we have analyzed the medium- and long-range contacts in mesophilic and thermophilic proteins of 16 different families. We found that the thermophiles prefer to have contacts between residues with hydrogen-bond-forming capability. Apart from hydrophobic contacts, more contacts are observed between polar and non-polar residues in thermophiles than mesophiles. Residue-wise analysis showed that Tyr has good contacts with several other residues, and Cys has considerably higher long-range contacts in thermophiles compared with mesophiles. Furthermore, the residues occurring in the range of 31-34 residues apart in the sequence contribute significant long-range contacts to the stability of thermophilic proteins.     

Modelling disease spread through random and regular contacts in clustered populations

An epidemic spreading through a network of regular, repeated, contacts behaves differently from one that is spread by random interactions: regular contacts serve to reduce the speed and eventual size of an epidemic. This paper uses a mathematical model to explore the difference between regular and random contacts, considering particularly the effect of clustering within the contact network. In a clustered population random contacts have a much greater impact, allowing infection to reach parts of the network that would otherwise be inaccessible. When all contacts are regular, clustering greatly reduces the spread of infection; this effect is negated by a small number of random contacts.     

Myosin VI and vinculin cooperate during the morphogenesis of cadherin cell cell contacts in mammalian epithelial cells

Cooperation between cadherins and the actin cytoskeleton controls many aspects of epithelial biogenesis. We report here that myosin VI critically regulates the morphogenesis of epithelial cell-cell contacts. As epithelial monolayers mature in culture, discontinuous cell-cell contacts are initially replaced by continuous (cohesive) contacts. Myosin VI is recruited to cell contacts as they become linear and cohesive, where it forms a biochemical complex with epithelial cadherin (E-cadherin). Myosin VI is necessary for strong cadherin adhesion, for cells to form cohesive linear contacts, and for the integrity of the apical junctional complex. We find that vinculin mediates this effect of myosin VI. Myosin VI is necessary for vinculin and E-cadherin to interact. A combination of gain and loss of function approaches identifies vinculin as a downstream effector of myosin VI that is necessary for the integrity of intercellular contacts. We propose that myosin VI and vinculin form a molecular apparatus that generates cohesive cell-cell contacts in cultured mammalian epithelia.     

Statistical analysis of domains in interacting protein pairs

MOTIVATION: Several methods have recently been developed to analyse large-scale sets of physical interactions between proteins in terms of physical contacts between the constituent domains, often with a view to predicting new pairwise interactions. Our aim is to combine genomic interaction data, in which domain-domain contacts are not explicitly reported, with the domain-level structure of individual proteins, in order to learn about the structure of interacting protein pairs. Our approach is driven by the need to assess the evidence for physical contacts between domains in a statistically rigorous way. RESULTS: We develop a statistical approach that assigns p-values to pairs of domain superfamilies, measuring the strength of evidence within a set of protein interactions that domains from these superfamilies form contacts. A set of p-values is calculated for SCOP superfamily pairs, based on a pooled data set of interactions from yeast. These p-values can be used to predict which domains come into contact in an interacting protein pair. This predictive scheme is tested against protein complexes in the Protein Quaternary Structure (PQS) database, and is used to predict domain-domain contacts within 705 interacting protein pairs taken from our pooled data set.     

Comprehensive statistical analysis of residues interaction specificity at protein-protein interfaces

We calculated interchain contacts on the atomic level for nonredundant set of 4602 protein-protein interfaces using an unbiased Voronoi-Delaune tessellation method, and made 20x20 residue contact matrixes both for homodimers and heterocomplexes. The area of contacts and the distance distribution for these contacts were calculated on both the residue and the atomic levels. We analyzed residue area distribution and showed the existence of two types of interresidue contacts: stochastic and specific. We also derived formulas describing the distribution of contact area for stochastic and specific interactions in parametric form. Maximum pairing preference index was found for Cys-Cys contacts and for oppositely charged interactions. A significant difference in residue contacts was observed between homodimers and heterocomplexes. Interfaces in homodimers were enriched with contacts between residues of the same type due to the effects of structure symmetry.     

Nonlinear scaling of foraging contacts with rodent population density

Density‐dependent shifts in population processes like territoriality, reproduction, dispersal, and parasite transmission are driven by changes in contacts between individuals. Despite this, surprisingly little is known about how contacts change with density, and thus the mechanisms driving density‐dependent processes. A simple linear contact–density function is often assumed, but this is not based on a sound basis of empirical data. We addressed this question using a replicated, semi‐natural experiment in which we measured contacts at feeding stations between multimammate mice, Mastomys natalensis, across ten distinct, linearly increasing densities between 10 and 272 animals/ha. Unexpectedly, unique contacts increased not linearly but sigmoidally with density, which we attribute to the species’ scramble competition mating system, small‐scale dominance/avoidance and absence of territoriality. These results provide new insights into how species’ characteristics can relate to density‐dependent changes in contacts, and the unexpected shape of the contact–density function warrants that density‐dependence in ecological models, such as parasite transmission models, must be parameterized with care.     

Effective discrimination between biologically relevant contacts and crystal packing contacts using new determinants

In the structural models determined by X‐ray crystallography, contacts between molecules can be divided into two categories: biologically relevant contacts and crystal packing contacts. With the growth in the number and quality of available large crystal packing contacts structures, distinguishing crystal packing contacts from biologically relevant contacts remains a difficult task, which can lead to wrong interpretation of structural models. In this study, we performed a systematic analysis on the biologically relevant contacts and crystal packing contacts. The analysis results reveal that biologically contacts are more tightly packed than crystal packing contacts. This property of biologically contacts may contribute to the formation of their interfacial core region. Meanwhile, the differences between the core and surface region of biologically contacts in amino acid composition and evolutionary measure are more dramatic than crystal packing contacts and these differences appear to be useful in distinguishing these two categories of contacts. On the basis of the features derived from our analysis, we developed a random forest model to classify biological relevant contacts and crystal packing contacts. Our method can achieve a high receiver operating curve of 0.923 in the 5‐fold cross‐validation and accuracies of 91.4% and 91.7% for two different test sets. Moreover, in a comparison study, our model outperforms other existing methods, such as DiMoVo, Pita, Pisa, and Eppic. We believe that this study will provide useful help in the validation of oligomeric proteins and protein complexes. The model and all data used in this paper are freely available at http://cic.scu.edu.cn/bioinformatics/bio‐cry.zip . Proteins 2014; 82:3090–3100. © 2014 Wiley Periodicals, Inc.     

A role for local calcium signaling in rapid synaptic partner selection by dendritic filopodia

Synapse elimination is an important process underlying the establishment of functional neuronal networks during development. Here, we tested the idea that neurons select among potential synaptic partners already during initial contact formation between dendritic filopodia and axons-well before mature synapses are established. We show that filopodia frequently make contact with axons, and while some contacts are selectively stabilized, many are short-lived. More specifically, we demonstrate that contacts with a certain population of GABAergic axons never get stabilized, indicating that filopodia already early on select between different types of axons. Local dendritic calcium transients that are independent of glutamate occur within seconds after contact formation, and their frequency is high where contacts become stabilized and low at short-lived contacts. Thus, filopodia are capable of choosing between potential synaptic partners well before a mature synapse is established.     

Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils

We describe solid-state nuclear magnetic resonance (NMR) measurements on fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)) that place constraints on the identity and symmetry of contacts between in-register, parallel beta-sheets in the fibrils. We refer to these contacts as internal and external quaternary contacts, depending on whether they are within a single molecular layer or between molecular layers. The data include (1) two-dimensional 13C-13C NMR spectra that indicate internal quaternary contacts between side chains of L17 and F19 and side chains of I32, L34, and V36, as well as external quaternary contacts between side chains of I31 and G37; (2) two-dimensional 15N-13C NMR spectra that indicate external quaternary contacts between the side chain of M35 and the peptide backbone at G33; (3) measurements of magnetic dipole-dipole couplings between the side chain carboxylate group of D23 and the side chain amine group of K28 that indicate salt bridge interactions. Isotopic dilution experiments allow us to make distinctions between intramolecular and intermolecular contacts. On the basis of these data and previously determined structural constraints from solid-state NMR and electron microscopy, we construct full molecular models using restrained molecular dynamics simulations and restrained energy minimization. These models apply to Abeta(1-40) fibrils grown with gentle agitation. We also present evidence for different internal quaternary contacts in Abeta(1-40) fibrils grown without agitation, which are morphologically distinct.     

Separation of distinct adhesion complexes and associated cytoskeleton by a micro-stencil-printing method

Adhesion between cells and the extracellular matrix is mediated by different types of transmembraneous proteins. Their associations to specific partners lead to the assembly of contacts such as focal adhesions and hemidesmosomes. The spatial overlap between both contacts within cells has however limited the study of each type of contact. Here we show that with “stampcils” focal contacts and hemidesmosomes can be spatially separated: cells are plated within the cavities of a stencil and the grids of the stencil serve as stamps for grafting an extracellular matrix protein—fibronectin. Cells engage new contacts on stamped zones leading to the segregation of adhesions and their associated cytoskeletons, i.e., actin and intermediate filaments of keratins. This new method should provide new insights into cell contacts compositions and dynamics.     

Selectivity in metabolic cooperation between cultured mammalian cells

Selective communication between cultured mammalian cells was detected as selectivity in metabolic cooperation. Whilst the majority of the cell types examined (human skin fibroblast, PC13, G3, Don, PyY) showed metabolic cooperation at almost all (>95%) of their homotypic cell-to-cell contacts, they did not necessarily show cooperation at such a high proportion of their heterotypic contacts. Less than 10% of G3/human fibroblast contacts, and usually less than 30% of G3/PC13 contacts were observed to be positive for metabolic cooperation. L cells differed from these other cell types in that they formed permeable junctions at a greater proportion of their heterotypic cell-to-cell contacts (contacts between L and PyY cells) than their homotypic contacts. We question why it was that the contacts between any two poorly-compatible cell types were positive for metabolic cooperation in only a small proportion of cases. We could find no indication that this phenomenon was attributable to heterogeneity within the cell stocks. Time course studies upon PC13 and G3 cells showed that the proportion of cooperation-positive contacts was not constant but that it continued to increase over many hours of co-culture. In comparing the homotypic and heterotypic interactions of these cell types, selectivity manifested as a difference in the rate of appearance of permeable junctions. We discuss possible explanations for these findings.     

Non-native interactions play an effective role in protein folding dynamics

Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well‐defined order. The detailed study of the folding dynamics of protein‐like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non‐native interactions in the folding process), reveals significant differences in the corresponding locking scenarios—the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non‐native contacts. Furthermore, strong evidence for a positive role played by non‐native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non‐native contacts is observed also toward the end of the folding process, suggesting that non‐native contacts may indeed affect the overall folding process. For target models exhibiting clear two‐state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.