Protein model discrimination attempts using mutational sensitivity,predicted secondary structure,and model quality information

Structure prediction methods often generate a large number of models for a target sequence. Even if the correct fold for the target sequence is sampled in this dataset, it is difficult to distinguish it from other decoy structures. An attempt to solve this problem using experimental mutational sensitivity data for the CcdB protein was described previously by exploiting the correlation of residue depth with mutational sensitivity (r ~ 0.6). We now show that such a correlation extends to four other proteins with localized active sites, and for which saturation mutagenesis datasets exist. We also examine whether incorporation of predicted secondary structure information and the DOPE model quality assessment score, in addition to mutational sensitivity, improves the accuracy of model discrimination using a decoy dataset of 163 targets from CASP. Although most CASP models would have been subjected to model quality assessment prior to submission, we find that the DOPE score makes a substantial contribution to the observed improvement. We therefore also applied the approach to CcdB and four other proteins for which reliable experimental mutational data exist and observe that inclusion of experimental mutational data results in a small qualitative improvement in model discrimination relative to that seen with just the DOPE score. This is largely because of our limited ability to quantitatively predict effects of point mutations on in vivo protein activity. Further improvements in the methodology are required to facilitate improved utilization of single mutant data.     

Butterfly edge effects are predicted by a simple model in a complex landscape

Edge responses have been studied for decades and form a critical component of our understanding of how organisms respond to landscape structure and habitat fragmentation. Until recently, however, the lack of a general, conceptual framework has made it difficult to make sense of the patterns and variability reported in the edge literature. We present a test of an edge effects model which predicts that organisms should avoid edges with less-preferred habitat, show increased abundance near edges with preferred habitat or habitat containing complementary resources, and show no response to edges with similar-quality habitat that offers only supplementary resources. We tested the predictions of this model against observations of the edge responses of 15 butterfly species at 12 different edge types within a complex, desert riparian landscape. Observations matched model predictions more than would be expected by chance for the 211 species/edge combinations tested over 3 years of study. In cases where positive or negative edge responses were predicted, observed responses matched those predictions 70% of the time. While the model tends to underpredict neutral results, it was rare that an observed edge response contradicted that predicted by the model. This study also supported the two primary ecological mechanisms underlying the model, although not equally. We detected a positive relationship between habitat preferences and the slope of the observed edge response, suggesting that this basic life history trait underlies edge effects and influences their magnitude. Empirical evidence also suggested the presence of complementary resources underlies positive edge responses, but only when completely confined to the adjacent habitat. This multi-species test of a general edge effects model at multiple edge types shows that resource-based mechanisms can explain many edge responses and that a modest knowledge of life history attributes and resource availability is sufficient for predicting and understanding many edge responses in complex landscapes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Epitopic discrimination by monoclonal antibodies directed against the same alkylated nucleoside

Epitopic specificity of three monoclonal antibodies (mAb's) (coded as ER-6, ER-3, and EM-1) was examined through the utilization of haptenic structural analogs. The binding affinity expressed by the microscopic equilibrium constant (Ki) (Yuhasz, et al., Biochemistry 26, 2334-2342 (1987] of the immunizing hapten, O6-ethyl-2'-deoxy-guanosine (*G) and eight structural analogs, were analyzed by a nitrocellulose affinity filter assay (NAFA) and radioimmunoassay (RIA) for each mAb to determine the protein-hapten interaction between the epitope and the binding cavity. Several components of the *G hapten were determined to be critical for each mAb recognition, while all three mAb's were found to require the O6-ethyl moiety, conjugated guanine base ring, the glycosyl bond and the sugar ring C [1'] and C [2'] position. This investigation further probes and categorizes the binding specificity of the monoclonal antibodies after incorporation of the *G monomer into three short deoxyribooligomeric haptens: O6-ethyl-2'-deoxyguanylyl 3',5' deoxyadenosine (*GA), 2'-deoxyadenylyl 3',5' O6-ethyl-2'-deoxyguanylyl 3',5' 2'-deoxyadenosine (A*GA), and O6-ethyl-2'-deoxyguanylyl 3',5' 2'-deoxyadenylyl 3',5'-2'-deoxyadenylyl 3',5' 2'-deoxycytosine (*GAAC). Unlike the similar binding profiles for the monoclonal antibodies and the haptenic structural analogs, the binding profiles for the deoxyribooligomeric haptens were found to differ in their modes of recognition. These results will be compared to ascertain the key components of monomer and oligomer interaction of the binding cavity. It is important for investigations where monoclonal antibodies derived from small haptens are utilized in recognition of larger antigens containing those haptens.     

Adhesive and lateral E-cadherin dimers are mediated by the same interface

E-cadherin is a transmembrane protein that mediates Ca(2+)-dependent cell-cell adhesion. To study cadherin-cadherin interactions that may underlie the adhesive process, a recombinant E-cadherin lacking free sulfhydryl groups and its mutants with novel cysteines were expressed in epithelial A-431 cells. These cysteine mutants, designed according to various structural models of cadherin dimers, were constructed to reveal cadherin dimerization by the bifunctional sulfhydryl-specific cross-linker BM[PE0]3. Cross-linking experiments with the mutants containing a cysteine at strand B of their EC1 domains did show cadherin dimerization. By their properties these dimers correspond to those which have been characterized by co-immunoprecipitation assay. Under standard culture conditions the adhesive dimer is a dominant form. Calcium depletion dissociates adhesive dimers and promotes the formation of lateral dimers. Our data show that both dimers are mediated by the amino-terminal cadherin domain. Furthermore, the interfaces involved in both adhesive and lateral dimerization appear to be the same. The coexistence of the structurally identical adhesive and lateral dimers suggests some flexibility of the extracellular cadherin region.     

Multiple walking speed-frequency relations are predicted by constrained optimization

A person constrained to walk at a given speed v on a treadmill, chooses a particular step frequency f and step length d=v/f. Testing over a range of speeds generates a speed-frequency (v-f) relationship. This relationship is commonly posited as a basic feature of human gait. It is often further posited that this curve follows from minimum energy cost strategy. We observed that individuals walking under different constraint circumstances--walking to a range of fixed metronome frequencies (fixed f) or over a range of spaced markers (fixed d)--produce speed-frequency relations distinct from the constrained v relation. We show here that three distinct speed-frequency curves, similar to those observed, are predicted by the assumption that a walking person optimizes an underlying objective function F (v, f) that has a minimum at the preferred gait. Further, the metabolic cost of transport is a reasonable approximate candidate for the function F.     

The transducer model for contrast detection and discrimination: formal relations, implications, and an empirical test

The transducer function mu for contrast perception describes the nonlinear mapping of stimulus contrast onto an internal response. Under a signal detection theory approach, the transducer model of contrast perception states that the internal response elicited by a stimulus of contrast c is a random variable with mean mu(c). Using this approach, we derive the formal relations between the transducer function, the threshold-versus-contrast (TvC) function, and the psychometric functions for contrast detection and discrimination in 2AFC tasks. We show that the mathematical form of the TvC function is determined only by mu, and that the psychometric functions for detection and discrimination have a common mathematical form with common parameters emanating from, and only from, the transducer function mu and the form of the distribution of the internal responses. We discuss the theoretical and practical implications of these relations, which have bearings on the tenability of certain mathematical forms for the psychometric function and on the suitability of empirical approaches to model validation. We also present the results of a comprehensive test of these relations using two alternative forms of the transducer model: a three-parameter version that renders logistic psychometric functions and a five-parameter version using Foley's variant of the Naka-Rushton equation as transducer function. Our results support the validity of the formal relations implied by the general transducer model, and the two versions that were contrasted account for our data equally well.     

Finding protein-protein interaction patterns by contact map matching

We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature.     

Egg phenotype matching by cuckoos in relation to discrimination by hosts and climatic conditions

Although parasites and their hosts often coexist in a set of environmentally differentiated populations connected by gene flow, few empirical studies have considered a role of environmental variation in shaping correlations between traits of hosts and parasites. Here, we studied for the first time the association between the frequency of adaptive parasitic common cuckoo Cuculus canorus phenotypes in terms of egg matching and level of defences exhibited by its reed warbler Acrocephalus scirpaceus hosts across seven geographically distant populations in Europe. We also explored the influence of spring climatic conditions experienced by cuckoos and hosts on cuckoo-host egg matching. We found that between-population differences in host defences against cuckoos (i.e. rejection rate) covaried with between-population differences in degree of matching. Between-population differences in host egg phenotype were associated with between-population differences in parasitism rate and spring climatic conditions, but not with host level of defences. Between-population differences in cuckoo egg phenotype covaried with between-population differences in host defences and spring climatic conditions. However, differences in host defences still explained differences in mimicry once differences in climatic conditions were controlled, suggesting that selection exerted by host defences must be strong relative to selection imposed by climatic factors on egg phenotypes.     

Native fold and docking pose discrimination by the same residue‐based scoring function

Structure prediction and quality assessment are crucial steps in modeling native protein conformations. Statistical potentials are widely used in related algorithms, with different parametrizations typically developed for different contexts such as folding protein monomers or docking protein complexes. Here, we describe BACH‐SixthSense, a single residue‐based statistical potential that can be successfully employed in both contexts. BACH‐SixthSense shares the same approach as BACH, a knowledge‐based potential originally developed to score monomeric protein structures. A term that penalizes steric clashes as well as the distinction between polar and apolar sidechain‐sidechain contacts are crucial novel features of BACH‐SixthSense. The performance of BACH‐SixthSense in discriminating correctly the native structure among a competing set of decoys is significantly higher than other state‐of‐the‐art scoring functions, that were specifically trained for a single context, for both monomeric proteins (QMEAN, Rosetta, RF_CB_SRS_OD, benchmarked on CASP targets) and protein dimers (IRAD, Rosetta, PIE*PISA, HADDOCK, FireDock, benchmarked on 14 CAPRI targets). The performance of BACH‐SixthSense in recognizing near‐native docking poses within CAPRI decoy sets is good as well. Proteins 2015; 83:621–630. © 2015 Wiley Periodicals, Inc.     

Protein interaction: same network, different hubs

Recently, large-scale experiments have provided new insights into the complex protein interaction network in yeast. However, previous analyses have shown that the number of interacting pairs that are common to different methods is extremely low and, therefore, less informative than expected. In this article, we show that comparing the connectivities of individual proteins can reveal that a common tendency between methods has been missed by the pairwise comparison of interactions. We found significant correlations between experimental methods and also between various in silico methods. Exceptionally, a computational method, gene neighbourhood, correlates with both in silico and experimental approaches.     

Strains at the myotendinous junction predicted by a micromechanical model

The goal of this work was to create a finite element micromechanical model of the myotendinous junction (MTJ) to examine how the structure and mechanics of the MTJ affect the local micro-scale strains experienced by muscle fibers. We validated the model through comparisons with histological longitudinal sections of muscles fixed in slack and stretched positions. The model predicted deformations of the A-bands within the fiber near the MTJ that were similar to those measured from the histological sections. We then used the model to predict the dependence of local fiber strains on activation and the mechanical properties of the endomysium. The model predicted that peak micro-scale strains increase with activation and as the compliance of the endomysium decreases. Analysis of the models revealed that, in passive stretch, local fiber strains are governed by the difference of the mechanical properties between the fibers and the endomysium. In active stretch, strain distributions are governed by the difference in cross-sectional area along the length of the tapered region of the fiber near the MTJ. The endomysium provides passive resistance that balances the active forces and prevents the tapered region of the fiber from undergoing excessive strain. These model predictions lead to the following hypotheses: (i) the increased likelihood of injury during active lengthening of muscle fibers may be due to the increase in peak strain with activation and (ii) endomysium may play a role in protecting fibers from injury by reducing the strains within the fiber at the MTJ.     

Lipid-cell interactions: Liposome adsorption and cell-to-liposome lipid transfer are mediated by the same cell-surface sites

The competitive behavior of solid vs. fluid liposomes in liposome-to-cell adsorption and cell-to-liposome lipid transfer processes was investigated with L cells and FBT epithelial sheets. Binding, transfer and ³¹P-NMR experiments have demonstrated that: (i) solid liposomes adhere to the cell surface as integral vesicles retaining the entrapped substances; (ii) fluid liposomes are partly disintegrated at the cell surface with concomitant entry of entrapped substances into the cytoplasm, while their lipids remain on the cell surface; (iii) fluid liposomes that escape lysis dissociate from the cell, taking away cell lipid molecules. The latter process underlies the mechanism of cell-to-fluid liposome lipid transfer. In contrast, no lipid transfer occurs between the plasma membrane and solid liposomes. Cell-bound solid liposomes interfere with the transfer of cell lipids to fluid liposomes, while these in turn inhibit the binding of solid liposomes to the cell surface. Moreover, cell-induced aggregation of both fluid and solid freshly added liposomes is also inhibited by preincubation of the cells with either solid or fluid liposomes. Thus, different types of interaction of both fluid and solid liposomes with the cell are mediated by the same (or closely related) sites on the cell surface.     

Effects of directional environmental change on extinction dynamics in experimental microbial communities are predicted by a simple model

Global temperatures are expected to rise between 1.1 and 6.4°C over the next 100 years, although the exact rate will depend on future greenhouse emissions, and will vary spatially. Temperature can alter an individual's metabolic rate, and consequently birth and death rates. In declining populations, these alterations may manifest as changes in the rate of that population's decline, and subsequently the timing of extinction events. Predicting such events could therefore be of considerable use. We use a small‐scale experimental system to investigate how the rate of temperature change can alter a population's time to extinction, and whether it is possible to predict this event using a simple phenomenological model that incorporates information about population dynamics at a constant temperature, published scaling of metabolic rates, and temperature. In addition, we examine 1) the relative importance of the direct effects of temperature on metabolic rate, and the indirect effects (via temperature driven changes in body size), on predictive accuracy (defined as the proximity of the predicted date of extinction to the mean observed date of extinction), 2) the combinations of model parameters that maximise accuracy of predictions, and 3) whether substituting temperature change through time with mean temperature produces accurate predictions. We find that extinction occurs earlier in environments that warm faster, and this can be accurately predicted (R² > 0.84). Increasing the number of parameters that were temperature‐dependent increased the model's accuracy, as did scaling these temperature‐dependent parameters with either the direct effects of temperature alone, or with the direct and indirect effects. Using mean temperature through time instead of actual temperature produces less accurate predictions of extinction. These results suggest that simple phenomenological models, incorporating metabolic theory, may be useful in understanding how environmental change can alter a population's rate of extinction. Synthesis Understanding how populations will respond to future climatic change is a key goal in ecology, however the exact rate of future warming will vary both spatially and temporally. Consequently, mathematical models must be used to understand the potential range of future population dynamics under various warming scenarios. We use a combination of experimentation and modelling to show that the effects of varying rates of environmental change on population dynamics can be predicted by a simple model. However, the accuracy of these predictions depends upon, amongst other things, a detailed knowledge of how temperature will change over time, rather than approximating this change to mean temperature.     

Form from motion parallax and form from luminance contrast: vernier discrimination

Some objects are perfectly camouflaged when stationary, but are clearly visible when moving; the boundaries of such an object are defined entirely by motion parallax. Little is known about the eye's ability to make spatial discriminations between motion-defined objects. In this study, subjects viewed a pseudo-random pattern of dots within which a camouflaged bar was made visible by relative motion of dots. Vernier acuity for the motion-defined bar was 27-45 sec arc for three subjects, much less than the interdot separation of 360 sec arc, much less than the 2 deg receptive field size for motion, and comparable with the foveal intercone separation of 30 sec arc. It is proposed that an opponent-orientation process and an opponent-position process can both contribute to vernier judgements for motion-defined objects. Real-world motion contrast commonly confounds the following cues for figure-ground segregation: (1) different texture velocities on either side of the figure's boundary; (2) in any given time interval, texture in figure and ground moves different distances; and (3) texture continually appears and disappears along the figure's boundary. When cues (2) and (3) were eliminated, thus ensuring figure-ground segregation was achieved entirely by motion-sensitive neural elements, vernier acuity was 44 +/- 5 sec arc compared with 36 +/- 8 sec arc for a dotted bar defined by luminance contrast. Conclusion: Vernier acuity for a dotted bar whose boundary was defined entirely by motion-sensitive neural elements was similar to vernier acuity for a dotted bar whose boundary was defined by luminance contrast.