Spontaneous and Stress-Induced Pore Formation in Membranes: Theory, Experiments and Simulations.

The large plasticity, dynamics and adaptability of biological membranes allow different modes of intrinsic and inducible permeability. These phenomena are of physiological importance for a number of natural functions related to cell death and can also be manipulated artificially for practical purposes like gene transfer, drug delivery, prevention of infections or anticancer therapy. For these advances to develop in a controllable and specific way, we need a sufficient understanding of the membrane permeability phenomena. Since the formulation of early concepts of pore formation, there has been an enormous effort to describe membrane permeability by using theory, simulations and experiments. A major breakthrough has come recently through theoretical developments that allow building continuous trajectories of pore formation both in the absence and presence of stress conditions. The new model provides a coherent quantitative view of membrane permeabilization, useful to test the impact of known lipid properties, make predictions and postulate specific pore intermediates that can be studied by simulations. For example, this theory predicts unprecedented dependencies of the line tension on the pore radius and on applied lateral tension which explain previous puzzling results. In parallel, important concepts have also come from molecular dynamics simulations, of which the role of water for membrane permeabilization is of special interest. These advances open new challenges and perspectives for future progress in the study of membrane permeability, as experiments and simulations will need to test the theoretical predictions, while theory achieves new refinements that provide a physical ground for observations.

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

MOTIVATION: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. RESULTS: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs.

(19)F NMR screening of unrelated antimicrobial peptides shows that membrane interactions are largely governed by lipids.

Many amphiphilic antimicrobial peptides permeabilize bacterial membranes via successive steps of binding, re-alignment and/or oligomerization. Here, we have systematically compared the lipid interactions of two structurally unrelated peptides: the cyclic ß-pleated gramicidin S (GS), and the α-helical PGLa. (19)F NMR was used to screen their molecular alignment in various model membranes over a wide range of temperatures. Both peptides were found to respond to the phase state and composition of these different samples in a similar way. In phosphatidylcholines, both peptides first bind to the bilayer surface. Above a certain threshold concentration they can re-align and immerse more deeply into the hydrophobic core, which presumably involves oligomerization. Re-alignment is most favorable around the lipid chain melting temperature, and also promoted by decreasing bilayer thickness. The presence of anionic lipids has no influence in fluid membranes, but in the gel phase the alignment states are more complex. Unsaturated acyl chains and other lipids with intrinsic negative curvature prevent re-alignment, hence GS and PGLa do not insert into mixtures resembling bacterial membranes, nor into bacterial lipid extracts. Cholesterol, which is present in high concentrations in animal membranes, even leads to an expulsion of the peptides from the bilayer and prevents their binding altogether. However, a very low cholesterol content of 10% was found to promote binding and re-alignment of both peptides. Overall, these findings show that the ability of amphiphilic peptides to re-align and immerse into a membrane is determined by the physico-chemical properties of the lipids, such as spontaneous curvature. This idea is reinforced by the remarkably similar behavior observed here for two structurally unrelated molecules (with different conformation, size, shape, charge), which further suggests that their activity at the membrane level is largely governed by the properties of the constituent lipids, while the selectivity towards different cell types is additionally ruled by electrostatic attraction between peptide and cell surface. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.

Direct observation of nanometer-scale pores of melittin in supported lipid monolayers.

Melittin is the most studied membrane-active peptide and archetype within a large and diverse group of pore formers. However, the molecular characteristics of melittin pores remain largely unknown. Herein, we show by atomic force microscopy (AFM) that lipid monolayers in the presence of melittin are decorated with numerous regularly shaped circular pores that can be distinguished from nonspecific monolayer defects. The specificity of these pores is reinforced through a statistical evaluation of depressions found in Langmuir-Blodgett monolayers in the presence and absence of melittin, which eventually allows characterization of the melittin-induced pores at a quantitative low-resolution level. We observed that the large majority of pores exhibit near-circular symmetry and a Gaussian distribution in size, with a mean diameter of ∼8.7 nm. A distinctive feature is a ring of material found around the pores, made by, on average, three positive peaks, with a height over the level of the lipidic background of ∼0.23 nm. This protruding rim is most likely due to the presence of melittin near the pore border. Although the current resolution of the AFM images in the {x, y} plane does not allow distinction of the specific organization of the peptide molecules, these results provide an unprecedented view of melittin pores formed in lipidic interfaces and open new perspectives for future structural investigations of these and other pore-forming peptides and proteins using supported monolayers.

A Hooke׳s law-based approach to protein folding rate.

Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke׳s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons among structural classes and folding mechanisms were carried out showing the good performance of our model with proteins of different types. The present model constitutes a simple rationale for the structural and energetic factors involved in protein folding kinetics.

Sex Differences in Cognitive Reflection: A Meta-Analysis.

The current study presents a meta-analytic review of the differences between men and women in cognitive reflection (CR). The study also explores whether the type of CR test (i.e., numerical tests and verbal tests) moderates the relationship between CR and sex. The results showed that men score higher than women on CR, although the magnitude of these differences was small. We also found out that the type of CR test moderates the sex differences in CR, especially in the numerical tests. In addition, the results showed that the length of numerical tests (i.e., number of items) does not affect the differences between men and women in CR. Finally, the implications of these results are discussed, and future research is suggested.

Canonical azimuthal rotations and flanking residues constrain the orientation of transmembrane helices.

In biological membranes the alignment of embedded proteins provides crucial structural information. The transmembrane (TM) parts have well-defined secondary structures, in most cases α-helices and their orientation is given by a tilt angle and an azimuthal rotation angle around the main axis. The tilt angle is readily visualized and has been found to be functionally relevant. However, there exist no general concepts on the corresponding azimuthal rotation. Here, we show that TM helices prefer discrete rotation angles. They arise from a combination of intrinsic properties of the helix geometry plus the influence of the position and type of flanking residues at both ends of the hydrophobic core. The helical geometry gives rise to canonical azimuthal angles for which the side chains of residues from the two ends of the TM helix tend to have maximum or minimum immersion within the membrane. This affects the preferential position of residues that fall near hydrophobic/polar interfaces of the membrane, depending on their hydrophobicity and capacity to form specific anchoring interactions. On this basis, we can explain the orientation and dynamics of TM helices and make accurate predictions, which correspond well to the experimental values of several model peptides (including dimers), and TM segments of polytopic membrane proteins.

Hydrophobic mismatch of mobile transmembrane helices: Merging theory and experiments.

Hydrophobic mismatch still represents a puzzle for transmembrane peptides, despite the apparent simplicity of this concept and its demonstrated validity in natural membranes. Using a wealth of available experimental ((2))H NMR data, we provide here a comprehensive explanation of the orientation and dynamics of model peptides in lipid bilayers, which shows how they can adapt to membranes of different thickness. The orientational adjustment of transmembrane α-helices can be understood as the result of a competition between the thermodynamically unfavorable lipid repacking associated with peptide tilting and the optimization of peptide/membrane hydrophobic coupling. In the positive mismatch regime (long-peptide/thin-membrane) the helices adapt mainly via changing their tilt angle, as expected from simple geometrical predictions. However, the adaptation mechanism varies with the peptide sequence in the flanking regions, suggesting additional effects that modulate hydrophobic coupling. These originate from re-adjustments of the peptide hydrophobic length and they depend on the hydrophobicity of the flanking region, the strength of interfacial anchoring, the structural flexibility of anchoring side-chains and the presence of alternative anchoring residues.

Bax-derived membrane-active peptides act as potent and direct inducers of apoptosis in cancer cells.

Although many cancer cells are primed for apoptosis, they usually develop resistance to cell death at several levels. Permeabilization of the outer mitochondrial membrane, which is mediated by proapoptotic Bcl-2 family members such as Bax, is considered as a point of no return for initiating apoptotic cell death. This crucial role has placed Bcl-2 family proteins as recurrent targets for anticancer drug development. Here, we propose and demonstrate a new concept based on minimal active versions of Bax to induce cell death independently of endogenous Bcl-2 proteins. We show that membrane-active segments of Bax can directly induce the release of mitochondria-residing apoptogenic factors and commit tumor cells promptly and irreversibly to caspase-dependent apoptosis. On this basis, we designed a peptide encompassing part of the Bax pore-forming domain, which can target mitochondria, induce cytochrome c release and trigger caspase-dependent apoptosis. Moreover, this Bax-derived 'poropeptide' produced effective tumor regression after peritumoral injection in a nude mouse xenograft model. Thus, peptides derived from proteins that form pores in the mitochondrial outer membrane represent novel templates for anticancer agents.

Global stability of protein folding from an empirical free energy function.

The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded and unfolded states and electrostatic interactions between residues. The parameters of the model were fixed from a protein data set whose unfolding free energy has been measured at the "standard" experimental conditions proposed by Maxwell et al. (2005) and a large data set of 1151 monomeric proteins obtained from the PDB. A blind test with proteins taken from ProTherm database, at similar experimental conditions, was carried out. We found a good correlation with the test data set, proving the effectiveness of our model for predicting protein folding free energies in considered standard conditions. Such a prediction compares favorably against estimations made with FoldX's function and the force field GROMOS96. This model constitutes a valuable tool for the fast evaluation of protein structure stability in 3D structure prediction methods.

Comparative analysis of the orientation of transmembrane peptides using solid-state (2)H- and (15)N-NMR: mobility matters.

Many solid-state nuclear magnetic resonance (NMR) approaches for membrane proteins rely on orientation-dependent parameters, from which the alignment of peptide segments in the lipid bilayer can be calculated. Molecules embedded in liquid-crystalline membranes, such as monomeric helices, are highly mobile, leading to partial averaging of the measured NMR parameters. These dynamic effects need to be taken into account to avoid misinterpretation of NMR data. Here, we compare two common NMR approaches: (2)H-NMR quadrupolar waves, and separated local field (15)N-(1)H polarization inversion spin exchange at magic angle (PISEMA) spectra, in order to identify their strengths and drawbacks for correctly determining the orientation and mobility of α-helical transmembrane peptides. We first analyzed the model peptide WLP23 in oriented dimyristoylphosphatidylcholine (DMPC) membranes and then contrasted it with published data on GWALP23 in dilauroylphosphatidylcholine (DLPC). We only obtained consistent tilt angles from the two methods when taking dynamics into account. Interestingly, the two related peptides differ fundamentally in their mobility. Although both helices adopt the same tilt in their respective bilayers (~20°), WLP23 undergoes extensive fluctuations in its azimuthal rotation angle, whereas GWALP23 is much less dynamic. Both alternative NMR methods are suitable for characterizing orientation and dynamics, yet they can be optimally used to address different aspects. PISEMA spectra immediately reveal the presence of large-amplitude rotational fluctuations, which are not directly seen by (2)H-NMR. On the other hand, PISEMA was unable to define the azimuthal rotation angle in the case of the highly dynamic WLP23, though the helix tilt could still be determined, irrespective of any dynamics parameters.

Counterproductive Academic Behaviors and Academic Performance: A Meta-Analysis and a Path Analysis Model.

Counterproductive academic behaviors (CAB) are a complex phenomenon that affects academic institutions in multiple geographical areas with different cultures, values, and social norms. The high incidence of CAB causes problems of critical importance that transcend the educational domain. The current study aims to contribute to the knowledge of the CAB consequences by focusing on its impact on academic performance (AP). For this purpose, a meta-analysis was conducted in order to examine the relationship between CAB, its facets, and AP. The results show that overall CAB and students' performance are negatively related with a true effect size of ρ = -0.40 (K = 231, N = 127,269). Particularly, absenteeism appeared to be the facet most strongly related to AP (ρ = -0.48, K = 117, N = 69,453). A meta-analytic path analysis model was carried out in order to test the predictive validity of CAB, students' personality characteristics, and intelligence on AP. Results show that conscientiousness and cognitive intelligence have a negative relationship with CAB (ß = -0.28 and ß = -0.20, respectively), and that conscientiousness, openness to experience, intelligence, and CAB can explain 58% of AP true variance. Meta-analyses of moderator variables and hierarchical meta-analyses are also presented. The implications for research and practice are discussed at the end.

Synthetic multistability in mammalian cells.

In multicellular organisms, gene regulatory circuits generate thousands of molecularly distinct, mitotically heritable states through the property of multistability. Designing synthetic multistable circuits would provide insight into natural cell fate control circuit architectures and would allow engineering of multicellular programs that require interactions among distinct cell types. We created MultiFate, a naturally inspired, synthetic circuit that supports long-term, controllable, and expandable multistability in mammalian cells. MultiFate uses engineered zinc finger transcription factors that transcriptionally self-activate as homodimers and mutually inhibit one another through heterodimerization. Using a model-based design, we engineered MultiFate circuits that generate as many as seven states, each stable for at least 18 days. MultiFate permits controlled state switching and modulation of state stability through external inputs and can be expanded with additional transcription factors. These results provide a foundation for engineering multicellular behaviors in mammalian cells.

Solid state NMR analysis of peptides in membranes: Influence of dynamics and labeling scheme.

The functional state of a membrane-active peptide is often defined by its conformation, molecular orientation, and its oligomeric state in the lipid bilayer. These "static" structural properties can be routinely studied by solid state NMR using isotope-labeled peptides. In the highly dynamic environment of a liquid crystalline biomembrane, however, the whole-body fluctuations of a peptide are also of paramount importance, although difficult to address and most often ignored. Yet it turns out that disregarding such motional averaging in calculating the molecular alignment from orientational NMR-constraints may give a misleading, if not false picture of the system. Here, we demonstrate that the reliability of a simplified static or an advanced dynamic data analysis depends critically on the choice of isotope labeling scheme used. Two distinctly different scenarios have to be considered. When the labels are placed on the side chains of a helical peptide (such as a CD(3)- or CF(3)-group attached to the C(alpha)C(beta) bond), their nuclear spin interaction tensors are very sensitive to motional averaging. If this effect is not properly accounted for, the helix tilt angle tends to be severely underestimated. At the same time, the analysis of labels in the side chains allows to extract valuable dynamical information about whole-body fluctuations of the peptide helix in the membrane. On the other hand, the alternative labeling scheme where (15)N-labels are accommodated within the peptide backbone, will yield nearly correct helix tilt angles, irrespective as to whether dynamics are taken into account or not.

Switchable bactericidal effects from novel silica-coated silver nanoparticles mediated by light irradiation.

Here we report on the triggering of antibacterial activity by a new type of silver nanoparticle coated with porous silica, Ag@silica, irradiated at their surface plasmon resonant frequency. The nanoparticles are able to bind readily to the surface of bacterial cells, although this does not affect bacterial growth since the silica shell largely attenuates the intrinsic toxicity of silver. However, upon simultaneous exposure to light corresponding to the absorption band of the nanoparticles, bacterial death is enhanced selectively on the irradiated zone. Because of the low power density used for the treatments, we discard thermal effects as the cause of cell killing. Instead, we propose that the increase in toxicity is due to the enhanced electromagnetic field in the proximity of the nanoparticles, which indirectly, most likely through induced photochemical reactions, is able to cause cell death.

A lipocentric view of peptide-induced pores.

Although lipid membranes serve as effective sealing barriers for the passage of most polar solutes, nonmediated leakage is not completely improbable. A high activation energy normally keeps unassisted bilayer permeation at a very low frequency, but lipids are able to self-organize as pores even in peptide-free and protein-free membranes. The probability of leakage phenomena increases under conditions such as phase coexistence, external stress or perturbation associated to binding of nonlipidic molecules. Here, we argue that pore formation can be viewed as an intrinsic property of lipid bilayers, with strong similarities in the structure and mechanism between pores formed with participation of peptides, lipidic pores induced by different types of stress, and spontaneous transient bilayer defects driven by thermal fluctuations. Within such a lipocentric framework, amphipathic peptides are best described as pore-inducing rather than pore-forming elements. Active peptides bound to membranes can be understood as a source of internal surface tension which facilitates pore formation by diminishing the high activation energy barrier. This first or immediate action of the peptide has some resemblance to catalysis. However, the presence of membrane-active peptides has the additional effect of displacing the equilibrium towards the pore-open state, which is then maintained over long times, and reducing the size of initial individual pores. Thus, pore-inducing peptides, regardless of their sequence and oligomeric organization, can be assigned a double role of increasing the probability of pore formation in membranes to high levels as well as stabilizing these pores after they appear.

A Meta-Analysis of the Faking Resistance of Forced-Choice Personality Inventories.

This study presents a comprehensive meta-analysis on the faking resistance of forced-choice (FC) inventories. The results showed that (1) FC inventories show resistance to faking behavior; (2) the magnitude of faking is higher in experimental contexts than in real-life selection processes, suggesting that the effects of faking may be, in part, a laboratory phenomenon; and (3) quasi-ipsative FC inventories are more resistant to faking than the other FC formats. Smaller effect sizes were found for conscientiousness when the quasi-ipsative format was used (δ = 0.49 vs. δ = 1.27 for ipsative formats). Also, the effect sizes were smaller for the applicant samples than for the experimental samples. Finally, the contributions and practical implications of these findings are discussed.

Cognitive Reflection, Life Satisfaction, Emotional Balance and Job Performance.

BACKGROUND: The validity of individual difference variables for predicting important life phenomena, such as job performance, has been studied for over a century. However, the relationships between some of them have scarcely been investigated. This paper presents a study on the relationship between cognitive reflection (CR), satisfaction with life (SWL), and emotional balance (EB) with job performance. METHOD: The participants were 245 managers (140 men and 105 women) working in companies in various economic sectors. RESULTS: The results showed that CR was not significantly related to job performance but that SWL and EB were valid predictors. Moreover, CR correlated significantly with SWL and EB. Multiple regression analysis showed that neither CR nor EB showed incremental validity over SWL in predicting job performance. CONCLUSIONS: These findings suggest that CR may not be an important variable in the workplace, at least regarding job performance, and that it is not a fully cognitive construct because some degree of its variance may be shared with motivational and personality traits.

Personality, intelligence, and counterproductive academic behaviors: A meta-analysis.

Counterproductive academic behaviors (CAB) are a major problem for educational institutions all over the world. For this reason, to determine the potential predictors of CAB is relevant. After defining CAB and introducing a typology of seven CABs facets (i.e., cheating, absenteeism, plagiarism, deception, breach of rules, low effort, and misuse of resources), this study reports on a comprehensive meta-analysis carried out to estimate the relationships between CAB and its facets with the Big Five personality dimensions and intelligence. Results showed that conscientiousness (K = 77, N = 31,473, ρ = -.28) and agreeableness (K = 56, N = 24,436, ρ = -.14) were predictors of the student's propensity to engage in CAB. Conscientiousness also predicted the 7 facets of CAB, particularly absenteeism (ρ = -.30), cheating (ρ = -.34), misuse of resources (ρ = -.32), low effort (ρ = -.29), and breach of rules (ρ = -.27). Intelligence showed a negative relationship with CAB (K = 55, N = 30,052, ρ = -.19), and it was the best predictor of deception (K = 18, N = 3,575 ρ = -.48). The educational level, the type of cognitive tests, and the intelligence factor assessed were relevant moderators of the validity estimates. The validity of a compound of conscientiousness, agreeableness, and intelligence was .42 for predicting overall CAB. Finally, we discuss the theoretical and practical implications of the findings. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Criterion Validity of Cognitive Reflection for Predicting Job Performance and Training Proficiency: A Meta-Analysis.

This article presents a meta-analysis of the validity of cognitive reflection (CR) for predicting job performance and training proficiency. It also examines the incremental validity of CR over cognitive intelligence (CI) for predicting these two occupational criteria. CR proved to be an excellent predictor of job performance and training proficiency, and the magnitude of the true validity was very similar across the two criteria. Results also showed that the type of CR is not a moderator of CR validity. We also found that CR showed incremental variance over CI for the explanation of job performance, although the magnitude of the contribution is small. However, CR shows practically no incremental validity over CI validity in the explanation of training proficiency. Finally, we discuss the implications of these findings for the research and practice of personnel selection.