Long-Range Coupling in an Allosteric Receptor Revealed by Mutant Cycle Analysis

The functional coupling of residues that are far apart in space is the quintessential property of allosteric proteins. For example, in Cys-loop receptors, the gating of an intrinsic ion channel is allosterically regulated by the binding of small molecule neurotransmitters 50–60 Å from the channel gate. Some residues near the binding site must have as their primary function the communication of the binding event to the gating region. These gating pathway residues are essential to function, but their identification and characterization can be challenging. This work introduces a simple strategy, derived from mutant cycle analysis, for identifying gating pathway residues using macroscopic measurements alone. In the exemplar Cys-loop receptor, the nicotinic acetylcholine receptor, a well-characterized reporter mutation (βL9′S) known to impact gating, was combined with mutations of target residues in the ligand-binding domain hypothesized or previously found to be functionally significant. A mutant cycle analysis of the macroscopic EC50 measurements can then provide insights into the role of the target residue. This new method, elucidating long-range functional coupling in allosteric receptors, can be applied to several reporter mutations in a wide variety of receptors to identify previously characterized and novel mutations that impact the gating pathway. We support our interpretation of macroscopic data with single-channel studies. Elucidating long-range functional coupling in allosteric receptors should be broadly applicable to determining functional roles of residues in allosteric receptors

The role of lipid composition on the interaction between a tryptophan-rich protein and model bacterial membranes

The interaction between tryptophan-rich puroindoline proteins and model bacterial membranes at the air-liquid interface has been investigated by FTIR spectroscopy, surface pressure measurements and Brewster angle microscopy. The role of different lipid constituents on the interactions between lipid membrane and protein was studied using wild type (Pin-b) and mutant (Trp44 to Arg44 mutant, Pin-bs) puroindoline proteins. The results show differences in the lipid selectivity of the two proteins in terms of preferential binding to specific lipid head groups in mixed lipid systems. Pin-b wild type was able to penetrate mixed layers of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) head groups more deeply compared to the mutant Pin-bs. Increasing saturation of the lipid tails increased penetration and adsorption of Pin-b wild type, but again the response of the mutant form differed. The results provide insight as to the role of membrane architecture, lipid composition and fluidity, on antimicrobial activity of proteins. Data show distinct differences in the lipid binding behavior of Pin-b as a result of a single residue mutation, highlighting the importance of hydrophobic and charged amino acids in antimicrobial protein and peptide activity

Bayesian optimization for materials design

We introduce Bayesian optimization, a technique developed for optimizing time-consuming engineering simulations and for fitting machine learning models on large datasets. Bayesian optimization guides the choice of experiments during materials design and discovery to find good material designs in as few experiments as possible. We focus on the case when materials designs are parameterized by a low-dimensional vector. Bayesian optimization is built on a statistical technique called Gaussian process regression, which allows predicting the performance of a new design based on previously tested designs. After providing a detailed introduction to Gaussian process regression, we introduce two Bayesian optimization methods: expected improvement, for design problems with noise-free evaluations; and the knowledge-gradient method, which generalizes expected improvement and may be used in design problems with noisy evaluations. Both methods are derived using a value-of-information analysis, and enjoy one-step Bayes-optimality

Selected wheat seed defense proteins exhibit competitive binding to model microbial lipid interfaces

Puroindolines (Pins) and purothionins (Pths) are basic, amphiphilic, cysteine-rich wheat proteins that play a role in plant defense against microbial pathogens. We have examined the co-adsorption and sequential addition of Pins (Pin-a, Pin-b and a mutant form of Pin-b with Trp-44 to Arg-44 substitution) and β-purothionin (β-Pth) model anionic lipid layers, using a combination of surface pressure measurements, external reflection FTIR spectroscopy and neutron reflectometry. Results highlighted differences in the protein binding mechanisms, and in the competitive binding and penetration of lipid layers between respective Pins and β-Pth. Pin-a formed a blanket-like layer of protein below the lipid surface that resulted in the reduction or inhibition of β-Pth penetration of the lipid layer. Wild-type Pin-b participated in co-operative binding with β-Pth, whereas the mutant Pin-b did not bind to the lipid layer in the presence of β-Pth. The results provide further insight into the role of hydrophobic and cationic amino acid residues in antimicrobial activity

The pseudophosphatase MK-STYX inhibits stress granule assembly independently of Ser149 phosphorylation of G3BP-1

The pseudophosphatase MK-STYX (mitogen-activated protein kinase phosphoserine/threonine/tyrosine-binding protein) has been implicated in the stress response pathway. The expression of MK-STYX inhibits the assembly of stress granules, which are cytoplasmic storage sites for mRNA that form as a protective mechanism against stressors such as heat shock, UV irradiation and hypoxia. Furthermore, MK-STYX interacts with a key component of stress granules: G3BP-1 (Ras-GTPase activating protein SH3 domain binding protein-1). Because G3BP-1 dephosphorylation at Ser149 induces stress granule assembly, we initially hypothesized that the inhibition of stress granules by MK-STYX was G3BP-1 phosphorylation-dependent. However, in the present study, using MK-STYX constructs and G3BP-1 phosphomimetic or nonphosphorylatable mutants, we show that MK-STYX inhibits stress granule formation independently of G3BP-1 phosphorylation at Ser149. The introduction of point mutations at the active site of MK-STYX that convert serine and phenylalanine to histidine and cysteine, respectively, is sufficient to generate an active enzyme. In separate experiments, we show that this active mutant, MK-STYXactive, has opposite effects to wild-type MK-STYK. Not only does MK-STYXactive induce stress granules, but also it has the capacity to dephosphorylate G3BP-1. Taken together, these results provide evidence that the pseudophosphatase MK-STYX plays a key role in the cellular response to stress

Alpha Band Signatures of Social Synchrony

Previous research has reported changes in mu rhythm, the central rhythm of the alpha frequency band, in both intentional and spontaneous interpersonal coordination. The current study was designed to extend existing findings on social synchrony to the pendulum swinging task and simultaneously measured time unfolding behavioral synchrony and EEG estimation of mu activity during spontaneous, intentional in-phase and intentional anti-phase interpersonal coordination. As expected, the behavioral measures of synchrony demonstrated the expected pattern of weak synchronization for spontaneous coordination, moderate synchronization for intentional anti-phase coordination, and strong synchronization for in-phase coordination. With respect to the EEG measures, we found evidence for mu enhancement for spontaneous coordination in contrast to mu suppression for intentional coordination (both in phase and anti-phase), with higher levels of synchronization associated with higher levels of mu suppression in the right hemisphere. The implications of the research findings and methodology for understanding the underlying mechanisms contributing to social problems in psychological disorders, leader-follower relationships, and inter-brain dynamics are discussed

Tryptophan to arginine substitution in puroindoline b alters binding to model eukaryotic membranes

We have studied how puroindoline-b (PINB) mutants bind to model eukaryotic membranes dependent on binary composition of anionic:zwitterionic phospholipids and the presence of cholesterol and sphingomyelin in the model membrane. We have found that the trends in lipid binding behavior are different for wild-type PINB compared to its naturally occurring PINB(Trp44Arg) mutant form and have seen evidence of protein-induced domain formation within the lipid layer structure. Results show that selective binding of antimicrobial peptides to different membrane types is as a result of differences in lipid composition and the arrangement of lipids within the membrane surface. However, membrane-binding behavior is not easily predicted; it is determined by net charge, hydrophobicity, and the amphiphilicity of the protein/peptide lipid-binding domain

Investigating the veracity of self-reported post-traumatic growth: a profile analysis approach

Research into posttraumatic growth—positive psychological change that people report in their relationships, priorities in life, and self-perception after experiences of adversity—has been severely critiqued. We investigated the degree to which community members’ friends and relatives corroborated targets’ self-perceived positive and negative changes as measured by the Posttraumatic Growth Inventory-42. We found corroboration only for negative changes when we examined overall (averaged) scores. However, using a profile analysis procedure, we found significant participant–informant agreement on the domains of change that had relatively higher scores in the target’s profile and those that had relatively lower scores. Our results demonstrate that informants were able to observe that targets had changed and were sensitive to the idiosyncratic ways in which these changes had manifested in targets’ behavior

Continuous Wavelets on Compact Manifolds

Let $\bf M$ be a smooth compact oriented Riemannian manifold, and let $\Delta_{\bf M}$ be the Laplace-Beltrami operator on ${\bf M}$. Say 0 \neq f \in \mathcal{S}(\RR^+), and that $f(0) = 0$. For $t > 0$, let $K_t(x,y)$ denote the kernel of $f(t^2 \Delta_{\bf M})$. We show that $K_t$ is well-localized near the diagonal, in the sense that it satisfies estimates akin to those satisfied by the kernel of the convolution operator $f(t^2\Delta)$ on \RR^n. We define continuous ${\cal S}$-wavelets on ${\bf M}$, in such a manner that $K_t(x,y)$ satisfies this definition, because of its localization near the diagonal. Continuous ${\cal S}$-wavelets on ${\bf M}$ are analogous to continuous wavelets on \RR^n in \mathcal{S}(\RR^n). In particular, we are able to characterize the H$\ddot{o}$lder continuous functions on ${\bf M}$ by the size of their continuous ${\mathcal{S}}-$wavelet transforms, for H$\ddot{o}$lder exponents strictly between 0 and 1. If $\bf M$ is the torus \TT^2 or the sphere $S^2$, and $f(s)=se^{-s}$ (the ``Mexican hat'' situation), we obtain two explicit approximate formulas for $K_t$, one to be used when $t$ is large, and one to be used when $t$ is small