Glen M. Hocky

Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model

The widely used Born model describes the electrostatic response of continuous media using static dielectric constants. However, when applied to a liquid environment, a comparison of Born model predictions with experimental values (e.g., transfer free energies and pKa shifts) found that agreement is only achieved by using physically unrealistic dielectric constants for proteins, lipids, etc., and/or equally unrealistic atomic radii. This leads to questions concerning the physical origins for this failure of the Born model. We partially resolve this question by applying the Langevin–Debye (LD) model of a continuous distribution of point, polarizable dipoles, a model that contains an added dependence of the electrostatic response on the solvents optical dielectric constant and both gas- and liquid-phase dipole moments, features absent in the Born model to which the LD model reduces for weak fields. The LD model is applied to simple representations of three biologically relevant systems: (i) globular proteins, (ii) lipid bilayers, and (iii) membrane proteins. The linear Born treatment greatly overestimates both the self-energy and the transfer free energy from water to hydrophobic environments (e.g., a protein interior). By using the experimental dielectric constant, the energy cost of charge burial in either globular or membrane proteins of the Born model is reduced by almost 50% with the nonlinear theory as is the pKa shift, and the shifts agree well with experimental trends.

Correlation of local order with particle mobility in supercooled liquids is highly system dependent.

We investigate the connection between local structure and dynamical heterogeneity in supercooled liquids. Through the study of four different models, we show that the correlation between a particles mobility and the degree of local order in nearby regions is highly system dependent. Our results suggest that the correlation between local structure and dynamics is weak or absent in systems that conform well to the mean-field picture of glassy dynamics and strong in those that deviate from this paradigm. Finally, we investigate the role of order-agnostic point-to-set correlations and reveal that they provide similar information content to local structure measures, at least in the system where local order is most pronounced.

Protein structure prediction enhanced with evolutionary diversity: SPEED.

For naturally occurring proteins, similar sequence implies similar structure. Consequently, multiple sequence alignments (MSAs) often are used in template‐based modeling of protein structure and have been incorporated into fragment‐based assembly methods. Our previous homology‐free structure prediction study introduced an algorithm that mimics the folding pathway by coupling the formation of secondary and tertiary structure. Moves in the Monte Carlo procedure involve only a change in a single pair of ϕ,ψ backbone dihedral angles that are obtained from a Protein Data Bank‐based distribution appropriate for each amino acid, conditional on the type and conformation of the flanking residues. We improve this method by using MSAs to enrich the sampling distribution, but in a manner that does not require structural knowledge of any protein sequence (i.e., not homologous fragment insertion). In combination with other tools, including clustering and refinement, the accuracies of the predicted secondary and tertiary structures are substantially improved and a global and position‐resolved measure of confidence is introduced for the accuracy of the predictions. Performance of the method in the Critical Assessment of Structure Prediction (CASP8) is discussed.

Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction.

Metadynamics is an enhanced sampling method designed to flatten free energy surfaces uniformly. However, the highest-energy regions are often irrelevant to study and dangerous to explore because systems often change irreversibly in unforeseen ways in response to driving forces in these regions, spoiling the sampling. Introducing an on-the-fly domain restriction allows metadynamics to flatten only up to a specified energy level and no further, improving efficiency and safety while decreasing the pressure on practitioners to design collective variables that are robust to otherwise irrelevant high energy driving. This paper describes a new method that achieves this using sequential on-the-fly estimation of energy wells and redefinition of the metadynamics hill shape, termed metabasin metadynamics. The energy level may be defined a priori or relative to unknown barrier energies estimated on-the-fly. Altering only the hill ensures that the method is compatible with many other advances in metadynamics methodology. The hill shape has a natural interpretation in terms of multiscale dynamics, and the computational overhead in simulation is minimal when studying systems of any reasonable size, for instance proteins or other macromolecules. Three example applications show that the formula is accurate and robust to complex dynamics, making metadynamics significantly more forgiving with respect to CV quality and thus more feasible to apply to the most challenging biomolecular systems.

Equilibrium ultrastable glasses produced by random pinning

Ultrastable glasses have risen to prominence due to their potentially useful material properties and the tantalizing possibility of a general method of preparation via vapor deposition. Despite the importance of this novel class of amorphous materials, numerical studies have been scarce because achieving ultrastability in atomistic simulations is an enormous challenge. Here, we bypass this difficulty and establish that randomly pinning the position of a small fraction of particles inside an equilibrated supercooled liquid generates ultrastable configurations at essentially no numerical cost, while avoiding undesired structural changes due to the preparation protocol. Building on the analogy with vapor-deposited ultrastable glasses, we study the melting kinetics of these configurations following a sudden temperature jump into the liquid phase. In homogeneous geometries, we find that enhanced kinetic stability is accompanied by large scale dynamic heterogeneity, while a competition between homogeneous and heterogeneous melting is observed when a liquid boundary invades the glass at constant velocity. Our work demonstrates the feasibility of large-scale, atomistically resolved, and experimentally relevant simulations of the kinetics of ultrastable glasses.

Crossovers in the dynamics of supercooled liquids probed by an amorphous wall.

We study the relaxation dynamics of a binary Lennard-Jones liquid in the presence of an amorphous wall generated from equilibrium particle configurations. In qualitative agreement with the results presented by Kob et al. [Nat. Phys. 8, 164 (2012).] for a liquid of harmonic spheres, we find that our binary mixture shows a saturation of the dynamical length scale close to the mode-coupling temperature T(c). Furthermore we show that, due to the broken symmetry imposed by the wall, signatures of an additional change in dynamics become apparent at a temperature well above T(c). We provide evidence that this modification in the relaxation dynamics occurs at a recently proposed dynamical crossover temperature T(s) > T(c), which is related to the breakdown of the Stokes-Einstein relation. We find that this dynamical crossover at T(s) is also observed for the harmonic spheres as well as a WCA liquid, showing that it may be a general feature of glass-forming systems.

Mechanoregulated inhibition of formin facilitates contractile actomyosin ring assembly

Cytokinesis physically separates dividing cells by forming a contractile actomyosin ring. The fission yeast contractile ring has been proposed to assemble by Search-Capture-Pull-Release from cytokinesis precursor nodes that include the molecular motor type-II myosin Myo2 and the actin assembly factor formin Cdc12. By successfully reconstituting Search-Capture-Pull in vitro, we discovered that formin Cdc12 is a mechanosensor, whereby myosin pulling on formin-bound actin filaments inhibits Cdc12-mediated actin assembly. We mapped Cdc12 mechanoregulation to its formin homology 1 domain, which facilitates delivery of new actin subunits to the elongating actin filament. Quantitative modeling suggests that the pulling force of the myosin propagates through the actin filament, which behaves as an entropic spring, and thereby may stretch the disordered formin homology 1 domain and impede formin-mediated actin filament elongation. Finally, live cell imaging of mechano-insensitive formin mutant cells established that mechanoregulation of formin Cdc12 is required for efficient contractile ring assembly in vivo.The fission yeast cytokinetic ring assembles by Search-Capture-Pull-Release from precursor nodes that include formin Cdc12 and myosin Myo2. The authors reconstitute Search-Capture-Pull in vitro and find that Myo2 pulling on Cdc12-associated actin filaments mechano-inhibits Cdc12-mediated assembly, which enables proper ring assembly in vivo.

Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits

Ions regulate the assembly and mechanical properties of actin filaments. Recent work using structural bioinformatics and site-specific mutagenesis favors the existence of two discrete and specific divalent cation binding sites on actin filaments, positioned in the long axis between actin subunits. Cation binding at one site drives polymerization, while the other modulates filament stiffness and plays a role in filament severing by the regulatory protein, cofilin. Existing structural methods have not been able to resolve filament-associated cations, and so in this work we turn to molecular dynamics simulations to suggest a candidate binding pocket geometry for each site and to elucidate the mechanism by which occupancy of the “stiffness site” affects filament mechanical properties. Incorporating a magnesium ion in the “polymerization site” does not seem to require any large-scale change to an actin subunit’s conformation. Binding of a magnesium ion in the “stiffness site” adheres the actin DNase-binding loop (D-loop) to its long-axis neighbor, which increases the filament torsional stiffness and bending persistence length. Our analysis shows that bound D-loops occupy a smaller region of accessible conformational space. Cation occupancy buries key conserved residues of the D-loop, restricting accessibility to regulatory proteins and enzymes that target these amino acids.

Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks

The fission yeast actin cytoskeleton is an ideal, simplified system to investigate fundamental mechanisms behind cellular self-organization. By focusing on the stabilizing protein tropomyosin Cdc8, bundling protein fimbrin Fim1, and severing protein coffin Adf1, we examined how their pairwise and collective interactions with actin filaments regulate their activity and segregation to functionally diverse F-actin networks. Utilizing multi-color TIRF microscopy of in vitro reconstituted F-actin networks, we observed and characterized two distinct Cdc8 cables loading and spreading cooperatively on individual actin filaments. Furthermore, Cdc8, Fim1, and Adf1 all compete for association with F-actin by different mechanisms, and their cooperative association with actin filaments affects their ability to compete. Finally, competition between Fim1 and Adf1 for F-actin synergizes their activities, promoting rapid displacement of Cdc8 from a dense F-actin network. Our findings reveal that competitive and cooperative interactions between actin binding proteins help define their associations with different F-actin networks. DOI: http://dx.doi.org/10.7554/eLife.23152.001

The F-actin bundler α-actinin Ain1 is tailored for ring assembly and constriction during cytokinesis in fission yeast

The highly dynamic bundling activity of fission yeast α-actinin SpAin1 was biochemically characterized, and its importance for contractile ring formation in vivo was tested. Investigation of a mutant with higher bundling activity, SpAin1(216E), revealed that dynamic SpAin1-mediated bundling is crucial for proper ring assembly and constriction.