Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains.

Protein binding to negatively charged lipids is essential for maintaining numerous vital cellular processes where its dysfunction can lead to various diseases. One such protein that plays a crucial role in this process is lactadherin, which competes with coagulation factors for membrane binding sites to regulate blood clotting. Despite identifying key binding regions of these proteins through structural and biochemical studies, models incorporating membrane dynamics are still lacking. In this study, we report on the multimodal binding of lactadherin and use it to gain insight into the binding mechanisms of its C domain homologs, factor V and factor VIII. Molecular dynamics simulations enhanced with the highly mobile mimetic model enabled the determination of lactadherin's multimodal binding on membranes that revealed critical interacting residues consistent with prior NMR and mutagenesis data. The binding occurred primarily via two dynamic structural ensembles: an inserted state and an unreported, highly conserved side-lying state driven by a cationic patch. We utilized these findings to analyze the membrane binding domains of coagulation factors V and VIII and identified their preferred membrane-bound conformations. Specifically, factor V's C domains maintained an inserted state, while factor VIII preferred a tilted, side-lying state that permitted antibody binding. Insight into lactadherin's atomistically resolved membrane interactions from a multistate perspective can guide new therapeutic opportunities in treating diseases related to blood coagulation.

RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting.

Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. Uridylation plays a particularly prominent role in RNA processing pathways of kinetoplastid protists typified by the causative agent of African sleeping sickness, Trypanosoma brucei In mitochondria of this pathogen, most mRNAs are internally modified by U-insertion/deletion editing while guide RNAs and rRNAs are U-tailed. The founding member of TUTase family, RNA editing TUTase 1 (RET1), functions as a subunit of the 3' processome in uridylation of gRNA precursors and mature guide RNAs. Along with KPAP1 poly(A) polymerase, RET1 also participates in mRNA translational activation. RET1 is divergent from human TUTases and is essential for parasite viability in the mammalian host and the insect vector. Given its robust in vitro activity, RET1 represents an attractive target for trypanocide development. Here, we report high-resolution crystal structures of the RET1 catalytic core alone and in complex with UTP analogs. These structures reveal a tight docking of the conserved nucleotidyl transferase bi-domain module with a RET1-specific C2H2 zinc finger and RNA recognition (RRM) domains. Furthermore, we define RET1 region required for incorporation into the 3' processome, determinants for RNA binding, subunit oligomerization and processive UTP incorporation, and predict druggable pockets.

Redox Active Colloids as Discrete Energy Storage Carriers.

Versatile and readily available battery materials compatible with a range of electrode configurations and cell designs are desirable for renewable energy storage. Here we report a promising class of materials based on redox active colloids (RACs) that are inherently modular in their design and overcome challenges faced by small-molecule organic materials for battery applications, such as crossover and chemical/morphological stability. RACs are cross-linked polymer spheres, synthesized with uniform diameters between 80 and 800 nm, and exhibit reversible redox activity as single particles, as monolayer films, and in the form of flowable dispersions. Viologen-based RACs display reversible cycling, accessing up to 99% of their capacity and 99 ± 1% Coulombic efficiency over 50 cycles by bulk electrolysis owing to efficient, long-distance intraparticle charge transfer. Ferrocene-based RACs paired with viologen-based RACs cycled efficiently in a nonaqueous redox flow battery employing a simple size-selective separator, thus demonstrating a possible application that benefits from their colloidal dimensions. The unprecedented versatility in RAC synthetic and electrochemical design opens new avenues for energy storage.

Impact of electrolyte composition on the reactivity of a redox active polymer studied through surface interrogation and ion-sensitive scanning electrochemical microscopy.

Elucidating the impact of interactions between the electrolyte and electroactive species in redox active polymers is key to designing better-performing electrodes for electrochemical energy storage and conversion. Here, we present on the improvement of the electrochemical activity of poly(para-nitrostyrene) (PNS) in solution and as a film by exploiting the ionic interactions between reduced PNS and K(+), which showed increased reactivity when compared to tetrabutylammonium (TBA(+))- and Li(+)-containing electrolytes. While cyclic voltammetry enabled the study of the effects of cations on the electrochemical reversibility and the reduction potential of PNS, scanning electrochemical microscopy (SECM) provided new tools to probe the ionic and redox reactivity of this system. Using an ion-sensitive Hg SECM tip allowed to probe the ingress of ions into PNS redox active films, while surface interrogation SECM (SI-SECM) measured the specific kinetics of PNS and a solution phase mediator in the presence of the tested electrolytes. SI-SECM measurements illustrated that the interrogation kinetics of PNS in the presence of K(+) compared to TBA(+) and Li(+) are greatly enhanced under the same surface concentration of adsorbed radical anion, exhibiting up to a 40-fold change in redox kinetics. We foresee using this new application of SECM methods for elucidating optimal interactions that enhance polymer reactivity for applications in redox flow batteries.

Enhanced Glassy State Mechanical Properties of Polymer Nanocomposites via Supramolecular Interactions.

It is now well accepted that the addition of nanoparticles (NPs) can strongly affect the thermomechanical properties of the polymers into which they are incorporated. In the solid (glassy) state, previous work has implied that optimal mechanical properties are achieved when the NPs are well dispersed in the matrix and when there is strong interfacial binding between the grafted NPs and the polymer matrix. Here we provide strong evidence supporting the importance of intermolecular interactions through the use of NPs grafted with polymers that can hydrogen bond with the matrix, yielding to significant improvements in the measured mechanical properties. Our finding thus supports the previously implied central role of strong interfacial binding in optimizing the mechanical properties of polymer nanocomposites.

Impact of redox-active polymer molecular weight on the electrochemical properties and transport across porous separators in nonaqueous solvents.

Enhancing the ionic conductivity across the electrolyte separator in nonaqueous redox flow batteries (NRFBs) is essential for improving their performance and enabling their widespread utilization. Separating redox-active species by size exclusion without greatly impeding the transport of supporting electrolyte is a potentially powerful alternative to the use of poorly performing ion-exchange membranes. However, this strategy has not been explored possibly due to the lack of suitable redox-active species that are easily varied in size, remain highly soluble, and exhibit good electrochemical properties. Here we report the synthesis, electrochemical characterization, and transport properties of redox-active poly(vinylbenzyl ethylviologen) (RAPs) with molecular weights between 21 and 318 kDa. The RAPs reported here show very good solubility (up to at least 2.0 M) in acetonitrile and propylene carbonate. Ultramicroelectrode voltammetry reveals facile electron transfer with E1/2 ∼ -0.7 V vs Ag/Ag(+)(0.1 M) for the viologen 2+/+ reduction at concentrations as high as 1.0 M in acetonitrile. Controlled potential bulk electrolysis indicates that 94-99% of the nominal charge on different RAPs is accessible and that the electrolysis products are stable upon cycling. The dependence of the diffusion coefficient on molecular weight suggests the adequacy of the Stokes-Einstein formalism to describe RAPs. The size-selective transport properties of LiBF4 and RAPs across commercial off-the-shelf (COTS) separators such as Celgard 2400 and Celgard 2325 were tested. COTS porous separators show ca. 70 times higher selectivity for charge balancing ions (Li(+)BF4(-)) compared to high molecular weight RAPs. RAPs rejection across these separators showed a strong dependence on polymer molecular weight as well as the pore size; the rejection increased with both increasing polymer molecular weight and reduction in pore size. Significant rejection was observed even for rpoly/rpore (polymer solvodynamic size relative to pore size) values as low as 0.3. The high concentration attainable (>2.0 M) for RAPs in common nonaqueous battery solvents, their electrochemical and chemical reversibility, and their hindered transport across porous separators make them attractive materials for nonaqueous redox flow batteries based on the enabling concept of size-selectivity.

Mitochondrial clearance and increased HSF-1 activity are coupled to promote longevity in fasted Caenorhabditis elegans.

Fasting has emerged as a potent means of preserving tissue function with age in multiple model organisms. However, our understanding of the relationship between food removal and long-term health is incomplete. Here, we demonstrate that in the nematode worm Caenorhabditis elegans, a single period of early-life fasting is sufficient to selectively enhance HSF-1 activity, maintain proteostasis capacity and promote longevity without compromising fecundity. These effects persist even when food is returned, and are dependent on the mitochondrial sirtuin, SIR-2.2 and the H3K27me3 demethylase, JMJD-3.1. We find that increased HSF-1 activity upon fasting is associated with elevated SIR-2.2 levels, decreased mitochondrial copy number and reduced H3K27me3 levels at the promoters of HSF-1 target genes. Furthermore, consistent with our findings in worms, HSF-1 activity is also enhanced in muscle tissue from fasted mice, suggesting that the potentiation of HSF-1 is a conserved response to food withdrawal.

Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters.

SWEETs and their prokaryotic counterparts SemiSWEETs were recently classified as transporters that translocate sugar across cellular membranes. SemiSWEETs are commonly used as a model system to infer biological properties of SWEETs; however, this presumes that the homologues are comparable to begin with. We evaluate this presumption by comparing their protein dynamics and substrate transport mechanism using 532 µs of simulation data in conjunction with Markov state models (MSMs). MSM weighted conformational landscape plots reveal significant differences between SWEETs and SemiSWEETs despite having similar structural topology. The presence of glucose reduces the free energy barrier between the functionally important intermediate states to enhance the transport process, while the substrate has no effect on SemiSWEET. The glucose adopts more rotational degrees of freedom in SWEET, while its conformation is restricted for SemiSWEET. Our study provides biological insights on the unexplored novelty of difference in the functional mechanism of two close homologous proteins.

Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes.

One of the key limitations of Molecular Dynamics (MD) simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long time scales. To overcome this bottleneck, we present the REinforcement learning based Adaptive samPling (REAP) algorithm that aims to efficiently sample conformational space by learning the relative importance of each order parameter as it samples the landscape. To achieve this, the algorithm uses concepts from the field of reinforcement learning, a subset of machine learning, which rewards sampling along important degrees of freedom and disregards others that do not facilitate exploration or exploitation. We demonstrate the effectiveness of REAP by comparing the sampling to long continuous MD simulations and least-counts adaptive sampling on two model landscapes (L-shaped and circular) and realistic systems such as alanine dipeptide and Src kinase. In all four systems, the REAP algorithm consistently demonstrates its ability to explore conformational space faster than the other two methods when comparing the expected values of the landscape discovered for a given amount of time. The key advantage of REAP is on-the-fly estimation of the importance of collective variables, which makes it particularly useful for systems with limited structural information.

A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases.

African trypanosomiasis occurs in 36 countries in sub-Saharan Africa with 10,000 reported cases annually. No definitive remedy is currently available and if left untreated, the disease becomes fatal. Structural and biochemical studies of trypanosomal terminal uridylyl transferases (TUTases) demonstrated their functional role in extensive uridylate insertion/deletion of RNA. Trypanosoma brucei RNA Editing TUTase 1 (TbRET1) is involved in guide RNA 3' end uridylation and maturation, while TbRET2 is responsible for U-insertion at RNA editing sites. Two additional TUTases called TbMEAT1 and TbTUT4 have also been reported to share similar function. TbRET1 and TbRET2 are essential enzymes for the parasite viability making them potential drug targets. For this study, we clustered molecular dynamics (MD) trajectories of four TUTases based on active site shape measured by Pocket Volume Measurer (POVME) program. Among the four TUTases, TbRET1 exhibited the largest average pocket volume, while TbMEAT1's and TbTUT4's active sites displayed the most flexibility. A side pocket was also identified within the active site in all TUTases with TbRET1 having the most pronounced. Our results indicate that TbRET1's larger side pocket can be exploited to achieve selective inhibitor design as FTMap identifies it as a druggable pocket.