Molecular Orientation of -PO3H2 and -COOH Functionalized Dyes on TiO2, Al2O3, ZrO2, and ITO: A Comparative Study.

Modification of transparent metal oxide (MOx) surfaces with organic monolayers is widely employed to tailor the properties of interfaces in organic electronic devices, and MOx substrates modified with light-absorbing chromophores are a key component of dye-sensitized solar cells (DSSCs). The effects of an organic modifier on the performance of a MOx-based device are frequently assessed by performing experiments on model monolayer|MOx interfaces, where an "inert" MOx (e.g., Al2O3) is used as a control for an "active" MOx (e.g., TiO2). An underlying assumption in these studies is that the structure of the MOx-monolayer complex is similar between different metal oxides. The validity of this assumption was examined in the present study. Using UV-Vis attenuated total reflection spectroscopy, we measured the mean dipole tilt angle of 4,4'-(anthracene-9,10-diyl)bis(4,1-phenylene)diphosphonic acid (A1P) adsorbed on indium tin oxide (ITO), TiO2, ZrO2, and Al2O3. When the surface roughness of the MOx substrate and the surface coverage (𝛤) of the A1P film were constant, the molecular orientation of A1P was the same on these substrates. The study was extended to 4,4'-(anthracene-9,10-diyl)bis(4,1-phenylene)dicarboxylic acid (A1C) adsorbed on the same group of MOx substrates. The mean tilt angle of A1C and A1P films on ITO was the same, which is likely due the intermolecular interactions resulting from the high and approximately equal 𝛤 of both films. Comparing A1C films at the same 𝛤 on TiO2 and Al2O3 having the same surface roughness, there was no difference in the mean tilt angle. MD simulations of A1C and A1P on TiO2 produced nearly identical tilt angle distributions, which supports the experimental findings. This study provides first experimental support for the assumption that the structure of the MOx-modifer film is the same on an "active" substrate vs. a "inert" control substrate.

Bioequivalence and Relative Bioavailability Studies to Assess a New Acalabrutinib Formulation That Enables Coadministration With Proton-Pump Inhibitors.

Acalabrutinib is a Bruton tyrosine kinase (BTK) inhibitor approved to treat adults with chronic lymphocytic leukemia, small lymphocytic lymphoma, or previously treated mantle cell lymphoma. As the bioavailability of the acalabrutinib capsule (AC) depends on gastric pH for solubility and is impaired by acid-suppressing therapies, coadministration with proton-pump inhibitors (PPIs) is not recommended. Three studies in healthy subjects (N = 30, N = 66, N = 20) evaluated the pharmacokinetics (PKs), pharmacodynamics (PDs), safety, and tolerability of acalabrutinib maleate tablet (AT) formulated with pH-independent release. Subjects were administered AT or AC (orally, fasted state), AT in a fed state, or AT in the presence of a PPI, and AT or AC via nasogastric (NG) route. Acalabrutinib exposures (geometric mean [% coefficient of variation, CV]) were comparable for AT versus AC (AUCinf 567.8 ng h/mL [36.9] vs 572.2 ng h/mL [38.2], Cmax 537.2 ng/mL [42.6] vs 535.7 ng/mL [58.4], respectively); similar results were observed for acalabrutinib's active metabolite (ACP-5862) and for AT-NG versus AC-NG. The geometric mean Cmax for acalabrutinib was lower when AT was administered in the fed versus the fasted state (Cmax 255.6 ng/mL [%CV, 46.5] vs 504.9 ng/mL [49.9]); AUCs were similar. For AT + PPI, geometric mean Cmax was lower (371.9 ng/mL [%CV, 81.4] vs 504.9 ng/mL [49.9]) and AUCinf was higher (AUCinf 694.1 ng h/mL [39.7] vs 559.5 ng h/mL [34.6]) than AT alone. AT and AC were similar in BTK occupancy. Most adverse events were mild with no new safety concerns. Acalabrutinib formulations were comparable and AT could be coadministered with PPIs, food, or via NG tube without affecting the PKs or PDs.

Bioavailability of acalabrutinib suspension delivered via nasogastric tube in the presence or absence of a proton pump inhibitor in healthy subjects.

AIMS: Acalabrutinib, a selective Bruton tyrosine kinase inhibitor, is approved for the treatment of mantle cell lymphoma and chronic lymphocytic leukaemia. Many critically ill patients are unable to swallow and need oral medications to be delivered via a nasogastric (NG) tube. Furthermore, critically ill patients are typically administered proton-pump inhibitors (PPIs) to prevent stress ulcers. Concomitant administration with PPIs reduces acalabrutinib exposure and is not currently recommended. To evaluate acalabrutinib in subjects co-administered with PPIs who require NG delivery, a phase 1, open-label, randomized, crossover, single-dose study was conducted in healthy subjects. METHODS: The study assessed the relative bioavailability of an acalabrutinib suspension-in regular, degassed Coca-Cola-administered via NG tube (Acala-NG) versus the pharmacokinetics (PK) of an acalabrutinib capsule administered orally with water. In addition, the PPI effect was evaluated by comparing the PK following Acala-NG in the presence or absence of rabeprazole. RESULTS: Exposure of acalabrutinib and its active metabolite (ACP-5862) were comparable following administration of Acala-NG versus the oral capsule (Geo mean ratio, % ref [90% confidence interval, CI]: acalabrutinib AUCinf : 103 [93-113]; Cmax : 144 [120-173]). In addition, exposure was similar following administration of Acala-NG with and without a PPI (Geo mean ratio, % ref [90% CI]: acalabrutinib AUCinf : 105 [79-138]; Cmax : 95 [66-137]). No safety or tolerability concerns were observed, and all adverse events were mild and resolved without treatment. CONCLUSIONS: Acala-NG with or without a PPI is safe and well-tolerated without impeding bioavailability.

Dynamic Hand Gesture Recognition in In-Vehicle Environment Based on FMCW Radar and Transformer.

Hand gesture recognition technology plays an important role in human-computer interaction and in-vehicle entertainment. Under in-vehicle conditions, it is a great challenge to design gesture recognition systems due to variable driving conditions, complex backgrounds, and diversified gestures. In this paper, we propose a gesture recognition system based on frequency-modulated continuous-wave (FMCW) radar and transformer for an in-vehicle environment. Firstly, the original range-Doppler maps (RDMs), range-azimuth maps (RAMs), and range-elevation maps (REMs) of the time sequence of each gesture are obtained by radar signal processing. Then we preprocess the obtained data frames by region of interest (ROI) extraction, vibration removal algorithm, background removal algorithm, and standardization. We propose a transformer-based radar gesture recognition network named RGTNet. It fully extracts and fuses the spatial-temporal information of radar feature maps to complete the classification of various gestures. The experimental results show that our method can better complete the eight gesture classification tasks in the in-vehicle environment. The recognition accuracy is 97.56%.

Radar Transformer: An Object Classification Network Based on 4D MMW Imaging Radar.

Automotive millimeter-wave (MMW) radar is essential in autonomous vehicles due to its robustness in all weather conditions. Traditional commercial automotive radars are limited by their resolution, which makes the object classification task difficult. Thus, the concept of a new generation of four-dimensional (4D) imaging radar was proposed. It has high azimuth and elevation resolution and contains Doppler information to produce a high-quality point cloud. In this paper, we propose an object classification network named Radar Transformer. The algorithm takes the attention mechanism as the core and adopts the combination of vector attention and scalar attention to make full use of the spatial information, Doppler information, and reflection intensity information of the radar point cloud to realize the deep fusion of local attention features and global attention features. We generated an imaging radar classification dataset and completed manual annotation. The experimental results show that our proposed method achieved an overall classification accuracy of 94.9%, which is more suitable for processing radar point clouds than the popular deep learning frameworks and shows promising performance.

Examining the influence of bilayer structure on energy transfer and molecular photon upconversion in metal ion linked multilayers.

Metal ion linked multilayers is a unique motif to spatially control and geometrically restrict molecules on a metal oxide surface and is of interest in a number of promising applications. Here we use a bilayer composed of a metal oxide surface, an anthracene annihilator molecule, Zn(II) linking ion, and porphyrin sensitizers to probe the influence of the position of the metal ion binding site on energy transfer, photon upconversion, and photocurrent generation. Despite being energetically similar, varying the position of the carboxy metal ion binding group (i.e. ortho, meta, para) of the Pt(II) tetraphenyl porphyrin sensitizer had a large impact on energy transfer rates and upconverted photocurrent that can be attributed to differences in their geometries. From polarized attenuated total reflectance measurements of the bilayers on ITO, we found that the orientation of the first layer (anthracene) was largely unperturbed by subsequent layers. However, the tilt angle of the porphyrin plane varies dramatically from 41° to 64° to 57° for the para-, meta-, and ortho-COOH substituted porphyrin molecules, which is likely responsible for the variation in energy transfer rates. We go on to show using molecular dynamics simulations that there is considerable flexibility in porphyrin orientation, indicating that an average structure is insufficient to predict the ensemble behavior. Instead, even a small subset of the population with highly favorable energy transfer rates can be the primary driver in increasing the likelihood of energy transfer. Gaining control of the orientation and its distribution will be a critical step in maximizing the potential of the metal ion linked structures.

Management of a patient with mantle cell lymphoma who developed severe neurotoxicity after chimeric antigen receptor T-cell therapy in ZUMA-2.

Cerebral edema following chimeric antigen receptor (CAR) T-cell therapy can be fatal. ZUMA-2 is a pivotal phase 2, multicenter study evaluating KTE-X19, an autologous anti-CD19 CAR T-cell therapy, in relapsed/refractory mantle cell lymphoma. We describe a 65-year-old patient in ZUMA-2 who developed cerebral edema following CAR T-cell therapy and had complete recovery after multimodality clinical intervention including rabbit antithymocyte globulin (ATG). Biomarker results show early and robust CAR T-cell expansion and related induction of inflammatory cytokines, followed by rapid declines in CAR T-cell and proinflammatory cytokine levels after ATG administration. This clinical profile highlights a potential relevance of ATG in treating severe CAR T-cell-related neurotoxicity.

KTE-X19 CAR T-Cell Therapy in Relapsed or Refractory Mantle-Cell Lymphoma.

BACKGROUND: Patients with relapsed or refractory mantle-cell lymphoma who have disease progression during or after the receipt of Bruton's tyrosine kinase (BTK) inhibitor therapy have a poor prognosis. KTE-X19, an anti-CD19 chimeric antigen receptor (CAR) T-cell therapy, may have benefit in patients with relapsed or refractory mantle-cell lymphoma. METHODS: In a multicenter, phase 2 trial, we evaluated KTE-X19 in patients with relapsed or refractory mantle-cell lymphoma. Patients had disease that had relapsed or was refractory after the receipt of up to five previous therapies; all patients had to have received BTK inhibitor therapy previously. Patients underwent leukapheresis and optional bridging therapy, followed by conditioning chemotherapy and a single infusion of KTE-X19 at a dose of 2×106 CAR T cells per kilogram of body weight. The primary end point was the percentage of patients with an objective response (complete or partial response) as assessed by an independent radiologic review committee according to the Lugano classification. Per the protocol, the primary efficacy analysis was to be conducted after 60 patients had been treated and followed for 7 months. RESULTS: A total of 74 patients were enrolled. KTE-X19 was manufactured for 71 patients and administered to 68. The primary efficacy analysis showed that 93% (95% confidence interval [CI], 84 to 98) of the 60 patients in the primary efficacy analysis had an objective response; 67% (95% CI, 53 to 78) had a complete response. In an intention-to-treat analysis involving all 74 patients, 85% had an objective response; 59% had a complete response. At a median follow-up of 12.3 months (range, 7.0 to 32.3), 57% of the 60 patients in the primary efficacy analysis were in remission. At 12 months, the estimated progression-free survival and overall survival were 61% and 83%, respectively. Common adverse events of grade 3 or higher were cytopenias (in 94% of the patients) and infections (in 32%). Grade 3 or higher cytokine release syndrome and neurologic events occurred in 15% and 31% of patients, respectively; none were fatal. Two grade 5 infectious adverse events occurred. CONCLUSIONS: KTE-X19 induced durable remissions in a majority of patients with relapsed or refractory mantle-cell lymphoma. The therapy led to serious and life-threatening toxic effects that were consistent with those reported with other CAR T-cell therapies. (Funded by Kite, a Gilead company; ZUMA-2 ClinicalTrials.gov number, NCT02601313.).

A Gyroidal MOF with Unprecedented Interpenetrating utc-c Network Exhibiting Exceptional Thermal Stability and Ultrahigh CO2 Affinity.

A zeolite-like gyroidal MOF (denoted as SCNU-1) constructed with Cu ions and 4-(1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)phenol has a featured interpenetrating uninodal utc-c network which is for the first time found in the real structure. Moreover, SCNU-1 exhibits high thermal (>773 K), solvent, and acid/base stabilities; the largest CO2 affinity, 90 kJ/mol, among the MOFs functionalized with an aromatic hydroxyl group; and excellent CO2/N2 selectivity.

Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean.

Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley.

Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method.

In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment analysis suggests that because essential conformational events are mainly driven by the compensating fluctuations of essential solute-solvent and solute-solute interactions, commonly employed "predictive" sampling methods are unlikely to be effective on this seemingly "simple" system. The gOST development presented in this paper illustrates how to employ the OSS scheme for physics-based sampling method designs.

Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.

Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc.

Free energy landscape of a minimalist salt bridge model.

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations.

Payoffs, not tradeoffs, in the adaptation of a virus to ostensibly conflicting selective pressures.

The genetic architecture of many phenotypic traits is such that genes often contribute to multiple traits, and mutations in these genes can therefore affect multiple phenotypes. These pleiotropic interactions often manifest as tradeoffs between traits where improvement in one property entails a cost in another. The life cycles of many pathogens include periods of growth within a host punctuated with transmission events, such as passage through a digestive tract or a passive stage of exposure in the environment. Populations exposed to such fluctuating selective pressures are expected to acquire mutations showing tradeoffs between reproduction within and survival outside of a host. We selected for individual mutations under fluctuating selective pressures for a ssDNA microvirid bacteriophage by alternating selection for increased growth rate with selection on biophysical properties of the phage capsid in high-temperature or low-pH conditions. Surprisingly, none of the seven unique mutations identified showed a pleiotropic cost; they all improved both growth rate and pH or temperature stability, suggesting that single mutations even in a simple genetic system can simultaneously improve two distinct traits. Selection on growth rate alone revealed tradeoffs, but some mutations still benefited both traits. Tradeoffs were therefore prevalent when selection acted on a single trait, but payoffs resulted when multiple traits were selected for simultaneously. We employed a molecular-dynamics simulation method to determine the mechanisms underlying beneficial effects for three heat-shock mutations. All three mutations significantly enhanced the affinities of protein-protein interfacial bindings, thereby improving capsid stability. The ancestral residues at the mutation sites did not contribute to protein-protein interfacial binding, indicating that these sites acquired a new function. Computational models, such as those used here, may be used in future work not only as predictive tools for mutational effects on protein stability but, ultimately, for evolution.

Lipid changes after leaf wounding in Arabidopsis thaliana: expanded lipidomic data form the basis for lipid co-occurrence analysis.

A direct-infusion electrospray ionization triple-quadrupole mass spectrometry method with multiple reaction monitoring (MRM) was employed to measure 264 lipid analytes extracted from leaves of Arabidopsis thaliana subjected to mechanical wounding. The method provided precise measurements with an average coefficient of variation of 6.1%. Lipid classes analyzed comprised galactolipids and phospholipids (including monoacyl molecular species, molecular species with oxidized acyl chains, phosphatidic acids (PAs)), tri- and tetra-galactosyldiacylglycerols (TrGDGs and TeGDGs), head-group-acylated galactolipids, and head-group-acylated phosphatidylglycerol (acPG), sulfoquinovosyldiacylglycerols (SQDGs), sphingolipids, di- and tri-acylglycerols (DAGs and TAGs), and sterol derivatives. Of the 264 lipid analytes, 254 changed significantly in response to wounding. In general, levels of structural lipids decreased, whereas monoacyl molecular species, galactolipids and phosphatidylglycerols (PGs) with oxidized fatty acyl chains, PAs, TrGDGs, TeGDGs, TAGs, head-group-acylated galactolipids, acPG, and some sterol derivatives increased, many transiently. The observed changes are consistent with activation of lipid oxidizing, hydrolyzing, glycosylating, and acylating activities in the wounding response. Correlation analysis of the levels of lipid analytes across individual control and treated plants was used to construct a lipid dendrogram and to define clusters and sub-clusters of lipid analytes, each composed of a group of lipids which occurred in a coordinated manner. Current knowledge of metabolism supports the notion that observed sub-clusters comprise lipids generated by a common enzyme and/or metabolically downstream of a common enzyme. This work demonstrates that co-occurrence analysis, based on correlation of lipid levels among plants, is a powerful approach to defining lipids generated in vivo by a common enzymatic pathway.

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.

An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.

Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment.

Molecular dynamics sampling can be enhanced via the promoting of potential energy fluctuations, for instance, based on a Hamiltonian modified with the addition of a potential-energy-dependent biasing term. To overcome the diffusion sampling issue, which reveals the fact that enlargement of event-irrelevant energy fluctuations may abolish sampling efficiency, the essential energy space random walk (EESRW) approach was proposed earlier. To more effectively accelerate the sampling of solute conformations in aqueous environment, in the current work, we generalized the EESRW method to a two-dimension-EESRW (2D-EESRW) strategy. Specifically, the essential internal energy component of a focused region and the essential interaction energy component between the focused region and the environmental region are employed to define the two-dimensional essential energy space. This proposal is motivated by the general observation that in different conformational events, the two essential energy components have distinctive interplays. Model studies on the alanine dipeptide and the aspartate-arginine peptide demonstrate sampling improvement over the original one-dimension-EESRW strategy; with the same biasing level, the present generalization allows more effective acceleration of the sampling of conformational transitions in aqueous solution. The 2D-EESRW generalization is readily extended to higher dimension schemes and employed in more advanced enhanced-sampling schemes, such as the recent orthogonal space random walk method.

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering.

The orthogonal space random walk (OSRW) method, which enables synchronous acceleration of the motions of a focused region and its coupled environment, was recently introduced to enhance sampling for free energy simulations. In the present work, the OSRW algorithm is generalized to be the orthogonal space tempering (OST) method via the introduction of the orthogonal space sampling temperature. Moreover, a double-integration recursion method is developed to enable practically efficient and robust OST free energy calculations, and the algorithm is augmented by a novel θ-dynamics approach to realize both the uniform sampling of order parameter spaces and rigorous end point constraints. In the present work, the double-integration OST method is employed to perform alchemical free energy simulations, specifically to calculate the free energy difference between benzyl phosphonate and difluorobenzyl phosphonate in aqueous solution, to estimate the solvation free energy of the octanol molecule, and to predict the nontrivial Barnase-Barstar binding affinity change induced by the Barnase N58A mutation. As demonstrated in these model studies, the DI-OST method can robustly enable practically efficient free energy predictions, particularly when strongly coupled slow environmental transitions are involved.

Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase.

Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of IMP dehydrogenase (IMPDH) by monovalent cations. Therefore, we investigated the mechanism of K(+) activation in IMPDH by delineating the kinetic mechanism in the absence of monovalent cations. Surprisingly, the K(+) dependence of k(cat) derives from the rate of flap closure, which increases by ≥65-fold in the presence of K(+). We performed both alchemical free energy simulations and potential of mean force calculations using the orthogonal space random walk strategy to computationally analyze how K(+) accelerates this conformational change. The simulations recapitulate the preference of IMPDH for K(+), validating the computational models. When K(+) is replaced with a dummy ion, the residues of the K(+) binding site relax into ordered secondary structure, creating a barrier to conformational exchange. K(+) mobilizes these residues by providing alternate interactions for the main chain carbonyls. Potential of mean force calculations indicate that K(+) changes the shape of the energy well, shrinking the reaction coordinate by shifting the closed conformation toward the open state. This work suggests that allosteric regulation can be under kinetic as well as thermodynamic control.