Frustration and folding of a TIM barrel protein.

Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture that supports a myriad of enzymatic functions, but also a conserved folding mechanism that involves on- and off-pathway intermediates. Although experiments have proven to be invaluable in defining the folding free-energy surface, they provide only a limited understanding of the structures of the partially folded states that appear during folding. Coarse-grained simulations employing native centric models are capable of sampling the entire energy landscape of TIM barrels and offer the possibility of a molecular-level understanding of the readout from sequence to structure. We have combined sequence-sensitive native centric simulations with small-angle X-ray scattering and time-resolved Förster resonance energy transfer to monitor the formation of structure in an intermediate in the Sulfolobus solfataricus indole-3-glycerol phosphate synthase TIM barrel that appears within 50 µs and must at least partially unfold to achieve productive folding. Simulations reveal the presence of a major and 2 minor folding channels not detected in experiments. Frustration in folding, i.e., backtracking in native contacts, is observed in the major channel at the initial stage of folding, as well as late in folding in a minor channel before the appearance of the native conformation. Similarities in global and pairwise dimensions of the early intermediate, the formation of structure in the central region that spreads progressively toward each terminus, and a similar rate-limiting step in the closing of the ß-barrel underscore the value of combining simulation and experiment to unravel complex folding mechanisms at the molecular level.

Will My Tibial Fracture Heal? Predicting Nonunion at the Time of Definitive Fixation Based on Commonly Available Variables.

BACKGROUND: Accurate prediction of tibial nonunions has eluded researchers. Reliably predicting tibial nonunions at the time of fixation could change management strategies and stimulate further research. QUESTIONS/PURPOSES: We asked (1) whether data from medical records, fracture characteristics, and radiographs obtained at the time of fixation would identify features predictive of tibial fracture nonunion; and (2) whether this information could be used to create a model to assess the chance of nonunion at the time of intramedullary (IM) nail fixation of the tibia. METHODS: We retrospectively reviewed all tibial shaft fractures treated at our center from 2007 to 2014. We conducted a literature review and collected data on 35 factors theorized to contribute to delayed bone healing. Patients were followed to fracture healing or surgery for nonunion. Patients with planned prophylactic nonunion surgery were excluded because their nonunions were anticipated and our focus was on unanticipated nonunions. Our cohort consisted of 382 patients treated with IM nails for tibial shaft fractures (nonunion, 56; healed, 326). Bivariate and multivariate regression techniques and stepwise modeling approaches examined the relationship between variables available at definitive fixation. Factors were included in our model if they were identified as having a modest to large effect size (odds ratio > 2) at the p < 0.05 level. RESULTS: A multiple variable logistic regression model was developed, including seven factors (p < 0.05; odds ratio > 2.0). With these factors, we created the Nonunion Risk Determination (NURD) score. The NURD score assigns 5 points for flaps, 4 points for compartment syndrome, 3 points for chronic condition(s), 2 points for open fractures, 1 point for male gender, and 1 point per grade of American Society of Anesthesiologists Physical Status and percent cortical contact. One point each is subtracted for spiral fractures and for low-energy injuries, which were found to be predictive of union. A NURD score of 0 to 5 had a 2% chance of nonunion; 6 to 8, 22%; 9 to 11, 42%; and > 12, 61%. CONCLUSIONS: The proposed nonunion prediction model (NURDS) seems to have potential to allow clinicians to better determine which patients have a higher risk of nonunion. Future work should be directed at prospectively validating and enhancing this model. LEVEL OF EVIDENCE: Level III, diagnostic study.

Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study.

Recent molecular dynamics simulations have suggested important roles for nanoscale dewetting in the stability, function, and folding dynamics of proteins. Using a synergistic simulation-experimental approach on the αTS TIM barrel protein, we validated this hypothesis by revealing the occurrence of drying inside hydrophobic amino acid clusters and its manifestation in experimental measures of protein stability and structure. Cavities created within three clusters of branched aliphatic amino acids [isoleucine, leucine, and valine (ILV) clusters] were found to experience strong water density fluctuations or intermittent dewetting transitions in simulations. Individually substituting 10 residues in the large ILV cluster at the N-terminus with less hydrophobic alanines showed a weakening or diminishing effect on dewetting that depended on the site of the mutation. Our simulations also demonstrated that replacement of buried leucines with isosteric, polar asparagines enhanced the wetting of the N- and C-terminal clusters. The experimental results on the stability, secondary structure, and compactness of the native and intermediate states for the asparagine variants are consistent with the preferential drying of the large N-terminal cluster in the intermediate. By contrast, the region encompassing the small C-terminal cluster experiences only partial drying in the intermediate, and its structure and stability are unaffected by the asparagine substitution. Surprisingly, the structural distortions required to accommodate the replacement of leucine by asparagine in the N-terminal cluster revealed the existence of alternative stable folds in the native basin. This combined simulation-experimental study demonstrates the critical role of drying within hydrophobic ILV clusters in the folding and stability of the αTS TIM barrel.

A biomimetic chip to assess subcutaneous bioavailability of monoclonal antibodies in humans.

Subcutaneous (subQ) injection is a common route for delivering biotherapeutics, wherein pharmacokinetics is largely influenced by drug transport in a complex subQ tissue microenvironment. The selection of good drug candidates with beneficial pharmacokinetics for subQ injections is currently limited by a lack of reliable testing models. To address this limitation, we report here a Subcutaneous Co-Culture Tissue-on-a-chip for Injection Simulation (SubCuTIS). SubCuTIS possesses a 3D coculture tissue architecture, and it allows facile quantitative determination of relevant scale independent drug transport rate constants. SubCuTIS captures key in vivo physiological characteristics of the subQ tissues, and it differentiates the transport behavior of various chemically distinct molecules. We supplemented the transport measurements with theoretical modeling, which identified subtle differences in the local absorption rate constants of seven clinically available mAbs. Accounting for first-order proteolytic catabolism, we established a mathematical framework to assess clinical bioavailability using the local absorption rate constants obtained from SubCuTIS. Taken together, the technology described here broadens the applicability of organs-on-chips as a standardized and easy-to-use device for quantitative analysis of subQ drug transport.

Revisiting the polyoxometalate-based late-transition-metal-oxo complexes: the "oxo wall" stands.

Terminal oxo complexes of the late transition metals Pt, Pd, and Au have been reported by us in Science and Journal of the American Chemical Society. Despite thoroughness in characterizing these complexes (multiple independent structural methods and up to 17 analytical methods in one case), we have continued to study these structures. Initial work on these systems was motivated by structural data from X-ray crystallography and neutron diffraction and (17)O and (31)P NMR signatures which all indicated differences from all previously published compounds. With significant new data, we now revisit these studies. New X-ray crystal structures of previously reported complexes K(14)[P(2)W(19)O(69)(OH(2))] and "K(10)Na(3)[Pd(IV)(O)(OH)WO(OH(2))(PW(9)O(34))(2)]" and a closer examination of these structures are provided. Also presented are the (17)O NMR spectrum of an (17)O-enriched sample of [PW(11)O(39)](7-) and a careful combined (31)P NMR-titration study of the previously reported "K(7)H(2)[Au(O)(OH(2))P(2)W(20)O(70)(OH(2))(2)]." These and considerable other data collectively indicate that previously assigned terminal Pt-oxo and Au-oxo complexes are in fact cocrystals of the all-tungsten structural analogues with noble metal cations, while the Pd-oxo complex is a disordered Pd(II)-substituted polyoxometalate. The neutron diffraction data have been re-analyzed, and new refinements are fully consistent with the all-tungsten formulations of the Pt-oxo and Au-oxo polyoxometalate species.

Pseudoaneurysm of the distal thigh after manipulation of a total knee arthroplasty.

The authors describe a unique complication after manipulation of a stiff total knee arthroplasty in a 47-year-old man. Four days after undergoing manipulation under anesthesia (MUA), the patient presented with increasing pain and swelling of the affected knee and decreased hemoglobin/hematocrit. Computed tomographic angiogram revealed a ruptured pseudoaneurysm of a segmental branch of the deep femoral artery that was treated with embolization and anterior thigh compartment fasciotomy. Although many complications of MUA have been described, we present a novel finding of a ruptured pseudoaneurysm. Ruptured pseudoaneurysm should be included in the differential diagnosis whenever a patient presents with pain and swelling of the thigh after MUA given its potential morbidity.

Synthesis and characterization of a metal-to-polyoxometalate charge transfer molecular chromophore.

[P(4)W(35)O(124){Re(CO)(3)}(2)](16-) (1), a Wells-Dawson [α(2)-P(2)W(17)O(61)](10-) polyoxometalate (POM)-supported [Re(CO)(3)](+) complex containing covalent W(VI)-O-Re(I) bonds has been synthesized and characterized by several methods, including X-ray crystallography. This complex shows a high visible absorptivity (ε(470 nm) = 4000 M(-1) cm(-1) in water) due to the formation of a Re(I)-to-POM charge transfer (MPCT) band. The complex was investigated by computational modeling and transient absorption measurements in the visible and mid-IR regions. Optical excitation of the MPCT transition results in instantaneous (<50 fs) electron transfer from the Re(I) center to the POM ligand.

Machine Learning Feature Selection for Predicting High Concentration Therapeutic Antibody Aggregation.

Protein aggregation can hinder the development, safety and efficacy of therapeutic antibody-based drugs. Developing a predictive model that evaluates aggregation behaviors during early stage development is therefore desirable. Machine learning is a widely used tool to train models that predict data with different attributes. However, most machine learning techniques require more data than is typically available in antibody development. In this work, we describe a rational feature selection framework to develop accurate models with a small number of features. We applied this framework to predict aggregation behaviors of 21 approved monospecific monoclonal antibodies at high concentration (150 mg/mL), yielding a correlation coefficient of 0.71 on validation tests with only two features using a linear model. The nearest neighbors and support vector regression models further improved the performance, which have correlation coefficients of 0.86 and 0.80, respectively. This framework can be extended to train other models that predict different physical properties.

NURD 2.0: Prediction of tibial nonunion after intramedullary nail fixation at any time within 3 months after injury.

Introduction Nonunion after fixation of long bones negatively impacts outcomes and requires additional surgery. The ability to predict likelihood of nonunion after tibial shaft fracture would be helpful to clinicians and patients. The goal of this work was to combine three previous models of tibial shaft nonunion at different time points into one overall model that incorporates time as a continuous variable. Methods We conducted a retrospective review at a Level I academic trauma center. The study cohort consisted of patients with tibial shaft fractures treated with nail insertion from 2007 through 2014, excluding patients who did not have contact between bone ends, those who had planned bone grafting for acute bone defects, and those who lacked adequate follow-up. Three previous models were combined: 382 patients at time 0, 323 at 6 weeks, and 240 at 12 weeks. The primary outcome variable was surgery for nonunion. Bivariate and multivariate regression analyses determined which of 42 clinical and radiographic variables were significantly associated with nonunion. Predictive power was evaluated using area under the curve (AUC). Results The original nonunion risk determination (NURD) score was significantly improved through addition of 6- and 12-week radiographic union scores for tibial fractures, infection and complications, smoking status, and need for flaps. Overall, over the course of 12 weeks, the NURD-based model produced an AUC of 0.87 at initial time of fixation that improved to >0.9 at 6 and 12 weeks. Data were used to bin patients into five clinically important risk strata (p < 0.001). Patients in the lowest risk strata had 0% probability of nonunion (0 of 97 patients); in the second lowest risk strata, 4% (three of 73 patients); and in the highest risk strata, 48% (38 of 80 patients). Conclusions We created a NURD 2.0 score that predicts nonunion at various time points during the first 3 months after fracture. The new model is a notable improvement over previous models. A computerized version allows surgeons and patients to use the score when making treatment decisions regarding need for nonunion surgery.

A single molecular descriptor to predict solution behavior of therapeutic antibodies.

Despite the therapeutic success of monoclonal antibodies (mAbs), early identification of developable mAb drug candidates with optimal manufacturability, stability, and delivery attributes remains elusive. Poor solution behavior, which manifests as high solution viscosity or opalescence, profoundly affects the developability of mAb drugs. Using a diverse dataset of 59 mAbs, including 43 approved products, and an array of molecular descriptors spanning colloidal, conformational, charge-based, hydrodynamic, and hydrophobic properties, we show that poor solution behavior is prevalent (>30%) in mAbs and is singularly predicted (>90%) by the diffusion interaction parameter (k D), a dilute-solution measure of colloidal self-interaction. No other descriptor, individually or in combination, was found to be as effective as k D. We also show that well-behaved mAbs, a substantial subset of which bear high positive charge and pI, present no disadvantages with respect to pharmacokinetics in humans. Here, we provide a systematic framework with quantitative thresholds for selecting well-behaved therapeutic mAbs during drug discovery.

Predicting tibia shaft nonunions at initial fixation: An external validation of the Nonunion Risk Determination (NURD) score in the SPRINT trial data.

BACKGROUND: Predictive models are common in orthopedic research; however, most models are not validated in an external population. The Nonunion Risk Determination (NURD) score was developed using a single-center cohort of 382 patients to reliably predict tibia shaft nonunions at the time of initial intramedullary nail fixation. The purpose of this study was to externally validate the NURD score using data from the SPRINT Trial. METHODS: The SPRINT trial was a multicenter study comparing reamed versus unreamed intramedullary nails in tibial shaft fracture patients. We assessed the prognostic performance of the NURD score in the SPRINT trial data with comparisons of the c-statistics, calibration plots, and a comparison of predicted probabilities at cut-points defined in the study to derive the NURD score. In addition, we compared the odds ratios of the NURD score components between the derivation (NURD) and external validation (SPRINT) data. RESULTS: The NURD score demonstrated significantly worse discrimination in the SPRINT data than was observed in the original data (c-statistic: 0.61 vs. 0.85, p<0.01). The NURD score was well-calibrated in the derivation and SPRINT data. The SPRINT data had less heterogeneity, as determined by the standard deviation of the linear predictors (NURD: 1.4 vs. SPRINT: 0.4). Once we adjusted for case-mix differences, the NURD score had similarly strong discrimination in the SPRINT data (c-statistic: 0.81 vs. 0.85, p = 0.17). DISCUSSION: Based on our external validation, the NURD score lacks generalizability as it underperforms with respect to discrimination in the SPRINT trial data. However, after adjusting for case-mix differences, the performance of the NURD score is comparable between the two datasets, suggesting robust reproducibility.

Altered bone marrow dendritic cell cytokine production to toll-like receptor and CD40 ligation during chronic feline immunodeficiency virus infection.

Impaired dendritic cell (DC) function is thought to be central to human immunodeficiency virus-associated immunodeficiency. In this study, we examined the effect of chronic feline immunodeficiency virus (FIV) infection on DC cytokine production in response to microbial and T-cell stimulation. Cytokine production after either Toll-like receptor (TLR) or CD40 ligation in bone marrow-derived DCs (BM-DCs) was measured in naïve and chronically FIV-infected cats. The BM-DCs were stimulated with ligands to TLR-2, -3, -4, -7 and -9 or cocultured with 3T3 cells expressing feline CD40 ligand. Ligation of TLR-4 and TLR-9 in BM-DCs from infected cats resulted in a significant decrease in the ratio of interleukin-12 (IL-12) to IL-10. Conversely, TLR-7 ligation produced a significant increase in the IL-12 : IL-10 ratio in BM-DCs from infected cats. No difference was noted for TLR-3 ligation. RNA expression levels of TLR-2, -3, -4, -7 and -9 were not significantly altered by FIV infection. CD40 ligation significantly elevated both IL-10 and IL-12 messenger RNA production but did not alter the IL-12 : IL-10 ratio. Chronic FIV infection alters the ratio of immunoregulatory cytokines produced by BM-DCs in response to certain pathogen-derived signals, which is probably relevant to the increased risk of opportunistic infections seen in lentiviral infection.

Multifunctional multilayer films containing polyoxometalates and bismuth oxide nanoparticles.

Multifunctional multilayer films consisting of the Keggin-type polyoxometalate [SiW(9)V(3)O(40)](7-) (SiW(9)V(3)) and bismuth oxide nanoparticles (Bi(2)O(3)) were prepared by the layer-by-layer assembly method. For the first time, electrochromic and photochromic studies were done on a film containing both polyoxometalates and nanoparticles. The films were characterized by UV-vis absorption, emission spectra, and atomic force microscopy. Their electrochromic and photochromic properties were investigated by cyclic voltammetry and UV-vis spectroscopy. The results show that the reduction of SiW(9)V(3) is very reversible and tunable with the addition of Bi(2)O(3) layers into the film. The electrocatalytic activity of the films toward oxidation of l-cysteine hydrochloride hydrate (l-cysteine) and reduction of nitrite were studied with cyclic voltammetry. The results show that the incorporation of Bi(2)O(3) nanoparticles into the films changed the films' photoluminescence properties and electrocatalytic efficiency.

Effect of Network Architecture and Linker Polarity on Ion Aggregation and Conductivity in Precise Polymerized Ionic Liquids.

Four polymerized ionic liquids (PILs) were systematically designed to study the effect of polymer architecture and linker polarity on ion aggregation and transport. Specifically, linear and network PILs with the same ammonium cations (Am) and bis(trifluoromethane)sulfonimide (TFSI) anions were prepared by step-growth polymerization, and polarity was tuned by incorporating two precise linkers, either polar tetra(ethylene oxide) (4EO) linker or nonpolar undecyl (C11) linker. The glass transition temperature (Tg) substantially increased with the nonpolar C11 linker or upon cross-linking to form a network. The low wave-vector (q) ion aggregation peak from wide-angle X-ray scattering (WAXS) was not observable in the linear 4EO PIL, while it was most pronounced in the network C11 PIL. The network C11 PIL exhibited the strongest decoupling, where the ionic conductivity at Tg is greater than 1 order of magnitude higher than the other PILs. This systematic comparison suggests that network structure and nonpolar linkers can promote both ion aggregation and ionic conductivity close to Tg.

Development and application of a quantitative real-time PCR assay to detect feline leukemia virus RNA.

We previously defined four categories of feline leukemia virus (FeLV) infection, designated as abortive, regressive, latent, and progressive. To determine if detectable viral DNA is transcriptionally active in the absence of antigenemia, we developed and validated a real-time viral RNA qPCR assay. This assay proved to be highly sensitive, specific, reproducible, and allowed reliable quantitation. We then applied this methodology, together with real-time DNA qPCR and p27 capsid antigen capture ELISA, to examine cats challenged with FeLV. We found that circulating viral RNA and DNA levels were highly correlated and the assays were almost in perfect agreement. This indicates that the vast majority of viral DNA is transcriptionally active, even in the absence of antigenemia. The real-time qPCR assays are more sensitive than the most commonly used FeLV diagnostic assay, the p27 capsid antigen capture ELISA. Application of qPCR assays may add greater depth in understanding of FeLV-host relationships.

A Hyperthermophilic Phage Decoration Protein Suggests Common Evolutionary Origin with Herpesvirus Triplex Proteins and an Anti-CRISPR Protein.

Virus capsids are protein shells that protect the viral genome from environmental assaults, while maintaining the high internal pressure of the tightly packaged genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of the hyperthermophilic phage P74-26. We determined the structure of capsid protein gp87 and show that it has the same fold as decoration proteins in many other phages, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than mesophilic homologs. Our analysis of the gp87 structure reveals that the core "ß tulip" domain is conserved in trimeric capsid components across numerous double-stranded DNA viruses, including Herpesviruses. Moreover, this ß barrel domain is found in anti-CRISPR protein AcrIIC1, suggesting a mechanism for the evolution of this Cas9 inhibitor. Our work illustrates the principles for increased stability of gp87, and extends the evolutionary reach of the ß tulip domain.

Polyoxometalate-encapsulated twenty-nuclear silver-tetrazole nanocage frameworks as highly active electrocatalysts for the hydrogen evolution reaction.

Two unprecedented polyoxometalate-encapsulated twenty-nuclear silver-tetrazole nanocage frameworks have been synthesized, which exhibit high activity in hydrogen evolution reaction. HUST-100 shows an onset overpotential of 148 mV and a Tafel slope of 82 mV dec-1, and the catalytic current density approaches 10 mA cm-2 at an overpotential of 234 mV.

Prediction of tibial nonunion at the 6-week time point.

INTRODUCTION: Intramedullary (IM) nail fixation is a common operative treatment, yet concerns regarding the frequency of complications, such as nonunion, remain. Treatment of tibial shaft fractures remains a challenge, and little evidence of prognostic factors that increase risk of nonunion is available. The aim of this study was to develop a predictive model of tibial shaft fracture nonunion 6 weeks after reamed intramedullary (IM) nail fixation based on commonly collected clinical variables and the radiographic union score for tibial fractures (RUST). METHODS: A retrospective case-control study was conducted. All tibial shaft fractures treated at our level I trauma center from 2007 to 2014 were retrospectively reviewed. Only patients with follow-up until fracture healing or secondary operation for nonunion were included. Fracture gaps ≥3 mm were excluded. A total of 323 patients were included for study. RESULTS: Infection within 6 weeks of operation, standard RUST, and the Nonunion Risk Determination (NURD) score had statistically significant associations with nonunion (odds ratio > or < 1.0; p < 0.01). The NURD score was increasingly predictive of nonunion with decreasing RUST. All patients in the high RUST group (RUST ≥ 10), achieved union regardless of NURD score. In the medium RUST group (RUST 6-9), 25% of patients with a NURD score ≥7 experienced nonunion. In the low RUST group (RUST <6 or infection within 6 weeks), 69% of patients with a NURD score ≥7 experienced nonunion. CONCLUSION: Three variables predicted nonunion. Based on these variables, we created a clinical prediction tool of nonunion that could aid in clinical decision making and discussing prognosis with patients.

An unprecedented 3D POM-MOF based on (7,8)-connected twin Wells-Dawson clusters: synthesis, structure, electrocatalytic and photocatalytic properties.

The first (7,8)-connected polyoxometalate-based metal-organic framework (POM-MOF) has been constructed from seven- and eight-connected twin Wells-Dawson clusters, and possesses the highest connection number of polyoxometalates to any mixed-connected POM-MOF to date and a unique structural motif that contains both organic-inorganic and all-inorganic networks.