The crystallation of estrogen-binding protein from Candida albicans

In the past decade scientists have discovered that the pathogenic fungus Candida albicans contains a highly specific estrogen-binding protein (EBP). Since it is known that the use of estrogen-containing compounds causes one to be more prone to infection by this organism, it is hypothesized that this estrogen system may have a role in infection. Understanding the structure and function of EBP would be helpful in developing treatments for infection by C. albicans. One way to approach the structure and function question of any protein is to crystallize the protein and solve its structure using X-ray diffraction. In the past few months, crystal~ of EBP have been produced using the hanging drop method of vapor diffusion. These crystals are yellow and spiky in appearance and grow as clusters within two weeks at 4°C in a solution containing the following: 0.1 M sodium cacodylate, pH 6.5; 0.1 M sodium acetate; and 25% polyethylene glycol (PEG) 8000. Crystals of similar appearance have been grown in less than one week using the technique of microseeding. Because neither the unseeded nor the seeded crystals grow singly, they cannot be subjected to X-ray diffraction in order for structural data to be taken. Since the jagged appearance of these crystals may be due to some microheterogeneity in the T.BP sample used, I believe that the future work on this project include an attempt to grow diffraction-grade EBP crystals with a more homogeneous EBP sample. Additionally, since other conditions have been found in which EBP crystalizes, I believe that these conditions should be explored to determine whether or not sharper crystals can be grown

Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes

AbstractAccurate free-energy calculations provide mechanistic insights into molecular recognition and conformational equilibrium. In this work, we performed free-energy calculations to study the thermodynamic properties of different states of molecular systems in their equilibrium basin, and obtained accurate absolute binding free-energy calculations for protein-ligand binding using a newly developed M2 algorithm. We used a range of Asp-Phe-Gly (DFG)-in/out p38α mitogen-activated protein kinase inhibitors as our test cases. We also focused on the flexible DFG motif, which is closely connected to kinase activation and inhibitor binding. Our calculations explain the coexistence of DFG-in and DFG-out states of the loop and reveal different components (e.g., configurational entropy and enthalpy) that stabilize the apo p38α conformations. To study novel ligand-binding modes and the key driving forces behind them, we computed the absolute binding free energies of 30 p38α inhibitors, including analogs with unavailable experimental structures. The calculations revealed multiple stable, complex conformations and changes in p38α and inhibitor conformations, as well as balance in several energetic terms and configurational entropy loss. The results provide relevant physics that can aid in designing inhibitors and understanding protein conformational equilibrium. Our approach is fast for use with proteins that contain flexible regions for structure-based drug design

Predictors of intra-abdominal coagulopathic hemorrhage after living donor liver transplantation

AbstractBackgroundResults of preoperative conventional coagulation assays are a poor predictor of hemorrhage after liver transplantation. In this study, we evaluated the factors that are predictive of intra-abdominal coagulopathic hemorrhage after living donor liver transplantation surgery.MethodsDuring the period from January 2009 to December 2012, 118 adults underwent living donor liver transplantation (LDLT) in our institution. Of those patients, 18 (15.3%) developed intra-abdominal coagulopathic hemorrhage (n = 7) or hemorrhage due to non-coagulopathic causes (n = 11) that required emergency medical, radiological, or surgical intervention within the first month after LDLT. Possible predictors of postoperative coagulopathic hemorrhage included donor-related factors, age, body mass index, MELD score, INR value, intra-operative blood transfusion, graft/recipient weight ratio, anhepatic phase, cold ischemia time, operative time, APACHE II score, onset of re-bleeding, and hemoglobin levels during rebleeding episodes.ResultsThere were no differences in any of the variables between the two groups (coagulopathic and noncoagulopathic hemorrhage) except for cold ischemia time. We found that cold ischemia time was significantly longer in patients with postoperative coagulopathic hemorrhage (160.50 ± 45.02 min) than in patients with hemorrhage due to non-coagulopathic causes (113.55 ± 29.31 min; P = 0.027).ConclusionProlonged cold ischemia time is associated with postoperative intra-abdominal coagulopathic hemorrhage in patients after LDLT. It is, therefore, necessary to shorten the cold ischemia time in order to reduce the risk of postoperative intra-abdominal hemorrhage due to coagulopathic causes

Development of a Piezoelectric Vacuum Sensing Component for a Wide Pressure Range

In this study, we develop a clamped-clamped beam-type piezoelectric vacuum pressure sensing element. The clamped-clamped piezoelectric beam is composed of a PZT layer and a copper substrate. A pair of electrodes is set near each end. An input voltage is applied to a pair of electrodes to vibrate the piezoelectric beam, and the output voltage is measured at the other pair. Because the viscous forces on the piezoelectric beam vary at different air pressures, the vibration of the beam depends on the vacuum pressure. The developed pressure sensor can sense a wide range of pressure, from 6.5 × 10(-6) to 760 Torr. The experimental results showed that the output voltage is inversely proportional to the gas damping ratio, and thus, the vacuum pressure was estimated from the output voltage

Terahertz generation in multiple laser-induced air plasmas

This is the published version. Copyright 2008 American Institute of PhysicsAn investigation of the terahertz wavegeneration in multiple laser-induced air plasmas is presented. First, it is demonstrated that the intensity of the terahertz wave increases as the number of air plasmas increases. Second, the physical mechanism of this enhancement effect of the terahertz generation is studied by quantitatively measuring the intensity of the generated terahertz wave as a function of phase difference between adjacent air plasmas. It is found out that the superposition is the main mechanism to cause this enhancement. Thus, the results obtained in this paper not only provide a technique to generate stronger terahertz wave but also enable a better understanding of the mechanism of the terahertz generation in air plasma

Local Implicit Normalizing Flow for Arbitrary-Scale Image Super-Resolution

Flow-based methods have demonstrated promising results in addressing the ill-posed nature of super-resolution (SR) by learning the distribution of high-resolution (HR) images with the normalizing flow. However, these methods can only perform a predefined fixed-scale SR, limiting their potential in real-world applications. Meanwhile, arbitrary-scale SR has gained more attention and achieved great progress. Nonetheless, previous arbitrary-scale SR methods ignore the ill-posed problem and train the model with per-pixel L1 loss, leading to blurry SR outputs. In this work, we propose "Local Implicit Normalizing Flow" (LINF) as a unified solution to the above problems. LINF models the distribution of texture details under different scaling factors with normalizing flow. Thus, LINF can generate photo-realistic HR images with rich texture details in arbitrary scale factors. We evaluate LINF with extensive experiments and show that LINF achieves the state-of-the-art perceptual quality compared with prior arbitrary-scale SR methods.Comment: CVPR 2023 camera-ready versio

Substrate Specificity and Plasticity of FERM-Containing Protein Tyrosine Phosphatases

SummaryEpidermal growth factor receptor (EGFR) pathway substrate 15 (Eps15) is a newly identified substrate for protein tyrosine phosphatase N3 (PTPN3), which belongs to the FERM-containing PTP subfamily comprising five members including PTPN3, N4, N13, N14, and N21. We solved the crystal structures of the PTPN3-Eps15 phosphopeptide complex and found that His812 of PTPN3 and Pro850 of Eps15 are responsible for the specific interaction between them. We defined the critical role of the additional residue Tyr676 of PTPN3, which is replaced by Ile939 in PTPN14, in recognition of tyrosine phosphorylated Eps15. The WPD loop necessary for catalysis is present in all members but not PTPN21. We identified that Glu instead of Asp in the WPE loop contributes to the catalytic incapability of PTPN21 due to an extended distance beyond protonation targeting a phosphotyrosine substrate. Together with in vivo validations, our results provide novel insights into the substrate specificity and plasticity of FERM-containing PTPs

In vitro assay to estimate tea astringency via observing flotation of artificial oil bodies sheltered by caleosin fused with histatin 3

AbstractAstringency, a sensory characteristic of food and beverages rich in polyphenols, mainly results from the formation of complexes between polyphenols and salivary proteins, causing a reduction of the lubricating properties of saliva. To develop an in vitro assay to estimate the astringency of oolong tea infusion, artificial oil bodies were constituted with sesame oil sheltered by a modified caleosin fused with histatin 3, one of the human salivary small peptides. Aggregation of artificial oil bodies was induced when they were mixed with oolong tea infusion or its major polyphenolic compound, (−)-epigallocatechin gallate (EGCG) of 100μM as observed in light microscopy. The aggregated artificial oil bodies gradually floated on top of the solution and formed a visible milky layer whose thickness was in proportion to the concentrations of tea infusion. This assay system was applied to test four different oolong tea infusions with sensory astringency corresponding to their EGCG contents. The result showed that relative astringency of the four tea infusions was correlated to the thickness of floated artificial oil bodies, and could be estimated according to the standard curve generated by simultaneously observing a serial dilution of the tea infusion with the highest astringency