Achieving Low-Dose Rate X-Ray Imaging Based on 2D/3D-Mixed Perovskite Films.

X-ray detection and imaging are widely used in medical diagnosis, product inspection, security monitoring, etc. Large-scale polycrystalline perovskite thick films possess high potential for direct X-ray imaging. However, the notorious problems of baseline drift and high detection limit caused by ions migration are still remained. Here, ion migration is reduced by incorporating 2D perovskite into 3D perovskite, thereby increasing the ion activation energy. This approach hinders ion migration within the perovskite film, consequently suppressing baseline drift and reducing the lowest detection limit(LOD) of the device. As a result, the baseline drifting declines by 20 times and the LOD reduces to 21.1 nGy s-1, while the device maintains a satisfactory sensitivity of 5.6 × 103 µC Gy-1 cm-2. This work provides a new strategy to achieve low ion migration in large-scale X-ray detectors and may provide new thoughts for the application of mixed-dimension perovskite.

Application of a Modified Extracorporeal Circulation Perfusion Method During Surgery for Acute Stanford Type A Aortic Dissection.

AIM: The aim of this study was to investigate the effect of the modified extracorporeal circulation perfusion method during surgery for acute Stanford type A aortic dissection in patients who underwent stented elephant trunk implantation and arch replacement. METHOD: A total of 69 patients with acute Stanford type A aortic dissection who underwent stented elephant trunk implantation and arch replacement were retrospectively analysed from 2017 to 2018. According to the perfusion method of extracorporeal circulation, patients were divided into a routine perfusion (RP) group and a modified perfusion (MP) group. Clinical data were collected, including the time of extracorporeal circulation and deep hypothermic circulatory arrest, incidence of acute kidney injury and neurological complications, and comparisons between the two groups were conducted by using independent sample t-tests for normally distributed qualitative data, the Mann-Whitney U-test for skewed qualitative data, and the chi square test or Fisher's exact test for categorical data. RESULTS: There were 55 (80%) males and 14 (20%) females in the entire cohort, and the mean ± standard deviation age was 50.4±9.0 years. A total of 53 (77%) patients were included in the RP group, and 16 (23%) were included in the MP group. Patients in the MP group were older (55.5±7.8 vs 48.8±8.9 years), and the difference was significant (p=0.008). Compared with the RP group, the time of extracorporeal circulation (218.0 [44.7] vs 246.0 [58.0] min; p=0.005) and deep hypothermic circulatory arrest (4.0 [2.0] vs 25.0 [10.0] min; p<0.001) was shorter, and the incidence of postoperative acute kidney injury (n=6 [37.5%] vs n=36 [67.9%]; p=0.029) was lower in the MP group; the differences were significant. Six (6) patients died in the RP group; no patients died in the MP group. The total in-hospital mortality rate was 8.7%. CONCLUSIONS: The modified extracorporeal circulation perfusion method is feasible, with satisfactory results.

[Synthesis of transdermal aloesin loaded zinc oxide nanoparticles and its inhibitory effect on the activity of tyrosinase].

Zinc oxide quantum dots (ZnO QDs) were synthesized by gel-sol method and employed as the transdermal aloesin (Alo) carriers. ZnO QDs were surface-functionalized with amino using aminopropyltriethoxysilane (APTES). Alo was covalently bonded on the surface of ZnO QDs via N,N'-carbonyldiimidazole to obtain Alo NPs, which were characterized by transmission electron microscope (TEM), dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR) and thermal gravimetric analyzer (TGA). TEM images showed that ZnO QDs were analogously sphere and monodisperse with a reasonably narrow size distribution, of which was around 4 nm. The size of Alo NPs increased to around 8 nm due to the surface modification. The intense bands at around 3 400 cm -1 and 1 200 cm -1 in the FTIR spectrum of Alo NPs from the vibration of -OH indicated the linkage of Alo on the surface of ZnO QDs. The results of TGA analysis showed that the mass ratio of ZnO QDs and Alo were 39.27% and 35.14%, respectively. The penetration of Alo NPs was much higher than raw Alo according to the passive penetration experiments with Franz-type diffusion cells instrument using full-thickness cavy skin, which manifested the improvement of the penetration for Alo delivered by ZnO QDs. The pH-controlled drug release behavior in vitro was investigated. At pH 7.4, only a small amount of Alo (1.45% ± 0.21%) had been released after 2 h. In contrast, as incubation at pH 5.0 of which pH was similar to endosomal environment, Alo was released very fast (87.63% ± 0.46% in 2 h) from Alo NPs, confirming that Alo NPs could response to the pH and realize the intracellular drug release. The inhibitory effect of Alo NPs on tyrosinase was in a dose dependent manner. When the concentration of Alo NPs was 12.5 µg/mL, the inhibition rate was up to 40.32% ± 1.57%. All the results show that the Alo NPs hold a great potential in transdermal tyrosinase inhibition.

Nimbolide Exhibits Potent Anticancer Activity Through ROS-Mediated ER Stress and DNA Damage in Human Non-small Cell Lung Cancer Cells.

The non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancers. It is usually diagnosed at an advanced stage with poor prognosis. Nimbolide (NB), a terpenoid limonoid isolated from the flowers and leaves of neem tree, possesses anticancer properties in various cancer cell lines. However, the underlying mechanism of its anticancer effect on human NSCLC cells remains unclear. In the present study, we investigated the effect of NB on A549 human NSCLC cells. We found that NB treatment inhibits A549 cells colony formation in a dose-dependent manner. Mechanistically, NB treatment increases cellular reactive oxygen species (ROS) level, leading to endoplasmic reticulum (ER) stress, DNA damage, and eventually induction of apoptosis in NSCLC cells. Furthermore, all these effects of NB were blocked by pretreatment with antioxidant glutathione (GSH), the specific ROS inhibitor. We further knockdown CHOP protein by siRNA markedly reduced NB-induced apoptosis in A549 cells. Taken together, our findings reveal that NB is an inducer of ER stress and ROS; these findings may contribute to increasing the therapeutic efficiency of NSCLC.

Preparation of pH-responsive polyurethane nano micelles and their antibacterial application.

Considering the differences in pH between bacterial infection microenvironment and normal tissues, a series of pH-responsive drug-release amphiphilic polyurethane copolymers (DPU-g-PEG) have been prepared in this work. Fourier transform infrared (FT-IR) spectroscopy and 1H NMR was selected to detect the structure of the condensed polymers. The DPU-g-PEG amphiphilic copolymers could form stable micelles with a hydrophilic shell of polyethylene glycol (PEG) and a hydrophobic core of polylactic acid (PLA). We loaded a model drug called triclosan onto DPU-g-PEG micelles and studied how pH affects their particle size, Zeta potential, and drug release performance. The results revealed that when exposed to acidic conditions, the surface potential of DPU-g-PEG micelles changed, the micelles' particle size increased, and the drug release performance was significantly enhanced. These results suggested that the micelles prepared in this study can release more antibacterial substances at sites of bacterial infection. Meanwhile, we also investigated the impact of different ratios of soft and hard segments on the properties of micelles, and the results showed that the pH responsiveness of micelles was strongest when the ratio of soft segments (PLLA diol + PEG 2000): 1,6-hexamethylene diisocyanate (HDI): 2,6-Bis-(2-hydroxy-ethyl)-pyrrolo[3,4-f]isoindole-1,3,5,7-tetraone (DMA) = 1: 1.2: 0.2. Furthermore, the results of inhibition zone test, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) all confirmed the antibacterial activity of triclosan-load DPU-g-PEG micelles. In conclusion, the DPU-g-PEG micelles produced in this study have the potential to be used as intelligent drug delivery systems in the biomedical field.

Using N-I-N Photodiodes Made of Perovskite Single Crystals for Low Noise Gamma-Ray Spectroscopy.

Solution-processed lead halide perovskite single crystals (LHPSCs) are believed to have great potential in gamma-ray spectroscopy. However, obtaining low-defect LHPSCs from a solution at low temperatures is difficult compared to obtaining Bridgman single crystals such as CdTe and Si. Herein, noise from the intrinsic defects of LHPSCs is considered as the main problem hindering their gamma-ray detection performance. By isolating the defect-induced holes in LHPSCs via energy barriers, we show that NIN photodiodes based on three types of LHPSCs, i.e., MAPbBr3 (MA = CH3NH3), MAPbBr2.5Cl0.5, and cascade LHPSCs, have demonstrated good energy resolution in the range of 6.7-10.3% for 662 keV 137Cs gamma-ray photons. The noise for >10 mm3 devices is low, in the order of 340-860 electrons, and the electron collection efficiency reaches 23-43%. These results pave the way for obtaining low-cost, large, high energy-resolution gamma-ray detectors at room temperature (300 K).

Photodiodes Made of Cascade Perovskite Single Crystals with Passivation Layers for High-Energy-Resolution γ-ray Spectroscopy.

Lead halide perovskite single crystals (LHPSC) are promising for room-temperature γ-ray spectroscopy in radiation detection. While MA(CH3NH3)-based LHPSCs are the most straightforward and cost-effective to synthesize from solution, their performance in γ-ray spectroscopy is hindered by significant noise and ion migration at high bias, which degrades their energy resolution (ER). The work introduced an n-type/intrinsic/n-type photodiode incorporating passivation layers of MA-based LHPSCs, grown through solution-process epitaxial growth. This single-polarity device demonstrated an outstanding ER of 3.6% for 662 keV γ-ray photons. Overall, this work provides useful information for developing room-temperature γ-ray detectors based on solution-processed lead halide perovskites.

Cascade perovskite single crystal for gamma-ray spectroscopy.

The halide lead perovskite single crystals (HLPSCs) have great potential in gamma-ray detection with high attenuation coefficient, strong defects tolerance, and large mobility-lifetime product. However, mobile halide ions would migrate under high external bias, which would both weaken the gamma-ray response and cause additional noise. Here, we report the gamma-ray PIN photodiodes made of cascade HLPSCs including both ion-formed and electron-hole-formed electrical junctions that could suppress the ions migration and improve the charges collection. Our photodiodes based on cascade HLPSCs (MAPbBr3/MAPbBr2.5Cl0.5/MAPbCl3) show a wide halide-ion-formed depletion layer of ∼52 µm. The built-in potential along the wide ionic-formed junction ensures a high mobility-lifetime product of 1.1 × 10-2 cm2V-1. As a result, our gamma-ray PIN photodiodes exhibit compelling response to 241Am, 137Cs, and 60Co; the energy resolution can reach 9.4%@59.5keV and 5.9%@662keV, respectively. This work provides a new path toward constructing high-performance gamma-ray detectors based on HLPSCs.

Fast Response, High Spectral Rejection Ratio, Self-Filtered Ultranarrowband Photodetectors Based on Perovskite Single-Crystal Heterojunctions.

Narrowband photodetectors have wide application potential in high-resolution imaging and encrypted communication, due to their high-precision spectral resolution capability. In this work, we report a fast response, high spectral rejection ratio, and self-filtered ultranarrowband photodetector with a new mechanism, which introduces bulk recombination by doping Bi3+ and cooperates with surface recombination for further quenching photogenerated charges generated by short-wavelength-light excitation in perovskite single-crystal. A perovskite film focused on collecting charges is fabricated on the single crystal by a lattice-matched solution-processed epitaxial growth method. Due to the formation of PN heterojunctions, a narrowband photodetector in this mechanism has remarkable spectral selectivity and detection performance with an ultranarrow full width at half-maximum (FWHM) of 7.7 nm and a high spectral rejection ratio of 790, as well as a high specific detectivity up to 1.5 × 1010 Jones, a fast response speed with a rise time and fall time of ∼8 and 137 µs. The ultrafast and ultranarrow spectra response of self-filtered narrowband photodetector provides a new strategy in high-precision and high-resolution photoelectric detection.

Sensitive Thermography via Sensing Visible Photons Detected from the Manipulation of the Trap State in MAPbX3.

Sensitive thermometry or thermography by responding to blackbody radiation is urgently desired in the intelligent information life, including scientific research, medical diagnosis, remote sensing, defense, etc. Even though thermography techniques based on infrared sensing have undergone unprecedented development, the poor compatibility with common optical components and the high diffraction limit impose an impediment to their integration into the established photonic integrated circuit or the realization of high-spatial-resolution and high-thermal-resolution imaging. In this work, we present a sensitive temperature-dependent visible photon detection in Bi-doped MAPbX3 (X = Cl, Br, and I) and employ it for uncooled thermography. Systematic measurements reveal that the Bi dopant introduces trap states in MAPbX3, thermal energy facilitates the carriers jumping from trap states to the conduction band, while the vacancies of trap states ensure the sequential absorption of visible photons with energy less than the band gap. Subsequently, the change of response toward the visible photon is applied to construct the thermograph, and it possesses a specific sensitivity of 2.11% K-1 along temperature variation. As a result, our thermograph presents a temperature resolution of 0.21 nA K-1, a high responsivity of 2.06 mA W-1, and a high detectivity of 2.08 × 109 Jones at room temperature. Furthermore, remote thermal imaging is successfully achieved with our thermograph.

Electrically Modulated Near-Infrared/Visible Light Dual-Mode Perovskite Photodetectors.

Dual-mode photodetectors (PDs) have attracted increasing interest owing to their potential optoelectrical applications. However, the widespread use of PDs is still limited by the high cost of epitaxial semiconductors. In contrast, the solution processability and wide spectral tunability of perovskites have led to the development of various inexpensive and high-performance optoelectronic devices. In this study, we develop a high-performance electronically modulated dual-mode PD with near-infrared (NIR) narrowband and visible light broadband detection based on organic-inorganic hybrid methylammonium lead halide perovskite (MAPbX3; MA = CH3NH3 and X = Cl, Br, and I) single crystals with a pnp configuration. The operating mode of the dual-mode PD can be switched according to voltage bias polarity because the photon absorption region and carrier transport performance are tuned at different bias voltages. The dual-mode PD exhibits a NIR light responsivity of 0.244 A/W and a narrow full width at half-maximum of ∼12 nm at 820 nm at positive voltages and an average visible light responsivity of ∼0.13 A/W at negative voltages. The detectivities of both modes are high (∼1012 Jones), and the linear dynamic range is wide (>100 dB). Our study provides a new method for fabricating multifunctional PDs and can expand their application in integrated imaging systems.

Epitaxial Perovskite Single-Crystalline Heterojunctions for Filter-Free Ultra-Narrowband Detection with Tunable Spectral Responses.

Narrowband photodetectors (NPDs) with the capability of detecting light within a selective wavelength range are in high demand for numerous emerging applications such as imaging systems, machine vision, and optical communication. Halide perovskite materials have been developed for eliminating the current complex filtering systems in NPDs due to their beneficial properties, while currently NPDs using perovskite materials are limited by hardly fully eliminated short wavelength response, low charge collection efficiency (CCE), complex fabrication process, and so forth. Herein, a series of perovskite single-crystalline heterojunctions (PSCHs) with a structure of Bi-MAPbX3/MAPbY3 are fabricated by liquid phase epitaxy for filter-free narrowband detection. By varying the halide component in the PSCH, the PSCH-based NPDs can realize continuously tunable spectral response range from blue to NIR regions and ultra-narrow full width at half-maximum (FWHM) of <20 nm. Specifically, the PSCH-based NPD with a high CCE under a large electric filed shows a high spectra rejection ratio of >1000, a fast response speed with rise/fall time of ∼160/∼225 µs, and long-term stability more than 3 months in ambient air. This work provides a simple strategy for designing low-cost and high-performance filter-free NPDs with a tunable spectral response.

Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses.

Periplasmic oligopeptide-binding protein (OppA) is the initial receptor in the ATP-binding cassette (ABC) system of bacteria, which exhibits a broad specificity in binding oligopeptides without regard to sequence. Here, we present a computational study on the structural properties and energetic landscapes of OppA protein interacting with its cognate ligands on the basis of 28 structure/affinity-known OppA-tripeptide complexes. By employing a well-designed protocol that couples the hybrid quantum mechanical/molecular mechanical (QM/MM) scheme and the sophisticated Poisson-Boltzmann/surface area (PB/SA) solvent model together to analyze and decompose the energy components associated with the OppA-peptide binding, we demonstrate that the broad specificity of OppA-recognizing peptides is originated from a series of exquisite balances between the free energy contributions from, for example, the direct nonbonded interactions and indirect desolvation effects, the main chains and side chains, and the different residue positions of the tripeptide ligands. We also show that, in a framework of structure-based quantitative structure-activity relationship (SB-QSAR) methodology, the QM/MM-PB/SA-derived energy terms could be used as a good descriptor to characterize the interaction profile of OppA with peptides and correlate pretty well with the experimentally measured affinities of the binding.

SNHG16 accelerates the proliferation of primary cardiomyocytes by targeting miRNA-770-5p.

The present study aimed to clarify the influence of long non-coding RNA small nuclear host gene 16 (lncRNA SNHG16) on cardiomyocyte proliferation following ischemia/reperfusion injury (IRI) and the potential mechanism. An IRI model in mice was established by performing ligation of the anterior descending coronary artery (LAD). Primary cardiomyocytes were isolated from newborn mice and subjected to H2O2 treatment to mimic in vitro IRI. Relative levels of SNHG16 and miRNA-770-5p in both in vivo and in vitro IRI models were examined. The regulatory effects of SNHG16 and miRNA-770-5p on the proliferative ability of H2O2-treated cardiomyocytes were assessed by Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) assay. The binding relationship between SNHG16 and miRNA-770-5p was verified through dual-luciferase reporter gene assay. It is found that SNHG16 was time-dependently downregulated in the IRI models. Overexpression of SNHG16 enhanced the proliferative ability of the cardiomyocytes. miRNA-770-5p was found to be a direct target of SNHG16. Moreover, SNHG16 was able to negatively regulate the miRNA-770-5p level. Overexpression of miRNA-770-5p partially reversed the role of SNHG16 on accelerating cardiomyocyte proliferation. Collectively, SNHG16 accelerates the proliferative ability of cardiomyocytes following IRI by negatively regulating miRNA-770-5p.

Perovskite Photodetectors Based on p-i-n Junction With Epitaxial Electron-Blocking Layers.

Organic-inorganic hybrid perovskite single crystals (PSCs) have been emerged as remarkable materials for some optoelectronic applications such as solid-state photodetectors, solar cells and light emitting diodes due to their excellent optoelectronic properties. To decrease the dark current, function layers based on spin-coating method are frequently requested for intrinsic PSCs to block the injected current by forming energy barrier. However, the amorphous function layers suffer from small carrier mobility and high traps density, which limit the speed of the photoelectric response of perovskite devices. This work supposes to grow thick MAPbBr3 and MAPbI3 mono-crystalline thin films on the surface of intrinsic MAPbBr2.5Cl0.5 PSCs substrate by a heteroepitaxial growth technique to act as electron-blocking layers. Meanwhile, C60 and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) layers are deposited on the opposite surface of substrate PSCs by spin-coating method to block injected holes. This Au-MAPbI3-MAPbBr3-MAPbBr2.5Cl0.5PSCs-C60-PCBM-Ag heterostructure can be used as excellent X-ray photodetector (XPD) due to its low dark current density of 6.97 × 10-11 A cm-2 at -0.5 V bias, high responsivity of 870 mA/W at -100 V bias and X-ray sensitivity as high as 59.7 µC mGy-1 cm-2 at -50 V bias.

Enhanced Performance of Perovskite Single-Crystal Photodiodes by Epitaxial Hole Blocking Layer.

Introducing hole/electron transporting and blocking layers is considered to enhance the performance of electronic devices based on organic-inorganic hybrid halide perovskite single crystals (PSCs). In many photodiodes, the hole/electron transporting or blocking materials are spin-coated or thermal-evaporated on PSC to fabricate heterojunctions. However, the heterojunction interfaces due to lattice mismatch between hole/electron, transporting or blocking materials and perovskites easily form traps and cracks, which cause noise and leakage current. Besides, these low-mobility transporting layers increase the difficulty of transporting carriers generated by photons to the electrode; hence, they also increase the response time for photo detection. In the present study, MAPbCl3-MAPbBr2.5Cl0.5 heterojunction interfaces were realized by liquid-phase epitaxy, in which MAPbBr2.5Cl0.5 PSC acts as an active layer and MAPbCl3 PSC acts as a hole blocking layer (HBL). Our PIN photodiodes with epitaxial MAPbCl3 PSC as HBL show better performance in dark current, light responsivity, stability, and response time than the photodiodes with spin-coated organic PCBM as HBL. These results suggest that the heterojunction interface formed between two bulk PSCs with different halide compositions by epitaxy growth is very useful for effectively blocking the injected charges under high external electric field, which could improve the collection of photo-generated carriers and hereby enhance the detection performance of the photodiode. Furthermore, the PIN photodiodes made of PSC with epitaxial HBL show the sensitivities of 7.08 mC Gyair -1 cm-2, 4.04 mC Gyair -1 cm-2, and 2.38 mC Gyair -1 cm-2 for 40-keV, 60-keV, and 80-keV X-ray, respectively.

[Empirical study of the transportation of pulmonary surfactant-super oxide dismutase liposome to lung tissue in rats].

OBJECTIVE: To study the feasibility of the transportation of pulmonary surfactant-super oxide dismutase (PS-SOD) liposome to lung tissue in rats. METHODS: 32 Wistar rats were randomly divided into 4 groups (8 rats in each group): normal saline group, PS group, SOD group, PS-SOD liposome group. Each group was further divided into two groups (4 rats in each group), and the rats were respectively killed 2 and 24 hours after the operation. While the biological activity of SOD in irrigating solution and tissue homogenate were detected, lung tissue were labeled with fluorescent and then observed under microscope and transmission electron microscope. RESULTS: PS-SOD liposome was corps rounds with monolayer lipid with stable surface tension and antioxidative activity. At the point of 2 hours after operation, while the SOD biological activity of irrigating solution in PS-SOD liposome group (32.87 +/- 5.47) and SOD group (33.14 +/- 5.61) were obviously higher than that in normal saline group (2.15 +/- 0.17, P < 0.01), there was no difference between them (P > 0.05). The mean fluorescence optical density in PS-SOD liposome group (0.109 +/- 0.018) was lower than that in normal saline group (0.144 +/- 0.052) and PS group (0.143 +/- 0.026, P < 0.01). 24 hours after operation, the SOD biological activity of irrigating solution in PS-SOD liposome group (11.54 +/- 1.42) was the highest (P < 0.01) and the mean fluorescence optical density in PS-SOD liposome group (0.112 +/- 0.018) was the lowest (P < 0.01). The SOD biological activity of tissue homogenate in PS-SOD liposome group (2 h: 16.83 +/- 2.69, 24 h: 15.70 +/- 2.75) was higher than that in normal saline group (2 h: 5.79 +/- 0.93, 24 h: 5.84 +/- 1.31) and in SOD group (2 h: 7.07 +/- 1.04, 24 h: 6.11 +/- 1.06, P < 0.01) both at the point of 2 and 24 hours after the operation. Lots of PS-SOD liposome was observed in type II alveolar epithelial cells under transmission electron microscope. CONCLUSION: Intrathecal administ ration of PS-SOD liposome enhanced the transportation of SOD into lung tissue and its antioxidative activity.

Structure-based prediction of the mobility and disorder of water molecules at protein-DNA interface.

Water plays an invaluable role in governing the structure, stability, dynamics, and function of biomolecules, which has also been demonstrated to be critical in mediating biomolecular recognition and association. Accurate determination of the dynamic behavior of water molecules at biological complex interface is important for the understanding of the molecular mechanism of water contributing to the binding between biomolecules and could be exploited as an alternative tool to refine the water's positions in X-ray electron density map. In the present study, a method called local hydrophobic descriptors (LHDs) is used to characterize the hydrophobic landscapes of the hydration sites at protein-DNA interface. The resulting variables of the characterization are then correlated with the experimentally measured B-factor values of 4445 elaborately selected water samples derived from a panel of thematically nonredundant, high-quality protein-DNA interfaces by using a variety of machine learning methods, including PLS, BPNN, SVM, LSSVM, RF, and GP. The results show that the dynamic behavior of interfacial water molecules is primarily governed by the local hydrophobic feature of the hydration sites that water molecules located, and the nonlinear dependence dominates over the linear component in the water B-factor system. We expect that this structured-based approach can be used for predicting the B-factor profile of other biomolecules as well.

Characterization of the binding profile of peptide to transporter associated with antigen processing (TAP) using Gaussian process regression.

Although MHC-peptide binding is the most selective event in epitope presentation process, the protein fragments generated by proteasomal cleavage require to be recognized by transporter associated with antigen processing (TAP) and translocated from cytosol to endoplasmic reticulum before they can be loaded into the ligand-binding groove of MHC. In this article, we report the use of a new and powerful machine learning tool called Gaussian process (GP) to model the linear and nonlinear relationships between the sequence pattern and binding affinity of peptide to TAP, and to explain the physicochemical properties and structural implications underlying the specific recognition and association of peptide with TAP. The resulting statistics are compared systematically with those obtained by sophisticated PLS, ANN and SVM. Results show that: (i) Nonlinear methods such as the ANN and GP perform much better than the linear PLS. (ii) GP is capable of handling both linearity- and nonlinearity-hybrid relationship and thus exhibits a good performance relative to other two nonlinear methods. (iii) Investigation of the GP model shows that the P1, P2, P3 and P9 of peptide are the most important positions that dominate TAP-peptide recognition, P5 contributes slightly to the peptide binding, whereas P4, P6, P7 and P8 can only exert very limited potency on the binding. (iv) Diverse properties cast remarkable effects on the interaction between TAP and peptide. In particular, hydrophobility, electronic property and hydrogen bond contribute most significantly to the binding affinity of TAP-peptide association.

Prediction of Water's Mobility and Disorder in Protein Crystals Using Novel Local Hydrophobic Descriptors.

The B-factors of crystal structures reflect the atomic fluctuations about their average positions and provide important information about molecular dynamics. Although numerous works have been addressed on theoretical and computational studies of B-factor profile of protein atoms, the methods used for predicting B-factor values of water molecules in protein crystals still remain unexploited. In this article, we describe a new approach that we named local hydrophobic descriptors (LHDs) to characterize the hydrophobic landscapes of protein hydration sites. Using this approach coupled with partial least squares (PLS) regression and least-squares squares support vector machine (LSSVM), we perform a systematic investigation on the linear and nonlinear relationships between the LHDs and water B-factors. Based upon an elaborately selected, large-scale dataset of crystal water molecules, our method predicts B-factor profile with coefficient of determination rpred of 0.554. We demonstrate that (i) the dynamics of water molecules is primarily governed by the local features of hydrophobic potential landscapes, and (ii) the accuracy of predicted B-factor values depends on water packing density.