2-D graphical representation of proteins based on virtual genetic code

We consider a novel 2-D graphical representation of proteins in which individual nucleic acids are represented as "spots" within a square frame distributed according to specific construction rules. The resulting "images" of proteins can not only serve to facilitate visual comparison of similarities and dissimilarities between lengthy protein sequences, but also offer a way for mathematical characterization of protein sequences, analogous to similar considerations for lengthy DNA sequences. Basically the approach is based on the concept of virtual genetic code, which is a hypothetical string of RNA nucleic acid bases, A, C, U and G, which generates reported protein sequences, without the knowledge of the actual genetic code that produces the protein.     

Utilizing the pH hysteresis effect for versatile and simple electrophoretic analysis of proteins in bare fused-silica capillaries

The analysis of peptides and proteins by CE is often desirable due to low sample consumption and possibilities for nondenaturing yet highly effective separations. However, adsorption to the inner surfaces of fused-silica capillaries often is detrimental to such analyses. This phenomenon is especially pronounced in the analysis of basic proteins and proteins containing exposed positively charged patches. To avoid wall interactions numerous buffer additives and static and dynamic wall coating principles have been devised. We previously showed (J. Chromatogr. A 2004, 1059, 215-222) that CE of the basic protein beta2-glycoprotein was rendered possible by an acidic pretreatment step, and we attributed this observation to the so-called pH hysteresis effect that influences the time for pH equilibration of the capillary wall and thus the effective wall charge and the electroosmotic mobility. We here investigate the effects of different pretreatment techniques on EOF values and on the rate of the deprotonation of silanol groups when performing the electrophoresis at neutral pH. We show the utility of this simple approach for the CE analysis of a number of basic proteins in plain silica capillaries at physiological pH.     

Capillary electrochromatography with bare silicas of different pore sizes as stationary phases

Bare silica can be used with reversed phase eluents for the chromatographic separation of basic analytes. It provides high surface charge density within a certain pH range, thus generating a high electroosmotic flow (EOF) when applied in electrochromatography. The influence of pore size on EOF velocity and mass transport is demonstrated. High EOF and fast mass transfer were encountered with 100 nm and 200 nm material and related to a pore perfusion mechanism. On a silica with 200 nm average pore size at pH 7, an EOF velocity of 2 mm/s was obtained at 600 V/cm. Silicas with pore diameters between 6 nm and 200 nm, corresponding to surface areas between 500 m/g and 10 m/g (data calculated from inverse size exclusion chromatography experiments), were used for CEC and HPLC separation of strongly basic solutes. On separation of tricyclic antidepressants by CEC, “normal” and “abnormal” efficiencies were achieved and were found to vary with the charge density within the separation column.     

Scaling of mesoscale simulations of polymer melts with the bare friction coefficient

Both the Rouse and reptation model predict that the dynamics of a polymer melt scale inversely proportional with the Langevin friction coefficient xi. Mesoscale Brownian dynamics simulations of polyethylene validate these scaling predictions, providing the reptational friction xi(R)=xi+xi(C) is used, where xi(C) reflects the fundamental difference between a deterministic and a stochastic propagator even in the limit of xi to zero. The simulations have been performed with Langevin background friction and with pairwise friction, as in dissipative particle dynamics. Both simulation methods lead to equal scaling behavior with xi(C) having almost the same value in both cases. The scaling is tested for the diffusion g(t), the shear relaxation modulus G(t), and the Rouse mode autocorrelations of melts of C(120)H(242), C(400)H(802), and C(1000)H(2002). The derived dynamical scaling procedure is very useful to reduce run-time in mesoscale computer simulations, especially if pairwise friction is applied.     

抚触护理对新生儿高胆红素血症的影响

目的探讨抚触护理对新生儿高胆红素血症的影响。方法选取江西省萍乡湘雅萍矿医院2012年8月至2015年1月收治的96例高胆红素血症患儿作为研究对象。按照入院顺序随机均分为实验组和对照组,对照组患儿进行常规护理,实验组患儿在对照组护理的基础上进行抚触护理。观察患儿经皮胆红素指数、住院时间、黄疸持续时间。结果护理干预前,两组患儿经皮胆红素指数水平对比,差异无统计学意义(P0.05);护理干预后,两组患儿经皮胆红素指数水平均低于护理干预前,差异有统计学意义(P0.05);护理干预后,实验组患儿经皮胆红素指数水平低于对照组,差异有统计学意义(P0.05)。实验组患儿住院时间、黄疸持续时间均低于对照组,差异有统计学意义(P0.05)。结论抚触护理对新生儿高胆红素血症有积极的影响,能够改善患儿经皮胆红素指数水平,缩短患儿住院时间、黄疸持续时间,临床应用价值较高。     

Interaction of bare and gold-coated superparamagnetic iron oxide nanoparticles with fetal bovine serum

Superparamagnetic iron oxide nanoparticles (SPIONs) are being increasingly used in various biomedical processes such as hyperthermia, cell and protein separation, enhancing resolution of magnetic resonance imaging and drug delivery. Here, SPIONs were prepared by optimized co-precipitation of iron chlorides in basic medium and then coated with gold. Bare SPIONs and Aucoated SPIONs were characterized by TEM before incubation with fetal bovine serum for 0.5, 1, 2, 4, 8 and 24 h. After these interaction times, the mixture was deposed on a small column in a strong magnetic field (MACS?system). The SPIONs were retained; different washing fractions were collected and studied by UV-Vis spectroscopy and by 1D gel electrophoresis. The study revealed the presence of proteins in the washing solutions and confirmed the strong interaction of the protein with the SPIONs.     

Hemin interaction with bare and 4,4'-thio-bis-benzene-thiolate covered n-GaAs (110) electrodes

Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) investigations on the redox behavior of hemin at bare and 4,4'-thio-bis-benzene-thiolate (TBBT) covered n-GaAs (110) electrodes in dimethylsulfoxide (DMSO) revealed the high irreversibility of the electroreduction process, which appeared to be closely related to the stable adsorbed species strongly interfering with the electronic properties of the semiconducting substrate. The subsequent exploration of the hemin-modified electrodes by second harmonic generation (SHG), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) measurements pointed to significant differences between the iron protoporphyrin species adsorbed on the bare- and TBBT-GaAs (110) electrodes. Only Fe(2+) species having a flat configuration with the porphyrin plane oriented parallel to the surface were detected on GaAs, unlike the TBBT-GaAs, where Fe(2+) and Fe(3+) species having both flat and vertical adsorption positions could be observed. These differences originate from the mutual interactions between the solvent, hemin and dithiolate molecules as well as their competition for the surface sites found to play a key role in the electrochemical process under discussion.     

Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications

ABSTRACT: BACKGROUND: Identification of the target proteins of bioactive compounds is critical for elucidating the mode of action; however, target identification has been difficult in general, mostly due to the low sensitivity of detection using affinity chromatography followed by CBB staining and MS/MS analysis. RESULTS: We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown mechanism. One hundred eighty-two target protein candidates were computationally predicted to bind to incednine by the statistical prediction method, and the predictions were verified by in vitro binding of incednine to seven proteins, whose expression can be confirmed in our cell system. As a result, 40% accuracy of the computational predictions was achieved successfully, and we newly found 3 incednine-binding proteins. CONCLUSIONS: This study revealed that our proposed protocol of predicting target protein combining in silico screening and experimental verification is useful, and provides new insight into a strategy for identifying target proteins of small molecules.     

Computation-led design of pollutant gas sensors with bare and carbon nanotube supported rhodium alloys

Quantum chemical study has been performed on finite-sized bi-metallic Rh3M alloys, M = Ag, Ir, Pd, Pt, Au, derived from magic cluster, Rh4. Bond length of C–O and N–O are noticed to be elongated in the presence of rhodium alloy clusters. CO2 and NO2 gases are found to be highly adsorbed on Rh3M clusters, which is confirmed by stretching frequency of C–O and N–O. DFT evaluated dipole moment and electronic charge redistribution suggests the sensing capability of CO2 and NO2 gases by Rh3M clusters which is further confirmed by the calculated HOMO–LUMO gap. Mixed rhodium alloy clusters supported on single-wall carbon nanotube (SWCNT) exhibits much higher ability to sense CO2 and NO2. On the other hand, SWCNT@Rh3M shows higher catalytic activity for the activation of CO2 and NO2 in comparison to bare Rh3M because of the higher electronic charge redistribution in the case of SWCNT@Rh3M. In case of SWCNT-supported gas adsorbed clusters, p electrons play a major role in bonding.     

Magnetic moments of bare and benzene-capped cobalt clusters

Magnetic moments of bare cobalt clusters Co(n) (n=7-32) and benzene-capped cobalt clusters Co(n)(bz)(m) have been measured at temperatures ranging from 54 to 150 K using a molecular beam deflection method. It was observed that Co(12-32) produced at temperatures greater than approximately 100 K display high-field-seeking behavior at all temperatures in the range investigated, indicating that they are superparamagnetic species. At temperatures below approximately 100 K, the field-on beam profiles of Co(7-11) and some larger clusters displayed substantial symmetric broadening, indicating that some fraction of the clusters in the beam were no longer superparamagnetic, but rather were in a blocked (locked-moment) state. In the superparamagnetic regime (T=150 K) Co(n) clusters in the n=7-32 size range were found to possess per-atom moments ranging from 1.96+/-0.04 micro(b)(Co(24)) to 2.53+/-0.04 micro(b)(Co(16)), significantly above the bulk value of 1.72 micro(b). Locked-moment isomers were found to display moments of approximately 1 micro(b) per atom. Cobalt clusters containing a layer of adsorbed benzene molecules were found to possess significantly lower moments per cobalt atom than the corresponding bare cobalt clusters.     

A systematic CI procedure with modified virtual orbitals

The use of modified virtual orbitals is studied in a systematic conventional CI procedure which offers considerable potential in regard to convergence and extension to larger systems. The method is applied to the HCN molecule by using 37 basis functions, and analysis of energy expectation values, together with the one-electron density, yields some insight into the physical content of CI wavefunctions.     

Calculation of second-order properties with improved virtual orbitals

¹³C---H nuclear spin coupling and ¹³C shielding constants of CH₄, C₂H₆, C₂H₄, C₂H₂ are calculated by means of the second-order perturbation theory and MO LCAO wavefunctions. The aim of this paper is to test the ability of the recently proposed virtual orbitals to accelerte the convergence of the sum over states, compared to the calculation with canonical MO's. The ¹³C---H nuclear spin coupling constants show a significant improvement, the changes of the ¹³C shielding are insignificant.     

Interactions of adsorbed poly(ethylene oxide) mushrooms with a bare silica-ionic liquid interface

The interaction of adsorbed poly(ethylene oxide) (PEO) mushrooms with clean silica-ethylammonium nitrate (EAN, a protic ionic liquid) interfaces is investigated using atomic force microscopy (AFM). 10 kDa, 35 kDa and 100 kDa PEO was used to prepare polymer layers ex situ by drop casting from 0.01 wt% EAN solutions. AFM tapping mode measurements of dried, solvent free PEO layers revealed oblate structures, which increase in size with molecular weight. Colloid probe force curve measurements of these surfaces re-solvated with EAN suggest PEO adopts a mushroom morphology, with the interaction range (layer thickness) increasing with molecular weight. Attractive forces on approach and single strand stretching forces on retraction show PEO has a strong affinity for the silica-EAN interface. The single polymer strand stretching forces follow the freely jointed chain model under good solvent conditions. Contour lengths close to the theoretical limits of 120 nm for the 10 kDa, 290 nm for the 35 kDa and 1240 nm for the 100 kDa PEO samples are observed, while fitted Kuhn lengths are small, at 0.14 nm.     

Genetic modulation of metalloprotein electron transfer at bare gold

Engineered metalloproteins and enzymes can be self assembled on pristine gold electrodes in robust, electrochemically-addressable, arrays.     

Sonoelectroanalytical detection of lead at a bare copper electrode

The sonochemically facilitated, mercury free detection of Pb2+ at a copper electrode has been investigated as a means of simplifying the quantification of this important analyte and to minimise the interference of copper ion. The procedure relies upon maximising the formation of Pb-Cu intermetallic compounds leading to the emergence of a single, easily quantifiable stripping signal. Linear responses to Pb2+ were obtained with a sensitivity comparable to that obtained at a bare glassy carbon electrode. Interference from Cu2+, Zn2+ and Cd2+ was assessed on the copper electrode with no appreciable change in the Pb2+ voltammetric profile observed. In contrast, bare glassy carbon showed a significant change in Pb2+ voltammetric profile as Cu2+ was added, due to the formation of intermetallic species.     

Sonoelectroanalytical detection of lead at a bare copper electrode

The sonochemically facilitated, mercury free detection of Pb²⁺ at a copper electrode has been investigated as a means of simplifying the quantification of this important analyte and to minimise the interference of copper ion. The procedure relies upon maximising the formation of Pb-Cu intermetallic compounds leading to the emergence of a single, easily quantifiable stripping signal. Linear responses to Pb²⁺ were obtained with a sensitivity comparable to that obtained at a bare glassy carbon electrode. Interference from Cu²⁺, Zn²⁺ and Cd²⁺ was assessed on the copper electrode with no appreciable change in the Pb²⁺ voltammetric profile observed. In contrast, bare glassy carbon showed a significant change in Pb²⁺ voltammetric profile as Cu²⁺ was added, due to the formation of intermetallic species.     

Direct oxidation of haemoglobin at bare boron-doped diamond electrodes

The communication reports the direct oxidation of human haemoglobin at a bare boron-doped diamond electrode under moderately alkaline conditions with detection limit of 0.4 microM.