Protein‐protein docking by shape‐complementarity and property matching

We present a computational approach to protein‐protein docking based on surface shape complementarity (“ProBinder”). Within this docking approach, we implemented a new surface decomposition method that considers local shape features on the protein surface. This new surface shape decomposition results in a deterministic representation of curvature features on the protein surface, such as “knobs,” “holes,” and “flats” together with their point normals. For the actual docking procedure, we used geometric hashing, which allows for the rapid, translation‐, and rotation‐free comparison of point coordinates. Candidate solutions were scored based on knowledge‐based potentials and steric criteria. The potentials included electrostatic complementarity, desolvation energy, amino acid contact preferences, and a van‐der‐Waals potential. We applied ProBinder to a diverse test set of 68 bound and 30 unbound test cases compiled from the Dockground database. Sixty‐four percent of the protein‐protein test complexes were ranked with an root mean square deviation (RMSD) < 5 Å to the target solution among the top 10 predictions for the bound data set. In 82% of the unbound samples, docking poses were ranked within the top ten solutions with an RMSD < 10 Å to the target solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Assessment of linear finite‐difference Poisson–Boltzmann solvers

CPU time and memory usage are two vital issues that any numerical solvers for the Poisson–Boltzmann equation have to face in biomolecular applications. In this study, we systematically analyzed the CPU time and memory usage of five commonly used finite‐difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson–Boltzmann equation. It turns out that the time‐limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson–Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

在导电高分子薄膜表面沉积密度可控的银纳米粒子

<正>由于导电高分子的导电性和化学性质可以在导体和半导体区间内快速调节[1],因此其复合材料受到了越来越多的关注[2].金属纳米粒子在光电子器件、检测及传感等诸多领域表现出独特的性能[3],在生物技术领域中的重要性尤为突出[4].因此,如果将导电高分子和金属纳米粒子结合在一起,将有利于拓展导电高分子的应用范围.本文研究了银纳米粒子在聚苯胺薄膜表面的沉积行为,分别用原子力显微镜(AFM)和扫描电子显     

Analysis of E. coli soluble proteins by non‐denaturing micro 2‐DE/3‐DE and MALDI‐MS‐PMF

Escherichia coli (strain K‐12)‐soluble proteins were analyzed by nondenaturing micro 2‐DE and MALDI‐MS‐PMF. The reported conditions of nondenaturing IEF in agarose column gels [Jin, Y., Manabe, T., Electrophoresis 2009, 30, 939–948] were modified to optimize the resolution of cellular soluble proteins. About 300 CBB‐stained spots, the apparent molecular masses of which ranged from ca. 6000 to 10 kDa, were detected. All the spots on two reference 2‐DE gels (one for wide mass range and one for low‐molecular‐mass range) were numbered and subjected to MALDI‐MS‐PMF for the assignment of constituting polypeptides. Most of the spots (310 spots out of 329) provided significant match (p<0.05) with polypeptides in Swiss‐Prot database and totally 228 polypeptide species were assigned. Activity staining of enzymes such as alkaline phosphatase and catalases was performed on the 2‐DE gels and the locations of the activity spots matched well with those of the MS‐assigned polypeptides of the enzymes. Most of the polypeptides with subunit information in Swiss‐Prot (119 polypeptides as homo‐multimers and 25 as hetero‐multimers out of the 228), such as pyruvate dehydrogenase complex which is composed of three enzymatic components, were detected at the apparent mass positions of their polymers, suggesting that the proteins were separated retaining their subunit structures. When a nondenaturing 2‐DE gel was vertically cut into 2 mm strips and one of the strips was subjected to a third‐dimension micro SDS‐PAGE (micro 3‐DE), about 190 CBB‐stained spots were detected. The assignment of the polypeptides separated on the 3‐DE gel would further provide information on protein/polypeptide interactions.     

QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Investigation of the mechanism of protein adsorption on ordered mesoporous silica using flow microcalorimetry

The adsorption of bovine serum albumin (BSA) and lysozyme (LYS) on siliceous SBA-15 with 24 nm pores was studied using flow microcalorimetry; this is the first attempt to understand the thermodynamics of protein adsorption on SBA-15 using flow microcalorimetry. The adsorption mechanism is a strong function of protein structure. Exothermic events were observed when protein–surface interactions were attractive. Entropy-driven endothermic events were also observed in some cases, resulting from lateral protein–protein interactions and conformational changes in the adsorbed protein. The magnitudes of the enthalpies of adsorption for primary protein–surface interactions decrease with increased surface coverage, indicating the possibility of increased repulsion between adsorbed protein molecules. Secondary exothermic events were observed for BSA adsorption, presumably due to secondary adsorption made possible by conformational changes in the soft BSA protein. These secondary adsorption events were not observed for lysozyme, which is structurally robust. The results of this study emphasize the influence of solution conditions and protein structure on conformational changes of the adsorbed protein and the value of calorimetry in understanding protein–surface interactions.     

Poly(divinylbenzene-alkyl methacrylate) monolithic stationary phases in capillary electrochromatography

In this study, a series of poly(divinylbenzene-alkyl methacrylate) monolithic stationary phases, which were prepared by single step in situ polymerization of divinylbenzene and various alkyl methacrylates (butyl-, octyl-, or lauryl-methacrylate), were developed as separation columns of benzophenone compounds for capillary electrochromatography (CEC). In addition to the presence of plenty of benzene moieties, the stationary phases contained long and flexible alkyl groups on the surface. With an increase in the molecular length of alkyl methacrylate, the polymeric monolith, which had higher hydrophobicity, effectively reduced the peak tailing of benzophenones, but a weaker retention was observed. The unusual phenomenon was likely due to the π–π interaction between the aromatic compound and the polymeric material. The usage of longer alkyl methacrylate as reaction monomer limited the retention of aromatic compounds on the stationary phase surface, thus the π–π interaction between them was possibly reduced. Consequently, the retention time of aromatic compounds was markedly decreased with an increase in carbon length of alkyl methacrylate that was carried on the polymeric monolith. Compared to previous reports on polystyrene-based columns in which the peak-tailing problem was reduced by decreasing the benzene moieties on the stationary phase, this study demonstrated that the undesirable retention (peak-tailing) could also be improved by the inclusion of long alkyl methacrylate to the polystyrene-based columns.     

Structure elucidation of highly polar basic degradants by on-line hydrogen/deuterium exchange hydrophilic interaction chromatography coupled to tandem mass spectrometry

A hydrophilic interaction liquid chromatography (HILIC) method was used to separate a commonly used pharmaceutical starting material, 4-aminomethylpyridine (4-AMP), and its degradants. The structures of the major degradants were characterized and elucidated without prior isolation by accurate mass measurement, MS/MS analysis and on-line hydrogen/deuterium (H/D) exchange experiments. The mass spectra obtained from H/D exchange experiments are particularly useful to differentiate structural isomers, to elucidate the fragmentation pathways, and to aid in structure elucidation in the absence of MS/MS fragmentation information. The impact of deuterium oxide and temperature on HILIC separation has also been explored here. The integration of H/D exchange with HILIC has been described here for the first time and has been demonstrated to be a powerful structure elucidation tool via the study of degradants in 4-AMP.     

Ionic polymers and oligomers with expanded π-conjugation system derived from through-space interaction in piperazinium ring

Reactions of N-(2,4-dinitrophenyl)-4-arylpyridinium chlorides (aryl (Ar) = phenyl and 4-pyridyl) with piperazines caused the ring opening of the pyridinium ring and yielded polymers that consisted of 5-piperazinium-3-aryl-penta-2,4-dienylideneammonium chloride units [N(CH(R)CH₂)₂N⁺(Cl⁻)CHCHC(Ar)CHCH, RH, Me, and phenyl]. However, the same reactions occurring in the presence of piperidine yielded oligomers that consisted of 5-piperazinium-3-aryl-penta-2,4-dienylideneammonium chloride units having piperidine and/or piperazine rings at both ends. ¹H NMR spectra suggested that π-electrons of the penta-2,4-dienylideneammonium group of the polymers and the oligomers were delocalized. UV-vis measurements revealed that the π-conjugation system expanded along the polymer and oligomer chains due to the orbital interaction between electrons on the two nitrogen atoms of the piperazinium ring. Conversion of the piperazinium ring from the boat form to the chair form caused decrease in the π-conjugation length. The rate constants of the conversion of the oligomers depended on their chain lengths. The surface of pellets that were molded from the polymers and oligomers exhibited metallic luster. These polymers and oligomers underwent electrochemical oxidation in solution.     

聚乙烯醇、聚乙烯胺与淀粉酶相互作用荧光光谱

采用荧光光谱和紫外吸收光谱法研究聚乙烯醇(PEG)和四乙烯五胺(TEPA)与淀粉酶相互作用。结果表明,PEG会增强淀粉酶内源性荧光和酪氨酸残基所处微环境的疏水性;TEPA对淀粉酶内源性荧光的猝灭机制属于动态猝灭,但同时也存在静态猝灭特征,并使色氨酸残基所处微环境的极性增大;在所考察的范围内,PEG与淀粉酶的结合常数在40℃达到最高,TEPA对淀粉酶荧光的动态猝灭结合常数在30℃以上趋于最大,PEG、TEPA与淀粉酶之间的作用力属于疏水与静电作用相结合。