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Protein–protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains. Characterizing
the interaction interface of domain–peptide complexes and analyzing binding specificity for modular domains are critical for
deciphering protein–protein interaction networks. In this article, we report the successful use of an integrated computational
protocol to dissect the energetic profile and structural basis of peptide binding to third PDZ domain (PDZ3) from the PSD-95
protein. This protocol employs rigorous quantum mechanics/molecular mechanics (QM/MM), semi-empirical Poisson–Boltzmann/surface
area (PB/SA), and empirical conformational free energy analysis (CFEA) to quantitatively describe and decompose systematic
energy changes arising from, respectively, noncovalent interaction, desolvation effect, and conformational entropy loss associated
with the formation of 30 affinity-known PDZ3–peptide complexes. We show that the QM/MM-, PB/SA-, and CFEA-derived energy components
can work together fairly well in reproducing experimentally measured affinity after a linearly weighting treatment, albeit
they are not compatible with each other directly. We also demonstrate that: (1) noncovalent interaction and desolvation effect
donate, respectively, stability and specificity to complex architecture, while entropy loss contributes modestly to binding;
(2) P0 and P−2 of peptide ligand are the most important positions for determining both the stability and specificity of the PDZ3–peptide
complex, P−1 and P−3 can confer substantial stability (but not specificity) for the complex, and N-terminal P−4 and P−5 have only a very limited effect on binding. 相似文献
996.
Tian F Cziferszky M Jiao D Wahlström K Geng J Scherman OA 《Langmuir : the ACS journal of surfaces and colloids》2011,27(4):1387-1390
We demonstrate a supramolecular peptide separation approach by the selective immobilization of peptides bearing an N-terminal tryptophan onto a CB[8]-modified gold substrate, followed by electrochemical release. The CB[8]-stabilized heteroternary complexes were characterized by (1)H NMR, ESI-MS, UV/vis, and fluorescence spectroscopy and cyclic voltammetry. Micropatterned CB[8]-modified gold substrates were found to trap only the recognizable N-tryptophan-containing peptides from a peptide mixture that could be visualized as green peptide arrays under fluorescence microscopy. Subsequently, the bound peptides were released from the modified substrates by the controlled single-electron reduction of viologen. The fully reversible trap-and-release process was repeated for 13 cycles, and the cumulative release profile of the dye-peptide conjugate was monitored by fluorescence spectroscopy, indicating that no degradation occurred. 相似文献
997.
Cao D Wu YP Fu ZF Tian Y Li CJ Gao CY Chen ZL Feng XZ 《Colloids and surfaces. B, Biointerfaces》2011,84(1):26-34
Nanostructured biocomposite scaffolds of poly(l-lactide) (PLLA) blended with collagen (coll) or hydroxyapatite (HA), or both for tissue engineering application, were fabricated by electrospinning. The electrospun scaffolds were characterized for the morphology, chemical and tensile properties by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), water contact angle (WCA), Fourier transform infrared (FTIR) measurement, and tensile testing. Electrospun biocomposite scaffolds of PLLA and collagen or (and) HA in the diameter range of 200-700 nm mimic the nanoscale structure of the extracellular matrix (ECM) with a well-interconnection pore network structure. The presence of collagen in the scaffolds increased their hydrophility, and enhanced cell attachment and proliferation, while HA improved the tensile properties of the scaffolds. The biocompatibility of the electrospun scaffolds and the viability of contacting cells were evaluated by 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) nuclear staining and by fluorescein diacetate (FDA) and propidium iodide (PI) double staining methods. The results support the conclusion that 293T cells grew well on composite scaffolds. Compared with pure PLLA scaffolds a greater density of viable cells was seen on the composites, especially the PLLA/HA/collagen scaffolds. 相似文献
998.
Hao XuHua Tian Liangyu Zheng Qingwen LiuLi Wang Suoqin Zhang 《Tetrahedron letters》2011,52(22):2873-2875
A novel and efficient microwave-assisted one-step reaction was developed to synthesize chiral N-sulfonylaziridines by the reaction of different chiral amino alcohols and sulfonic chlorides. The newly developed microwave synthetic method has the advantage of reducing the reaction time from 24 to 0.5 h with improved yields (84-93%) and minimizing by-products. 相似文献
999.
Xiaofang Zhang Li Dong Juwei Zhang Yajun Tian Guangwen Xu 《Journal of Analytical and Applied Pyrolysis》2011,91(1):241-250
Simulating the conditions of pyrolytic topping in a fluidized bed reactor integrated into a CFB boiler, the study was devoted to the reaction fundamentals of coal pyrolysis in terms of the production characteristics of pyrolysis oil in fluidized bed reactors, including pyrolysis oil yield, required reaction time and the chemical species presented in the pyrolysis oil. The results demonstrated that the maximal pyrolysis oil yield occurred on conditions of 873 K, with a reaction time of 3 min and in a reaction atmosphere gas simulating the composition of pyrolysis gas. Adding H2 and CO2 into the reaction atmosphere decreased the pyrolysis oil yield, while the oil yield increased with increasing the CO and CH4 contents in the atmosphere. TG-FTIR analysis was conducted to reveal the effects of reaction atmosphere on the chemical species present in the pyrolysis oil. The results clarified that the pyrolysis oil yield reached its maximum when the simulated pyrolysis gas was the reaction atmosphere, but there were slightly fewer volatile matters in the pyrolysis oil than the oil generated in the N2 atmosphere. All of these results are expected not only to reveal the composition characteristics of the pyrolysis oil from different conditions of the coal topping process but also to optimize the pyrolysis conditions in terms of maximizing the light pyrolysis oil yield and quality. 相似文献
1000.
A temperature-responsive composite based on poly (N-isopropylacrylamide) (PNIPAAm) and ordered mesoporous carbons (OMCs) has been successfully prepared by a simple wetness impregnation technique. The structures and properties of the composite were characterized by infrared spectroscopy (IR), X-ray diffraction (XRD), transmission electron microscopy (TEM), N2 sorption, thermogravimetric analysis (TG) and differential scanning calorimetry (DSC). The results showed that the inclusion of PNIPAAm had not greatly changed the basic ordered pore structure of the OMCs. Ibuprofen (IBU) was selected as model drug, and in vitro test of IBU release exhibited a temperature-responsive controlled release delivery. 相似文献