Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Rate-equilibrium relationships in hydride transfer reactions: the role of intrinsic barriers

A literature survey on the kinetics of hydride abstractions from CH-groups by carbocations reveals a general phenomenon: Variation of the hydride acceptor affects the rates of hydride transfer to a considerably greater extent than an equal change of the thermodynamic driving force caused by variation of the hydride donor. The origin of this relationship was investigated by quantum chemical calculations on various levels of ab initio and DFT theory for the transfer of an allylic hydrogen from 1-mono- and 1,1-disubstituted propenes (XYC=CH-CH(3)) to the 3-position of 1-mono- and 1,1-disubstituted allyl cations (XYC=CH-CH(2)(+)). The discussion is based on the results of the MP2/6-31+G(d,p)//RHF/6-31+G(d,p) calculations. Electron-releasing substituents X and Y in the hydride donors increase the exothermicity of the reaction, while electron-releasing substituents in the hydride acceptors decrease exothermicity. In line with Hammond's postulate, increasing exothermicity shifts the transition states on the reaction coordinate toward reactants, as revealed by the geometry parameters and the charge distribution in the activated complexes. Independent of the location of the transition state on the reaction coordinate, a value of 0.72 is found for Hammond-Leffler's alpha = deltaDeltaG/deltaDelta(r)G degrees when the hydride acceptor is varied, while alpha = 0.28 when the hydride donor is varied. The value of alpha thus cannot be related with the position of the transition state. Investigation of the degenerate reactions XYC=CH-CH(3) + XYC=CH-CH(2)(+) indicates that the migrating hydrogen carries a partial positive charge in the transition state and that the intrinsic barriers increase with increasing electron-releasing abilities of X and Y. Substituent variation in the donor thus influences reaction enthalpy and intrinsic barriers in the opposite sense, while substituent variation in the acceptor affects both terms in the same sense, in accord with the experimental findings. Marcus theory is employed to treat these effects quantitatively.     

A highly sensitive assay for protein with dibromochloro-arsenazo-Al(3+) using resonance light scattering technique and its application

A simple, sensitive and selective method has been developed for the determination of protein using resonance light scattering (RLS) technique. The method is based on the interaction of protein and arsenazo-DBC-Al(3+) in the pH range of 5.0-7.0, which causes a substantial enhancement of the resonance scattering signal of arsenazo-DBC-Al(3+) in the wavelength range of 300-550 nm with the maximum RLS platform at 405-420 nm. With this method, 2.50-50.00 mug ml(-1) of bovine serum albumin (BSA) and 2.50-60.00 mug ml(-1) of human serum albumin (HSA) can be determined, and the detection limits, calculated three times the standard deviation (S.D.) of six blank measurements, for BSA and HSA were 123.4 and 89.6 ng ml(-1), respectively. Moreover, the method is free from interference from many amino acids and metal ions. The method, with high sensitivity, selectivity and reproducibility, was satisfactorily applied to the determination of total protein in human serum samples. Mechanism studies indicated that arsenazo-DBC-Al(3+) could bind to BSA depending mainly on electrostatic forces, which results in enhanced RLS in the arsenazo-DBC-Al(3+)-protein system.     

High pressure Raman studies of 7,7,8,8-tetracyanoquinodimethane (TCNQ) and CuTCNQ

The high-pressure Raman studies of 7,7,8,8-tetracyanoquinodimethane (TCNQ) single crystals and polycrystalline CuTCNQ are presented in this paper. TCNQ shows a phase transition at 22 kbar, a pressure higher than reported earlier. CuTCNQ undergoes a first order phase transition at 30 kbar, which is characterized by the abrupt disappearance of all the Raman bands.     

1,2,2,6,6-五甲基哌啶醇对聚丙烯光稳定作用的研究

<正> 关于受阻胺类光稳定剂的稳定作用机理,是近年来光稳定研究领域中广泛探讨的课题,我们用异辛烷溶液研究了1,2,2,6,6-五甲基哌啶醇的光稳定作用,结果已在前文报道,本工作是上述研究的继续,主要研究五甲基哌啶醇对聚丙烯膜的光稳定作用。     

环氧丙烯酸酯的紫外光固化

制备了适于配制紫外光固化涂料的环氧丙烯酸酯，研究了反应温度、阻聚剂、催化剂等因素对环氧树脂与丙烯酸反应的影响；讨论了反应机理和动力学；并利用红外光谱观察了产物的紫外光固化行为。季铵盐能有效地催化环氧树脂和丙烯酸的反应，当其用量为０．６％～１．２％时，在９０～１１０℃反应４．５～８小时后，环氧基转化率大于９７％。由此配制的光固化涂料经紫外光辐照能快速固化。     

Influence of the three-dimensional heterogeneous roughness on electrokinetic transport in microchannels

Surface roughness has been considered as a passive means of enhancing species mixing in electroosmotic flow through microfluidic systems. It is highly desirable to understand the synergetic effect of three-dimensional (3D) roughness and surface heterogeneity on the electrokinetic flow through microchannels. In this study, we developed a three-dimensional finite-volume-based numerical model to simulate electroosmotic transport in a slit microchannel (formed between two parallel plates) with numerous heterogeneous prismatic roughness elements arranged symmetrically and asymmetrically on the microchannel walls. We consider that all 3D prismatic rough elements have the same surface charge or zeta potential, the substrate (the microchannel wall) surface has a different zeta potential. The results showed that the rough channel's geometry and the electroosmotic mobility ratio of the roughness elements' surface to that of the substrate, epsilon(mu), have a dramatic influence on the induced-pressure field, the electroosmotic flow patterns, and the electroosmotic flow rate in the heterogeneous rough microchannels. The associated sample-species transport presents a tidal-wave-like concentration field at the intersection between four neighboring rough elements under low epsilon(mu) values and has a concentration field similar to that of the smooth channels under high epsilon(mu) values.     

Two 3D supramolecular polymers constructed from an amino acid and a high-nuclear Ln6Cu24 cluster node

The first successful attempt to construct 3D supramolecular frameworks with high-nuclear 3d-4f heterometallic clusters as a node is reported. The self-assembly of Ln3+, Cu2+ and amino acid in solution leads to the formation of two polymers, 35-nuclear complex [Sm6Cu29] 1 with a primitive cubic net-like structure and 36-nuclear complex [Nd6Cu30] 2 with a face-centred cubic network type structure. Glycine and L-proline, respectively, were used as ligands. It should be noted that 2 has a chiral framework. X-ray structure analyses show that 1 crystallizes in the triclinic P1 space group (a=19.6451(8), b=20.4682(8), c=20.7046(8) A, alpha=89.453(1), beta=66.290(1), gamma=68.572(1) degrees, V=7003.0(5) A3 and Z=1) and 2 belongs to the cubic P2(1)3 space group (a=b=c=32.4341(3) A, V=34 119.7(5) A3 and Z=4). Both complexes utilize Ln6Cu24 octahedral clusters as nodes and trans-Cu(amino acid)2 groups as bridges. Electrical conductivity measurements reveal that both polymers behave as semiconductors.     

Transmembrane ion conductance by an acyclic bolaamphiphile

[reaction in text] An acyclic bolaamphiphile forms ion channels in vesicles and planar bilayer membranes that are closely similar to the channels formed by related bismacrocyclic compounds. Thus the function of these ion channels does not depend on synthetically difficult macrocyclic subunits.