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.     

Speciation analysis of aluminium(III) in natural waters and biological fluids by complexing with various catechols followed by differential pulse voltammetry detection

The biological effects of aluminium have received much attention in recent years. Speciation of Al is of basic relevance as it concerns its reactivity and bioavailability. A differential pulse voltammetry (DPV) procedure is proposed for speciation analysis of Al(III) in natural waters and biological fluids using six catechols (L-dopa, dopamine, epinephrine, norepinephrine, caffeic acid and o-benzenediol) as electroactive ligands. The decrease of the DPV anodic peak current for each catechol ligand is linear with the increase of Al concentration. This speciation analysis idea is based on the measurement of the complexation capacity, namely, different affinities of Al(III) for catechols and organic ligands under two pH conditions. The labile monomeric Al fraction (mainly inorganic aluminium) is determined at pH 4.6, while the total monomeric Al fraction is determined at pH 8.5. The principle for Al(III) speciation analysis by an electrochemical method is discussed. This sensitive and simple fractionation method is successfully applied to the speciation analysis of Al in natural waters and the results agree well with those of Driscoll's method. The speciation analysis of Al in biological fluids is also explored and the results are compared with those obtained by ultrafiltration and dialysis. Compared with other speciation protocols the electrochemical method possesses some remarkable advantages: rapidity, high sensitivity, cheap instrumentation and a simple operation procedure.     

一步室温固相化学反应合成纳米氨基酸杂多电荷转移配合物(HPhe)3PMo12O40·2H2O

以Keggin结构的钼磷酸(H3PMo12O40·13H2O)与苯丙氨酸(Phe)为原料,利用一步固相化学反应于室温合成了纳米氨基酸杂多电荷转移配合物(HPhe)3PMo12O40·2H2O,采用元素分析,IR,XRD,TEM,UV和循环伏安法等手段对其进行了结构表征及性质研究.结果表明,标题化合物纳米粒子为均匀的球状,粒径约为30～40nm.该化合物中杂多阴离子部分仍保持Keggin结构,但在钼磷酸与苯丙氨酸之间发生了显著的电荷转移.     

Bis[bis­(methoxy­carbimido)amine‐κ2N,N′]bis­(perchlorato‐κO)copper(II) bis­[bis­(methoxy­carbimido)amine‐κ2N,N′]bis­(methanol‐κO)copper(II) bis­(perchlorate) methanol disolvate

The title compound, [Cu(ClO₄)₂(C₄H₉N₃O₂)₂][Cu(C₄H₉N₃O₂)₂(CH₄O)₂](ClO₄)₂·2CH₃OH, comprises two independent Cu^II species lying on different inversion sites. In the Cu complexes, a distorted octa­hedral geometry arises (from basic square‐planar N₄ coordination) from the weak coordination of two perchlorate ions (as Cu—O) in one species and two methanol mol­ecules in the other (also as Cu—O). Inter­actions between the O atoms of the perchlorate anions or methanol groups and the imide or amine NH groups afford an extensive inter­molecular hydrogen‐bonding network.     

Electrochemical formation and clevage of bis-imidazolyls

Bis-(2,4,5-triphenylimidazolyls) result from the dimerization of 2,4,5-triphenylimidazolyls and from the nucleophilic attack of 2,4,5-triphenylimidazole anions upon 2,4,5-triphenylimidazolylium cations. The isomeric bis-imidazolyls consist of imidazole and isoimidazole systems. Imidazoles undergo only anodic oxidation, isoimidazoles only cathodic reduction. Therefore the bis-imidazolyls may be analyzed from their electrochemical behaviour. Bis-(2,4,5-triphenylimidazolyl)-1,2′ and bis-(2,4,5-triphenylimidazolyl)-1,4′ undergo reductive bond cleavage in an ē.c?.ē. mechanism from which 2,4,5-triphenyl-imidazole anions result. The electrochemical properties of one of the bis-imidazolyls agree with that of 1,4,5-triphenyl-2-(2,4,5-triphenylisoimidazolyl-4)-imidazole and not with that of bis-(2,4,5-triphenylimidazolyl)-2,4′ as reported in literature.     

Thermodynamic properties of the spin-Peierls transition in CuGeO3

We present an investigation of the spin-Peierls transition atT _SP=14.5 K in polycrystalline CuGeO₃ through specific-heat and thermal-expansion measurements. Clear second-order phase-transition anomalies are found in both properties atT _SP, although only a small entropy of S0.1 Rn2 is released at the transition. Most of the entropy is released atT _SP<T<150 K, where the temperature dependence of the magnetic contribution to the specific heat as well as the thermal expansion exhibit extrema atT ^*40 K. These are caused by one-dimensional antiferromagnetic fluctuations along the Cu chains, possibly accompanied by structural fluctuations. Using Ehrenfest's relation, a hydrostatic pressure coefficient (T _SP/_p)_p0 (0.45±0.06) K/kbar is derived.