A fast method for large‐scale De Novo peptide and miniprotein structure prediction

Although peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large‐scale experiments is still missing. We introduce a new approach—PEP‐FOLD—to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model‐derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse‐grained energy score. On a benchmark of 52 peptides with 9–23 amino acids, PEP‐FOLD generates lowest‐energy conformations within 2.8 and 2.3 Å Cα root‐mean‐square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27–49 amino acids, PEP‐FOLD reaches an accuracy of 3.6 and 4.6 Å Cα root‐mean‐square deviation for the most‐native and lowest‐energy conformations, using the nonflexible regions identified by NMR. PEP‐FOLD simulations are fast—a few minutes only—opening therefore, the door to in silico large‐scale rational design of new bioactive peptides and miniproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.     

Second Dissociation Constants of 4-[N-morpholino]butanesulfonic Acid and N-[2-hydroxyethyl]piperazine-N′-4-butanesulfonic Acid from 5 to 55°C

The values of the second dissociation constant, pK ₂, for the dissociation of the NH⁺ charge center of the zwitterionic buffer compounds 4-(N-morpholino)butanesulfonic acid (MOBS), and N-(2-hydroxyethyl)piperazine-N-4-butanesulfonic acid (HEPBS) have been determined from 5 to 55°C, including, 37°C at intervals of 5°C. The electromotive-force (emf) measurements have been made utilizing hydrogen electrodes and silver–silver chloride electrodes. The value of pK ₂ for MOBS was found to be 7.702 ± 0.0005, and 8.284 ± 0.0004 for HEPBS, at 25°C, respectively. The related thermodynamic quantities, G ^o, H ^o, S ^o, and C _p ^o for the dissociation processes of MOBS and HEPBS have been derived from the temperature coefficients of pK ₂. Both the MOBS and HEPBS buffer materials are useful as primary pH standards for the control of pH 7.3 to 8.6 in the region close to that of physiological fluids.     

Controlling the self-assembly of a deoxiguaninosine on mica

We report a tapping mode scanning force microscopy investigation on the growth from solutions of a lipophilic deoxiguanosine derivative on the basal plane of a muscovite mica surface. By varying the chemical composition of the substrate surface it is possible to drive the self-assembly towards either layered thin films, which are very likely to consist of guanosine quartets, or nanoribbons, comprising hydrogen bonded networks. Both these two architectures, which are peculiar to the guanine base itself, are of notable importance for the fabrication of molecular nanowires. Moreover, the first arrangement provides evidence that the guanosine is able to behave as ionophore, thus, suggesting its utilization in the development of solid-state ion selective sensors.     

铜在空气中生成碱式碳酸铜的热力学分析

从热力学角度研究了酸度、湿度、水的存在状态不同时,单质铜在空气中生成碱式碳酸铜的电动势及其自由能变。通过计算发现:在酸性条件下,p H的大小对于反应的自发性没有影响;大气中二氧化碳溶解达到饱和时,空气湿度增加,反应的自发性略微增加;相同条件下,水由气态变为液态时,反应的自发性增幅较大。     

超支化聚合反应的多尺度模拟

超支化聚合物具有与树枝状大分子相似的物理和化学性质,其具有合成简单、分子量分布宽等突出特点,超支化聚合物分子的结构形成取决于聚合反应过程,本文介绍了超支化聚合反应模拟研究的最新进展.首先介绍了八位置键涨落粗粒化格子模型在超支化聚合反应模拟中的应用,该方法考虑了聚合物分子空间位阻效应、分子内成环和反应点活性等影响因素,从而可以模拟不同类型的超支化聚合反应;为了定量描述单体和聚合物分子结构,研究者进一步发展了杂化多尺度超支化聚合反应模拟方法,该方法通过玻尔兹曼反演迭代方法获取单体和聚合物特异性粗粒化力场,然后通过粗粒化分子动力学方法结合反应性Monte Carlo方法对特异性超支化聚合反应进行定量模拟.多尺度聚合反应模拟不仅可以精确计算超支化聚合物分子量、多分散性指数和支化度等一般性聚合物参数,还可以获取分子成环率、超支化大分子构象等重要分子结构信息,在超支化聚合反应基础研究与预测方面具有重要应用价值.     

微波辐射下秸秆纤维微观结构的变化

利用原子力显微镜(AFM)对微波处理前后秸秆纤维表面的变化进行了研究,并结合XRD和FTIR研究了处理前后其化学结构及结晶形态的变化情况。结果表明,未经微波处理的秸秆纤维表面比较光滑,平均粗糙度(Ra)为(86.7±6.335)nm,均方根粗糙度(Rq)为(141.1±9.055)nm;经微波处理的秸秆纤维表面比较粗糙,并出现许多细小孔洞,其Ra为(445.0±28.14)nm,Rq为(558.9±33.458)nm,微波辐射处理前后秸秆纤维的表面形态差异较大。经微波辐射处理后,秸秆纤维在2θ=22.3°处的衍射峰移至21.8°,且峰宽稍有增加,在38.1°、44.3°、64.6°、78.9°处出现的4个衍射峰,除强度稍有增强,其峰形和位置与未经处理秸秆纤维的衍射峰基本一致,表明微波处理没有改变纤维的结晶形态。FTIR光谱表明,微波处理样中未产生新的官能团,但分子间氢键及分子内氢键发生变化。微波作用未引起秸秆纤维化学结构的变化。     

A sensitive, rapid ferricyanide-mediated toxicity bioassay developed using Escherichia coli

A need for rapid toxicity techniques has seen recent research into developing new microbiological assays and characterising their toxicity responses using a range of substances. A microbiological bioassay that determines changes in ferricyanide-mediated respiration for toxicity measurement (FM-TOX) shows particular promise. The development and optimisation of an improved FM-TOX method, incorporating novel features, is described using Escherichia coli as the biocatalyst. Omission of an exogenous carbon source, used in previously described FM-TOX assays, substantially improves the assay sensitivity. In addition, the development of a two-step procedure (toxicant exposure followed by determination of microbial respiratory activity) was found to enhance the inhibition of E. coli by 3,5-dichlorophenol and four other toxicants, compared to single-step procedures. Other assay parameters, such as the ferricyanide concentration, exposure times and optical density of the biocatalyst were also optimised, sometimes based on practical aspects. Toxicity tests were carried out using the adopted technique on both organic and inorganic toxicants, with classic sigmoid-shaped dose-response curves observed, as well as some non-standard responses. IC₅₀ data is presented for a number of common toxicants. The optimised assay provides a good foundation for further toxicity testing using E. coli, as well as the potential for expanding the technique to utilise other bacteria with complementary toxicity responses, thereby allowing use of the assay in a range of applications.     

Open tubular capillary electrochromatography: A useful microreactor for collagen I glycation and interaction studies with low-density lipoprotein particles

Diabetes, a multifunctional disease and a major cause of morbidity and mortality in the industrialized countries, strongly associates with the development and progression of atherosclerosis. One of the consequences of high level of glucose in the blood circulation is glycation of long-lived proteins, such as collagen I, the most abundant component of the extracellular matrix (ECM) in the arterial wall. Glycation is a long-lasting process that involves the reaction between a carbonyl group of the sugar and an amino group of the protein, usually a lysine residue. This reaction generates an Amadori product that may evolve in advanced glycation end products (AGEs). AGEs, as reactive molecules, can provoke cross-linking of collagen I fibrils. Since binding of low-density lipoproteins (LDLs) to the ECM of the inner layer of the arterial wall, the intima, has been implicated to be involved in the onset of the development of an atherosclerotic plaque, collagen modifications, which can affect the affinity of native and oxidized LDL for collagen I, can promote the entrapment of LDLs in the intima and accelerate the progression of atherosclerosis.In this study, open tubular capillary electrochromatography is proposed as a new microreactor to study in situ glycation of collagen I. The kinetics of glycation was first investigated in a fused silica collagen I-coated capillary. Dimethyl sulphoxide, injected as an electroosmotic flow marker, gave information about the charge of coating. Native and oxidized LDL, and selected peptide fragments from apolipoprotein B-100, the protein covering LDL particles, were injected as marker compounds to clarify the interactions between LDLs and the glycated collagen I coating. The method proposed is simple and inexpensive, since only small amounts of collagen and LDL are required. Atomic force microscopy images complemented our studies, highlighting the difference between unmodified and glycated collagen I surfaces.     

Electron density distribution in potassium bis -(carbonato)cuprate(II)

The electron density distribution in potassiumbis-(carbonato)cuprate(II) has been analyzed using x-ray diffraction data from an earlier structure determination. While the copper-ligand geometry is close to square planar the deformation density near the metal is strongly asymmetric. There are local maxima near the copper atom along the line of the Cu-K vectors. These resemble features found in corresponding regions in normal length metal-metal bonds. The observation is consistent with the long range nature of the Coulomb potential associated with the potassium ion.