Sequence-Dependent Nanofiber Structures of Phenylalanine and Isoleucine Tripeptides

The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and assembled supramolecular structures. We report a hybrid-resolution model to computationally explore the sequence–structure relationship of self-assembly for tripeptides containing only phenylalanine and isoleucine. We found that all these tripeptides have a tendency to assemble into nanofibers composed of laterally associated filaments. Molecular arrangements within the assemblies are diverse and vary depending on the sequences. This structural diversity originates from (1) distinct conformations of peptide building blocks that lead to different surface geometries of the filaments and (2) unique sidechain arrangements at the filament interfaces for each sequence. Many conformations are available for tripeptides in solution, but only an extended β-strand and another resembling a right-handed turn are observed in assemblies. It was found that the sequence dependence of these conformations and the packing of resulting filaments are determined by multiple competing noncovalent forces, with hydrophobic interactions involving Phe being particularly important. The sequence pattern for each type of assembly conformation and packing has been identified. These results highlight the importance of the interplay between conformation, molecular packing, and sequences for determining detailed nanostructures of peptides and provide a detailed insight to support a more precise design of peptide-based nanomaterials.     

Photoresponsive peptide and polypeptide systems: part II. Photochromism of poly(l-ornithine) containing various azo-contents in side chains

Poly(L-ornithine)s having various azo-contents in the side chains were synthesized by the water-soluble carbodiimide procedure. The photochemical properties of the polypeptides poly[N^δ-p-(phenylazo)benzoyl-L-ornithine] (PPABLO) containing 3–77 mol% azobenzene were investigated by absorption and circular dichroism spectroscopy in hexafluoro-2-propanol (HFIP) or water, and in HFIP-water or methanol-water solvent mixtures. The photochromism of the dichroic bands of the PPABLOs containing 20–77 mol% azobenzene in the visible and ultraviolet wavelength regions was found to be mostly reversible as a function of irradiation time at different wavelengths due to the photostationary state (above 80% trans-cis photoisomerization) of the azo aromatic moieties. The PPABLO containing 3.2 mol% azobenzene in water exhibited conformational changes from random coil to helix by the addition of methanol or sodium dodecyl sulphate (SDS). The photo-induced conformational change was observed in HFIP-water-SDS solvent mixtures, while no conformational change was seen in water and HFIP-water solvent mixtures.     

Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling

Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of accuracy and efficacy since the ligand may bind in a number of thermally accessible conformations. The conformational rotamer ensemble sampling tool (CREST) uses an iterative scheme to efficiently sample the conformational space and calculates energies using the semi-empirical ‘Geometry, Frequency, Noncovalent, eXtended Tight Binding’ (GFN2-xTB) method. This combined approach is applied to blind predictions of the modes and free energies of binding for a set of 10 drug molecule ligands to the cucurbit[n]urils CB[8] receptor from the recent ‘Statistical Assessment of the Modeling of Proteins and Ligands’ (SAMPL) challenge including morphine, hydromorphine, cocaine, fentanyl, and ketamine. For each system, the conformational space was sufficiently sampled for the free ligand and the ligand-receptor complexes using the quantum chemical Hamiltonian. A multitude of structures makes up the final conformer-rotamer ensemble, for which then free energies of binding are calculated. For those large and complex molecules, the results are in good agreement with experimental values with a mean error of 3 kcal/mol. The GFN2-xTB energies of binding are validated by advanced density functional theory calculations and found to be in good agreement. The efficacy of the automated QM sampling workflow allows the extension towards other complex molecular interaction scenarios.     

The Histidine Phosphocarrier Kinase/Phosphorylase from Bacillus Subtilis Is an Oligomer in Solution with a High Thermal Stability

The histidine phosphocarrier protein (HPr) kinase/phosphorylase (HPrK/P) modulates the phosphorylation state of the HPr protein, and it is involved in the use of carbon sources by Gram-positive bacteria. Its X-ray structure, as concluded from crystals of proteins from several species, is a hexamer; however, there are no studies about its conformational stability, and how its structure is modified by the pH. We have embarked on the conformational characterization of HPrK/P of Bacillus subtilis (bsHPrK/P) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, small-angle X-ray-scattering (SAXS) and dynamic light-scattering (DLS)). bsHPrK/P was mainly a hexamer in solution at pH 7.0, in the presence of phosphate. The protein had a high conformational stability, with an apparent thermal denaturation midpoint of ~70 °C, at pH 7.0, as monitored by fluorescence and CD. The protein was very pH-sensitive, precipitated between pH 3.5 and 6.5; below pH 3.5, it had a molten-globule-like conformation; and it acquired a native-like structure in a narrow pH range (between pH 7.0 and 8.0). Guanidinium hydrochloride (GdmCl) denaturation occurred through an oligomeric intermediate. On the other hand, urea denaturation occurred as a single transition, in the range of concentrations between 1.8 and 18 µM, as detected by far-UV CD and fluorescence.     

日光照射对荧光增白剂VBL顺-反异构现象影响的研究

用紫外光谱和荧光光谱法对日光照射荧光增白剂VBL溶液进行了研究。结果表明、随日光照射时间的延长，VBL溶液在432nm处荧光强度下降；而在267nm处有所增强，低浓度溶液对日光照射更加敏感。1mg／1在避光时测得吸光度为0.449，而在日光照射15分钟后，其吸光度下降至0.141，证明日光照射使VBL溶液中的顺式异构体增加。     

Nucleophilic substitution onto poly(methylmethacrylate): 4. Dilute solution properties of substituted polymethacrylates

The morphological and hydrodynamic properties of a series of homogeneous fractions of substituted poly(methylmethacrylate) (A units) bearing keto-β-functional groups (B units) of the general structureCOCH₂R, with R = SO_xCH₃ (x = 1,2) or SO₂N(CH₃)₂, were investigated by intrinsic viscosity, light scattering and partial specific volume measurements in dimethylformamide (DMF) solution at 25°C. For molar substitution degrees $\text{DS}{}_{\mathrm{m}}\text{< 0.5}$, the copolymers behave as flexible random coils. The Stockmayer-Fixman-Yamakawa analysis of the $\text{[η]-}\text{M}\text{?}{}_{\mathrm{w}}$ data leads to slightly higher unperturbed dimensions K_o and steric factor σ than those for PMMA, and to stronger chain expansion as a result of the weak hydrogen bonding between DMF and COCH₂R units and a positive X_AB interaction parameter. For $\text{DS}{}_{\mathrm{m}}\text{> 0.5}$ however, copolymers bearing COCH₂SO₂N(CH₃)₂ groups behave as worm-like chains, as derived from the Fujii-Yamakawa analysis of the $\text{[η]-}\text{M}\text{?}{}_{\mathrm{w}}\text{-}\text{v}\text{?}$ data: the persistence length increases from 380 to 570 Å within the $\text{DS}$_m range 0.57–0.75. This transition from a random coil to a worm-like chain for $\text{DS}{}_{\mathrm{m}}\text{> 0.5}$ was tentatively correlated with the accumulation of B units in sterically hindered and self-associated short blocks of average length l_B ? 1.6 which provide drastically increased rigidity to the copolymer chain.     

基于XML的DNA公共数据模型

针对目前DNA数据组织与处理中存在的数据异构问题,提出一个基于XML的DNA公共数据模型（DCDM）。该模型具有很强的可扩展性,能克服一般公共数据模型的作用范围小的缺点,可用于构建DNA研究领域统一的DNA数据描述模式。实验结果表明,该模型能解决DNA数据异构中的语义异构。     

动态小生境半径两阶段多模态差分进化算法

针对多模态优化问题, 提出一种动态小生境半径两阶段多模态差分进化算法. 基于构象空间退火思想, 设计一种两阶段退火策略来动态调整小生境半径, 并根据退火过程将整个优化过程分为两个阶段. 在第1 阶段, 通过差分限制变异策略生成高质量的新个体来维持种群的多样性, 促进多模收敛; 在第2 阶段, 利用种子邻近变异策略对已探测到的生境高度搜索, 加快算法的收敛速度. 实验结果表明, 所提出算法能够有效实现从全局探测到局部增强的自适应平滑过渡, 是一种有效的多模态优化算法.

     

Semiempirical and ab initio conformational analysis of 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane with application of GIAO-SCF methods to NMR spectrum interpretation

The GIAO-SCF method for calculating isotropic nuclear magnetic shielding values has been utilized to explain certain features in the ¹H-NMR spectrum of 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane. Population distributions of the low-energy conformers based on their ab initio energies were used to produce weighting factors for the individual calculated shielding values to calculate the weighted average of the shielding values for a complete set of conformers. The differences in ¹H chemical shifts between the hydrogens of the two methyl groups and between the axial and equatorial hydrogens in 2-methylene-8,8-dimethyl-1,4,6,10-tetraoxaspiro[4.5] decane were shown to be due to energy differences between the chair and boat orientations of the six-membered ring and contribution from a twist-boat conformation. Results suggest a hypothesis that intramolecular differences in chemical shift might be calculated to a greater degree of accuracy than chemical shifts calculated relative to a standard.