高等植物铁氧还蛋白的结构与功能

该文介绍了高等植物中铁氧还蛋白（Fd）的结构,铁氧还蛋白与铁氧还蛋白：NADP^＋氧化还原酶（FNR）的相互作用,氧化还原电势和电子传递活性;阐述了铁氧还蛋白结构与功能的关系。     

紫色非硫光合细菌Rhodopseudomonas capsulata铁氧还蛋白氧化还原电位的研究

本文介绍了从紫色非硫光合细菌Rhodopseudomonas capsulata分离纯化的铁氧还蛋白,经固体硫酸铵分级盐析沉淀和透析进一步纯化的样品,通过循环伏安法检测其对温度的敏感性,所引起的蛋白变性;然后应用定电位电量法和电位阶跃电量法,研究它的电量-电位关系,根据Nernst公式进而计算铁氧还蛋白的中点电位分别为-378mV和-375mV,在其参与氧化-还原反应时,每分子铁氧还蛋白传递电子数目≈2。并对不同菌种来源的铁氧还蛋白的标准氧化-还原电位及其传递电子数目进行了讨论。     

紫色非硫光合细菌Rhodopseudomonas capsulata铁氧还蛋白氧化还原电位的研究

本文介绍了从紫色非硫光合细菌Rhodopseudomanas capsulata 分离纯化的铁氧还蛋白,经固体硫酸铵分级盐析沉淀和透析进一步纯化的样品,通过循环伏安法检测其对温度的敏感性,所引起的蛋白变性;然后应用定电位电量法和电位阶跃电量法,研究它的电量-电位关系,根据Nernst 公式进而计算铁氧还蛋白的中点电位分别为-378mV 和-375mV,在其参与氧化-还原反应时,每分子铁氧还蛋白传递电子数目≈2。并对不同菌种来源的铁氧还蛋白的标准氧化-还原电位及其传递电子数目进行了讨论。     

紫色非硫光合细菌Rhodopseudomonas capsulata铁氧还蛋白的分离纯化

采用超声破碎,Triton X-100处理,30％丙酮提取,经三次DEAE-52纤维素离子交换柱层析分离纯化,我们第一次从紫色非硫光合细菌Rps.capsulata N-3菌株中,获得聚丙烯酰胺凝胶电泳纯的铁氧还蛋白(Ferredoxin)及其结晶。吸收光谱的峰值位于275舳,375nm;在450 nm、480 nm处各有较小的吸收峰。特征吸收峰比A375nm/A275nm=0.74。凝胶过滤测定它的分子量为9,000道尔顿;每分子含有8个非血红素铁和等数量的酸性不稳定硫。铁氧还蛋白能被连二亚硫酸钠化学还原,氢气和氢酶构成的酶体系还原,亦能作为电子传递载体参与菠菜叶绿体催化的DCPIPH_2→铁氧还蛋白→NADP~ 光还原。     

紫色非硫光合细菌Rhodopseudomonas capsulata铁氧还蛋白(Ferredoxin)一些特性的研究

作者报导了(朱长喜等1980)从紫色非硫光合细菌Rhodopseudomonas capsulata N-3菌株中,分离纯化获得了聚丙烯酰胺凝胶电泳纯的铁氧还蛋白(Ferredoxin),通过对其生物活性、分子量的测定,铁、硫含量的化学分析以及电子自旋共振波谱(EPR)的研究,确认它是具有8Fe—8S簇活性中心结构的铁—硫蛋白。已知铁氧还蛋白的生物化学特性随它的来源有变化,因而表现它作为电子传递载体,在光合作用、生物固氮、氢代谢等方面的电子传递过程中,行使的功能也有差异(Rao和Hall 1977),为了进一步研究Rps.capsulata铁氧还蛋白的生理功能,我们测定了它的氨基酸组份,克分子消光系数以及与细菌载色体光合膜的结合状态等生化特性。     

高等植物铁氧还蛋白的结构装配和基因表达调控的研究进展

本文综述高等植物铁氧还蛋白的结构和装配研究近况,并着重讨论其基因克隆和表达调控方面的最新进展。     

嗜酸氧化亚铁硫杆菌中铁氧还蛋白的生物信息学分析

从NCBI数据库中下载了3种铁氧还蛋白(ACK79261.1,ACK79281.1和ACK80954.1)序列,利用网站在线预测结合软件分析,对其基本理化性质、蛋白修饰、保守结构域、亚细胞定位、二级和三级结构预测和蛋白相互作用网络等方面进行分析和预测。所得数据表明,3种蛋白质均为不稳定的亲水性蛋白质,等电点偏酸性,不含信号肽,均在细胞质中发挥作用;蛋白相互作用分析预测ACK79261.1在核酸代谢过程中发挥重要作用,ACK79281.1主要参与了细胞内的2Fe-2S簇的组装,ACK80954.1对于能量和电子传递必不可少。本研究利用生物信息学预测了铁氧还蛋白结构和功能,为后续研究嗜酸氧化亚铁硫杆菌中的电子传递过程以及菌株改良、应用推广提供理论上的依据。     

人心肌缺血/再灌注期间红细胞膜分子流动性改变的机理研究

对开心手术病人心肌缺血／再灌注过程中冠状静脉窦血中的红细胞流变性变化和红细胞膜分子结构的改变进行了研究。结果表明,再灌注即刻心脏产生大量自由基,并持续到再灌注第２０分钟时才大幅度回落;于再灌注后的２０分钟的自由基产生时相期间,除红细胞膜蛋白分子和脂质分子的τｐ、τｌ均明显延长外,还伴有血浆ＭＤＡ水平的明显增加和ＳＯＤ活性的显著降低,及红细胞内ＧＳＨ－Ｐｘ活性升高;与此同时其红细胞膜蛋白分子的α螺旋先减少后渐回复和β折叠渐增加并伴有羧基（ＣＯＯＨ）和氨基（ＮＨ３）的减少,而其红细胞膜脂质分子的磷氧双键（Ｐ＝Ｏ）、羰基（Ｃ＝Ｏ）和多不饱和键（Ｃ＝Ｃ）则增加;说明（１）再灌注期间氧自由基分别引起了红细胞膜蛋白分子碳端和氮端的改变及膜磷脂分子亲水区和疏水区化学结构的变化,（２）蛋白分子碳、氮端的变化造成了膜蛋白分子构象的改变,（３）蛋白分子和磷脂分子化学结构及构象的改变是红细胞膜这些分子流动性明显恶化的根本原因。     

近两年细胞生物学的进展（1991—1992）

从80年代末期以来,生物大分子结构和功能的研究又取得很大的进展。一批重要的生物大分子(如受体、离子通道、间隙连结、光合作用中心Ⅰ和固氮酶铁钼蛋白等)的三维结构,陆续得到解决。这些成就使细胞的结构和功能活动在分子水平得到更为圆满的解释。另一方面,用各种分子遗传学和基因工程方法(重组DNA技术、PCR、同源重组和转基因动、植物等)对高等生物的细胞分化、发育和遗传的分析取得     

阴道毛滴虫铁氧还蛋白与甲硝唑抵抗的研究进展

氢化酶体是阴道毛滴虫重要的代谢器官,该器官内存在的铁氧还蛋白不仅是虫体代谢过程中主要的电子传递介体,而且也在甲硝唑的激活中起关键作用。近年来阴道毛滴虫的甲硝唑抵抗株在临床和实验室都有报道,实验研究发现活化药物的铁氧还蛋白减少或缺失,因此对铁氧还蛋白与甲硝唑抵抗的相关性研究越来越受到医学及药学界的重视。本文总结近年来该领域的研究成果及发展动态,以期对滴虫药物抵抗的发生机制以及滴虫病防治的研究提供有价值的资料。     

The Crystal and Molecular Structure of 5-Fluoro-2′-Deoxy-β-Uridine

The crystal structure of 5-fluoro-2′-deoxy-β-uridine (FUDR) has been solved and the details of the molecular structure determined by x-ray analysis. The bond lengths and angles have been measured and are compared with the dimensions found for calcium thymidylate and adenylic acid. In all three compounds the bonds formed by the nitrogen atom involved in the glycosidic bond are not coplanar. Furthermore, it is found that in FUDR the C2′ carbon atom is out of the plane of the ribose ring. The possible effect of these observations on nucleic acid structures is discussed.     

Crystal structure analyses of reduced (CuI) poplar plastocyanin at six pH values

The structure of poplar plastocyanin in the reduced (CuI) state has been determined and refined, using counter data recorded from crystals at pH 3.8, 4.4, 5.1, 5.9, 7.0 and 7.8 (resolution 1.9 A, 1.9 A, 2.05 A, 1.7 A, 1.8 A and 2.15 A; the final residual R value was 0.15, 0.15, 0.16, 0.17, 0.16 and 0.15, respectively). The molecular and crystal structure of the protein is substantially the same in the reduced state as in the oxidized state. The refinements of the structures of the six forms of the reduced protein could therefore be commenced with a model derived from the known structure of CuII-plastocyanin. The refinements were made by reciprocal space least-squares calculations interspersed with inspections of electron-density difference maps. Precautions were taken to minimize any bias of the results of the refinements in the direction of the starting model. The most significant differences among the structures of the reduced protein at the six pH values, or between them and the structure of the oxidized protein, are concentrated at the Cu site. In the reduced protein at high pH (pH 7.8), the CuI atom is co-ordinated by the N delta(imidazole) atoms of His37 and His87, the S gamma(thiolate) atom of Cys84, and the S delta(thioether) atom of Met92, just as in CuII-plastocyanin. The distorted tetrahedral geometry and the unusually long Cu-S(Met92) bond are retained. The only effects of the change in oxidation state are a lengthening of the two Cu-N(His) bonds by about 0.1 A, and small changes in two bond angles involving the Cu-S(Cys) bond. The high-pH form of reduced plastocyanin accordingly meets all the requirements for efficient electron transfer. As the pH is lowered, the Cu atom and the four Cu-binding protein side-chains appear to undergo small but concerted movements in relation to the rest of the molecule. At low pH (pH 3.8), the CuI atom is trigonally co-ordinated by N delta(His37), S gamma(Cys84) and S delta(Met92). The fourth Cu-ligand bond is broken, the Cu atom making only a van der Waals' contact with the imidazole ring of His87. The trigonal geometry of the Cu atom strongly favours CuI, so that this form of the protein should be redox-inactive. This is known to be the case.(ABSTRACT TRUNCATED AT 400 WORDS)     

Structures for polyinosinic acid and polyguanylic acid

X-ray-diffraction analysis of oriented, partially crystalline fibres of polyinosinic acid has resulted in a new molecular model. This model consists of four identical polynucleotide chains related to one another by a fourfold rotation axis. The coaxial helices are righthanded (screw symmetry 23(2)) and have an axial translation per residue h=0.341nm and a rotation per residue t=31.3 degrees . Incorporated in the model are standard bond lengths, bond angles and C-2-endo furanose rings. The nucleotide conformation angles, determined by linked-atom least-squares methods, are orthodox and the fit with the X-ray intensities is good. Each hypoxanthine base is linked to two others by hydrogen bonds involving O-6 and N-1. Further stability may arise from intrachain hydrogen bonds between each ribose hydroxyl group and the phosphate oxygen O-3. If guanine were to be substituted for hypoxanthine in an isogeometrical molecular structure, additional hydrogen bonds could be made between every N-2 and N-7.     

Synthesis, X-ray crystallographic structures of thio substituted N-acetyl N'-methylamide alanine and evaluation of sp sulfur parameters of the CFF91 force field.

Acetyl thioalanine N-methyl (Ac-Alat-NHMe) and thioacetyl alanine N-methyl (Act-Ala-NHMe) were synthesized, crystallized and their X-ray diffraction structures determined for the first time. Both molecules adopted beta-sheet conformations and showed similar hydrogen bonding patterns with one molecular surface forming two oxo hydrogen bonds and the other forming two thio hydrogen bonds. The crystal structure data for the two thioamides provided a validation of the thioamide parameters for the newly derived CFF91 force field because the observed crystal (phi, psi) angles were situated in the global minimum regions of the theoretical (phi, psi) map predicted using the parameters. In addition, the parameters were further validated because conformational energy minimization of the crystal structure produced low deviations in unit cell dimensions, bond lengths, bond angles and torsional angles, and a 120-ps molecular dynamics simulation also gave a low deviation for the most probable N-H...S=C bond distance.     

Structure of oxidized bacteriophage T4 glutaredoxin (thioredoxin). Refinement of native and mutant proteins.

The structure of wild-type bacteriophage T4 glutaredoxin (earlier called thioredoxin) in its oxidized form has been refined in a monoclinic crystal form at 2.0 A resolution to a crystallographic R-factor of 0.209. A mutant T4 glutaredoxin gives orthorhombic crystals of better quality. The structure of this mutant has been solved by molecular replacement methods and refined at 1.45 A to an R-value of 0.175. In this mutant glutaredoxin, the active site residues Val15 and Tyr16 have been substituted by Gly and Pro, respectively, to mimic that of Escherichia coli thioredoxin. The main-chain conformation of the wild-type protein is similar in the two independently determined molecules in the asymmetric unit of the monoclinic crystals. On the other hand, side-chain conformations differ considerably between the two molecules due to heterologous packing interactions in the crystals. The structure of the mutant protein is very similar to the wild-type protein, except at mutated positions and at parts involved in crystal contacts. The active site disulfide bridge between Cys14 and Cys17 is located at the first turn of helix alpha 1. The torsion angles of these residues are similar to those of Escherichia coli thioredoxin. The torsion angle around the S-S bond is smaller than that normally observed for disulfides: 58 degrees, 67 degrees and 67 degrees for wild-type glutaredoxin molecule A and B and mutant glutaredoxin, respectively. Each sulfur atom of the disulfide cysteines in T4 glutaredoxin forms a hydrogen bond to one main-chain nitrogen atom. The active site is shielded from solvent on one side by the beta-carbon atoms of the cysteine residues plus side-chains of residues 7, 9, 21 and 33. From the opposite side, there is a cleft where the sulfur atom of Cys14 is accessible and can be attacked by a nucleophilic thiolate ion in the initial step of the reduction reaction.     

Program for the visualization and interactive study of molecules on a calligraphic display system

Mops is a computer program for the visualization and interactive analysis of crystallographic and molecular structures on a calligraphic PS 300 display system. This system allows the interactive display of bond lengths, bond angles and torsion angles with colour coding of atom types as well as crystalline packing interactions. Mops is also capable of easily drawing a chosen image on the screen using the Ortep program. This facility allows the very fast preparation of slides or illustrations.     

Conformational analysis of phosphatides: Mapping and minimization of the intramolecular energy

Empirical intramolecular energy calculations were carried out on molecular fragments related to phosphatides in order to find the preferred conformations. The energy was mapped as a function of several pairs of torsional angles in progressively larger molecular fragments, with energy minimization being carried out at each map point with respect to other significant variables. The energy mapping results were used as starting points for energy minimization on diheptanoyl L-α-phosphatidic acid-C, which consisted of the named molecule plus a carbon atom attached to one of the phosphate oxygens. It was found that there are 6 pairs of values for 2 of the torsional angles at the 3-way branch point in the glyceryl group which give sterically acceptable conformations; only 4 of these are compatible with lipid bilayer structure in that they can give a parallel arrangement of the acyl chains. The several acceptable conformations of the phosphate and acyl ester groups within each of these conformational classes are enumerated. The results obtained may be used as a guide for further experimental and theoretical work on phosphatide structures.     

ProDCoNN: Protein design using a convolutional neural network

Designing protein sequences that fold to a given three-dimensional (3D) structure has long been a challenging problem in computational structural biology with significant theoretical and practical implications. In this study, we first formulated this problem as predicting the residue type given the 3D structural environment around the C _α atom of a residue, which is repeated for each residue of a protein. We designed a nine-layer 3D deep convolutional neural network (CNN) that takes as input a gridded box with the atomic coordinates and types around a residue. Several CNN layers were designed to capture structure information at different scales, such as bond lengths, bond angles, torsion angles, and secondary structures. Trained on a very large number of protein structures, the method, called ProDCoNN (protein design with CNN), achieved state-of-the-art performance when tested on large numbers of test proteins and benchmark datasets.     

Periodic conformations of deoxyribonucleic acids

The conformation of a deoxyribonucleotide unit in a deoxyribonucleic acid molecule can be defined by six angles, each of which specifies the relative orientations between two groups of atoms adjacent to a covalent bond. With the assumption that these atoms are hard spheres with fixed van der Waal radii, conformations are sought to minimize their overlapping. The additional requirement of the polymer having a periodic structure further reduces the allowable conformations.     

Molecular interactions between terpenoid mosquito repellents and human-secreted attractants

Molecular interactions between terpenoid mosquito repellents and three typical human-secreted attractants, ammonia, 1-octen-3-ol, and formic acid were studied. Relative energies, bond distances, and bond angles of the molecular interactions were obtained at HF level to evaluate the interaction intensity and types. The effects of molecular interactions on repellency were investigated by the subsequent quantitative structure–activity relationship (QSAR) study. The results of this study suggest that attractant–repellent interaction should not be ignored and could be helpful for future research on the repelling mechanism of mosquito repellents.