蛋白质构象的可变性及其在胰岛素结构中的反映

我们对蛋白质三维结构的认识,主要来源于对蛋白质晶体的X射线衍射分析。应用该方法已测定了一百多个蛋白质分子的结构。这些结构分析表明,蛋白质分子具有一个特定的空间结构,并且是相当稳定的致密结构。蛋白质多肽链的卷曲方式,主要取决于非共价力。除了少数的二硫键外,蛋白质结构中有大量的次级键。水溶性蛋白质结构内部由空间上契合得很好的疏水氨基酸侧链组成,带电或极性侧链,除了为行使特殊的功能而藏于凹窝或沟槽的深处,一般都分布在分子的表面。由较长肽链组成的结构,常常可以被划分为相对独立的较稳定的结构域;而含有多条肽链的蛋白质,通常形     

嗜压蛋白氨基酸残基溶剂可及性对其稳定性的影响

【目的】研究嗜压微生物中蛋白质在不同结构区域的特点对了解其稳定的结构基础及设计新型嗜压酶具有重要意义。【方法】利用43对嗜压和非嗜压同源蛋白的晶体结构信息,将氨基酸所处结构分成3种:分子表面、中间区及内核区,统计了不同结构状态中氨基酸的差异。【结果】统计分析结果表明,嗜压蛋白具有明显的溶剂可及性结构特点:其分子表面Cys、Asp、Asn和Lys含量显著高于非嗜压蛋白,而Pro和Arg则相反;中间区域Ile、Met含量显著高,而Trp则相反;内核区Cys、Ile含量显著高,而Ala则相反。同时,非嗜压氨基酸在嗜压蛋白分子表面及内核区含量均显著高于非嗜压蛋白。【结论】嗜压和非嗜压蛋白在分子表面差异最为明显,将是改造嗜压酶的首选区域;同时,需要统计更多的样本,对氨基酸压力不对称指数进行修订。     

脂质筏在信号转导中的作用

细胞质膜对膜上受体的细胞外到细胞内的跨膜信号转导具有十分重要的意义。目前的研究表明膜上受体在介导跨膜信号转导时,通常是在细胞质膜上的胞膜窖和脂质筏结构中进行的。胞膜窖和脂质筏都是细胞膜上富含胆固醇和鞘磷脂的脂质有序结构域。其中,胞膜窖是一种有窖蛋白包被的特殊的脂质筏结构,通常在细胞膜上形成内陷的小窝。许多细胞膜上的受体都已经被发现位于胞膜窖和脂质筏中。同时,在脂质筏的胞质侧富集了大量的细胞内信号分子,这些信号分子集聚形成信号分子复合体,使得受体的细胞内结构域很容易就与大量的细胞内信号分子发生相互作用,为信号的起始和交叉作用提供了一个结构平台。     

高碱性pH诱导紫膜片层表面结构变化的原子力显微镜直接观测

报道了在高碱性pH下,紫膜中细菌视紫红质(BR)表面结构变化的直观信息.紫外可见光谱实验发现,当pH上升到12.6,BR分子上的生色团视黄醛脱落,分子完全变性;原子力显微镜实验观测到在此pH下,紫膜片层的晶格结构瓦解,BR分子在紫膜上无规则聚集,同时出现非特征“岛屿”结构和特征“岛屿”结构.     

多肽分子疏水性的电喷雾飞行时间质谱法快速测定

疏水作用是决定生物分子的结构和性质的重要因素,特别是在蛋白质的折叠,药物分子与受体(蛋白质、DNA等)的相互作用中起着关键作用.分子疏水性的强弱决定于分子内非极性基团的含量.在一定的实验条件下,电喷雾所获得的信号与多肽分子内非极性基团的面积呈现良好的相关性.因此,采用电喷雾飞行时间质谱法,在数分钟之内快速测定了不同多肽之间的疏水性,所获得结果与色谱法结果一致.     

植物环肽及其可能的生物合成途径

植物环肽是一个庞大的小分子天然产物家族,通常由4—10个氨基酸残基组合而成。该类化合物广泛存在于全球多种植物的根、茎、枝、叶及种子中,中草药中也时有发现。由于对其生物合成途径及机理研究较少,环肽分子的利用价值尚未得到有效的开发。和常见的非环状基因编码的多肽或蛋白质相比,环肽结构更为复杂。本文将对植物环肽的生物合成途径及其机理做初步探讨。     

真核生物mRNA非翻译区结构特征与mRNA翻译

真核生物中蛋白质合成通常在翻译水平受到调控,而mRNA非翻译区与mRNA翻译之间关系密切。真核生物mRNA非翻译区长度、mRNA二级结构、GC含量、顺式作用元件与反式作用因子、mRNA帽端结构和多聚腺苷酸尾等结构对翻译具有重要的调控作用。本文就真核生物mRNA非翻译区结构特征对其翻译的影响做一综述。     

环形RNA分子揭秘

环形RNA分子是一类不具有5'末端帽子和3'末端poly(A)尾巴、并以共价键形成环形结构的非编码RNA分子。利用针对环形结构RNA分子的实验和计算方法,并结合新一代高通量测序,现已在多种细胞内发现了大量环形RNA分子的稳定存在。目前,尽管环形RNA分子的产生机制及其代谢仍然不清楚,但是已有的研究表明环形RNA分子具有调控基因表达的功能。对环形RNA分子的产生机制和功能等的进一步研究,将为人们深入理解生命活动在转录水平的复杂性调控提供重要的分子基础和研究依据。     

核酸分子中碱基含量的计算

关于核酸分子中碱基含量的计算,在遗传学和高中生物教学中相当重要,但在教科书中通常没有专门讲述。我们根据碱基互补配对规律及中心法则进行归纳总结,从DNA结构、DNA复制、转录、翻译等方面探讨了DNA、RNA、蛋白质3者之间的关系,分析了核酸分子中碱基的含量。互核酸分子中碱基含量的计算1．且已知双链DNA分子中一种碱基的含量,推断其他碱基的含量：例1：一双链‘DNA分子中,（A－C）占碱基总量的Zo％。求A、T、G、C各占多少？解：在双链DNA分子中,据规律知,1．2由碱基含量推断核酸分子的结构——单链或双链、DNA或RNA…     

Molecular polytomies

This paper focuses on polytomies, especially molecular polytomies. The distinction between molecular and species polytomies is important, but is often not made. Likelihood ratio tests are an easier method for detecting molecular polytomies than other methods cited herein. Simulation shows that parsimony will generally falsely resolve molecular polytomies, which is worrisome because a simple mathematical model described herein predicts that molecular polytomies will occur often when the mean branch length is small. A test of the model using several real molecular data sets indicates that molecular polytomies may actually occur more often than predicted by the model. This suggests that at least some published molecular parsimony trees contain clades that are false resolutions of polytomies. Finally, a possible method for detecting species polytomies from molecular data is described.     

Heterogeneous genomic molecular clocks in primates

Using data from primates, we show that molecular clocks in sites that have been part of a CpG dinucleotide in recent past (CpG sites) and non-CpG sites are of markedly different nature, reflecting differences in their molecular origins. Notably, single nucleotide substitutions at non-CpG sites show clear generation-time dependency, indicating that most of these substitutions occur by errors during DNA replication. On the other hand, substitutions at CpG sites occur relatively constantly over time, as expected from their primary origin due to methylation. Therefore, molecular clocks are heterogeneous even within a genome. Furthermore, we propose that varying frequencies of CpG dinucleotides in different genomic regions may have contributed significantly to conflicting earlier results on rate constancy of mammalian molecular clock. Our conclusion that different regions of genomes follow different molecular clocks should be considered when inferring divergence times using molecular data and in phylogenetic analysis.     

The non-virus proteins associated with tobacco mosaic virus

1. Exhaustive fractionation of leaves from tobacco plants systemically infected with TMV has led to the isolation of two non-virus proteins, B3 and B6, and the detection of a third, A4, which do not occur in comparable uninfected plants. 2. Components B3 and B6 have been found consistently in a series of ten extracts from plants grown over an 18 month period in all seasons of the year. It is concluded that these components are as characteristic of the infected plant as TMV itself. 3. As they occur in the initial extracts, the non-virus proteins are of low molecular weight (S₂₀ ca. 3). On treatment, each component tends to form a high molecular weight polymer with an electrophoretic mobility considerably greater than that of the starting material. The high molecular weight derivatives of A4, B3, and B6 have been designated A8, B8, and B7 respectively. There is no evidence that these high molecular weight components occur as such in the infected leaf. 4. The non-virus proteins are free of nucleic acid and are not infectious. They cross-react immunochemically with TMV. 5. Compared with TMV content, the amounts of the non-virus proteins found in infected leaf are relatively small, falling in the range of 10 to 150 micrograms per gm. of tissue.     

Pitfalls in the molecular genetic diagnosis of Leber hereditary optic neuropathy (LHON).

Pathogenetic mutations in mtDNA are found in the majority of patients with Leber hereditary optic neuropathy (LHON), and molecular genetic techniques to detect them are important for the diagnosis. A false-positive molecular genetic error has adverse consequences for the diagnosis of this maternally inherited disease. We found a number of mtDNA polymorphisms that occur adjacent to known LHON-associated mutations and that confound their molecular genetic detection. These transition mutations occur at mtDNA nt 11779 (SfaNI site loss, 11778 mutation), nt 3459 (BsaHI site loss, 3460 mutation), nt 15258 (AccI site loss, 15257 mutation), nt 14485 (mismatch primer Sau3AI site loss, 14484 mutation), and nt 13707 (BstNI site loss, 13708 mutation). Molecular genetic detection of the most common pathogenetic mtDNA mutations in LHON, using a single restriction enzyme, may be confounded by adjacent polymorphisms that occur with a false-positive rate of 2%-7%.     

Coordinating Multi-Protein Mismatch Repair by Managing Diffusion Mechanics on the DNA

DNA mismatch repair (MMR) corrects DNA base-pairing errors that occur during DNA replication. MMR catalyzes strand-specific DNA degradation and resynthesis by dynamic molecular coordination of sequential downstream pathways. The temporal and mechanistic order of molecular events is essential to insure interactions in MMR that occur over long distances on the DNA. Biophysical real-time studies of highly conserved components on mismatched DNA have shed light on the mechanics of MMR. Single-molecule imaging has visualized stochastically coordinated MMR interactions that are based on thermal fluctuation-driven motions. In this review, we describe the role of diffusivity and stochasticity in MMR beginning with mismatch recognition through strand-specific excision. We conclude with a perspective of the possible research directions that should solve the remaining questions in MMR.     

Impaired light detection of the circadian clock in a zebrafish melanoma model

The circadian clock controls the timing of the cell cycle in healthy tissues and clock disruption is known to increase tumourigenesis. Melanoma is one of the most rapidly increasing forms of cancer and the precise molecular circadian changes that occur in a melanoma tumor are unknown. Using a melanoma zebrafish model, we have explored the molecular changes that occur to the circadian clock within tumors. We have found disruptions in melanoma clock gene expression due to a major impairment to the light input pathway, with a parallel loss of light-dependent activation of DNA repair genes. Furthermore, the timing of mitosis in tumors is perturbed, as well as the regulation of certain key cell cycle regulators, such that cells divide arhythmically. The inability to co-ordinate DNA damage repair and cell division is likely to promote further tumourigenesis and accelerate melanoma development.     

Uterine receptivity and the plasma membrane transformation

This review begins with a brief commentary on the diversity of placentation mechanisms, and then goes on to examine the extensive alterations which occur in the plasma membrane of uterine epithelial cells during early pregnancy across species. Ultrastructural, biochemical and more general morphological data reveal that strikingly common phenomena occur in this plasma membrane during early pregnancy despite the diversity of placental types--from epitheliochorial to hemochorial, which ultimately form in different species. To encapsulate the concept that common morphological and molecular alterations occur across species, that they are found basolaterally as well as apically, and that moreover they are an ongoing process during much of early pregnancy, not just an event at the time attachment, the term ‘plasma membrane transformation‘ is suggested which also emphasises that alterations in this plasma membrane during early pregnancy are key to uterine receptivity.     

Synchronized conformational fluctuations and binding site desolvation during molecular recognition

Binding site desolvation is a poorly understood prerequisite to ligand binding. Although structural fluctuations may be expected to have an important role, little is known about which fluctuations are important or the mechanism by which they promote desolvation. This investigation examines whether and how specific structural fluctuations contribute to desolvation of the ligand binding site in glycopeptide antibiotics. Backbone peptide group rotations in vancomycin, known to occur by experimental observation, were examined in this work with a two-dimensional adaptive umbrella sampling molecular dynamics simulation technique. Results indicate that energetic barriers to rotation are relatively small for two of the peptide groups intimately involved in ligand recognition. When they occur, these rotations strip water molecules away from key hydrogen bond donors and simultaneously cause significant distortions in the macrocyclic rings of the antibiotic that force water into and out of the binding site. Both events are intricately synchronized on the molecular level and have consequences that are clearly necessary to prepare the binding site for receiving a ligand. These results suggest that previously reported observations concerning structural dynamics and binding kinetics in these compounds are mechanistically linked, and they illustrate a heretofore unrecognized degree of preorganization, complexity, and synchronization that may be involved in specific molecular recognition. They also suggest that strategies for increasing antibiotic affinity through covalent dimerization may be counterproductive.     

The theory of everything and molecular evolution

The theory of everything is discussed in relationship to early bacterial molecular evolution. The emphasis is on time, space (or location at the molecular level), the universal construction kit (elements contained in periodic table) and change per units of time that were necessary for early bacterial molecular evolution to occur.