分子系统学在微体古生物及相关领域中的应用

核酸（ＤＮＡ和ＲＮＡ）和蛋白等生物大分子（尤其是它们的序列资料）可作为重要的生物性状用于系统分类和演化等主题的研究。相对于形态学性状而言,分子性状不仅是前者的补充,而且具有许多前者无法比拟的优点;比如ＤＮＡ作为遗传信息的直接载体能较准确地反映生物类群之间的系统发生关系、信息量巨大、易于定量化和进行计算机分析等等。分子古生物研究包含两个方面：一、发掘化石生物分子,以提供历史生物界演化过程中的直接遗传学证据以及检验分子演化速率等方面的独特数据;二、利用现代分子生物学数据,探讨化石生物界的系统发生问题。上述两个研究方向均已成为当今演化生物学领域的热点。有孔虫等具有重要化石记录的微体生物的分子系统学研究已经开始。随着现生的和化石的生物分子资料的逐渐积累,预期在不久的将来,分子资料将成为微体古生物研究中不可缺少的重要数据之一。     

Molecular pathology in the diagnosis and treatment of non-Hodgkin's lymphomas

The non-Hodgkin's lymphomas encompass a wide spectrum of hematologic neoplasms that exhibit different clinical and biological features. Lymphomas classically have been initially assessed based on their cytologic and histologic features. Morphology alone is often inadequate as similar appearing neoplasms may be immunophenotypically and molecularly heterogeneous. Molecular diagnostic methods can provide an additional level of testing that not only helps refine diagnoses but can provide prognostic information. New methods are being refined that may provide information to establish precise diagnostic profiles, provide targets for therapy and provide more sensitive methods for monitoring the success of treatment. Molecular methods will be increasingly utilized and eventually required as the accepted method of diagnosis and for monitoring the disease. Understanding of the molecular abnormality and the pathogenesis of the neoplasm hopefully will lead to therapeutic intervention aimed at the specific molecular defect or its product. The molecular pathology of the non-Hodgkin's lymphomas is discussed.     

分子伴侣HdeA与底物蛋白SurA作用机制的模拟研究

分子伴侣HdeA与底物蛋白间的相互作用可帮助底物蛋白复性,这是肠道致病菌得以在酸性环境中幸存的重要原因之一.为探究HdeA发挥伴侣活性的作用机制,本研究采用分子对接和分子动力学的方法,模拟了HdeA与底物蛋白SurA间的相互作用,计算了二者的结合自由能.通过分析HdeA-SurA复合物体系的作用模式、氢键作用以及能量分解的结果,确定了HdeA与底物蛋白SurA结合时发挥重要作用的关键氨基酸残基.该研究结果为以后采用实验手段探究HdeA与底物蛋白之间的作用提供了重要的理论参考,同时为今后设计与开发HdeA的抑制剂提供了理论指导依据.     

Hydrophobic patches on the surfaces of protein structures

A survey of hydrophobic patches on the surface of 112 soluble, monomeric proteins is presented. The largest patch on each individual protein averages around 400 Ų but can range from 200 to 1,200 Ų. These areas are not correlated to the sizes of the proteins and only weakly to their apolar surface fraction. Ala, Lys, and Pro have dominating contributions to the apolar surface for smaller patches, while those of the hydrophobic amino acids become more important as the patch size Increases. The hydrophilic amino acids expose an approximately constant fraction of their apolar area independent of patch size; the hydrophobic residue types reach similar exposure only in the larger patches. Though the mobility of residues on the surface is generally higher, it decreases for hydrophilic residues with Increasing patch size. Several characteristics of hydrophobic patches catalogued here should prove useful in the design and engineering of proteins. © 1996 Wiley-Liss, Inc.     

纳米狭缝中Aβ蛋白构象变化的间距作用

目的 金属表面对蛋白质分子具有吸附作用,然而在纳米尺度内,蛋白质分子构象受到狭缝的间距作用尚未明确。本文通过在分子动力学模拟中建立不同间距的金原子层,研究纳米级金属狭缝中蛋白质分子构象变化。方法 使用GOIPCHARMM力场在Au (111)金原子界面间对Aβ1-42蛋白单体进行分子动力学仿真,研究无狭缝的水溶液环境下和由5.0、5.5以及8.5 nm狭缝结构与Aβ蛋白相互作用及蛋白质构象变化。结果 当金狭缝结构间距从5.0 nm增加到8.5 nm,Aβ蛋白分子与两侧金层相互作用可由单表面吸附、双表面吸附过渡到无吸附。结论 Aβ蛋白分子在金狭缝结构中与表面发生相互作用,随狭缝间距和蛋白质分子距界面距离的变化,蛋白质分子的状态可能表现为单表面吸附、双表面吸附和无吸附3种状态。     

分子表面的计算机表示

提出了一种用于生成分子光滑表面的新算法.该算法从分布在一个包含整个分子表面的椭球上的三角网络开始,逐步收缩网络直到所有的三角形最佳贴近分子表面.所使用的收缩包络椭球的技术只要稍加修改就可用于蛋白质空腔的表示.     

The selectivity of protein‐imprinted gels and its relation to protein properties: A computer simulation study

Polymer‐based protein recognition systems have enormous potential within clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. Imprinted polymer matrices have been extensively studied and applied as a simple technique for creating artificial polymer‐based recognition gels for a target molecule. Although this technique has been proven effective when targeting small molecules (such as drugs), imprinting of proteins have so far resulted in materials with limited selectivity due to the large molecular size of the protein and aqueous environment. Using coarse‐grained molecular simulation, we investigate the relation between protein makeup, polymer properties, and the selectivity of imprinted gels. Nonspecific binding that results in poor selectivity is shown to be strongly dependent on surface chemistry of the template and competitor proteins as well as on polymer chemistry. Residence time distributions of proteins diffusing within the gels provide a transparent picture of the relation between polymer constitution, protein properties, and the nonspecific interactions with the imprinted gel. The pronounced effect of protein surface chemistry on imprinted gel specificity is demonstrated.     

Imaging gene expression using oligonucleotides and peptide nucleic acids

The development of methods for non-invasive, real-time imaging of gene expression would provide powerful tools for biomedical research and medical diagnostics. A broadly applicable strategy for achieving this goal is the use of complementary oligonucleotide probes for recognition of mRNA. The major challenge for molecular imaging is the development of specific and efficient transducers for signaling probe-target interaction. This review summarizes the strengths and limitations of reported molecular approaches for imaging of mRNA expression and discusses the challenges to development of in vivo methods.     

The molecular reaction vessels for a transesterification process created by molecular imprinting technique

A polymeric catalyst was synthesized by co-polymerizing 4(5)-vinylimidazole and itaconic acid with trimethylpropanol trimethacrylate micro spheres. The catalyst obtained catalysed the transesterification process between p-nitrophenyl acetate and hexanol with maximal initial velocity(nu(max)) of 4.73 +/- 0.47 microM min(-1) mg(-1), and turnover rate (k(cat)) of 8.67 min(-1). Using p-nitrophenyl acetate as template, molecular imprinting process enhanced the nu(max) of the polymeric catalyst 3-fold. Each imprinted site can be considered as a single molecular reaction vessel, and achieved a k(cat) of 169 min(-1) towards the conversion of p-nitrophenyl acetate in hexanol.     

Molecular magnetic materials from polyoxometalates

The significance of polyoxometalates in the field of molecular magnetism is discussed. We show that this kind of inorganic complexes provides remarkable examples for the study of the exchange interactions in clusters. On the other hand, we examine the possibility of using these metal oxide anions as magnetic components of molecular materials containing organic tetrathiafulvalenes as electron donor molecules.     

P-糖蛋白结构及作用机制

ABC (ATP-binding cassette) 转运蛋白广泛存在于各种生物体细胞中,例如细菌的内层细胞浆膜和真核生物的细胞膜和细胞器膜.其利用与ATP的结合和水解供能进行底物的跨膜转运,其中一部分ABC转运蛋白能转运多种疏水性分子.P-糖蛋白隶属于ABC转运蛋白超家族,是研究最为透彻的一员,主要功能是防止机体对外来有害物质的摄入.P-糖蛋白(P-glycoprotein)由4 个基本结构域组成,2 个跨膜区和2 个位于细胞浆内的核苷酸结合区.核苷酸结合区参与ATP的结合和水解,而各由6 个α 跨膜螺旋组成的2个跨膜区联合构成了底物跨膜转运的通道.P 糖蛋白能转运多种不同结构的底物,包括脂类、胆汁酸、多肽和外源性化学物质,这对机体的生存至关重要,但同时也存在不利的一面,包括干扰了药物的运输,从而导致了多药耐药现象的产生.本文就P-糖蛋白的分子结构和作用机制的最新研究进展进行综述.     

Identification of the PcrA DNA helicase reaction pathway by applying advanced targeted molecular dynamic simulations

PcrA DNA helicase uses the free energy of hydrolysis and binding of ATP to unwind double-stranded DNA (ds-DNA). There are two states of PcrA, termed the substrate and product complexes and, through the conformational changes between these two states, PcrA moves along ds-DNA and separates the two strands. In this study, two different methods, namely chain minimisation (CM, less reliable method) and auto targeted molecular dynamic (TMD) simulation (more reliable), were performed to generate two different initial reaction pathways between these two states, and then fixed root mean square distance (RMSD) TMD simulation was performed to optimise these two initial pathways. In general, the two optimised pathways share very similar major conformational changes, but are different in the minor motions. The potential energy profiles of the two improved pathways are generally similar, but the one generated by the improved TMD path is slightly lower. Considering the poor reliability of the initial path generated by CM and insignificant improvements of the auto-TMD path, our study suggests that fixed RMSD TMD simulation can generate reliable reaction pathways, but the different initial paths still have some influence on the detailed conformational analysis.     

Sitting above the maze: recent model discoveries in molecular science

The 2013 Nobel Prize in Chemistry has convinced the world that how important the role that computational sciences play in chemical and materials sciences. In this review, computational methods and rational molecule design, including quantum mechanics and molecular mechanics methods, have been applied to study electronic structures and the interactions in a number of important applications at molecular level. The applications which include bioactive compounds, drug candidates and photoactive molecules at Swinburne University in the past several years are discussed. The research is in close collaboration with world class experimental groups from spectroscopy, organic and medicinal synthesis laboratories and most recently to γ-ray spectroscopy as well as other theory groups in the world. Ionisation spectra of biomolecules and bioactive compounds including amino acids, DNA bases, cyclic dipeptides, drug candidates, complexes and photoactive molecules are discussed. Most recent projects such as infrared spectral studies of ferrocene, rational design of organic dyes in solar cell applications, and recent development in γ-ray spectra of positron annihilation in molecules are highlighted.     

Training in molecular cytopathology testing

Training in molecular cytopathology testing is essential in developing and maintaining skills in modern molecular technologies as they are introduced to a universal health care system such as extant in the UK and elsewhere. We review the system in place in Northern Ireland (NI) for molecular testing of solid tumours, as an example to train staff of all grades, including pathologists, clinical scientists, biomedical scientists and equivalent technical grades. We describe training of pathologists as part of the NI Deanery medical curriculum, the NI training programme for scientists and laboratory rotation for Biomedical Scientists. Collectively, the aims of our training are two‐fold: to provide a means by which individuals may extend their experience and skills; and to provide and maintain a skilled workforce for service delivery. Through training and competency, we introduce new technologies and tests in response to personalised medicine therapies with a competent workforce. We advocate modifying programmes to suit individual needs for skill development, with formalised courses in pre‐analytical, analytical and postanalytical demands of modern molecular pathology. This is of particular relevance for cytopathology in small samples such those from formalin‐fixed paraffin‐embedded cell blocks. We finally introduce how university courses can augment training and develop a skilled workforce to benefit the delivery of services to our patients.     

Hsp90 and co‐chaperones twist the functions of diverse client proteins

Hsp90 molecular chaperones are required for the stability and activity of a diverse range of client proteins that have critical roles in signal transduction, cellular trafficking, chromatin remodeling, cell growth, differentiation, and reproduction. Mammalian cells contain three types of Hsp90s: cytosolic Hsp90, mitochondrial Trap‐1, and Grp94 of the endoplasmic reticulum. Each of the Hsp90s, as well as the bacterial homolog, HtpG, hydrolyze ATP and undergo similar conformational changes. Unlike the other forms of Hsp90, cytosolic Hsp90 function is dependent on a battery of co‐chaperone proteins that regulate the ATPase activity of Hsp90 or direct Hsp90 to interact with specific client proteins. This review will summarize what is known about Hsp90's ability to mediate the folding and activation of diverse client proteins that contribute to human diseases, such as cancer and fungal and viral infections. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 211–217, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

植物分子系统地理学及其研究进展

系统地理学这个概念框架来源于早期对线粒体DNA(mitochondrial DNA,mtDNA)的研究。随着系统地理学研究方法的不断拓展和分子生物学实验技术的渗透,出出了一门新的交叉学科——分子系统地理学(Mokcular phylogeography)。本文简述了分子系统地理学的发展简史和植物分子系统地理学研究常用的分子标记,回顾了近年来植物分子系统地理学方面的研究进展以及存植物研究中的应用。并对植物分子系统地理学研究进行了展望。     

Standardized nonculture techniques recommended for European reference laboratories

Culture-confirmed diagnosis of meningococcal invasive infections is often hindered by early antibiotic treatment. Nonculture molecular standardized methods are now essential tools for the immediate management of meningococcal infections. The European Monitoring Group on Meningococci (EMGM) recommends the following measures. (1) The implementation of standardized protocols of extraction methods for DNA isolation from clinical specimens for PCR-based identification and genogrouping of Neisseria meningitidis. (2) The use of molecular approaches (sequencing of target genes) for the determination of meningococcal susceptibility to antibiotics, such as sequencing of penA and rpoB genes for susceptibility to penicillin G and rifampicin, respectively. (3) The use of nonculture strain characterization by multilocus sequence typing (MLST) and sequence typing of porA and fetA. These approaches can be implemented either by individual reference laboratories or through collaboration and referral between centres.