Integrating experimental data with molecular simulations to investigate RNA structural dynamics

Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule Förster resonance energy transfer, or even thermal or mechanical denaturation experiments probe RNA dynamics at different time and space resolutions. Their combination with accurate atomistic molecular dynamics (MD) simulations paves the way for quantitative and detailed studies of RNA dynamics. First, experiments provide a quantitative validation tool for MD simulations. Second, available data can be used to refine simulated structural ensembles to match experiments. Finally, comparison with experiments allows for improving MD force fields that are transferable to new systems for which data is not available. Here we review the recent literature and provide our perspective on this field.     

The progress of DNA analyzing techniques and its impact on plant molecular systematics

Recent advances in manipulating nucleic acids have opened a new research field called plant molecular systematics. This short review provides an overview of molecular techniques which have been used in the analysis of DNA molecules for the study of plant systematics, with a special emphasis on PCR. The early application of DNA analysis, DNA/DNA hybridization, has not become popular with plant systematists, because of several disadvantages inherent in the method. The survey of restriction fragment length polymorphisms (RFLPs), on the contrary, has become one of the preferred methods used by plant molecular systematists, since the method is relatively easy to perform. Although unambiguous data can be obtained by both long-range restriction mapping and nucleotide sequencing, these approaches may have limited use in plant molecular systematics because of their laborious experimental procedures relying on conventional molecular cloning techniques. To date, PCR based analyses of the DNA molecule seem to be the most suitable experimental approach for plant molecular systematics. Several advantages of the method have changed both the quality and quantity of the DNA data. Further application of PCR to plant molecular systematics will open up a new era in the field. The present paper is based on the contribution which was read in a symposium entitled “Organellar DNA Variations in Higher Plants and their Taxonomic Significance”, at the 50th Annual Meeting of the Botanical Society of Japan in Shizuoka on October 2, 1990, under the auspices of the Japan Society of Plant Taxonomists.     

我国巢鼠属分类和分子系统学分析

本研究对2018至2021年采集的9号巢鼠(Micromys minutus)标本、22号红耳巢鼠(M. erythrotis)标本和19号待厘定的巢鼠属标本,进行形态分类和分子系统学分析,进一步揭示我国巢鼠属的分类和系统分化问题。待厘定的巢鼠属标本形态特征为：标本体背毛黑棕,体腹毛基灰色,毛尖灰白,体侧毛色具明显区分,尾背部毛色黑棕,尾腹部毛色灰棕色;尾长长于头体长的120%;头骨背面观可见颧弓明显弯曲;颅全长[(18.59 ± 0.48)mm]和颅基长[(17.43 ± 0.48 mm)]较长,腭长[(9.35 ± 0.11)mm]较长,脑颅高[(7.43 ± 0.06)mm]较高。待厘定的巢鼠属标本形态特征与巢鼠和红耳巢鼠均存在差异。待厘定巢鼠属标本与巢鼠和红耳巢鼠之间的遗传距离分别为0.115和0.136,接近于巢鼠与红耳巢鼠之间的遗传距离(0.126)。利用Cyt b基因全序列和核基因IRBP1、RAG1和RAG2序列分别构建的巢鼠属系统发生树均以较高的置信度分化成3个进化支,即巢鼠、红耳巢鼠和待厘定的巢鼠属样本的进化支。形态学和分子系统学分析结果均支持待厘定的巢鼠属标本为独立物种分类单元,对应于文献记载的巢鼠川西亚种(M. m. pygmaeus)。根据产地、遗传距离和形态分化,建议将巢鼠川西亚种提升为种,命名为川西巢鼠(M. pygmaeus comb. nov.)。利用Cyt b基因全序列构建的巢鼠系统发生树分化成6个进化谱系：日韩谱系、欧洲谱系、俄罗斯新西伯利亚谱系、中国东北和俄罗斯远东谱系、中国安徽谱系和中国台湾谱系。     

Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure

Summary A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived from complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect (NOE) spectral peak intensities. As in the case of restrained molecular dynamics (rMD) refinement of structures, the experimental distance restraints and bounds are incorporated as a pseudo-energy term (or penalty function) into the mathematical expression for the molecular energy. However, the use of generalized helical parameters, rather than Cartesian coordinates, to define DNA conformation increases efficiency by decreasing by an order of magnitude the number of parameters needed to describe a conformation and by simplifying the potential energy profile. The Metropolis Monte Carlo method is employed to simulate an annealing process. The rMC method was applied to experimental 2D NOE data from the octamer duplex d(GTA-TAATG)·d(CATTATAC). Using starting structures from different locations in conformational space (e.g. A-DNA and B-DNA), the rMC calculations readily converged, with a root-mean-square deviation (RMSD) of <0.3 Å between structures generated using different protocols and starting structures. Theoretical 2D NOE peak intensities were calculated for the rMC-generated structures using the complete relaxation matrix program CORMA, enabling a comparison with experimental intensities via residual indices. Simulation of the vicinal proton coupling constants was carried out for the structures generated, enabling a comparison with the experimental deoxyribose ring coupling constants, which were not utilized in the structure determination in the case of the rMC simulations. Agreement with experimental 2D NOE and scalar coupling data was good in all cases. The rMC structures are quite similar to that refined by a traditional restrained MD approach (RMSD<0.5 Å) despite the different force fields used and despite the fact that MD refinement was conducted with additional restraints imposed on the endocyclic torsion angles of deoxyriboses. The computational time required for the rMC and rMD calculations is about the same. A comparison of structural parameters is made and some limitations of both methods are discussed with regard to the average nature of the experimental restraints used in the refinement.Abbreviations MC Monte Carlo - rMC restrained Monte Carlo - MD molecular dynamics - rMD restrained molecular dynamics - DG distance geometry - EM energy minimization - 2D NOE two-dimensional nuclear Overhauser effect - DQF-COSY double-quantum-filtered correlation spectroscopy - RMSD root-mean-square deviation To whom correspondence should be addressed.     

Molecular mimicry in Lyme disease: monoclonal antibody H9724 to b. burgdorferi flagellin specifically detects chaperonin-HSP60

A monoclonal antibody (H9724), specific for the 41-kDa flagellar protein of the Lyme disease pathogen Borrelia burgdorferi, cross-reacts with human axons and detects one major protein in human neuroblastoma cell extracts. The homologous cross-reacting protein has now been isolated from calf adrenal and identified as chaperonin-HSP60 by N-terminal sequencing.     

越南槐根的抗HIV活性成分研究

为研究越南槐(Sophora tonkinensis)根的抗HIV蛋白酶活性成分及其分子对接机制,采用硅胶、MCI、Sephadex LH-20等多种色谱分离方法,对越南槐根的化学成分进行分离,采用HIV蛋白酶对化合物进行体外抗HIV活性筛选,运用分子对接手段初步探究活性化合物与HIV-1蛋白酶的结合机制。结果表明,从越南槐中共分离得到8个化合物,根据波谱数据分别鉴定为三叶豆紫檀苷(1)、苦参碱(2)、N-acetylnicotinamide (3)、2′-O-甲基腺苷(4)、毛蕊异黄酮苷(5)、玫瑰花苷(6)、环广豆根素(7)、芒柄花苷(8),此外还分离得到塑化剂衍生物邻苯二甲酸二(2-乙基)己酯(9)和邻苯二甲酸二异丁酯(10)。抗HIV蛋白酶活性测试显示化合物1和2的IC50分别为13.2和38.6μg/m L,分子对接表明其与HIV蛋白酶有一定的结合作用。化合物3～5为首次从该植物中分离得到,化合物1和2显示中等的抗HIV蛋白酶活性。     

Phylogenomic study of Amorphophallus (Alismatales; Araceae): When plastid DNA gene sequences help to resolve the backbone subgeneric delineation

Encompassing ca. 200 species distributed in paleotropical Africa and Asia, Amorphophallus is one of the largest genera of Araceae. In spite of the great economic interest in its glucomannan production, only a few studies have attempted to grasp the evolutionary history of this genus. In the current state of knowledge, four main clades, mostly linked to biogeographical delineation, have been identified from phylogenies based on a few genes. However, relationships among and within these clades still remain unclear, due to the rapid radiation that occurred during the early evolutionary history of the genus. Here, we generated genome skimming libraries for 43 specimens from 36 species distributed across the 4 clades, which allowed us to produce a phylogenetic matrix for a set of 71 plastid genes. Our phylogenies confirm the monophyly of these clades but show a new and well-resolved arrangement among these clades. Our analyses therefore provide a new scenario and timeline for the evolution of the main Amorphophallus clades, consistent with the morphological characteristics of the clades. The inferred scenario is also in agreement with climate dynamics and the onset of long-distance dispersal by the earliest migratory birds near the Oligocene/Miocene transition around 23 million years ago. Our study provides an up-to-date baseline to understand biogeographic and ecological processes that shaped the current diversity and distribution of Amorphophallus, paving the way for larger-scale phylogenomic studies based on plastid and nuclear genomes.     

Using Molecular Dynamics to Predict Factors Affecting Binding Strength and Magnetic Relaxivity of MRI Contrast Agents

We demonstrate the use of molecular dynamics and molecular mechanics methods to calculate properties and behavior of metal-chelate complexes that can be used as MRI contrast agents. Static and dynamic properties of several known agents were calculated and compared with experiment. We calculated the static properties such as the q-values (number of inner shell waters) and binding distances of chelate atoms to the metal ion for a set of chelates with known X-ray structure. The dynamic flexibility of the chelate arms was also calculated. These computations were extended to a series of exploratory chelate structures in order to estimate their potential as MRI contrast agents. We have also calculated for the first time the NMR relaxivity of an MRI contrast agent using a long (5 nsec) molecular dynamics simulation. Our predictions are promising enough that the method should prove useful for evaluating novel candidate compounds before they are synthesized. One novel static property, the projected area of chelate atoms onto a virtual surface centered on the metal ion (gnomonic projection), was found to give an effective measure of how well the chelate atoms use the free space around the metal ion.     

Exploiting the complete yeast genome sequence

The completion of the genome sequence of the budding yeast Saccharomyces cerevisiae marks the dawn of an exciting new era in eukaryotic biology that will bring with it a new understanding of yeast, other model organisms, and human beings. This body of sequence data benefits yeast researchers by obviating the need for piecemeal sequencing of genes, and allows researchers working with other organisms to tap into experimental advantages inherent in the yeast system and learn from functionally characterized yeast gene products which are their proteins of interest. In addition, the yeast post-genome sequence era is serving as a testing ground for powerful new technologies, and proven experimental approaches are being applied for the first time in a comprehensive fashion on a complete eukaryotic gene repertoire.