Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide

Summary The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 s at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.     

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules

Summary A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with diferent force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.Abbreviations D diffusion constant in cm²/s - Er-2 pheromone 2 from Euplotes raikovi - GFlop one billion floating point operations per second - Grx(C14S)-SG mixed disulfide between a mutant E. coli glutaredoxin, with Cys¹⁴ replaced by Ser, and glutathione - MD molecular dynamics - NOE nuclear Overhauser enhancement - rmsd root-mean-square deviation - density in g/cm³     

Isolation of carp cDNA clones,representing developmentally-regulated genes,using a subtractive-hybridization strategy

A subtractive-hybridization technique, combined with differential screenings and subsequent whole mount in situ hybridization (ISH) reactions, was used to isolate novel cDNA clones representing developmentally-regulated genes of carp. Small-scale differential screenings of an oocyte and a segmentation-stage cDNA library using oocyte-specific and segmentation stage-specific enriched probes, yielded 75 positive clones. ISH screening showed that 65% (15) of the oocyte-stage clones and 50% (26) of the segmentation-stage clones were indeed stage-specific. Partial sequence analysis suggests that approximately 65% of the 41 stage-specific clones represent novel genes. In addition, an Otxl clone was isolated. Two novel clones and the Otxl clone are of special interest for developmental studies. The clones represent genes that are locally expressed during embryonic development. The expression patterns of Otxl and one of the novel clones suggest functions in specification of the anterior-posterior axis. The three clones provide molecular markers for the study of gastrulation and the patterning of the a-p axis in teleosts.     

HCV5＇端非编码区cDNA的体外转录

采用逆转录聚合酶链反应（ＲＴ－ＰＣＲ）从广东省一例慢性丙型肝炎病人血清中获得丙型肝炎病毒（ＨＣＶ）５＇端非编码区（５＇ＮＣＲ）３０２ｂｐ的ｃＤＮＡ片段,经补齐和提纯后插入ｐＵＣ１９质粒,获得的重组体ｐＵＮ进行序列测定。将ｐＵＮ的目的基因亚克隆进体外转录载体ｐＳＰＯＲＴＩ多克隆位点的ＥｏｏＲＩ和ＰｓｔＩ切点之间,所得重组体ｐＳＮ线性化后由Ｔ＿７ＲＮＡ多聚酶及ＳＰ６ＲＮＡ多聚酶引导体外转录反应,产物经凝胶电泳及特异引物ＲＴ－ＰＣＲ,证实ＳＰ６引导的是正义ＲＮＡ,Ｔ７合成的是反义ＲＮＡ,其大小分别力４２９ｂｐ和３６２ｂｐ。并证实所得ＲＮＡ力ＨＣＶ５＇ＮＣＲｃＤＮＡ转录而来。获得的ＨＣＶ５＇ＮＣＲｃＤＮＡ和ＲＮＡ在常规逆转录和ＰＣＲ步骤中用于设立有效的模板对照,对消除假用性及评估试剂有重要意义。同时,ＨＣＶ５＇ＮＣＲ体外转录载体的构建可用于制各ＲＮＡ探针和反义ＲＮＡ,改进后还可作为定量ＰＣＲ的竞争性模板。     

Development of a new method for obtaining osteoclasts from endosteal surfaces

Summary Techniques for the isolation of ahhighly pure population of viable osteoclasts are limited. For this reason, we developed an isolation procedure that results in a high yield of osteoclast-like cells, up to 92% pure, from 3-wk-old chicken tibias. The unique feature of the method is the migration of cells from marrow-free endosteal surfaces to vitronectin-coated plates. The cells retain the osteoclast phenotype and remain viable in culture for a minimum of 1 wk. The cells were characterized and compared to two populations of authentic avian osteoclasts, which were isolated on the basis of association with fibronectin-coated plates. The cells contained substantial amounts of tartrate-resistant acid phosphatase. Alkaline phosphatase levels were negligible, suggesting little contamination by osteoblasts. Response to parathyroid hormone, dibutyryl cyclic adenosine monophosphate, calcitonin, acetazolamide, 17β-estradiol, and prostaglandin E₂ was evident, as detected by measuring acid production. The vitronectin-associating cells contained numerous mitochondria, had the ability to resorb bone in anin vitro bone slice assay, and specifically bound biotinylated vitronectin. At 5 d of culture, the cells demonstrated marginal multinuclearity, having two to three nuclei. A large number (∼1×10⁶ cells/tibia) of viable cells that exhibit characteristics of authentic osteoclasts can be obtained by the method described. Potentially, this method could be applied to other species.     

限制性核酸内切酶Bsp 63Ⅰ的纯化及性质研究

用Ｂａｃｉｌｌｕｓｓｐｈａｅｒｉｃｕｓ６３菌为材料,经ＤＮＡ－Ｓｅｐｈａｒｏｓｅ和ＣｉｂａｃｒｏｎＢｌｕｅＦ３ＧＡ－Ｓｅｐｈａｒｏｓｅ两步亲和层析,将Ｂｓｐ６３Ⅰ纯化到均一程度。酶比活力达６１４００Ｕ／ｍｇ蛋白。用凝胶过滤法测得该酶分子量为１１３８００。该酶样品在ＳＤＳ－ＰＡＧＥ中呈现为一条蛋白带,并测得其亚基分子量为５６８００。用ＤＮＳ－Ｃｌ法测得该酶Ｎ－末端氨基酸为丙氨酸。上述结果表明该酶分子是由两个相同亚基组成。     

鼠肝DNA甲基化酶的纯化及物理化学性质的研究

以Ｗｉｓｔａｒ大鼠肝为材料,确立了一个简便的纯化鼠肝ＤＮＡ甲基化酶的程序,包括：细胞的超声破碎、去内源核酸、硫酸铵盐析、磷酸纤维素亲和层析、ＤＥＡＥ－ＳｅｐｈａｄｅｘＡ－５０柱层析及ＳｅｐｈａｄｅｘＧ－１５０凝胶过滤。用不同浓度聚丙烯酰胺凝胶电泳和孔梯度凝胶电泳检测,纯化后的酶已达电泳均一,且酶的比活力提高１１２倍。以聚丙烯酰胺孔梯度凝胶电泳测得其天然酶的分子量为３６５ｋＤ,以ＳＤＳ－聚丙烯酰胺凝胶电泳测得该酶有两种亚基,大亚基为９５ｋＤ,小亚基为８５ｋＤ,推测该酶由两个大亚基和两个小亚基组成。     

The Influence of Genotype and Environment on the Physiological and Metabolic Diversity ofFusarium compactum

Talbot, N. J., Vincent, P., and Wildman, H. G. 1996. The influence of genotype and environment on the physiological and metabolic diversity ofFusarium compactum. Fungal Genetics and Biology20,254–267. Fungal species produce a large variety of secondary metabolites which are of considerable interest to the pharmaceutical industry. It is clear that the secondary metabolite production of a species varies significantly in strains from different geographic locations and from different habitats. The influence of genotype and environment on metabolite production is, however, poorly understood. In this study we examined the influence of genotypic variability, physiological variability, environmental location, and habitat on metabolite production byFusarium compactum.Isolates of the fungus from two geographic locations and two distinct habitat types were examined for growth on 95 different carbon sources, and genotypic variability was determined using RAPDs and rDNA–RFLP analysis. In a blind test secondary metabolite production was assessed using HPLC profiles of methanolic cell extracts. A number of correlations were observed between genotypic groupings, as determined using parsimony, and specific metabolite production. Similar correlations were also observed with physiological groups although genotypic analysis proved to be a more sensitive predictor of metabolite variability. The data suggest a complex relationship between environment, genotype, and metabolite production but highlight the use of genetic screening as a means of optimizing the chances of identifying a wide range of metabolites from a given species.     

Tagging and mapping the thermo-sensitive genic male-sterile gene in rice (Oryza sativa L.) with molecular markers

The thermo-sensititve genic male-sterile (TGMS) gene in rice can alter fertility in response to temperature and is useful in the two-line system of hybrid rice production. However, little is known about the TGMS gene at the molecular level. The objective of this study was to identify molecular markers tightly linked with the TGMS gene and to map the gene onto a specific rice chromosome. Bulked segregant analysis of an F₂ population from 5460s (a TGMS mutant line) x Hong Wan 52 was used to identify RAPD markers linked to the rice TGMS gene. Four hundred RAPD primers were screened for polymorphisms between the parents and between two bulks representing fertile and sterile plants; of these, 4 primers produced polymorphic products. Most of the polymorphic fragments contained repetitive sequences. Only one singlecopy sequence fragment was found, a 1.2-kb fragment amplified by primer OPB-19 and subsequently named TGMS1.2. TGMS1.2 was mapped on chromosome 8 with a RIL population and confirmed by remapping with a DHL population. Segregation analysis using TGMS1.2 as a probe indicated that TGMS1.2 both consegregated and was lined with the TGMS gene in this population. It is located about 6.7 cM from the TGMS gene. As TGMS1.2 is linked to the TGMS gene, the TGMS gene must be located on chromosome 8.This research was supported by the Rockefeller Foundation and China National High-Tech Research and Development Program. The first author is a Rockefeller Career Fellow at Texas Tech University