Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures

Summary Two modifications to the commonly used protocols for calculating NMR structures are developed, relating to the treatment of NOE constraints involving groups of equivalent protons or nonstereoassigned diastereotopic protons. Firstly, a modified method is investigated for correcting for multiplicity, which is applicable whenever all NOE intensities are calibrated as a single set and categorised in broad intensity ranges. Secondly, a new set of values for pseudoatom corrections is proposed for use with calculations employing centre-averaging. The effect of these protocols on structure calculations is demonstrated using two proteins, one of which is well defined by the NOE data, the other less so. It is shown that failure to correct for multiplicity when using r^-6 averaging results in overly precise structures, higher NOE energies and deviations from geometric ideality, while failure to correct for multiplicity when using r^-6 summation can cause an avoidable degradation of precision if the NOE data are sparse. Conversely, when multiplicities are treated correctly, r^-6 averaging, r^-6 summation and centre averaging all give closely comparable results when the structure is well defined by the data. When the NOE data contain less information, r^-6 averaging or r^-6 summation offer a significant advantage over centre averaging, both in terms of precision and in terms of the proportion of calculations that converge on a consisten result.Abbreviations HMG high mobility group - NOE nuclear Overhauser enhancement - NOESY nuclear Overhauser enhancement spectroscopy - rmsd root-mean-square deviation - YASAP yet another simulated-annealing protocol     

丝氨酸蛋白酶抑制剂的研究及应用

丝氨酸蛋白酶抑制剂（serpin）是一类结构、序列同源的蛋白酶抑制剂,它是体内许多蛋白水解级联反应的调节因子,其遗传性结构或分泌异常将导致许多疾病．因此对于其结构及作用机理的研究将为临床应用提供依据．     

城郊景观动态模型研究──以沈阳市东陵区为例

基于渗透理论、马尔柯夫过程理论,采用中性模型方法,建立了3个不同的城郊景观动态模型,模型中分别介入不同自然因子和决策因子.利用模型对研究区景观进行了动态变化模拟.对模拟结果进行了评价,评价方法与指标包括:1)多分辨率拟合分析;2)最近邻概率;3)斑块大小和数目.结果发现,综合介入决策因素和自然因子的模型具有最好的效果.     

不同育秧方式和插植密度下晚籼稻群体动态结构的研究

不同育秧方式和插植密度下晚籼稻群体动态结构存在差异。旱育秧群体分蘖速度快,分蘖能力强。稀植可促进个体分蘖多发、有效穗数增多,但旱育稀植并无分蘖早发的优势。旱育稀植使主茎基部叶片变短而上部叶片变长,生育后期叶面积消长平稳,地上部干物质积累较多。旱育秧、稀植都使主茎叶总数增多,全生育期延长。     

Chemical shifts and three-dimensional protein structures

Summary During the past three years it has become possible to compute ab initio the ¹³C, ¹⁵N and ¹⁹F NMR chemical shifts of many sites in native proteins. Chemical shifts are beginning to become a useful supplement to more established methods of solution structure determination, and may find utility in solid-state analysis as well. From ¹³C NMR, information on , and torsions can be obtained, permitting both assignment verification, and structure refinement and prediction. For ¹⁵N, both torsional and hydrogen-bonding effects are important, while for ¹⁹F, chemical shifts are primarily indicators of the local charge field. Chemical shift calculations are still slow, but shielding hypersurfaces — the shift as a function of the dihedral angles that define the molecular conformation — are becoming accessible. Over the next few years, theoretical and computer hardware improvements will enable more routine use of chemical shifts in structural studies, including the study of metal-ligand interactions, the analysis of drug and substrate binding and catalysis, the study of folding/unfolding pathways, as well as the characterization of conformational substates. Rather than simply being a necessary prerequisite for multidimensional NMR, chemical shifts and chemical shift non-equivalence due to folding are now beginning to be useful for structural characterization.     

Conformational studies of chemotactic HCO-Met-Leu-Phe-OMe analogues

Summary In order to investigate the proper peptide backbone conformation able to elicit a biological activity, HCO-Met-Pro-Phe-OMe, HCO-Met-[COO]Leu-Phe-OMe, and HCO-Met-OLeu-Phe-OMe, analogues of the prototypical chemotactic peptide HCO-Met-Leu-Phe-OMe, were studied by CD and IR techniques. The results obtained comparing biological and conformational data evidence the critical presence of (i) the NH group at position 2, (ii) a rather flexible backbone, (iii) the chemical structure of the central residue which can affect the stability of a possible active conformer.     

Differentiation of vegetation zones and species strategies in the subalpine region of Mt. Fuji

The floristic and structural differentiation of vegetation along the altitudinal gradient in four subalpine forests of different developmental stages on Mt. Fuji has been studied. Near the forest limit a micropattern of vegetation corresponding to the altitudinal zonation has been observed which elucidated the mechanisms of development of the vegetation zonation. As to early stages of vegetation development only two types can be distinguished: the volcanic desert above 1500 m and the pioneer forests below. As to later stages a differentiation of subzones includes from higher to lower altitudes: the Alnus maximowiczii, Betula ermanii, Abies veitchii and Tsuga diversifolia forests. Larix leptolepis and Sorbus americana ssp. japonica, appear as co-dominants in ecotonal communities between the principal subzones and are also important pioneers in early stages. Similarity analyses reveal that the upper subalpine Alnus-Betula forests can be regarded as early successional phases of the climax Abies-Tsuga forests of the lower subalpine zone. The regular arrangement of A. maximowiczii-B. ermanii-A. veitchii is studied along the gradient from the margin to the interior of the forest growing near the forest limit where locally favourable conditions prevail. Growth form, height growth, photosynthetic activity, seed supply, and seedling distribution of the three principal species have been compared, as well as biomass and production relations in contiguous forests of these species. The marginal Alnus type community is productive and disturbance-tolerant, and has a wide ecological and sociological amplitude along the gradient, while the central Abies community is accumulative and disturbance-intolerant, and has a narrower tolerance range, but is superior in competition under stable habitat conditions. A vegetation organization, ‘temporal multi-storeyed structure’, is suggested which means that a zonal pattern of vegetation within a climax region develops by successive replacement of successional species along an environmental gradient.     

Age-dependent changes in myogenic precursor cell compartment sizes. Evidence for the existence of a stem cell

Individual myogenic cells were isolated from the pectoralis muscles of chick embryos from days 8-14 of embryogenesis. When separately cloned, these cells produced three types of colonies in culture: (1) Positive: all cells in the clone were terminally differentiated muscle cells; (2) negative: no cells in the clone were terminally differentiated muscle; (3) mixed: some cells in the clone were terminally differentiated muscle. Positive clones from all ages tended to contain 2n cells (n = 0, 1, 2, 3, 4). Negative clones were found in all sizes and did not cluster around powers of 2 in cell number. Mixed clones were, by far, the most common type among those clones larger than 24 in cell number. Estimates of cell numbers in embryonic muscle tissue revealed that, while the numbers of cells in all myogenic compartments increased steadily with embryonic age, the number and percentage of precursor cells that produced large mixed clones increased dramatically. Subclones, prepared from populations of cells equivalent to large mixed clones, yielded both small positive and large mixed colonies. This indicated that the precursors to the large mixed clones were also precursors to the smaller positive clones. These observations suggest a model for the myogenic lineage in which there exists a stem cell that can generate, by a series of asymmetric divisions, cohorts of terminally differentiated muscle cells. The model can explain the asynchrony of production of terminally differentiated muscle cells both in vitro and in vivo.     

Fusion of phosphatidylserine and mixed phosphatidylserine-phosphatidylcholine vesicles Dependence on calcium concentration and temperature

Dynamic light scattering has been used to study the temperature dependence of Ca²⁺-induced fusion of phosphatidylserine vesicles and mixed vesicles containing phosphatidylserine and different phosphatidylcholines. The final vesicle size after Ca²⁺ and EDTA incubation serves as a measure of the extent of fusion. With phosphatidylserine vesicles, the extent of fusion shows a sharp maximum at an incubation temperature which depends on the Ca²⁺ concentration between 0.8 and 2 mM. The shift in the fusion peak temperature with Ca²⁺ concentration is similar to the typical shift in the phase transition temperature with divalent cation concentration in acidic phospholipids. The results suggest a direct correlation between the fusion peak temperature and the phase transition temperature in the presence of Ca²⁺ prior to fusion. With mixed vesicles containing up to 33% of a phosphatidylcholine in at least 2 mM Ca²⁺, the extent of fusion as a function of incubation temperature also shows a maximum. The fusion peak temperature is essentially independent of the quantity and type of phosphatidylcholine and the Ca²⁺ concentration, and identical to that with pure phosphatidylserine in excess Ca²⁺. The results imply that Ca²⁺-induced molecular segregation occurs first, and fusion subsequently takes place between pure phosphatidylserine domains.     

Molecular mechanisms of the origin of chromosome aberrations and the structural organisation of eukaryotic DNA

Summary A new hypothesis on the appearance of exchange chromosomal aberrations has been suggested. According to this hypothesis, temporal duplex polynucleotide structure should arise during G₁ and G₂ phases during the correction of DNA. The size of the duplex, as a rule, should be restricted to the size of complementary nucleotide sequences in the regions of repetitions. Any polynucleotide break in a duplex zone would result in chromosome breakage and if complementary broken ends interact with each other, then exchange chromosome aberrations may be formed. This hypothesis would explain such previously obscure phenomena as extremely high frequencies of exchanges after mutagen treatment, the nature of mitotic crossing-over, negative interference, change of aberration types before replication, the low frequency of damaged structural genes during aberration formation, etc.