Determination of the backbone torsion angle ɛ in nucleic acids

Summary The multiplet structure of cross peaks in double-quantum-filtered COSY NMR spectra is analysed for those resonances that include passive heteronuclear couplings. Interestingly, the cross peak involving the sugar-ring protons H2 and H3 in nucleic acids display an E.COSY-type appearance exclusively when the backbone torsion angle (C4-C3-O3-P) adopts a gauche(-) conformation. This observation allows an unambiguous analysis of the conformation around , without the knowledge of ³J_cp coupling constants.     

锌离子对氨基酰化酶构象及其稳定性的影响

天然氨基酰化酶和脱谷氨基酰化酶无论在二级结构（用ＣＤ和ＦＴＩＲ监测）还是三级结构上（以荧光发射光谱监测）都有明显的差异,表明了脱锌后酶的有序度降低;当比较天然和脱锌氨基酸化酶对去圬剂的稳定性时,结果表明脱锌后酶的构象的稳定性明显降低．因此可以认为锌离子对维持酶分子活性部位的特定构象以及构象的稳定性具有重要的作用．     

Conformational properties of the —35 region of the trp promoter in solution: comparison of the wild-type sequence with an AT transversion

The majority of the ¹H NMR resonances of the protons in a tetradecamer containing the —35 region of the trp promoter d(GCTGTTGACAATTA): d(TAATTGTCAACAGC) and in the TA transversion have been assigned. The conformational properties of the nucleotides have been determined and compared in the two duplexes. Analysis of spin-spin coupling and NOES shows that all sugar puckers are in the south domain (i.e. near C2 endo) and the glycosidic torsion angles are anti (110°). The NMR data are consistent with the duplex being in the B family of conformations. Significant differences in chemical shifts between the two molecules were observed only for nearest neighbours to the transversion site, suggesting the absence of long range conformational effects. This was confirmed by the similarity of coupling constants and NOEs. Other properties are also not greatly affected at positions more than two base pairs from the mutation site. These results are consistent with the hypothesis that unconstrained oligonucleotides are highly flexible, and can readily accommodate significant perturbations of the local structure, such as a transversion.     

天然林内红松种群年龄更替数学模型及研究

本文给出天然林内红松种群年令更替数学模型（1）。通过对（1）进行定性分析,得到主要结论是：系统（1）在第一象限内存在唯一稳定周期解的充要条件是bk-bc-2d＞0其生态意义是天然林内红松幼树与母树随时间变化会产生一个有规律、互为消涨的变化特征。     

缢蛏碱性磷酸酶胍溶液中分子折叠与活力变化研究

报道了缢蛏碱性磷酸酶（简称ＡＬＰ）经不同浓度盐酸胍处理时酶的分子构象所发生的变化以及酶变化和失活的动力学过程。在胍中酶荧光发射峰强度下降,紫外差光谱在２４６ｎｍ和２８５ｎｍ处出现２个负峰,ＣＤ谱中酶的α螺旋度下降,且随浓度增大,变化程度也加大。动力学研究表明,酶在０．５ｍｏｌ／Ｌ、１．０ｍｏｌ／Ｌ、２．０ｍｏｌ／Ｌ３．０ｍｏｌ／Ｌ、４．０ｍｏｌ／Ｌ盐酸胍中的变性速度常数分别为３．２１×１０~（－４）ｓ~（－１）、６．３８×１０~（－４）ｓ~（－１）、２．１７×１０~（－３）ｓ~（－１）、２．３３×１０~（－３）ｓ~９－１）、５．１７×１０~（－３）ｓ~（－１）;而酶在相应盐酸胍中的失活速度常数分别为２．３３×１０~（－４）ｓ~（－１）、３．５７×１０~（－４）ｓ~（－１）、５．８６×１０~（－４）ｓ~（－１）、１．１４×１０~（－３）ｓ~（－１）、３．４５×１０~（－３）ｓ~（－１）;表现为失活与构象伸展变化基本平行。     

Conformational analysis of d-tubocurarine: Implications for minimal dimensions of its binding site within ion channels

All the minimum-energy conformations of d-tubocurarine were calculated by the method of molecular mechanics. The energy was minimized from 413 closed forms of the 18-member ring. The set of minimum-energy conformations includes 10 forms with energies less than 6 kcal/mol from the most stable one. Among the four lowest minimum-energy conformations, two forms correspond to those known from X-ray studies, whereas two conformations were not detected experimentally earlier. The flexibility of d-tubocurarine was estimated by calculating six paths of interconversion between the four lowest minimum-energy conformations. Using a molecular graphics technique, it was found that the most extended minimum-energy conformation of d-tubocurarine may fit in an ion channel of a rectangular profile of 8.7 × 11.2 Å, while one tetrahydroisoquinoline head may fit a profile as small as 6.9 × 11.0 Å. A possible model of d-tubocurarine location within the ion channel of the neuronal nicotinic acetylcholine receptor is suggested.     

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.     

Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

Summary The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.To whom correspondence should be addressed.     

The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example

 The availability of NOE constraints and of the relative solution structure of a paramagnetic protein permits the use of pseudocontact shifts as further structural constraints. We have developed a strategy based on: (1) determination of the χ tensor anisotropy parameters from the starting structure; (2) recalculation of a new structure by using NOE and pseudocontact shift constraints simultaneously; (3) redetermination of the χ tensor anisotropy parameters from the new structure, and so on until self-consistency. The system investigated is the cyanide derivative of a variant of the oxidized Saccharomyces cerevisiae iso-1-cytochrome c containing the Met80Ala mutation. The structure has been substantially refined. It is shown that the analysis of the deviation of the experimental pseudocontact shifts from those calculated using the starting structure may be unsound, as may the simple structure refinement based on the pseudocontact shift constraints only. Received: 11 July 1995 / Accepted: 30 October 1995     

Ce~（3＋）与G－肌动蛋白结合引起的构象变化及对聚合的影响

用Ａｅｄａｎｓ标记肌动蛋白单体Ｇ－Ａｃｔｉｎ上Ｃｙｓ３７４残基作为探针,研究了稀土离子Ｃｅ~（３＋）与Ｇ－Ａｃｔｉｎ的结合及引起的微构象变化。Ｃｅ~（３＋）在低浓度（Ｃｅ~（３＋）／Ａｃｔｉｎ摩尔比＜１）和Ｃａ~（２＋）竞争Ｇ－Ａｃｔｉｎ上二价离子的高亲合位点。Ｃｅ~（３＋）取代Ｃａ~（２＋）引起Ａｅｄａｎｓ荧光强度增强与Ｍｇ~（２＋）取代Ｃａ~（２＋）的结果相同。Ｃｅ~（３＋）／Ａｃｔｉｎ＞ｌ则导致Ａｅｄａｎｓ荧光强度下降。说明Ｃｅ~（３＋）在高低两种浓度条件下结合的位点及对Ｃｖｓ３７４的微构象的影响不同。时间分辩测得的Ａｅｄａｎｓ荧光寿命也支持这一结论。ＣＤ谱结果表明Ｃｅ~（３＋）／Ａｃｔｉｎ＜０．４,Ａｃｔｉｎ的二级结构增加,大于０．４又导致其失去。Ｃｅ~（３＋）－Ａｃｔｉｎ在有／无游离ＡＴＰ时用聚合液诱导的聚合结果表明,无游离ＡＴＰ时,极低浓度Ｃｅ~（３＋）促进聚合,高浓度虽有促进但有所减弱;有游离ＡＴＰ时,Ｃｅ~（３＋）／Ａｃｔｉｎ在实验范围内促进聚合。