Capping and alpha-helix stability

The first and last four residues of alpha-helices differ from the rest by not being able to make the intrehelical hydrogen bonds between the backbone greater than C=O groups of one turn and the greater than NH groups of the next. Physico-chemical arguments and statistical analysis suggest that there is a preference for certain residues at the C and N termini (The C- and N-caps) that can fulfil the hydrogen bonding requirements. We have tested this hypothesis by constructing a series of mutations in the two N-caps of barnase (Bacillus amyloliquefaciens ribonuclease, positions Thr 6 and Thr 26) and determining the change in their stability. The N-cap is found to stabilize the protein by up to approximately 2.5 kcal mol(-1). The presence of a negative charge of the N-cap adds some 1.6 kcal mol(-1) of stabilization energy because of the interaction with the macroscopic electrostatic dipole of the helix.     

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups.

Shortened forms of the group I intron from Tetrahymena catalyse sequence-specific cleavage of exogenous oligonucleotide substrates. The association between RNA enzyme (ribozyme) and substrate is mediated by pairing between an internal guide sequence on the ribozyme and a complementary sequence on the substrate. RNA substrates and cleavage products associate with a binding energy greater than that of base-pairing by approximately 4 kcal-mol-1 (at 42 degrees C), whereas DNA associates with an energy around that expected for base-pairing. It has been proposed that the difference in binding affinity is due to specific 2'-OH groups on an RNA substrate forming stabilizing tertiary interactions with the core of the ribozyme, or that the RNA.RNA helix formed upon association of an RNA substrate and the ribozyme might be more stable than an RNA.DNA helix of the same sequence. To differentiate between these two models, chimaeric oligonucleotides containing deoxynucleotide residues at successive positions along the chain were synthesized, and their equilibrium binding constants for association with the ribozyme were measured directly by a new gel electrophoresis technique. We report here that most of the extra binding energy can be accounted for by discrete RNA-ribozyme interactions, the 2'-OH group on the sugar residue three nucleotides from the cleavage site contributing the most interaction energy. Thus, in addition to the well documented binding of RNA to RNA by base-pairing, 2'-OH groups within a duplex can also mediate association between RNA molecules.     

离子—偶极混合物的MC分子模拟研究

在综合考虑电解质溶液中各种粒子相互作用的基础上，将电解质溶液简化为带有Ｌｅｎｎａｒｄ－Ｊｏｎｅｓ位能的离子—点偶极子混合物，用ＭｏｎｔｅＣａｒｌｏ分子模拟方法进行了初步模拟计算，对长程力采用了Ｅｗａｌｄ求和方法，得到了混合物的各种位能（离子—离子、离子—偶极、偶极—偶极和ＬＪ短程位能）以及径向分布函数。并考察了体系密度、温度、离子浓度和电荷对体系性质的影响。     

Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3

The centromere is a unique chromosomal locus that ensures accurate segregation of chromosomes during cell division by directing the assembly of a multiprotein complex, the kinetochore. The centromere is marked by a conserved variant of conventional histone H3 termed CenH3 or CENP-A (ref. 2). A conserved motif of CenH3, the CATD, defined by loop 1 and helix 2 of the histone fold, is necessary and sufficient for specifying centromere functions of CenH3 (refs 3, 4). The structural basis of this specification is of particular interest. Yeast Scm3 and human HJURP are conserved non-histone proteins that interact physically with the (CenH3-H4)(2) heterotetramer and are required for the deposition of CenH3 at centromeres in vivo. Here we have elucidated the structural basis for recognition of budding yeast (Saccharomyces cerevisiae) CenH3 (called Cse4) by Scm3. We solved the structure of the Cse4-binding domain (CBD) of Scm3 in complex with Cse4 and H4 in a single chain model. An α-helix and an irregular loop at the conserved amino terminus and a shorter α-helix at the carboxy terminus of Scm3(CBD) wraps around the Cse4-H4 dimer. Four Cse4-specific residues in the N-terminal region of helix 2 are sufficient for specific recognition by conserved and functionally important residues in the N-terminal helix of Scm3 through formation of a hydrophobic cluster. Scm3(CBD) induces major conformational changes and sterically occludes DNA-binding sites in the structure of Cse4 and H4. These findings have implications for the assembly and architecture of the centromeric nucleosome.     

磁性超晶格的静磁能和磁相图的唯像理论研究

计算了包含不同自旋取向的单畴粒子具有短程交换相互作用能,各向异性能及长程偶极相互作用能的磁性超晶格的静磁能,利用能面图和局域能量极小模型得到了磁相图和磁滞回线,研究了有限尺寸和温度效应,计算结果较好解释了在超薄磁性薄膜中观察到的两种磁相（磁化强度平行和垂直于薄膜平面）的转变行为。     

硝酸钾电解质溶液的结构和热力学性质的计算机分子模拟

对硝酸钾电解质溶液进行了分子动力学计算机模拟研究。水分子采用简单点电荷（SPC）三节点模型，钾离子被看作带电硬球，硝酸根离子采用刚性四节点模型，同时考虑节点间的库仑长程作用和L-J相互作用，对库仑长程作用采用EWALD求和方法进行计算。研究结果表明，随着溶液浓度的增加，水-水相互作用的总势能绝对值升高；高浓度溶液中水水作用能的升高与水分子排列有序化程度的提高有关，即在浓溶液中水分子的偶极取向更加有序化，说明有更多的水分子参与水化。     

SH2域与磷酸化多肽相互作用的连续溶剂模型研究

使用连续溶剂模型方法研究了SH2结构域与磷酸化多肽pYXXX(X为20种常见氨基酸残基中的任意一种)之间的相互作用.首先计算了已知的SH2域-磷酸化酪氨酸多肽复合物之间的结合能,理论计算的结果与实验测得的亲合能之间的相关系数为0.91,验证了理论模型的正确性.然后,用该模型方法计算了SH2域与pYXXX之间的结合能,分析了磷酸化酪氨酸多肽pYXXX中 1, 2, 3位置上残基对结合能的影响.结果表明 2, 3位置上残基的变化对结合能影响较大, 2位置上带负电的残基和 3位置上的疏水性残基有利于SH2域与pYXXX之间的相互作用,这与实验结果一致.     

A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution

The crystal structure of alamethicin in nonaqueous solvent has been determined, and refined at 1.5-A resolution. The molecular conformation of the three crystallographically independent molecules is largely alpha-helical with a bend in the helix axis at an internal proline residue. The helix structure is highly amphipathic as most of the solvent-accessible polar atoms lie on a narrow strip of surface parallel to the helix axis. Molecular models for the voltage-gated ion channel, with n-fold symmetry and based on the molecular conformations observed in the crystal, are characterized by strong surface complementarity, a hydrophilic interior and a hydrophobic exterior. The channel structures are stabilized by a hydrated annulus of hydrogen-bonded glutamine residues which produce the greatest restriction in the channel diameter.     

Primary structure of helix C to helix G of a new retinal protein in H.sp.xz515

The gene fragment encoding the retinal protein from helix C to helix G in a new strain of halobacteria, H.sp.xz515 has been amplified by PCR method. The nucleotide sequence of this fragment has been determined. The deduced amino acid sequence has been compared with halobium br and other two br-like proteins, ar-1 and ar-2. Results show that those amino acid residues in br, essential for proton pumping and binding to retinal, are conserved. The residue M145 in br may be important for isomerization reaction of retinal.     

Atomic model of the actin filament

The F-actin filament has been constructed from the atomic structure of the actin monomer to fit the observed X-ray fibre diagram from oriented gels of F-actin. A unique orientation of the monomer with respect to the actin helix has been found. The main interactions are along the two-start helix with a contribution from a loop extending across the filament axis provided by the molecule in the adjacent strand. There are also contacts along the left-handed genetic helix.     

Structural basis of cell surface receptor recognition by botulinum neurotoxin B

Botulinum neurotoxins (BoNTs) are potent bacterial toxins that cause paralysis at femtomolar concentrations by blocking neurotransmitter release. A 'double receptor' model has been proposed in which BoNTs recognize nerve terminals via interactions with both gangliosides and protein receptors that mediate their entry. Of seven BoNTs (subtypes A-G), the putative receptors for BoNT/A, BoNT/B and BoNT/G have been identified, but the molecular details that govern recognition remain undefined. Here we report the crystal structure of full-length BoNT/B in complex with the synaptotagmin II (Syt-II) recognition domain at 2.6 A resolution. The structure of the complex reveals that Syt-II forms a short helix that binds to a hydrophobic groove within the binding domain of BoNT/B. In addition, mutagenesis of amino acid residues within this interface on Syt-II affects binding of BoNT/B. Structural and sequence analysis reveals that this hydrophobic groove is conserved in the BoNT/G and BoNT/B subtypes, but varies in other clostridial neurotoxins. Furthermore, molecular docking studies using the ganglioside G(T1b) indicate that its binding site is more extensive than previously proposed and might form contacts with both BoNT/B and synaptotagmin. The results provide structural insights into how BoNTs recognize protein receptors and reveal a promising target for blocking toxin-receptor recognition.     

Aminoacylation of RNA minihelices with alanine

The genetic code is determined by both the specificity of the triplet anticodon of tRNAs for codons in mRNAs and the specificity with which tRNAs are charged with amino acids. The latter depends on interactions between tRNAs and their charging enzymes, and an advance in understanding such interactions was provided recently by the demonstration that a major determinant of the identity of alanine tRNA is located in the amino-acid acceptor helix. Multiple substitutions in many distinct parts of the molecule do not prevent aminoacylation with alanine. Substitution of the G3.U70 base pair with G3.C70 or A3.U70 in the acceptor helix prevents aminoacylation in vivo and in vitro, however, and the introduction of this base pair into tRNA(Cys) (ref. 1) or tRNA(Phe) (refs 1, 2) enables both to accept alanine. The importance of a single base pair in the acceptor helix and the results of recent footprinting experiments promoted us to investigate the possibility that a minihelix, composed only of the amino-acid acceptor-T psi C helix, could be a substrate for alanine tRNA synthetase. We show here that a synthetic hairpin minihelix can be enzymatically aminoacylated with alanine. Alanine incorporation requires a single G.U base pair, and occurs in helices that otherwise differ significantly in sequence. Aminoacylation can be achieved with only seven base pairs in the helix.     

Crystal structure of 15-mer DNA duplex containing unpaired bases

Errors during DNA replication or repair can lead to the presence of unpaired or inserted bases in the double helix, as well as to mismatched base pairs. So far only structures of the latter type have been characterized by X-ray crystallography. We report here a 3-A crystal structure of DNA 15-mer d(CGCGAAATTTACGCG), which forms a duplex with two unpaired adenine residues looped outside the B-type helix. This arrangement is in disagreement with the nuclear magnetic resonance spectroscopy results for the same 15-mer in solution, indicating polymorphic nature of the structure adopted by this sequence.     

Cloning and sequencing of a novel class of rice homeobox

Rice genomic DNA was surveyed by polymerase chain reaction (PCR) to detect homeobox sequences. The PCR product (183 bp) was cloned and sequenced. The nucleotide sequence and the deduced amino acid sequence of a homeobox, which was isolated in this study, and designated OSIHI1, were obtained. Comparison of the encoded polypeptide sequence with other homeodomains reveals that OSIHI1 has 85% and 87% identity to that of Antp, and quail Quox1, respectively at the protein level. An alignment of the OSIHI1 amino acid sequence with homeodoma in sequences from varlous other eukaryotes shows that OSIHI1 homeodomain contains identical residues in the eight positions most conserved among homeodomains, and also contains the four invariant residues present in the putative recognition helix (helix3) Supported by the National Natural Science Foundation of China Yi Qingming: born in Apr. 1938. Professor     

Structure of Arc repressor in solution: evidence for a family of beta-sheet DNA-binding proteins

The Arc repressor, which is involved in the switch between lysis and lysogeny of Salmonella bacteriophage P22, does not belong to any of the known classes of DNA-binding proteins. Mutagenesis studies show that the DNA-binding region is located in the 15 N-terminal amino-acid residues. We have now determined the three-dimensional structure of the Arc dimer from an extensive set of interproton-distance data obtained from 1H NMR spectroscopy. A priori, intra- and inter-monomer nuclear Overhauser effects (NOEs) cannot be distinguished for a symmetric dimer. But by using the homology with the Escherichia coli Met repressor we could interpret the NOEs unambiguously in an iterative structure refinement procedure. The final structure satisfies a large set of NOE constraints (1,352 for the dimer). It shows a strongly intertwined dimer, in which residues 8-14 of different monomers form an antiparallel beta-sheet. A model for the Arc repressor-operator complex can account for all available biochemical and genetic data. In this model two Arc dimers bind with their beta-sheet regions in successive major grooves on one side of the DNA helix, similar to the Met repressor interaction. Thus, Arc and Met repressors are members of the same family of proteins, which contain an antiparallel beta-sheet as the DNA-binding motif.     

飞机稳态失速螺旋特点仿真

针对现有飞机失速螺旋动力学本质和失速特点研究不足的现状,分析了飞机失速和失速螺旋产生的原因,从失速螺旋的进入、定常、改出三个阶段分析了失速螺旋的运动学特点,用力的平衡法推导出失速螺旋运动中的速度、半径、损失高度和时间的计算式及六自由度运动学方程,并运用MATLAB/Simulink平台搭建仿真模型对稳态平螺旋进行实时仿真计算,通过仿真可以直接观察失速螺旋过程中机体的实时姿态及运动轨迹,解决了飞机稳态尾旋过程状态获取困难的问题。仿真结果表明:构建的模型和使用的方法真实可靠,具有一定的实用性,相关方法也可以运用到其他机型稳态失速螺旋的研究过程中,研究结果可为相关飞行人员提供参考,为安全飞行,避免尾旋奠定理论基础。     

紫色光合细菌LH1和LH2的激子能级结构(I)——理论与模型

为了理解紫色光合细菌LH1和LH2的可能的光谱性质,解析地研究了二聚物环状链的激子能级结构.在叶绿素分子间偶极子-偶极子相互作用的近似下,利用偶极子间的相互作用能量和指向参数,解析地给出了激子能级、带宽和两个Davydov子能带间的带宽.提出的模型包括了系统中色素分子间所有的相互作用.