The molten globule protein conformation probed by disulphide bonds

The molten globule is a compact protein conformation that has a secondary structure content like that of the native protein, but poorly defined tertiary structure. It is a stable state for a few proteins under particular conditions and could be a ubiquitous kinetic intermediate in protein folding. The extent to which native interactions, above the level of the secondary structure, are preserved in this conformation is not so far known. Here we report that alpha-lactalbumin can adopt a molten globule conformation when one of its four disulphide bonds is reduced. In this state, the three other disulphide bonds rearrange spontaneously, at the same rate as when the protein is fully unfolded, to a number of different disulphide bond isomers that tend to maintain the molten globule conformation. That the molten globule state is compatible with a variety of disulphide bond pairings suggests that it is unlikely to be stabilized by many specific tertiary interactions.     

水杨醛甘氨酸Schiff碱的从头算构象研究

运用从头算HF方法对水杨醛甘氨酸Schiff碱的构象进行了理论研究.结果表明,C=N键与苯环的共轭以及分子内弱相互作用是分子能量降低的2个重要结构因素.在各存在形态的所有最稳定构象中c=N键均与苯环共轭,均至少存在1条H14的弱氢键.酸式结构最稳定构象羧基上羟基氢H22背离大共轭平面;酸根形态的稳定构象羧基与苯环共面形成平面分子,且存在2条氢键;钾盐酚式最稳定构象羧基螯合成键,而醌式最稳定构象为平面分子,羧基单齿成键,且存在H14的2条弱氢键.由于具有很大的能量优势,水杨醛甘氨酸Schiff碱在水中的主要存在形态为酸式,该结论与其水溶液的实验研究结果一致.     

Long-term decline of global atmospheric ethane concentrations and implications for methane

After methane, ethane is the most abundant hydrocarbon in the remote atmosphere. It is a precursor to tropospheric ozone and it influences the atmosphere's oxidative capacity through its reaction with the hydroxyl radical, ethane's primary atmospheric sink. Here we present the longest continuous record of global atmospheric ethane levels. We show that global ethane emission rates decreased from 14.3 to 11.3 teragrams per year, or by 21 per cent, from 1984 to 2010. We attribute this to decreasing fugitive emissions from ethane's fossil fuel source--most probably decreased venting and flaring of natural gas in oil fields--rather than a decline in its other major sources, biofuel use and biomass burning. Ethane's major emission sources are shared with methane, and recent studies have disagreed on whether reduced fossil fuel or microbial emissions have caused methane's atmospheric growth rate to slow. Our findings suggest that reduced fugitive fossil fuel emissions account for at least 10-21 teragrams per year (30-70 per cent) of the decrease in methane's global emissions, significantly contributing to methane's slowing atmospheric growth rate since the mid-1980s.     

丙烯酸的量子拓扑研究

用RHF自洽场从头计算在STO-3G基组水平上优化了顺式和反式丙烯酸的平衡构型.在此基础上对其进行了拓扑分析研究,发现顺式丙烯酸的平衡构型是一环状结构,H(5)和H(7)之间有弱键相连.但H(5)和H(7)之间键的键鞍点靠近环鞍点,说明它是一不稳定构型,H(5)-H (7)键有断裂的趋势.这也能说明反式结构比顺式更稳定.     

Unidirectional rotation in a mechanically interlocked molecular rotor

Molecular motor proteins are ubiquitous in nature and have inspired attempts to create artificial machines that mimic their ability to produce controlled motion on the molecular level. A recent example of an artificial molecular rotor is a molecule undergoing a unidirectional 120 degrees intramolecular rotation around a single bond; another is a molecule capable of repetitive unimolecular rotation driven by multiple and successive isomerization of its central double bond. Here we show that sequential and unidirectional rotation can also be induced in mechanically interlocked assemblies comprised of one or two small rings moving around one larger ring. The small rings in these [2]- and [3]catenanes move in discrete steps between different binding sites located on the larger ring, with the movement driven by light, heat or chemical stimuli that change the relative affinity of the small rings for the different binding sites. We find that the small ring in the [2]catenane moves with high positional integrity but without control over its direction of motion, while the two rings in the [3]catenane mutually block each other's movement to ensure an overall stimuli-induced unidirectional motion around the larger ring.     

线性金属配合物Cr3(dpa)4Cl2及其氧化态的Cr—Cr键的理论研究

用密度泛函理论对具有分子导线潜在应用前景的线性金属配合物Cr3(dpa)4Cl2的对称构型1,非对称构型2及其氧化态[Cr3(dpa)4Cl2]+3进行理论计算,并结合自然键轨道理论对配合物1～3的CrCr键进行分析.结果表明:(1)中性构型1和2中只形成Cr36+的dz2轨道组成的三中心三电子键,电子由两端向中间的Cr离域,电子由中间向两端的Cr离域,电子的离域更显著.由于离域和dpa-配体的螺旋盘绕作用,Cr36+的轨道中dxz和dyz轨道成份较小且绕金属轴(Z轴)发生不同程度的旋转,难以重叠形成键.(2)氧化态3中,因配体的螺旋作用,Cr的dxy轨道绕Z轴发生不同程度旋转而无法有效重叠形成键,故CrCr短键只存在1个键和2个键的三重键.(3)中性分子的HOMO轨道为非键轨道,电子云集中在两端Cr上,两端的Cr(2的长键端的Cr)是失电子形成氧化态3的中心.     

Observation of conformation-specific pathways in the photodissociation of 1-iodopropane ions.

Many molecules can rotate freely around single bonds and thereby interconvert between different conformations, such as gauche and anti 1,2-disubstituted ethane, a classic example of conformational isomerism. Even though rotation occurs rapidly at room temperature, the product selectivity seen in some reactions has been explained by conformation-dependent reaction mechanisms: if reactant molecules differing only in their conformation are located at different positions on the reaction path, they may undergo different reactions. But a direct verification of this effect is difficult, because the energy barrier separating conformational isomers is so low that under ambient conditions reactants with more than one conformation will be present. But by using temperatures low enough to suppress the interconversion between different conformations, gauche-1-iodopropane ions and anti-1-iodopropane ions have been selectively generated. Here we show that the kinetic energy released during the photodissociation of 1-iodopropane ions depends strongly on the conformation of the ions. Thermodynamic arguments and ab initio calculations indicate that this difference in kinetic energy release results from differences in the reaction mechanism, with gauche-1-iodopropane ions forming 2-propyl ions and anti-1-iodopropane ions forming protonated cyclopropane ions. These findings suggest that the well-known concept of conformation selection forms the basis of a simple scheme for reaction control, thus providing in some cases an attractive alternative for more involved schemes that utilize the phase and pulse shape of laser beams to control chemical reactions.     

基于量子化学计算的乙烷、乙烯、乙炔水合物主客体间相互作用特性研究

天然气水合物是一种特殊的笼状化合物,水合物中的客体分子不同,主客体间的相互作用存在差异。为了分析烃类水合物中主客体间相互作用的特征,利用量子化学方法,对乙烷、乙烯、乙炔这3种客体分子占据Ⅰ型水合物T笼时的结构、相互作用能及C—C键伸缩振动频率进行研究,讨论了客体分子在水笼中的赋存形态,揭示了主客体间的相互作用机制。结果表明：客体分子占据T笼后,与占据前相比,T笼会发生微小的膨胀或收缩,客体分子的原子间距减小;通过能量分析,发现主客体间相互作用能(ΔE_host-guest)的大小顺序为：ΔE_T笼-乙烯<ΔE_T笼-乙烷<ΔE_T笼-乙炔,色散矫正的加入使主客体间的相互作用能增大;能量分解结果显示C原子的杂化方式对水合物的主客体间相互作用影响较大,随着客体分子中C原子的杂化方式由sp³→sp²→sp杂化,客体分子与水笼间的相互作用中静电作用先略微减弱、然后增强,色散作用逐渐减弱;与未占据T笼相比,乙烷分子占据T笼后C—C键伸缩振动频率增加了6.79 cm^-1,乙烯和乙炔分子占据T笼后C—C键伸缩振动频率分别减小了5.86 cm^-1和15.87 cm^-1。     

Effect of protein packing structure on side-chain methyl rotor conformations

Protein molecules undergo a series of conformational fluctuations ranging in degree from atomic vibrations to transient denaturation, even in physiological conditions. The rotational motions of amino acid side chains form an important subset of the types of fluctuation a protein can undergo. NMR and molecular dynamics have shown that methyl groups in proteins are not held in fixed positions, but spin rapidly around their rotor axes. The question then arises as to whether methyl groups in proteins predominantly adopt the 'staggered' conformation, favoured by the intrinsic barrier to rotation of these groups, or whether cooperative packing effects in the folded protein perturb the average configurations to higher torsional energy. We report here an investigation of the rotational conformations of the methyl groups of aliphatic side chains in the protein crambin by neutron diffraction. We find that in the time-averaged structure of this protein, the majority of methyl rotors adopt the staggered conformation. This is consistent with rotation being a quantized event consisting of rapid reorientations of approximately 120 degrees steps to positions of highest stability. The fact that the local environment does not dictate the low energy state of methyl groups suggests that within the seemingly close-packed interior structure of a protein, mutual packing accommodation occurs as a consequence of the inherent flexibility and small packing defects in protein structures.     

混合溶剂热条件下DL-Trp晶体生成过程的研究

 以L-Trp和碳酸钕为原料,通过混合溶剂热法制得DL-Trp晶体,并进行红外光谱、单晶X-衍射等表征。该化合物属单斜晶系P2(1)/c空间群,具有中心对称结构。a=1.890 8(2) nm, b=0.572 67(11) nm,c=0.930 32(15) nm,Z=4。此晶体通过′C-O-H-N′氢键缔合作用形成三维空间构型。对构型转变原因进行了分析。通过测定溶液体系旋光度-时间曲线可知,L色氨酸构型变化是一个渐变过程,降温至90 ℃左右是色氨酸发生构型转变最显著的温度范围。     

非共价相互作用对中心手性的影响及中心手性的定义

建立在van't Hoff碳正四面体构型学说基础上的中心手性的概念未涉及非共价相互作用对分子中心手性的影响.可以想像,当某原子连有两个相同的原子或基团(如氢原子)时,可因非共价相互作用(如分子内氢键)的存在(如只与其中的一个氢原子形成氢键)成为不等性原子或基团.考虑到非共价相互作用对分子中心手性可能产生的影响,中心手性的概念似应为:一个原子(如C,N)的四支键分别指向四面体的各顶点,并分别键连四个不等性原子或基团(包括孤电子对)时,则该原子是手性的.     

Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB

Accurate translation of genetic information into protein sequence depends on complete messenger RNA molecules. Truncated mRNAs cause synthesis of defective proteins, and arrest ribosomes at the end of their incomplete message. In bacteria, a hybrid RNA molecule that combines the functions of both transfer and messenger RNAs (called tmRNA) rescues stalled ribosomes, and targets aberrant, partially synthesized, proteins for proteolytic degradation. Here we report the 3.2-A-resolution structure of the tRNA-like domain of tmRNA (tmRNA(Delta)) in complex with small protein B (SmpB), a protein essential for biological functions of tmRNA. We find that the flexible RNA molecule adopts an open L-shaped conformation and SmpB binds to its elbow region, stabilizing the single-stranded D-loop in an extended conformation. The most striking feature of the structure of tmRNA(Delta) is a 90 degrees rotation of the TPsiC-arm around the helical axis. Owing to this unusual conformation, the SmpB-tmRNA(Delta) complex positioned into the A-site of the ribosome orients SmpB towards the small ribosomal subunit, and directs tmRNA towards the elongation-factor binding region of the ribosome. On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome.     

氯汞二茂铁的晶体结构

氯汞二茂铁的晶体结构钱鹰刘举正陈健郑培菊（东南大学化学化工系，南京２１００９６）（复旦大学分析测试中心，上海２００４３３）在研制二茂铁类金属有机非线性光学材料时，首先需制备一种重要的中间体－氯汞二茂铁，由氯汞二茂铁再与共轭烯烃单体在催化剂的作用下生...     

轴向配位体和周边氢键对叶绿素结构的影响

应用密度泛函理论为基础的量子化学计算方法研究了周边氢键和Mg2+的轴向配位体对叶绿素分子结构的影响。结果表明:Mg2+的配位体(水和甲硫氨酸)使叶绿素a(Chla)分子的结构发生了很大的变化;由于水分子中的氧原子对Mg2+的吸引致使叶绿素a分子中N-Mg键发生明显改变,并且使卟啉面发生明显弯曲(二面角约为10°);另外也发现叶绿素a分子中乙烯基和C16-C17键对不同配位体很敏感。     

A stable silicon-based allene analogue with a formally sp-hybridized silicon atom

Carbon chemistry exhibits a rich variety in bonding patterns, with homo- or heteronuclear multiple bonds involving sp-hybridized carbon atoms as found in molecules such as acetylenes, nitriles, allenes and carbon dioxide. Carbon's heavier homologues in group 14 of the periodic table--including silicon, germanium and tin--were long thought incapable of forming multiple bonds because of the less effective p(pi)-p(pi) orbital overlap involved in the multiple bonds. However, bulky substituents can protect unsaturated bonds and stabilize compounds with formally sp-hybridized heavy group-14 atoms: stable germanium, tin and lead analogues of acetylene derivatives and a marginally stable tristannaallene have now been reported. However, no stable silicon compounds with formal sp-silicon atoms have been isolated. Evidence for the existence of a persistent disilaacetylene and trapping of transient 2-silaallenes and other X = Si = X' type compounds (X, X' = O, CR2, NR, and so on) are also known, but stable silicon compounds with formally sp-hybridized silicon atoms have not yet been isolated. Here we report the synthesis of a thermally stable, crystalline trisilaallene derivative containing a formally sp-hybridized silicon atom. We find that, in contrast to linear carbon allenes, the trisilaallene is significantly bent. The central silicon in the molecule is dynamically disordered, which we ascribe to ready rotation of the central silicon atom around the molecular axis.     

Distal residues in the oxygen binding site of haemoglobin studied by protein engineering

The geometries of the Fe-O2 and Fe-CO bonds in myoglobin and haemoglobin differ significantly from those in free porphyrin model compounds. It has been suggested that steric hindrance by Val-E11 and His-E7 and a hydrogen bond between His-E7 and oxygen affect the geometry and electronic state of the Fe-ligand bond, and that these interactions may be important in controlling oxygen affinity. We have produced mutant haemoglobins in E. coli having Val(67 beta)E11 replaced by Ala, Met, Leu or Ile and His(58 beta)E7 by Gln, Val or Gly. We have studied the effect of these mutations on the equilibrium and kinetics of ligand binding. The conformation of the new side chains and their effect on the protein structure have been examined by X-ray crystallography, and the vibrational properties of the Fe-CO bond observed by resonance Raman spectroscopy. We found that the steric hindrance of ligand binding by the E11 residue and the polarity of the E7 residue in the beta subunit are critical for fine-tuning ligand affinity.     

The crystal structure of a voltage-gated sodium channel

Voltage-gated sodium (Na(V)) channels initiate electrical signalling in excitable cells and are the molecular targets for drugs and disease mutations, but the structural basis for their voltage-dependent activation, ion selectivity and drug block is unknown. Here we report the crystal structure of a voltage-gated Na(+) channel from Arcobacter butzleri (NavAb) captured in a closed-pore conformation with four activated voltage sensors at 2.7?? resolution. The arginine gating charges make multiple hydrophilic interactions within the voltage sensor, including unanticipated hydrogen bonds to the protein backbone. Comparisons to previous open-pore potassium channel structures indicate that the voltage-sensor domains and the S4-S5 linkers dilate the central pore by pivoting together around a hinge at the base of the pore module. The NavAb selectivity filter is short, ～4.6?? wide, and water filled, with four acidic side chains surrounding the narrowest part of the ion conduction pathway. This unique structure presents a high-field-strength anionic coordination site, which confers Na(+) selectivity through partial dehydration via direct interaction with glutamate side chains. Fenestrations in the sides of the pore module are unexpectedly penetrated by fatty acyl chains that extend into the central cavity, and these portals are large enough for the entry of small, hydrophobic pore-blocking drugs. This structure provides the template for understanding electrical signalling in excitable cells and the actions of drugs used for pain, epilepsy and cardiac arrhythmia at the atomic level.     

High resolution structure of the RNA duplex [U(U-A)6A]2

RNA is involved in many biological functions, ranging from information storage and transfer to the catalysis of reactions involving both nucleic acids and proteins. Previous crystallographic studies on RNA oligomeric chains provide only averaged structures or information limited in resolution. The oligomer [U(U-A)6A]2 was chosen for the study of protein-RNA interactions in viruses. Its size and base composition mimic portions of the genomic RNA in alfalfa mosaic virus that bind to the amino terminus of the viral subunit. The actual sequence was designed to guarantee the formation of a single species of duplex and to facilitate the production of the pure oligomer in large quantities. The molecular structure, derived from the 2.25 A resolution X-ray diffraction data, allows the most detailed analysis of an A-RNA helix reported to date. Two kinks are observed that divide the duplex into three blocks, each close to a canonical A-helical conformation. A few intermolecular hydrogen bonds involving 2'-hydroxyl groups stabilize this peculiar conformation of the RNA, which may be related to the temperature used for the crystallization (35 degrees C). The structure demonstrates both the plasticity of the RNA molecule and the role of the 2'-hydroxyl groups in intermolecular interactions.