Crystal structure determination of desheptapeptide (B24--B30)-insulin

Desheptapeptide (B24--B30)-insulin (DHPI), an essentially inactive insulin analog, is crystallized in space group P212121 with two molecules in an asymmetric unit. The orientations of the molecules in the crystal cell have been determined by using Patterson search method at 6 A resolution and the positions of the molecules are deduced from translation function calculation and R search at 3 A resolution. After using the rigid body refinement (CORELS) further to refine the orientational and positional parameters as well as the initial energy restrained refinement (EREF) for the model, the crystallographic R value is reduced to 0.384 at 3 A resolution. The initial Fourier map shows that the B-chain N-terminal (B1-B8) and C-terminal (B20-B22) segments, compared with the native 2 zinc insulin, exhibit drastic conformational changes, but the three helices of B- and A-chains and their relative arrangement are essentially kept in DHPI.     

Studies on the Crystal Structure of [L-Met]~(B0) Bovine Insulin at 3.0 Resolution

Based on the crystal symmetry of [L-Met]~(B0) bovine insulin (LMBBI) and the fundamental theory of the molecular packing method, the scheme for the determination of the position and orientation of the molecules by only using one-dimensional rotation and one-dimensional translation was chosen to be used,and therefore the calculation of the rotation function of the molecular replacement method and the refinement of the rotational and translational parameters by using the R-factor search method were simplified greatly. After the preliminary refinement by using the macromolecular rigid body refinement technique, the molecular model was further refined and adjusted by using the energy-minimizing stereochemical-restrained least squares refinement technique assisted by the manual revision on the difference Fourier maps.The L-Met residues on the N-termlnus of the B-chain appeared clearly on the final electron density map.     

Effect of solvent molecular structure on vibration—rotation spectra of DCl and CO solutes in cycloalkanes

Infrared vibration—rotation spectra have been obtained for DCl and CO in a variety of cyclic and bicyclic alkanes and in alkyl-substituted cyclopentanes and cyclohexanes. The band shapes for CO depend on solvent free volume. For DCl they are sensitive to solvent structure, the rotation being perturbed by surface features (“roughness”) of the surrounding molecules. Molecular roughness is assessed qualitatively either through inspection of molecular models or through _V*, the solvent volume at close-packing, obtained from equation of state data.     

A personal reminiscence about theories used and misused in structural chemistry

In the last half-century, chemists acquired enough information about the structures and force fields of molecules to formulate what appeared to be successful theories (better called models) of molecular properties. For various reasons, chemists relied particularly heavily on studies of small hydrogen-containing compounds to shape their thinking. As discussed in the following text, this led to some inappropriate generalizations. In my first studies of molecular structure by gas-phase electron diffraction (GED), I was fortunate to find contradictions to the theories proposed at the time. What follows are reminiscences of how that came about and what happened subsequently. The main lesson to be earned, at least for molecules with central atoms that are not extremely large, is that the principal forces governing molecular structure are neither hybridization nor even the popular valence shell electron pair repulsions, explanations still taught routinely in chemistry courses but, instead, are the forces between geminal atoms resulting in the close-packing of ligands.     

The structure of the lowest electronic Rydberg state of CdAr complex determined by laser double resonance method in a supersonic jet-expansion beam

The lowest E1(3Sigma(+)) Rydberg state of the CdAr van der Waals (vdW) complex was investigated by means of an optical-optical double resonance (OODR) method of laser spectroscopy in conjunction with a free jet-expansion molecular beam. Two dye lasers were employed for the two-step excitation. The A0(+)(3Pi(+)) and B1(3Sigma(+)) states were used as intermediates in the excitation process from the X0(+)(1Sigma(+)) ground state. Two types of bound-bound excitation spectra of the E1<--A0(+) and E1<--B1 transitions were recorded indicating the existence of two, well defined minima in the E1-state potential energy (PE) curve. First, considerably deep, with the well depth of D(e)'(E1(2))=1309.0 cm(-1) and second, separated by a positive PE barrier, with D(e)'(E1(2))=24.2 cm(-1). Combination of bound-bound and first-time observed bound-free excitation spectra enabled a complete determination of the spectroscopical parameters of the PE curve of the E1-Rydberg state, the height of the PE barrier and its approximate location. In the excitation spectra of the E1<--B1 transition, a nodal structure of the bound-free transitions was observed and elucidated by a projection of the B1-state vibrational wave-functions onto the E1-state potential barrier and/or onto the repulsive part of the E1-state PE curve. The experimental results of our investigation coincides well with recently published results of ab initio calculation of Czuchaj and co-workers [Chem. Phys. 248 (1999) 1; Chem Phys. 263 (2001) 7; Theor. Chem Acc. 105 (2001) 219].     

[B10Glu,B24-Asp-B25]人胰岛素类似物的制备、鉴定与性质研究

采用PCR方法,将人胰岛素分子B链B10位His突变为Glu,在B24和B25位之间插入Asp,构建了[B10Glu,B24-Asp-B25]胰岛素原基因.利用通用型质粒pBV220构建表达载体,在大肠杆菌DH5α中表达,表达蛋白为包含体形式,约占菌体总蛋白的20%～30%.经过复性和凝胶过滤得到胰岛素原融合蛋白.用胰蛋白酶和羧肽酶B酶切,经DEAE离子交换和RP-HPLC纯化得胰岛素突变体类似物.用凝胶过滤法测定了蛋白质分子自身的缔合性质,用圆二色谱测定了构象变化.放射性免疫活性及受体结合活性测定结果表明,突变体分子缔合性明显下降,放免活性和受体结合活性分别约为人胰岛素的73.6%和146%.     

Crystal structural studies of destripeptide (B28-B30) insulin

Single crystals of destripeptide (B28-B30) insulin (DTRI) in three forms were obtained by hanging-drop vapor diffusion method. Form 1 belongs to P21 space group with cell parameters a-4.77 nm, b=6.19 nm, c=6.12 nm, β=110.3°. Form 2 belongs to P4122 or P4322 space group with cell parameters a= 6.45 nm, c=12.07 nm. Form 3 belongs to P212121 space group with cell parameters a=4.98 nm, b=5.16 nm, c=10.06 nm. The structure of form 1 crystal was determined by molecular replacement method and refined at 0.23 nm resolution. The R-factor of the final model is 18.8% with r.m.s. deviations of 0.001 5 nm and 3.3?for the bond lengths and the bond angles, respectively. Studies on the crystal structure show that the removal of B28 Pro has brought DTRI structural changes which made it dissociate more easily than native insulin although DTRI can still form a hexamer.     

Studies on the crystal structure of (D-Ala)-B0 porcine insulin at 1.9 A resolution

The crystal structure of (D-Ala)-B0 porcine insulin has been determined, using data to 1.9 A and atomic parameters of 2 Zn porcine insulin as a starting model, and through the use of the difference method and the restrained least square method, to a final R-factor of 0.211 and r.m.s. deviation of 0.057 A for the bond lengths. The electron densities of B0 residues were very clear. Introduction of B0 residues into the molecules had reduced the thermal vibration of the N-terminus of B-chain for both molecules I and II and made the molecules pack closer in the crystal. The obvious differences between the crystal structures of 2 Zn and (D-Ala)-B0 porcine insulin were the conformations of partial polar groups around the possible receptor binding surface and the assembly mode of two helixes of A-chain in molecule I. In the local environment of the N-terminus of B-chain there were great differences between the crystal structures of (D-Ala)-B0 porcine insulin, (Trp)-B1 porcine insulin and Des B1(Phe) bovine insulin. In this paper the structure-immunoactivity relationships of insulin molecule have also been discussed briefly.     

Similarity recognition of molecular structures by optimal atomic matching and rotational superposition

An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.     

The crystal structure of silver carp insulin at medium resolution

It is an important way of surveying the structure-function relationship of insulin to study insulins from different species. Based on the structure model of an orthorhombic crystal obtained by the molecular replacement method, the crystallographic refinement of a hexamer of silver carp insulin in an asymmetric unit has been carried out with 2.8 A resolution data using the restrained least-squares method. The comparisons of insulin structures have shown that the six silver carp insulin molecules have very similar but not identical three-dimensional structures which are similar to the known 2 Zn pig insulin structure but remarkably different in some local conformations.     

THE CRYSTAL STRUCTURE OF SILVER CARP INSULIN AT MEDIUM RESOLUTION

It is an important way of surveying the structure-functionrelationship of insulin tostudy insulins from different species. Based on the structure model of an orthorhombic crys-tal obtained by the molecular replacement method, the crystallographic refinement of a hex-amer of silver carp insulin in an asymmetric unit has been carried out with 2.8A resolutiondata using the restrained least- squares method. The comparisons of insulin structures haveshown that the six silver carp insulin molecules have very similar but not identical three- di-mensional structures which are similar to the known 2Zn pig insulin structure but remarka-bly different in some local conformations.     

Structure and dynamics of hydrated NH(4) (+): an ab initio QM/MM molecular dynamics simulation

A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to investigate solvation structure and dynamics of NH(4) (+) in water. The most interesting region, the sphere includes an ammonium ion and its first hydration shell, was treated at the Hartree-Fock level using DZV basis set, while the rest of the system was described by classical pair potentials. On the basis of detailed QM/MM simulation results, the solvation structure of NH(4) (+) is rather flexible, in which many water molecules are cooperatively involved in the solvation shell of the ion. Of particular interest, the QM/MM results show fast translation and rotation of NH(4) (+) in water. This phenomenon has resulted from multiple coordination, which drives the NH(4) (+) to translate and rotate quite freely within its surrounding water molecules. In addition, a "structure-breaking" behavior of the NH(4) (+) is well reflected by the detailed analysis on the water exchange process and the mean residence times of water molecules surrounding the ion.     

Microenvironment control of methyl rotation induced by proton transfer

Methyl rotation induced by proton transfer was found for cis-N-methylacetamide (NMA). More interestingly, it was found that the microenvironment could control the methyl rotation. The atom-centered density matrix propagation (ADMP) method, a recently developed ab initio molecular dynamics, was further carried out to depict the trajectories for methyl rotation of NMA. Moreover, trajectories for methyl rotation of NMA complexed with water molecules were also calculated, and water molecules at the two different sites of NMA were found to reverse or cease the rotational direction of the methyl groups of NMA. This finding that microenvironment can not only control rotational direction of methyl groups but can also cease the rotation may be of significant importance for the control of molecular machines.     

Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules

A method for estimating the configurational (i.e., non-kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest-neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi-harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information-theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters.     

Switching mechanism in polar columnar mesophases made of bent-core molecules.

The behaviour of polar, broken-layer-type columnar phases made of bent molecules (B(1Rev) and B(1RevTilted)) was studied under an applied electric field. There are two competing mechanisms of ferroelectric switching in the polar B(1RevTilted) columnar phase: collective rotation around the long molecular axis and collective rotation around the tilt cone. The proposed model shows that the main factor discriminating the type of switching is the width of the column cross-section.     

微波波谱法研究分子系统内基团大幅度运动动力学

分子中基团的运动方式、机制对分子体系性质、分子功能的表达等具有重要作用。微波波谱法在研究分子系统内部动力学、分子结构、构象变化、弱相互作用、基团大幅度运动以及探索量子溶剂等方面具有独特的能力,特别适合研究分子的精细结构、分子系统基团的内部转动运动,具有高灵敏度、高分辨率的特点。本文讨论了微波波谱法在研究分子系统基团大幅度运动动力学方面的应用,包括分子系统中甲基基团的内部转动、OH基团的运动、氨和氨基化合物的反演以及环状有机分子环运动等的动力学,同时结合作者使用微波波谱法研究的部分体系进行了分析。     

CuC、CuN分子基态的结构与分析势能函数

在Cu 的有效核势近似下, 运用密度泛函(B3LYP)方法, 对Cu采用基集合LANL2DZ, 但对其价电子基组的p轨道函数部分做了必要的修改, 而对C、N采用基集合6-311+G(d), 对CuC和CuN分子的微观结构进行了理论计算. 优化并计算了两分子基态的能量, 平衡结构和谐振频率. 根据原子分子反应静力学原理, 导出了CuC和CuN分子基态的合理离解极限和离解能. 应用密度泛函(B3LYP)方法扫描了CuC和CuN分子基态的势能曲线, 并采用最小二乘法拟合了两分子基态的Murrell-Sorbie势能函数及其在平衡位置附近的Dunham展开式. 同时根据Herzberg 和Dunham的公式, 计算了CuC和CuN分子基态的光谱参数.     

Molecular "compasses" and "gyroscopes." III. Dynamics of a phenylene rotor and clathrated benzene in a slipping-gear crystal lattice

Samples of 1,4-bis(3,3,3-triphenylpropynyl)benzene 3 were prepared by Pd(0)-catalyzed coupling of 3,3,3-triphenylpropyne (1) and 1,4-diiodobenzene. The structure of compound 3 is such that the central phenylene can play the role of a gyroscope wheel, while the alkyne bond and trityl groups can act as an axle and shielding frameworks, respectively. Crystals grown from benzene and dichloromethane were characterized by X-ray diffraction, variable-temperature (13)C CPMAS NMR, quadrupolar echo solid-state (2)H NMR, and thermal analyses. The rotational dynamics of benzene molecules and phenylene groups were characterized in terms of 6-fold rotation and 2-fold flipping models, respectively. The possibility of a gearing mechanism between adjacent benzene molecules and phenylene groups suggested by the clathrate structure was investigated. However, it was found that 6-fold rotation of benzene molecules at 300 K occurs in the gigahertz regime (or higher) and 2-fold flipping of phenylene groups in the kilohertz range in a structure that can be described as a slipping-gear lattice. The rotational dynamics of the phenylene group in the solvent-free structure were remarkably similar to those in the clathrate, and both are among the fastest known for phenylene rotation in solids. The results presented here provide a valuable starting point for the design and analysis of crystalline solids with correlated molecular motions.