Simple and efficient approach to preparation of molecular drawings

A convenient approach to the preparation of good quality molecular drawings is described. The method is based on transforming the atomic coordinates provided by a conventional crystallographic structure analysis or deduced from a model of a particular molecule, to a suitably weighted molecular inertia system and forming a projection of the molecule down the axis that corresponds to its highest moment of inertia. When implemented in a routine which prepares the input to the program ORTEP, the new method very nearly eliminates trial-and-error procedures from the preparation of a molecular diagram with suitable orientation of the molecule.     

The area moment of inertia of the tibia: A risk factor for stress fractures

In a prospective study of stress fractures among Israeli infantry recruits, the area moment of inertia of the tibia was found to have a statistically significant correlation with the incidence of tibial, femoral and total stress fractures. Recruits with "low" area moments of inertia of the tibia were found to have higher stress fracture morbidity than those with "high" area moments of inertia. The best correlation was obtained when the area moment of inertia was calculated about the AP axis of bending at a cross-sectional level corresponding to the narrowest tibial width on lateral X-rays, a point which is at the distal quarter of the tibia. This finding indicates that bending forces about the approximate AP axis are an important causal factor for tibial and many other stress fractures. The bone's bending strength, or ability to resist bending moments, as measured by the area moment of inertia, helps determine risk to stress fracture.     

Stabilization of the bio-membrane by small molecules: interaction of trehalose with the phospholipid bilayer

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A disaccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems. Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accommodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction.     

Stabilization of the Bio-membrane by Small Molecules: Interaction of Trehalose with the Phospholipid Bilayer

Abstract

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A di-saccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems (1). Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of l,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC (2) reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accomodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction.     

生物膜研究在生物物理研究所的兴起与发展

生物膜研究是现代生物学研究的前沿方向之一,本文对文革结束以后生物膜研究在中国科学院生物物理研究所(下称生物物理所)的兴起与发展进行了系统回顾.文革结束后,中国科学院领导了解到国外生物膜研究迅速发展的情况,迅即派遣以生物物理所杨福愉为组长,包括生物化学研究所、动物研究所、植物研究所、上海实验生物研究所等六人的代表团前往联邦德国进行考察.考察结束后院领导根据多学科交叉对生物膜研究的重要作用,组织了生物物理所、植物所、中国医学科学院、北京医科大学等单位联合申报国家自然科学基金委员会重大项目"膜脂-膜蛋白的相互作用及其在医学和农业上的应用",并获得立项.与此同时,院领导建议由中国生物物理学会、中国生化学会和中国细胞生物学会共同组织生物膜学术讨论会.首次会议于1979年3月在北京友谊宾馆举行,以后每3年召开1次,从未中断,有力地促进了生物膜研究的交流与发展.2003年举行的第200届香山会议专门组织讨论21世纪生物膜研究在中国的布局,进一步推动了生物膜研究的发展.本文还重点阐述了中国科学院生物物理研究所在生物膜研究方面所取得的代表性成果:a.金属离子通过膜脂-膜蛋白相互作用调控生物膜能量转换、物质运输及信号转导的分子机制;b.提出"克山病是一种心肌线粒体病"的重要观点;c.发现溶酶体内含有为量甚微、一般认为是消化酶的胰凝乳蛋白酶,并阐明了它通过溶酶体膜外泄后参与细胞凋亡的作用机制;d.确定了通过调控线粒体动态变化而干预肿瘤细胞迁移侵袭的新靶标.最后,特别值得一提的是,2004年,常文瑞与植物研究所匡廷云等在《自然》(Nature)发表了《菠菜中主要捕光色素复合体2.72魡分辨率的晶体结构分析》的研究论文,2005年饶子和与徐建兴等在《细胞》(Cell)发表了《猪心线粒体呼吸链复合体Ⅱ的晶体结构》的研究论文,充分标志着我国生物膜研究已在国际上占据一席之地.2004年,徐涛研究员因其在囊泡转运方面的丰厚学术积淀,作为首席科学家组织一批生物膜专家承担了国内首个生物膜973项目,这标志着国内生物膜研究开始进入一个新的发展时期.     

Local anesthetic-phospholipid interactions. The pH dependence of the binding of dibucaine to dimyristoylphosphatidylcholine vesicles

The interaction of the local anesthetic dibucaine with unilamellar vesicles of dimyristoylphosphatidylcholine was studied by equilibrium dialysis. Saturating binding profiles (as a function of dibucaine) were found, with apparent association constant ranging from 1.26 X 10(3)M-1 to 2.57 X 10(3)M-1 as pH is increased from 5.0 to 7.5. The number of phospholipid molecules comprising a binding site was found to be about 5 at each pH. Analysis of the data was also achieved using the Stern model, which takes into account the electrostatic effect on binding of the cationic drug due to the build up of a surface potential.     

Effects of small nonpolar molecules on membrane compressibility and permeability: A theoretical study of the effects of anesthetic gases

We explore from a theoretical perspective the effects of small nonpolar molecules, such as anesthetic gases, on membrane compressibility and permeability. As a model system we expand a previously proposed generalization of Nagle's model for biomembrane phase transitions. In this model anesthetic gases alter membrane compressibility, causing profound changes in membrane permeability. Anesthetics either increase or decrease membrane permeability, depending on whether the membrane lipid is originally in the solid or melted state, or in a two-phase region. These changes are reversed by high pressure, in agreement with experimental results. Anesthetic-induced changes in compressibility are predicted to inhibit fusion of phospholipid vesicles to each other and to planar bilayers, and thus might be expected to inhibit the fusion of presynaptic vesicles with the presynaptic nerve membrane. This work provides a detailed molecular theory for many of the effects of anesthetic gases on both synapse and axon, and provides a coherent framework for understanding diverse experimental results.     

The cooperativity between hydrogen and halogen bond in the XY···HNC···XY (X,Y = F,Cl, Br) complexes

The cooperativity between hydrogen and halogen bonds in XY···HNC···XY (X, Y = F, Cl, Br) complexes was studied at the MP2/aug-cc-pVTZ level. Two hydrogen-bonded dimers, five hydrogen-bonded dimers, and ten trimers were obtained. The hydrogen- and halogen-bonded interaction energies in the trimers were larger than those in the dimers, indicating that both the hydrogen bonding interaction and the halogen bonding interaction are enhanced. The binary halogen bonding interaction plays the most important role in the ternary system. The hydrogen donor molecule influences the magnitude of the halogen bonding interaction much more than the hydrogen bonding interaction in the trimers with respect to the dimers. Our calculations are consistent with the conclusion that the stronger noncovalent interaction has a bigger effect on the weaker one. The variation in the vibrational frequency in the HNC molecule was considered. The NH antisymmetry vibration frequency has a blue shift, whereas the symmetry vibration frequency has a red shift. A dipole moment enhancement is observed upon formation of the trimers. The variation in topological properties at bond critical points was obtained using the atoms in molecules method, and was consistent with the results of the interaction energy analysis.     

Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a Cyanophenylalanine Spectroscopic Probe

A nitrile-derived amino acid, Phe_CN, has been used as an internal spectroscopic probe to study the binding of an inhalational anesthetic to a model membrane protein. The infrared spectra from experiment showed a blue-shift of the nitrile vibrational frequency in the presence of the anesthetic halothane. To interpret the infrared results and explore the nature of the interaction between halothane and the model protein, all-atom molecular dynamics (MD) simulations have been used to probe the structural and dynamic properties of the protein in the presence and absence of one halothane molecule. The frequency shift analyzed from MD simulations agrees well with the experimental infrared results. Decomposition of the forces acting on the nitrile probes demonstrates an indirect impact on the probes from halothane, namely a change of the protein's electrostatic local environment around the probes induced by halothane. Although the halothane remains localized within the designed hydrophobic binding cavity, it undergoes a significant amount of translational and rotational motion, modulated by the interaction of the trifluorine end of halothane with backbone hydrogens of the residues forming the cavity. This dominant interaction between halothane and backbone hydrogens outweighs the direct interaction between halothane and the nitrile groups, making it a good “spectator” probe of the halothane-protein interaction. These MD simulations provide insight into action of anesthetic molecules on the model membrane protein, and also support the further development of nitrile-labeled amino acids as spectroscopic probes within the designed binding cavity.     

Interaction of steptolysin O with sterols.

A quantitative study of the specific inhibitory power of cholesterol and other sterols on the hemolytic properties of streptolysin O is reported. This streptococcal exocellular protein is a cytolytic toxin which disrupts cytoplasmic membranes of eukaryote cells. The structural characteristics, particularly the stereochemical ones required for a steroid molecule to inhibit the cytolytic activity of streptolysin O, have been investigated in detail. By immunodiffusion techniques, in agar gel plates or tubes containing sterols, the formation of hydrophobic complexes between streptolysin O and inhibitory steroids, but not non-inhibitory steroids except lanosterol, is shown. Upon interaction with inhibitory steroids streptolysin O loses its immunoreactive properties towards neutralizing and precipitating homologous antibodies. An interpretation of the mechanism of biomembrane disorganization by streptolysin O is discussed in the light of its steroid binding properties.     

A fluorescence study of the interaction and location of (+)-totarol, a diterpenoid bioactive molecule, in model membranes

(+)-Totarol, a diterpene extracted from Podocarpus totara, has been reported as a potent antioxidant and antibacterial agent. Although the molecular mechanism of action of this hydrophobic molecule remains unknown, recent work made in our laboratory strongly suggests that it could be lipid-mediated. Since (+)-totarol contains a phenolic ring, we have studied the intrinsic fluorescent properties of this molecule, i.e., quantum yield, lifetime, steady-state anisotropy and emission spectra, both in aqueous and in phospholipid phases, in order to obtain information on the interaction and location of (+)-totarol in biomembrane model systems. The phospholipid/water partition coefficient of (+)-totarol was found to be very high (K(p)=1.8x10(4)), suggesting that it incorporates very efficiently into membranes. In order to estimate the transverse location (degree of penetration) of the molecule in the fluid phase of DMPC model membranes, the spin labelled fatty acids 5-NS and 16-NS were used in differential quenching experiments. The results obtained show that (+)-totarol is located in the inner region of the membrane, far away from the phospholipid/water interface. Since (+)-totarol protects against oxidative stress, its interaction with an unsaturated fatty acid, trans-parinaric acid, was studied using fluorescence resonance energy transfer. No significant interactions were observed, molecules of trans-parinaric acid distributing themselves randomly amongst those of (+)-totarol in the phospholipid membrane.     

Role of aromatic side chains in the binding of volatile general anesthetics to a four-alpha-helix bundle

Currently, the mechanism by which anesthesia occurs is thought to involve the direct binding of inhaled anesthetics to ligand-gated ion channels. This hypothesis is being studied using four-alpha-helix bundles as model systems for the transmembrane domains of the natural "receptor" proteins. This study concerns the role in anesthetic binding played by aromatic side chains in the binding cavity of a four-alpha-helix bundle designed to assume a Rop-like fold. Specifically, the effect of the substitution W15Y on bundle structure, stability, and anesthetic binding energetics was investigated. No appreciable effect of substituting W for Y on the secondary structure or the thermodynamic stability of the four-alpha-helix bundle was identified. However, the substitution W15Y resulted in about 6- and 3-fold decreases in halothane and chloroform binding affinities, respectively. This effect may reflect weaker dipole-aromatic quadrupole interactions between the aromatic side chain and the anesthetic in the tyrosine-containing species, which possesses the smaller aromatic ring system. For these anesthetic binding proteins, this class of interaction occurs when the permanent nonspherical distribution of electrons in the aromatic ring systems interact with the weakly acidic CH group of the anesthetics.     

Effects of the Racket Polar Moment of Inertia on Dominant Upper Limb Joint Moments during Tennis Serve

This study examined the effect of the polar moment of inertia of a tennis racket on upper limb loading in the serve. Eight amateur competition tennis players performed two sets of 10 serves using two rackets identical in mass, position of center of mass and moments of inertia other than the polar moment of inertia (0.00152 vs 0.00197 kg.m²). An eight-camera motion analysis system collected the 3D trajectories of 16 markers, located on the thorax, upper limbs and racket, from which shoulder, elbow and wrist net joint moments and powers were computed using inverse dynamics. During the cocking phase, increased racket polar moment of inertia was associated with significant increases in the peak shoulder extension and abduction moments, as well the peak elbow extension, valgus and supination moments. During the forward swing phase, peak wrist extension and radial deviation moments significantly increased with polar moment of inertia. During the follow-through phase, the peak shoulder adduction, elbow pronation and wrist external rotation moments displayed a significant inverse relationship with polar moment of inertia. During the forward swing, the magnitudes of negative joint power at the elbow and wrist were significantly larger when players served using the racket with a higher polar moment of inertia. Although a larger polar of inertia allows players to better tolerate off-center impacts, it also appears to place additional loads on the upper extremity when serving and may therefore increase injury risk in tennis players.     

Reversal of cellular polarity and early cell-cell interaction in the embryos of Caenorhabditis elegans

During early embryogenesis of Caenorhabditis elegans the serial stem cell-like cleavages of the germ line cells P0-P3 generate a number of somatic founder cells with different developmental potentials. Observations on partial embryos show that in the first two of these unequal divisions in the germ line the somatic daughter cell comes to lie anterior to the new germ line cell. In the following two, however, the somatic daughter cell comes to lie posterior to the new germ line cell, suggesting a reversal of polarity in the germ line. By the use of a laser microbeam, egg fragments can be extruded from young embryos; the fragments often cleave like partial twins. Depending on whether the fragment is derived from the posterior region of the uncleaved zygote P0 or its daughter P1, the mirror image duplications that are generated are joined at their larger soma-like cells or at their smaller germ line-like cells, respectively. This result is best explained as a reversal of polarity taking place in the germ line cell P2. This notion is strengthened by the finding that partial embryos derived from the posterior region of the P2 cell in late interphase do not undergo stem cell-like (i.e., unequal) cleavages in contrast to those derived from P0 or P1. Finally, an apparent early cell-cell interaction is described which is inconsistent with the classical notion of "mosaic" nematode development: removal of the germline cell P2 results in an altered developmental pattern of its somatic sister cell EMS. A working model is presented linking reversal of polarity and cell-cell interaction and offers an explanation for the unique behavior of the EMS cell in normal development.     

400 MHz two-dimensional nuclear Overhauser spectroscopy on anesthetic interaction with lipid bilayer

Interaction between a volatile anesthetic, methoxyflurane, and dipalmitoylphosphatidylcholine (DPPC) vesicle membrane was analyzed by nuclear Overhauser effect (NOE) difference spectroscopy and two-dimensional nuclear Overhauser spectroscopy (NOESY). The NOE difference spectra were obtained by selectively irradiating methoxy protons (hydrophobic end) of the anesthetic: a negative nuclear Overhauser effect of -2.94% was observed with the choline methyl protons of DPPC. The NOESY spectra revealed a cross-peak between the anesthetic methoxy protons and the choline methyl protons. A dipole-dipole interaction exists between the hydrophobic end of the anesthetic and the hydrophilic head group of DPPC. No other cross-peaks were observed. The anesthetic orients itself at the membrane/water interface by interacting with the hydrophilic surface of the DPPC membrane, leaving the hydrophilic end of the anesthetic molecule in the aqueous phase. The preferred residence site of dipolar volatile anesthetics is the membrane/water interface.     

A new geometric-based model to accurately estimate arm and leg inertial estimates

Segment estimates of mass, center of mass and moment of inertia are required input parameters to analyze the forces and moments acting across the joints. The objectives of this study were to propose a new geometric model for limb segments, to evaluate it against criterion values obtained from DXA, and to compare its performance to five other popular models. Twenty five female and 24 male college students participated in the study. For the criterion measures, the participants underwent a whole body DXA scan, and estimates for segment mass, center of mass location, and moment of inertia (frontal plane) were directly computed from the DXA mass units. For the new model, the volume was determined from two standing frontal and sagittal photographs. Each segment was modeled as a stack of slices, the sections of which were ellipses if they are not adjoining another segment and sectioned ellipses if they were adjoining another segment (e.g. upper arm and trunk). Length of axes of the ellipses was obtained from the photographs. In addition, a sex-specific, non-uniform density function was developed for each segment. A series of anthropometric measurements were also taken by directly following the definitions provided of the different body segment models tested, and the same parameters determined for each model. Comparison of models showed that estimates from the new model were consistently closer to the DXA criterion than those from the other models, with an error of less than 5% for mass and moment of inertia and less than about 6% for center of mass location.     

Determination of the moment of inertia of limb segments by a simple method

A simple oscillation method to determine the moment of inertia of limb segments is described. The method involves coupling the limb segment to an elastic mechanical device. The resulting system has a lightly damped oscillatory response from which its resonant frequency can be measured and used to determine the moment of inertia of the limb. The method has been applied to the forearm and results produced compare favourably with those obtained by other methods.     

Interactions of colipase with bile salt micelles. 2. Study by dialysis and spectrophotometry.

The finding reported in the preceding paper that colipase is able to bind one sodium taurodeoxycholate micelle per molecule was confirmed by dialysis and spectrophotometry. Dialysis in the presence of labelled sodium taurodeoxycholate provided a direct qualitative proof of taurodeoxycholate binding to colipase. This binding was found to occur only above the critical micelle concentration. But, dialysis did not give any information about the composition of the associations, because equilibrium was not attained at the end of the assays. Addition of sodium taurodeoxycholate above the critical micelle concentration was also observed to induce a strong perturbation of the ultraviolet spectrum of one or several of the three tyrosines of colipase. The variation of the perturbation as a function of sodium taurodeoxycholate concentration was consistent with the binding of a single micelle to colipase. The dissociation constant calculated in "micelle molarity" was approximately 1 X 10(-4) M. The colipase-bile salt micelle association can fix one molecule of lipase to form a ternary complex which represents an interesting model of a protein-protein interaction mediated by an organized lipid structure. The ternary complex is probably also a model for lipase-substrate interactions in the presence of an amphipath.     

Epitope-dependent blocking of the angiotensin-converting enzyme dimerization by monoclonal antibodies to the N-terminal domain of ACE: possible link of ACE dimerization and shedding from the cell surface

In a biomembrane modeling system, reverse micelles, somatic ACE forms dimers via carbohydrate-mediated interaction, providing evidence for the existence of a carbohydrate-recognizing domain on the ACE molecule. We localized this putative region on the N-domain of ACE using monoclonal antibodies (mAbs) to seven different epitopes of ACE. Two mAbs, 9B9 and 3G8, directed to distinct, but overlapping, epitopes of the N-domain of ACE shielded the CRD. Only "simple" ACE-antibody complexes were found in the system. Five mAbs allowed the formation of "double" antibody-ACE-ACE-antibody complexes via carbohydrate-mediated interactions. The results were confirmed using the ACE N- and C-domains. Testicular ACE was unable to form carbohydrate-mediated ACE dimers in the reverse micelles, while the N-domain of ACE, obtained by limited proteolysis of the parent full-length ACE, retained the ability to form dimers. Furthermore, mAb 3G8, which blocked ACE dimerization in micelles, significantly inhibited ACE shedding from the surface of ACE-expressing cells. Galactose prevented ACE dimerization in reverse micelles and also affected antibody-induced ACE shedding in an epitope-dependent manner. Restricted glycosylation of somatic ACE, obtained by the treatment of CHO-ACE cells with the glucosidase inhibitor N-butyldeoxynojirimycin, significantly increased the rate of basal ACE shedding and altered antibody-induced ACE shedding. A chemical cross-linking approach was used to show that ACE is present (at least in part) as noncovalently linked dimers on the surface of CHO-ACE cells. These results suggest a possible link between putative ACE dimerization on the cell surface and the proteolytic cleavage (shedding) of ACE.     

Dynamic analysis of a simplified bone model during the process of fracture healing

The dynamic analysis of fracture healing is tackled numerically by means of a bone model which uses the finite element method. The model is of non-uniform cross-sectional area and moment of inertia. Shear and rotatory inertia are taken into account. Considerable variation of the upper natural frequencies is observed as the healing process progresses. The practical implications, as well as present limitations, of the technique are examined.