Quantitative comparison of experimental and simulated NOE intensities: Correlation with accuracy of oligonucleotide structure determination

Summary The relation between the match of experimental and simulated NOE intensities with the accuracy of structure determination of oligonucleotides has been investigated. A hypothetical experimental spectrum of the oligonucleotide d(CCAACGTTGG) from its known X-ray crystallographic structure (Privé, G.G. et al. (1991)J. Mol. Biol.,217, 177–199) has been generated with simplifying assumptions of single correlation time, leakage rate etc., and this spectrum has been simulated imposing various constraints in a manner as one would do in a real case. The hypothetical spectrum represents the case of an infinitely good experimental spectrum and therefore the study of quality of fit against quality of structure represents the limiting case of real situations. It has been shown that even with a limited number of NOEs, it is possible to approach the correct structure of the molecule by demanding a highly accurate fit between experimental and simulated NOE intensities. Distance geometry calculations have been used to probe the extent of structural degeneracies in the NOE intensity matching exercise.     

Formation of Transient Clusters on Nanoscopic Length Scales in a Simulated One-Component Supercooled Liquid

Dense liquids above their glass transition exhibit spatially heterogeneous dynamics in which regions within the liquid exhibit enhanced or diminished mobility relative to the average on some time scale. Substantial evidence suggests that these regions are confined to nanoscopic sizes at temperatures close to the mode coupling temperature T ^MCT, and reach well beyond the characteristic length scale over which the two-point static structure of the liquid is correlated. In this paper, we investigate the formation of clusters of mobile particles in a dynamically heterogeneous model liquid. We find that clusters are formed as a result of mobility propagation that begins from distributed locations confined within a nanoscopic local structure. This mobility is facilitated through the development of quasi-one dimensional string-like rearrangements within the nanoscopic region.     

Constructing ab initio models of ultra-thin Al–AlOx–Al barriers

The microscopic structure of ultra-thin oxide barriers often plays a major role in modern nano-electronic devices. In the case of superconducting electronic circuits, their operation depends on the electrical nonlinearity provided by one or more such oxide layers in the form of ultra-thin tunnel barriers (also known as Josephson junctions). Currently available fabrication techniques manufacture an amorphous oxide barrier, which is attributed as a major noise source within the device. The nature of this noise is currently an open question and requires both experimental and theoretical investigation. Here, we present a methodology for constructing atomic-scale computational models of Josephson junctions using a combination of molecular mechanics, empirical and ab initio methods. These junctions consist of ultra-thin amorphous aluminium-oxide layers sandwiched between crystalline aluminium. The stability and structure of these barriers as a function of density and stoichiometry are investigated, which we compare with experimentally observed parameters.     

On the mechanical characterization of compact bone structure using the homogenization theory

In a previous paper (Crolet et al., 1993, J. Biomechanics 26, 677–687), a modelling of the mechanical behavior of compact bone was presented, in which the homogenization theory was the basic tool of computation. In this simulation, approximations were used for the modelling of the lamellae and the osteons: the lamella and the osteon were divided into cylindrical sectors, each sector being approximated as a parallelepiped having a periodic structure (fibrous composite for the lamella, superimposition of plates for the osteon). The present study deals with a new model without these approximations. First, it can be proved that the homogenized elasticity tensor for a lamella, which has a non-periodic structure, is obtained at each geometrical point as a homogenized tensor of a periodic problem. Similarly, for the osteonal structure, the components of the homogenized tensor are determined at each point as the result of a periodic homogenization.

The software OSTEON, which is the computational method associated with this model, allows one to obtain a better understanding of the effects of many bony parameters. The obtained results are in accordance with experimental data.     

A Molecular Dynamics Study for Lithium Metasilicate: Liquid and Quenched Supercooled States

A molecular dynamics (MD) simulation of the lithium metasilicate (Li₂SiO₃) system has been performed to study the dynamics and geometrical structure of a liquid state at 1673 K and a glassy state at 700 K. The long term dynamics of the glassy state is shown for the self-part of the van Hove correlation functions. In the glassy state, diffusion of lithium ion was found to occur mainly through jump motions among equilibrium sites surrounded by oxygen atoms. A geometric structural analysis with polyhedra made of oxygen atoms around lithium was applied to characterize the structure and dynamical behavior.     

Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: A simulation study

The exchange-transferred NOE method to determine the three-dimensional structure of peptides bound to proteins, or other macromolecular systems, is becoming increasingly important in drug design efforts and for large or multicomponent assemblies, such as membrane receptors, where structural analysis of the full system is intractable. The exchange-transferred nuclear Overhauser effect spectroscopy (etNOESY) method allows the determination of the bound-state conformation of the peptide from the intra-molecular NOE interactions between ligand protons. Because only ligand–ligand NOEs are generally observable, the etNOESY method is restricted to fewer NOEs per residue than direct protein structure determination. In addition, the averaging of relaxation rates between free and bound states affects the measured cross-peak intensities, and possibly the accuracy of distance estimates. Accordingly, the study reported here was conducted to examine the conditions required to define a reliable structure. The program CORONA was used to simulate etNOE data using a rate-matrix including magnetic relaxation and exchange rates for two peptide–protein complexes derived from the reference complex of cAMP-dependent protein kinase ligated with a 24-residue inhibitor peptide. The results indicate that reasonably accurate peptide structures can be determined with relatively few NOE interactions when the interactions occur between non-neighboring residues. The reliability of the structural result is suggested from the pattern of NOE interactions. A structure with an accuracy of approximately 1.3 Å rms difference for the main-chain atoms can be obtained when etNOE interactions between non-neighboring residues occur over the length of the peptide. The global precision is higher (approximately 0.9 Å rms difference) but is not correlated to global accuracy. A local definition of precision along the backbone appears to be a good indicator of the local accuracy.     

Study of Liquid Dimethyl Sulfoxide by Computer Simulation

The paper reports Monte Carlo and molecular dynamicsresults for pure liquid dimethyl sulfoxide (DMSO) at298 K and 1 atm. The classical 6–12 Lennard–Jones plusCoulomb pairwise potential was used to calculateintermolecular interaction energy. Potentialparameters for the liquid were optimized in this work.Some thermodynamic and dynamical properties obtained,such as heat of vaporization, density and diffusioncoefficient, are in good agreement with theexperimental values. The present model is comparedwith other models for DMSO reported previously. It isshown to be an improvement over earlier potentials.The structure factors and the radial distributionfunctions (rdf), are compared with experimentalresults for the liquid. The analysis shows that thestructure of DMSO is not completely understood yet anddeserves deeper investigation. The geometry of thedimer that corresponds to the rdf plots obtained, isreported. The results suggest that the dipole momentof this dimer plays an important role in the structureof the liquid.     

The thermosetting resin prepared by curing reaction of typical soybean oil and properties of the product network structures: a multiscale simulation study

With our multiscale simulation strategy developed previously, we study the curing reaction of soybean oil and styrene to prepare a thermosetting resin. From atomistic simulation details, we estimate the parameters used in coarse-grained (CG) simulations. Then, with the mesoscopic dissipative particle dynamics simulation, the CG network structure and average cross-linking density of a material can be obtained. Finally, the reverse-mapping scheme of the CG structure to atomistic representation is carried out to analyse the mechanical properties and the glass transition temperature of the system. We find in such a system that the molar ratio of double bonds in the two reactants plays a significant role in determining the physical properties of a product. These results shed light on improved control and design of thermosetting resin material via curing reaction of soybean oil.     

Solution structure by nuclear magnetic resonance of the two lantibiotics 97518 and NAI‐107

Lantibiotics 97518 and NAI‐107, produced by the related genera Planomonospora and Microbispora respectively, are members of a family of nisin‐related compounds. They represent promising compounds to treat infections caused by multiresistant Gram‐positive pathogens. Despite their similar structure and a similar antibacterial spectrum, the two lantibiotics exhibit significant differences in their potency. To gain an insight into the structure–activity relationships, their conformational properties in solution are determined by NMR. After carrying out an NOE analysis of 2D ¹H NMR spectra, high‐resolution 3D structures are determined using molecular dynamics simulations. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water

The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using “realistic” potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.     

Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model

Biophysical forcefields have contributed less than originally anticipated to recent progress in protein structure prediction. Here, we have investigated the selectivity of a recently developed all‐atom free‐energy forcefield for protein structure prediction and quality assessment (QA). Using a heuristic method, but excluding homology, we generated decoy‐sets for all targets of the CASP7 protein structure prediction assessment with <150 amino acids. The decoys in each set were then ranked by energy in short relaxation simulations and the best low‐energy cluster was submitted as a prediction. For four of nine template‐free targets, this approach generated high‐ranking predictions within the top 10 models submitted in CASP7 for the respective targets. For these targets, our de‐novo predictions had an average GDT_S score of 42.81, significantly above the average of all groups. The refinement protocol has difficulty for oligomeric targets and when no near‐native decoys are generated in the decoy library. For targets with high‐quality decoy sets the refinement approach was highly selective. Motivated by this observation, we rescored all server submissions up to 200 amino acids using a similar refinement protocol, but using no clustering, in a QA exercise. We found an excellent correlation between the best server models and those with the lowest energy in the forcefield. The free‐energy refinement protocol may thus be an efficient tool for relative QA and protein structure prediction. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

耐热碱性磷酸酶突变体耐热性变化机理研究

从耐热碱性磷酸酶（TAP）200多个随机突变体的克隆库中选出耐热性明显下降的4株突变体,进行全序列及表达产物的最高耐受温度和最适反应温度测定和酶分子高级结构的模拟,分析突变位点、高级结构和耐热性表现三者的关系,探讨引起耐热性变化的机理。结构模拟显示所有突变位点都仅能引起细微的、局部的结构变化,除T320→I外都未直接触及酶的活性中心;结构上的细微改变虽然对最适反应温度影响不明显,但却使最高耐受温度降低了10℃左右;T320→I靠近酶的活性中心,尽管未能引起结构的较大变化,但却使最高耐受温度和最适反应温度同时显著降低。可见,多数点突变对高级结构的影响都不剧烈,但对耐热性尤其是最高耐受温度的影响却比较明显,一般地,在非活性区的突变通常只能引起最高耐受温度的降低,靠近活性区的突变则能同时引起最适反应温度和最高耐受温度的降低。     

Wetting control through topography and surface hydrophilic/hydrophobic property changes by coarse grained simulation

Abstract

The changes of wetting state of water droplet on the solid surface featuring pillared structures are quantitatively studied by Coarse Grained simulation. Our results demonstrate that wetting state changes with the different topography (surface roughness), and it depends on the intrinsic hydrophilic/hydrophobic property of surface as well. Only if the contact angle of water droplet on the smooth surface is larger than 93.13°, the wetting state translates from the Wenzel state to the Cassie state on the rough surface with certain pillar height and width, and the contact angle climb up to the highest point and then remain almost unchanged with the increasing of pillar height and the same pillar distance. However, the wetting state does not change if the contact angle on the smooth surface is 85.1° or less, no matter what pillar structure the surface has. Additionally, the contact angles will remain almost unchanged if the pillar height is higher than a certain value. Our simulation results provide a quantitative understanding about the wetting state of water droplet on solid rough surfaces, and the results show the wetting state can be controlled by combining rough structure design and hydrophilic/hydrophobic property change of surfaces.     

Impact of deglycosylation and thermal stress on conformational stability of a full length murine igG2a monoclonal antibody: Observations from molecular dynamics simulations

With the rise of antibody based therapeutics as successful medicines, there is an emerging need to understand the fundamental antibody conformational dynamics and its implications towards stability of these medicines. Both deglycosylation and thermal stress have been shown to cause conformational destabilization and aggregation in monoclonal antibodies. Here, we study instabilities caused by deglycosylation and by elevated temperature (400 K) by performing molecular dynamic simulations on a full length murine IgG2a mAb whose crystal structure is available in the Protein Data bank. C^α‐atom root mean square deviation and backbone root mean square fluctuation calculations show that deglycosylation perturbs quaternary and tertiary structures in the C_H2 domains. In contrast, thermal stress pervades throughout the antibody structure and both Fabs and Fc regions are destabilized. The thermal stress applied in this study was not sufficient to cause large scale unfolding within the simulation time and most amino acid residues showed similar average solvent accessible surface area and secondary structural conformations in all trajectories. C_H3 domains were the most successful at resisting the conformational destabilization. The simulations helped identify aggregation prone regions, which may initiate cross‐β motif formation upon deglycosylation and upon applying thermal stress. Deglycosylation leads to increased backbone fluctuations and solvent exposure of a highly conserved APR located in the edge β‐strand A of the C_H2 domains. Aggregation upon thermal stress is most likely initiated by two APRs that overlap with the complementarity determining regions. This study has important implications for rational design of antibody based therapeutics that are resistant towards aggregation. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods,sample size and population structure

The distribution of fitness effects (DFE) of new mutations has been of interest to evolutionary biologists since the concept of mutations arose. Modern population genomic data enable us to quantify the DFE empirically, but few studies have examined how data processing, sample size and cryptic population structure might affect the accuracy of DFE inference. We used simulated and empirical data (from Arabidopsis lyrata) to show the effects of missing data filtering, sample size, number of single nucleotide polymorphisms (SNPs) and population structure on the accuracy and variance of DFE estimates. Our analyses focus on three filtering methods—downsampling, imputation and subsampling—with sample sizes of 4–100 individuals. We show that (1) the choice of missing-data treatment directly affects the estimated DFE, with downsampling performing better than imputation and subsampling; (2) the estimated DFE is less reliable in small samples (<8 individuals), and becomes unpredictable with too few SNPs (<5000, the sum of 0- and 4-fold SNPs); and (3) population structure may skew the inferred DFE towards more strongly deleterious mutations. We suggest that future studies should consider downsampling for small data sets, and use samples larger than 4 (ideally larger than 8) individuals, with more than 5000 SNPs in order to improve the robustness of DFE inference and enable comparative analyses.     

Study of PE and iPP orientations on the surface of carbon nanotubes by using molecular dynamic simulations

In this study, the early stage of interfacial crystallisation behaviour of low molecular weight polyethylene (PE) and isotactic polypropylene (iPP) oligomer on the surface of carbon nanotubes (CNTs) with different diameters, chiralities and topography structures was studied using MD simulations. We started to simulate the effect of CNTs chirality and diameter on PE molecular chain orientation, and then the effect of CNTs topography structure on PE and iPP molecular chain orientation was investigated. Finally, some experiments were carried out to prove the simulated results. Our study shows that for CNTs with a diameter comparable with the radius of gyration (R_g) of a polymer chain, an easy orientation of PE chains along CNTs axis is observed for all the systems of the CNTs with different chiralities due to a geometric confinement effect. For CNTs with a much larger diameter, multiple orientation of PE chains is induced on its surface due to the lattice matching between graphite lattice and PE molecular chains. In this case, the chirality of CNTs dominates the orientation of graphite lattice, which determines the orientation of PE chains arrangement on CNTs surface. More importantly, it was found that the groove structure formed by CNT bundles is very useful for the stabilisation of polymer chain, and thus facilitates the orientation of molecular chain along the long axis of CNTs. As a result, a novel nanohybrid shish–kebab (NHSK) structure with CNTs acting as central shish while polymer lamellae as kebab can be successfully obtained for both PE with zigzag conformation and iPP with helical conformation. This simulation result was well supported by the experimental observation. Our study could provide not only a deep understanding of the origin of the polymer chain orientation on CNTs surface but also the guidance for the preparation of polymer/CNTs nanocomposites with novel NHSK structure.     

Modeling and simulation of musculoskeletal system of human lower limb based on tensegrity structure

Abstract

In this paper, a mechanical model of the skeletal muscle of human lower limb system is established by using the Hill muscle model and kinetic equation of the movement of lower extremities according to the attachment positions of skeletal muscle. State vector and neural control are delineated by the direct configuration method. Changes of gait and skeletal muscle stress during walking process are analyzed with energy consumption as objective function. Results illustrate that simulation data are in good agreement with actual walking gait data. Feasibility and correctness of the designed model and control behavior of skeletal muscle tension structure are also verified.     

HIV-1整合酶四聚体结构模拟及其活性位点分析

HIV-1复制需要HIV-1整合酶将其环状DNA整合进宿主DNA中,这其中包括2个重要反应,即“3′-加工”和“链转移”,两者均由HIV-1整合酶催化完成.阻断其中的任一反应,都能达到抑制HIV-1复制的目的.因此,了解HIV-1整合酶的完整结构和聚合状态,对深入探讨其作用机理及设计新型抑制剂具有重要的指导作用.然而,迄今为止仅有HIV-1整合酶单独结构域的晶体结构可供参考,而其全酶晶体结构尚未获得解析.本研究利用分子模拟技术,通过蛋白质 蛋白质/DNA分子对接、动力学模拟等方法,构建了全长整合酶四聚体的结构模型、HIV-1 DNA与整合酶复合物的结构模型,进一步从理论上证实HIV-1整合酶是以四聚体形态发挥催化作用,明确“3′-加工”和“链转移”在HIV-1整合酶上的催化位点.同时,通过与作用机理相似的细菌转座子Tn5转座酶等的结构比对,推测HIV-1整合酶的核心结构域中应有第2个Mg^２＋存在,其位置螯合于Asp64与Glu152之间.在HIV-1整合酶结构研究的基础上,有望进一步设计出新的抗艾滋病药物.     

Simulation of NOESY spectra of DNA segments: A new scaling procedure for iterative comparison of calculated and experimental NOE intensities

Summary A new algorithm for simulation of two-dimensional NOESY spectra of DNA segments has been developed. For any given structure, NOE intensities are calculated using the relaxation matrix approach and a new realistic procedure is suggested for 1:1 comparison of calculated and experimental intensities. The procedure involves a novel method for scaling of calculated NOE intensities to represent volumes of digitised cross peaks in NOESY spectra. A data base of fine structures of all the relevant cross peaks with Lorentzian line shapes and in-phase components, is generated in a digitised manner by two-dimensional Fourier transformation of simulated time domain data, assuming a total intensity of 1.0 for each of the cross peaks. With this procedure, it is shown that the integrated volumes of these digitised cross peaks above any given threshold scale exactly as the total intensity of the respective peaks. This procedure eliminates the repetitive generation of digitised cross peaks by two-dimensional Fourier transformation during the iterative process of structure alteration and NOE intensity calculation and thus enhances the speed of DNA structure optimization. Illustrative fits of experimental and calculated spectra obtained using the new procedure are shown.[/p]