Nonuniformity of nucleotide substitution rates in molecular evolution: Computer simulation and analysis of 5S ribosomal RNA sequences

Summary The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.     

Brownian dynamics simulation of the unsaturated lipidic molecules oleic and docosahexaenoic acid confined in a cellular membrane

A Brownian dynamics (BD) simulation of two unsaturated molecules, oleic and docosahexaenoic acid, in an environment that reproduces a cellular membrane, is presented. The results of the simulations, performed using mean-field potentials, were calibrated with experimental results obtained for oleic acid in a cellular membrane. The agreement between simulation and experimental results is excellent which validates subsequent simulation outcome for docosahexaenoic acid. This molecule is a major component of several cellular membranes thought to be involved in specific biological functions that require conformational changes of membrane components. The results for docosahexaenoic acid indicate that it is minimally influenced by temperature changes and that it presents great conformational variability.     

Computer simulation of Zn(II) speciation and effect of Gd(III) on Zn(II) speciation in human blood plasma

The speciation and distribution of Zn(II) and the effect of Gd(III) on Zn(II) speciation in human blood plasma were studied by computer simulation. The results show that, in normal blood plasma, the most predominant species of Zn(II) are [Zn(HSA)] (58.2%), [Zn(IgG)](20.1%), [Zn(Tf)] (10.4%), ternary complexes of [Zn(Cit)(Cys)] (6.6%) and of [Zn(Cys)(His)H] (1.6%), and the binary complex of [Zn(Cys)₂H] (1.2%). When zinc is deficient, the distribution of Zn(II) species is similar to that in normal blood plasma. Then, the distribution changes with increasing zinc(II) total concentration. Overloading Zn(II) is initially mainly bound to human serum albumin (HSA). As the available amount of HSA is exceeded, phosphate metal and carbonate metal species are established. Gd(III) entering human blood plasma predominantly competes for phosphate and carbonate to form precipitate species. However, Zn(II) complexes with phosphate and carbonate are negligible in normal blood plasma, so Gd(III) only have a little effect on zinc(II) species in human blood plasma at a concentration above 1.0×10⁻⁴ M.     

Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin

Molecular interaction between p53 tumor suppressor and the copper protein azurin (AZ) has been demonstrated to enhance p53 stability and hence antitumoral function, opening new perspectives in cancer treatment. While some experimental work has provided evidence for AZ binding to p53, no crystal structure for the p53-AZ complex was solved thus far. In this work the association between AZ and the p53 DNA-binding domain (DBD) was investigated by computational methods. Using a combination of rigid-body protein docking, experimental mutagenesis information, and cluster analysis 10 main p53 DBD-AZ binding modes were generated. The resulting structures were further characterized by molecular dynamics (MD) simulations and free energy calculations. We found that the highest scored docking conformation for the p53 DBD-AZ complex also yielded the most favorable free energy value. This best three-dimensional model for the complex was validated by using a computational mutagenesis strategy. In this structure AZ binds to the flexible L(1) and s(7)-s(8) loops of the p53 DBD and stabilizes them through protein-protein tight packing interactions, resulting in high degree of both surface matching and electrostatic complementarity.     

Computer simulation of the association of caffeine and actinocin derivatives in aqueous solutions

The association of caffeine and actinocin derivatives (ActII), analogs of the antitumor antibiotic actinomycin D, was studied by molecular dynamics simulation in explicit solvent (water and Na⁺ and Cl^? ions). Information was obtained describing in detail the association of caffeine and ActII in water and water-salt solution and the interaction of monomers and their associates with the ionic hydrate environment. The schemes of hydration of monomers of actinocin derivatives and caffeine and their self-and heteroassociates are determined. The calculated energies of monomer interaction in associates indicate that dimerization of these compounds in aqueous solutions is advantageous in energy. Both self-and heteroassociates are stabilized by van der Waals, electrostatic, and hydrophobic interactions, as well as intermolecular hydrogen bonds. The rearrangement of the hydration shells of monomers during their association in water is energy-unfavorable and destabilizes the associates. In water-salt solutions, it is energy-favorable for the systems containing associates of the singly charged ActII⁺ and caffeine-ActII⁺. The formation of caffeine-actinocin heterodimers is preferable in energy to the formation of self-associates. In this way caffeine can decrease the concentration of the actinocin derivatives in solution and thereby decrease their biological activity.     

Computer simulation of the effects of shoe cushioning on internal and external loading during running impacts

Biomechanical aspects of running injuries are often inferred from external loading measurements. However, previous research has suggested that relationships between external loading and potential injury-inducing internal loads can be complex and nonintuitive. Further, the loading response to training interventions can vary widely between subjects. In this study, we use a subject-specific computer simulation approach to estimate internal and external loading of the distal tibia during the impact phase for two runners when running in shoes with different midsole cushioning parameters. The results suggest that: (1) changes in tibial loading induced by footwear are not reflected by changes in ground reaction force (GRF) magnitudes; (2) the GRF loading rate is a better surrogate measure of tibial loading and stress fracture risk than the GRF magnitude; and (3) averaging results across groups may potentially mask differential responses to training interventions between individuals.     

Effect of nanostructure on heat transfer between fluid and copper plate: a molecular dynamics simulation study

A molecular simulation is developed to study the effect of surface nanostructures on nanoscale flows. Based on this method, particles equation of motion is solved through the Verlet algorithm. Meanwhile, a physically sound method is applied to control the momentum and temperature of the simulation box. By adding an external force on the top copper plate according to the velocity difference between on-the-fly and desired velocities, simulations on convection of argon flows between two solid walls are performed. The top wall, which holds a higher temperature, moves at a constant velocity relative to bottom one along with the streamwise direction. These simulation results show that the nanostructures particularly affect fluid density oscillations adjacent to solid wall and nanostructures. In addition, these nanostructures also have significant effects on temperature and velocity distributions in simulation system.     

The relationship between guard cell water potential and the aperture of stomata in Populus

Abstract Previous work with clones of Populus trichocarpa demonstrated that the water vapour conductance of leaves from well-watered cuttings of this species does not decline with loss of turgor from the bulk leaf. In the present study, stomatal responses to water potential in Populus were examined with detached epidermal strips. Stomata in epidermal strips from well-watered plants of P. trichocarpa did not close at low water potentials which led to plasmolysis of the guard cells. In contrast, stomata of P. deltoides and a P. trichocarpa×deltoides hybrid closed when the guard cells lost turgor. A period of water stress preconditioning resulted in modified stomatal responses in P. trichocarpa such that stomata of stressed and re-watered plants nearly closed when guard cell turgor was lost.     

Exploration of potential RSK2 inhibitors by pharmacophore modelling,structure-based 3D-QSAR,molecular docking study and molecular dynamics simulation

Abstract

The p90 ribosomal s6 kinase 2 (RSK2) is a promising target because of its over expression and activation in human cancer cells and tissues. Over the last few years, significant efforts have been made in order to develop RSK2 inhibitors to treat myeloma, prostatic cancer, skin cancer and etc., but with limited success so far. In this paper, pharmacophore modelling, molecular docking study and molecular dynamics (MD) simulation have been performed to explore the novel inhibitors of RSK2. Pharmacophore models were developed by 95 molecules having pIC₅₀ ranging from 4.577 to 9.000. The pharmacophore model includes one hydrogen bond acceptor (A), one hydrogen bond donor (D), one hydrophobic feature (H) and one aromatic ring (R). It is the best pharmacophore hypothesis that has the highest correlation coefficient (R² = 0.91) and cross validation coefficient (Q² = 0.71) at 5 component PLS factor. It was evaluated using enrichment analysis and the best model was used for virtual screening. The constraints used in this study were docking score, ADME properties, binding free energy estimates and IFD Score to screen the database. Ultimately, 12 hits were identified as potent and novel RSK2 inhibitors. A 15 ns molecular dynamics (MD) simulation was further employed to validate the reliability of the docking results.     

The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model

Abstract

The capacity of silencing genes makes small interfering RNA (siRNA) becomes potential candidates for curing many fatal diseases. Due to the low stability and delivery efficiency of siRNA, the design of amphiphilic carrier for siRNA delivery is vital for the practical gene therapy. In the present work, we explored how the complexation and dissociation of siRNA with poly (maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine (PMAL), which is a recent synthesised amphiphilic polymer and can be used in delivery of siRNAs and proteins, using traditional molecular dynamics simulations, together with steered molecular dynamics simulations. It was shown that the complexation of siRNA with PMALs can spontaneously occur, no matter what unit number of PMAL is. PMALs of different unit numbers form micelle-like structures and interact with siRNA surface. With the increase of unit number, PMAL becomes more flexible and interacts with siRNA from attachment to entanglement. The dissociation of PMAL from siRNA is an energy-consuming process. The free energy difference increases with the unit number of PMAL. The free energy for dissociation involves both the stretch of PMAL and the separation of PMAL from siRNA. Therefore, an optimal unit number of PMAL is critical for the delivery efficiency of siRNA when PMAL is used as carrier. In present work, when the radius of gyration of PMAL approaches to that of siRNA, PMAL gives a favoured both complexation and dissociation between siRNA and PMAL. Finally, we propose the mechanism of complexation and dissociation of PMAL with siRNA. The above simulation established a molecular insight of the interaction between siRNA and PMAL and was helpful for the design and applications of new PMAL-based polymers as siRNA delivery carriers.     

黄土高原不同类型旱区苜蓿草地水分生产潜力与土壤干燥化效应模拟

在模型验证和数据库组建基础上,用WinEPIC模型定量模拟研究了黄土高原半湿润区长武、半干旱区固原和半干旱偏旱区海原20～30年内苜蓿草地水分生产潜力、10m土层土壤有效含水量和土壤湿度剖面分布特征的动态变化.结果表明:长武、固原和海原苜蓿草地水分生产潜力模拟值随降水量变化而呈现波动性降低趋势,其平均值分别为8.81、3.83和2.48t.hm-2;长武、固原和海原苜蓿草地10m土层逐月土壤有效含水量模拟值均呈现明显的波动性降低趋势,模拟初期,4～8年生苜蓿草地土壤干燥化趋势十分强烈,此后,随降水量变化长期在较低水平上波动;随着苜蓿生长年限的延长,苜蓿草地土壤干层逐年加深、加厚,长武、固原和海原土壤干层分布深度达到10m所需时间依次为6、6和4年,此后苜蓿草地降水渗深以下土层长期维持较为稳定的干燥化状态;苜蓿草地水分持续利用的合理年限为半湿润区8～10年,半干旱区6～8年,半干旱偏旱区4～6年.     

Energetic and entropic contributions to the interactions between like-charged groups in cationic peptides: A molecular dynamics simulation study

The interaction between like-charged amino acid residues has been proposed to stabilize the folded state of peptides and proteins, and to modulate the substrate binding and the action mechanism of enzymes. We have used an alanine- and lysine-based peptide as a model system to study the interaction between like charges, and we have performed a 16-nsec molecular dynamics simulation in solution. The calculated potential of mean force for the approach of the lysine's Nzeta atoms showed a minimum at a distance of 0.7 nm, in agreement with the separation probabilities obtained from analysis of protein crystal structures. The analysis of the individual energy components showed that the solvent polarization pays for the approach of the like charges and that the van der Waals energies do not contribute significantly. The entropic contributions have been divided in conformational and desolvation terms. Both terms favor the formation of the charge pair. A 10-fold increase in counterion concentration was observed-with respect to its bulk concentration-next to the peptide charges, which helps to stabilize the peptide charges at a close distance.     

A relationship between the midpoint potential of the primary acceptor and low temperature photochemistry in photosystem II

Redox titrations of the photo-induced pheophytin EPR signal in Photosystem II show two transitions which reflect the redox state of Q. The high potential wave (E_m ? ?50 mV) can be photo-induced at 5 K and 77 K. The low potential wave (E_m ? ?275 mV) required illumination at 200 K. This indicates the presence of two kinds of PS-II reaction centres differing in terms of the competence of their donors at low temperature and the E_m-values of their acceptors. Measurements of the semiquinone-iron acceptor also demonstrate functional heterogeneity at low temperature. This is the first observation of the semiquinone-iron acceptor in a non-mutant species.     

The developing relationship between the study of fungal communities and community ecology theory

Plant and animal systems had a head start of several decades in community ecology and have largely created the theoretical framework for the field. I argue that the lag in fungal community ecology was largely due to the microscopic nature of fungi that makes observing species and counting their numbers difficult. Thus the basic patterns of fungal occurrence were, until recently, largely invisible. With the development of molecular methods, especially high-throughput sequencing, fungal communities can now be “seen”, and the field has grown dramatically in response. The results of these studies have given us unprecedented views of fungal communities in novel habitats and at broader scales. From these advances we now have the ability to see pattern, compare it to existing theory, and derive new hypotheses about the way communities are assembled, structured, and behave. But can fungal systems contribute to the development of theory in the broader realm of community ecology? The answer to this question is yes! In fact fungal systems already have contributed, because in addition to many important natural fungal communities, fungi also offer exceptional experimental communities that allow one to manipulate, control, isolate and test key mechanisms. I discuss five well-developed systems and some of the contributions they have made to community ecology, and I briefly mention one additional system that is amenable to development.