Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Extended topological indices and prediction of activities of chiral compounds

The activities/properties of two molecules with identical formula but different configuration states of the asymmetric atoms are different. Thus, usually the common topological indices are not suitable. In this study, the chiral topological indices were obtained by extending A(mi) indices suggested by our laboratory and molecular connectivity indices. The modified topologial indices have been used for the studies on D2 for dopamine receptor and a receptor activities of fourteen N-alkylated 3-(3-hydroxypyenyl)-piperidines. It has been observed that selected variables possess low correlations. The results obtained by using multiple regression analysis and artificial neural networks are satisfactory.

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.

Correlation analysis of the structures and gas-liquid chromatographic retention indices of amines

Quantitative structure-retention relationship(QSRR) was studied for amines to gas-liquid chromatography on three stationary phases of different polarities with the topological indices A(m) (A(m1), A(m2), A(m3)) and gravitational index GI. The algorithm of "Leaps and Bounds" was performed for selection of the variables. And the multi-regression and the quasi-Newton neural networks were employed for the calculation with better results.

Study on relationship between partition coefficient of compounds and topological indices

In this work, the A(m) indices and the molecular connectivity indices of fifty aromatic compounds have been calculated, and applied for studying on relationship between partition coefficient and structure of aromatic compounds. The results demonstrate that the property of compounds can be described better with revisionary A(m) indices.

Study on structure-property relationships between color reagents and sensitivity of color reactions with yttrium by topological indices

In this paper, three topological indices, Am-1, Am-2, and Am-3, multivariate analysis in structure-property studies. The topological indices of twenty asymmetrical phosphosphono bisazo derivatives of chromotropic acid have been calculated. The structure-property relationships between color reagents and molar absorptivity of color reactions with yttrium have been studied by A(m) indices and structure selective factors. Good results have been obtained by using correlation equation to predict the molar absorptivity of new color reagents.

Studies on structure-property relationship between color reagents and contrast of their color reactions with cerium by topological indices

In this paper, three topological indices A(m1), A(m2) and A(m3) have been applied to multivariate analysis in structure property relationship studies. The topological indices oi fourty-three asymmetrical phosphono bisazo derivatives of chromotropic acid have been calculated, The structure-property relationship between color reagents and contrast of color reactions with cerium has been studied by A, indices and structure selective factors, Good results have been obtained.

Genetic diversity of the subterranean Gansu zokor in a semi-natural landscape

We studied the relationship between genetic diversity of the subterranean Gansu zokor Myospalax cansus and habitat variability in the Loess Plateau, Qinghai Province, China. We used a combination of geographic information systems and molecular techniques to assess the impact of habitat composition and human activities on the genetic diversity of zokor populations in this semi-natural landscape. Although they occurred relatively infrequently in the landscape, woodland and high-coverage grassland habitats were the main positive contributors to the genetic diversity of zokor populations. Rural residential land, plain agricultural land and low-coverage grassland had a negative effect on genetic diversity. Hilly agricultural land and middle-coverage grassland had little impact on zokor genetic diversity. There were also interactions between some habitat types, that is, habitat types with relatively better quality together promoted conservation of genetic diversity, while the interaction between (among) bad habitat types made situations worse. Finally, habitat diversity, measured as patch richness and Shannon's diversity index, was positively correlated with the genetic diversity. These results demonstrated that: (1) different habitat types had different effects on the genetic diversity of zokor populations and (2) habitat quality and habitat heterogeneity were important in maintaining genetic diversity. Habitat composition was closely related to land use thus emphasizing the importance of human activities on the genetic diversity of subterranean rodent populations in this semi-natural landscape. Although the Gansu zokor was considered to be a pest species in the Loess Plateau, our study provides insights for the management and conservation of other subterranean rodent species.

A new method of predicting of gas chromatographic retention indices for polychlorinated dibenzofurans (PCDFs)

A new method has been developed to describe the quantitative relationship between molecular structures of PCDFs and their gas chromatographic retention indices on a 30-m fused silica column coated with DB-5 stationary phase. The regression equation is derived with a multiple correlation coefficient greater than 0.9995. The highest residual is 20 index units. The standard deviation is less than 7 index units. Using this regression equation, the retention indices of PCDFs for which data is not available have also been predicted. (C) 2000 Elsevier Science Ltd. All rights reserved.

Faith in the Landscape : Overseas Pilgrimages in 'The Book of Margery Kempe'

Watt, D. (2006). Faith in the Landscape: Overseas Pilgrimages in 'The Book of Margery Kempe'. In C. Lees and G. Overing (Eds.), A Place to Believe In: Locating Medieval Landscapes (pp.170-187). University Park (PA): Pennsylvania State University Press. RAE2008

In Comes I: Performance, Memory and Landscape

Pearson, Mike, In Comes I: Performance, Memory and Landscape (Exeter: University of Exeter Press, 2007) RAE2008