Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of 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. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. 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. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Computer perception of topological symmetry by all-paths algorithm

During the development of our ESESOC system (Expert System for the Elucidation of the Structures of Organic Compounds), computer perception of topological symmetry is essential in searching for the canonical description of a molecular structure, removing the irredundant connections in the structure generation process, and specifying the number of peaks in C-13- and H-1-NMR spectra in the structure evaluation process. In the present paper, a new path identifier is introduced and an algorithm for detection of topological symmetry from a connection table is developed by the all-paths method. (C) 1999 Elsevier Science B.V. All rights reserved.

Developing molecular identification numbers by an all-paths method

A new topological index is devised from an all-paths method. This molecular topological index has highly discriminating power for various kinds of organic compounds such as alkane trees, complex cyclic or polycyclic graphs, and structures containing heteroatoms and thus can be used as a Molecular IDentification number (MID) for chemical documentation. Some published MIDs derived from an all-paths method and their structural selectivity for alkane trees are also reviewed.

Plastic zone in front of mode I crack in phenolphthalein polyether ketone

The plastic zone size and crack opening displacement of phenolphthalein polyether ketone (PEK-C) at various conditions were investigated. Both of them increase with increasing temperature (decreasing strain rate), i.e. yield stress steadily falls. Thus, the mechanism increasing the yield stress leads to increased constraint in the crack tip and a corresponding reduction in the crack opening displacement and the plastic deformation zone. The effect of the plastic deformation on the fracture toughness is also discussed.

COMPARISON OF THE CRACK-GROWTH METHOD AND THE CRACK STRESS WHITENING ZONE METHOD FOR THE FRACTURE-TOUGHNESS DETERMINATION OF PHENOLPHTHALEIN POLY(ETHER KETONE)

Fracture toughness values of phenolphthalein poly(ether ketone) (PEK-C) at 190 degrees C were determined by two different methods, i. e. the conventional crack growth method and the crack stress whitening zone method, which show consistent results. This indicates that the crack stress whitening zone method can be used to determine the crack initiation of some polymers for which the blunting line concept is unsuitable.

J-INTEGRAL STUDIES OF CRACK INITIATION AND CRACK TIP-BLUNTING OF PHENOLPHTHALEIN POLYETHER KETONE

The J-integral is applied to characterize the fracture initiation of phenolphthalein polyether ketone (PEK-C) for which the concepts of linear elastic fracture mechanics (LEFM) are inapplicable at high temperatures for reasonably-sized specimens due to ex