The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase

This paper describes the application of PRO_–LEADS to the flexible docking of ligands into crystallographically derived enzyme structures that are assumed to be rigid. PRO_–LEADS uses a Tabu search methodology to perform the flexible search and an empirically derived estimate of the binding affinity to drive the docking process. The paper tests the extent to which the assumption of a rigid enzyme compromises the accuracy of the results. All-pairs docking experiments are performed for three enzymes (thrombin, thermolysin and influenza virus neuraminidase) based on six or more ligand-enzyme crystal structures for each enzyme. In 76% of the cases, PRO_–LEADS can successfully identify the correct ligand conformation as the lowest energy configuration when the enzyme structure is derived from that ligand's crystal structure, but the methodology only docks 49% of the cases successfully when the ligand is docked against enzyme crystal structures derived from other ligands. Small movements in the enzyme structure lead to an under-prediction in the energy of the correct binding mode by up to 14 kJ/mol and in some cases this under-prediction can lead to the native mode not being recognised as the lowest energy solution. The type of movements responsible for mis-docking are: the movement of sidechains as a result of changes in C position; the movement of sidechains without changes in C position; the movement of flexible portions of main chains to facilitate the formation of hydrogen bonds; and the movement of metal atoms bound to the enzyme active site. The work illustrates that the assumption of a rigid active site can lead to errors in identification of the correct binding mode and the assessment of binding affinity, even for enzymes which show relatively small shift in atomic positions from one ligand to the next. A good docking code, such as PRO_–LEADS, can usually dock successfully if there is induced fit in relatively rigid enzymes but there remains the need to develop improved strategies for dealing with enzyme flexibility. The work implies that treatments of enzyme flexibility which focus only on sidechain rotations will not deal with the critical shifts responsible for mis-docking of ligands in thrombin, thermolysin and neuraminidase. The paper demonstrates the utility of all pairs docking experiments as a method of assessing the effectiveness of docking methodologies in dealing with enzyme flexibility.     

Thermal and mechanical behavior of polyethylene film obtained by orientational crystallization

The thermal and mechanical behaviour was measured in the U. S.for a polyethylene that had been prepared and highly drawn in the U. S. S. R. The melting point and percent crystallinity were evaluated in this studies as a function of heating rate and recrystallization. The Young's modulus and tensile stress to break in the orientation direction were 4.1 and 0.15 GPa, respectively.The tensile strain to break was about 8%.

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Zusammenfassung Das thermische und mechanische Verhalten eines in der UdssR hergestellten und stark gezogenen Polyäthylens wurde in den U. S. A. gemessen. Schmelzpunkt und Prozentsatz der Kristallinität wurden als Funktion der Aufheizgeschwindigkeit und Rekristallisation in den Untersuchungen ausgewertet. Der Young-sche Modulus und die Zugspannung zum Reissen in der Orientierungsrichtung betrugen 4.1, bzw. 0.15 GPa. Die Dehnung bis zum Bruch betrug etwa 8 %.

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Résumé On a effectué, aux Etats Unis, l'étude du comportement thermique et mécanique d'un polyéthylène préparé et fortement étiré en URSS. Le point de fusion et le pourcentage de cristallinité ont été évalués en fonction de la vitesse de chauffage et de la recristallisation. Lesvaleurs respectives du module d'Young et de la limite de rupture dans la direction d'orientation s'élèvent respectivement à 4.1 et 0.15 GPa. L'allongement à la rupture est d'environ 8%.

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, . . . 4.1 0.15 . 8%.

     

Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies

Using a simple mean-field model, we analyze the surface and bulk dissolution properties of DNA-linked nanoparticle assemblies. We find that the dissolution temperature and the sharpness of the dissolution profiles increase with the grafting density of the single-stranded DNA "probes" on the surface of colloids. The surface grafting density is controlled by the linker occupation number, in analogy with quantum particles obeying fractional statistics. The dissolution temperature increases logarithmically with the salt concentration. This is in agreement with the experimental findings [R. Jin, G. Wu, Z. Li, C. A. Mirkin, and G. C. Schatz, J. Am. Chem. Soc. 125, 1643 (2003)]. By exploiting the unique phase behavior of DNA-coated colloids, it should be possible to detect multiple "targets" in a single experiment by essentially mapping the DNA base-pair sequence onto the phase behavior of DNA-linked nanoparticle solution.     

Synthese von 1α-Hydroxycholecalciferol. Vorläufige Mitteilung

1α-hydroxycholesterol ( 4a ) was synthesized from cholesterol and transformed via its diacetyl derivative 4b into 1α, 3β-diacetoxycholesta-5, 7-diene ( 6b ). Irradiation of the ring-B-diene 6b followed by thermal isomerization and saponification gave 1α-hydroxycholecalciferol ( 7 ).     

Switch-like surface binding of competing multivalent particles

Multivalent particles competing for binding on the same surface can exhibit switch-like behaviour, depending on the concentration of receptors on the surface. When the receptor concentration is low, energy dominates the free energy of binding, and particles having a small number of strongly-binding ligands preferentially bind to the surface. At higher receptor concentrations, multivalent effects become significant, and entropy dominates the binding free energy; particles having many weakly-binding ligands preferentially bind to the surface. Between these two regimes there is a “switch-point”, at which the surface binds the two species of particles equally strongly. We demonstrate that a simple theory can account for this switch-like behaviour and present numerical calculations that support the theoretical predictions. We argue that binding selectivity based on receptor density, rather than identity, may have practical applications.     

Low‐Temperature Transformation of Methane to Methanol on Pd1O4 Single Sites Anchored on the Internal Surface of Microporous Silicate

Direct conversion of methane to chemical feedstocks such as methanol under mild conditions is a challenging but ideal solution for utilization of methane. Pd₁O₄ single‐sites anchored on the internal surface of micropores of a microporous silicate exhibit high selectivity and activity in transforming CH₄ to CH₃OH at 50–95 °C in aqueous phase through partial oxidation of CH₄ with H₂O₂. The selectivity for methanol production remains at 86.4 %, while the activity for methanol production at 95 °C is about 2.78 molecules per Pd₁O₄ site per second when 2.0 wt % CuO is used as a co‐catalyst with the Pd₁O₄@ZSM‐5. Thermodynamic calculations suggest that the reaction toward methanol production is highly favorable compared to formation of a byproduct, methyl peroxide.     

Quasibinary amorphous phase in a three-dimensional system of particles with repulsive-shoulder interactions

We report a computer-simulation study of the equilibrium phase diagram of a three-dimensional system of particles with a repulsive-step potential. Using free-energy calculations, we have determined the equilibrium phase diagram of this system. At low temperatures, we observe a number of distinct crystal phases. However, under certain conditions the system undergoes a glass transition in a regime where the liquid appears thermodynamically stable. We argue that the appearance of this amorphous low-temperature phase can be understood by viewing this one-component system as a quasibinary mixture.     

Structural arrest in an ideal gas

We report a molecular dynamics study of a simple model system that has the static properties of an ideal gas, yet exhibits nontrivial "glassy" dynamics behavior at high densities. The constituent molecules of this system are constructs of three infinitely thin hard rods of length L, rigidly joined at their midpoints. The crosses have random but fixed orientation. The static properties of this system are those of an ideal gas, and its collision frequency can be computed analytically. For number densities NL(3)/V>1, the single-particle diffusivity goes to zero. As the system is completely structureless, standard mode-coupling theory cannot describe the observed structural arrest. Nevertheless, the system exhibits many dynamical features that appear to be mode-coupling-like. All high-density incoherent intermediate scattering functions collapse onto master curves that depend only on the wave vector.