Pathways of Enzymatic Phosphotransfer Reactions

Abstract

Mevalonate 5-pyrophosphate (MVAPP) decarboxylase catalyzes the decarboxylation of MVAPP to isopentenyl pyro-phosphate, an ATP-dependent process in which 3-phospho-MVAPP is a transient intermediate that undergoes concomitant decarboxylation and elimination of phosphate. Reaction of (S_p)-adenosine 5′-0-3-thio [3-17_{O 2},180] triphosphate in place of ATP produces (R)-[17O,18O] thiophosphate in place of phosphate. Therefore, the phosphotransfer step producing 3-phospho-MVAPP proceeds with inversion of configuration at P. Gentamicin nucleotidyl-transferase catalyzes the reaction of ATP with the C-2″ hydroxyl group of aminoglycoside antibiotics to produce AMP-2″-aminoglycosides, thereby inactivating the drugs. Enzymatic reaction of (S_p)-2′-deoxyadenosine 5′-O[α-17O] triphosphate with tobramycin produces (R_p)-[α-17O]dAMP-2″-tobramycin. Therefore, transfer of the 2′-deoxyadenosine 5′-phosphoryl group proceeds with inversion of configuration. Since both reactions are uncomplicated bisubstrate processes and both proceed with inversion at P, it is likely that both proceed by mechanisms involving direct, single-step phosphotransfer from the phospho-donor substrate to the acceptor, rather than by double-displacement mechanisms involving covalent, phosphoenzyme-intermediates.     

Tracer studies on f-actin fluctuations

We present a study on the fluctuations of semiflexible actin filaments using fluorescence videomicroscopy, focusing on the end-to-end fluctuations of single filaments. In order to specifically measure the position of the polymer's ends, we developed a novel noninvasive method that consists of annealing short end tags to the filaments. This allows us to probe polymer fluctuations to a very high accuracy. We compared the distribution of the end-to-end distance with recent theoretical results, and found excellent agreement. We also studied the dynamics of the mean-square end-to-end distance deltaR2(t) and orientation of the ends, deltaTheta(2)(t), finding power laws t(3/4) and t(1/4), respectively. Scaling behavior for deltaR2(t) is observed over several decades in relaxation time in agreement with theoretical results.     

Cyclic-inelastic deformation and fatigue resistance of notched-thin aluminum plates

The results of experiments designed to develop data to assess the accuracy and utility of the critical location concept in applications of fatigue-crack nucleation analysis at notch roots are presented and discussed. Fully reversed and nonzero mean-stress data are presented over a range of lives which encompass both elastic and inelastic deformations for thin-notched specimens and smooth specimens made of 2024 T351 aluminum-alloy sheet. Notch-root strains were measured via an extensometer, whereas the formation of small cracks was detected via an eddy-current transducer. Data reported indicated the validity of the assumption that smooth and notched specimens form cracks at the same cycle number when identical deformation histories are imposed at their respective critical locations. They also serve to demonstrate the accuracy and utility of the critical-location approach in analysis to predict the formation of small cracks at notches in coupons and components.     

Numerical integration and the constant strain condition

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Melting of colloidal molecular crystals on triangular lattices

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High-resolution imaging of single fluorescent molecules with the optical near-field of a metal tip

We show that a concentration of light at a metal tip allows near-field optical imaging of single fluorescent dye molecules at very high resolution, despite strong quenching effects. Details as small as 10 nm were observed in the fluorescence patterns of single Cy-3 dyes bound to the termini of DNA. Data evaluation by model fitting determines the positions of the dyes to an accuracy even better than 1 nm and also yields their 3D orientation. The metal tip simultaneously provides high-resolution topographic imaging complementing the optical signal for a detailed surface examination.     

Phase coexistence in driven one-dimensional transport

We study a one-dimensional totally asymmetric exclusion process with random particle attachments and detachments in the bulk. The resulting dynamics leads to unexpected stationary regimes for large but finite systems. Such regimes are characterized by a phase coexistence of low and high density regions separated by domain walls. We use a mean-field approach to interpret the numerical results obtained by Monte Carlo simulations, and we predict the phase diagram of this nonconserved dynamics in the thermodynamic limit.     

Elasticity of stiff polymer networks

We study the elasticity of a two-dimensional random network of rigid rods ("Mikado model"). The essential features incorporated into the model are the anisotropic elasticity of the rods and the random geometry of the network. We show that there are three distinct scaling regimes, characterized by two distinct length scales on the elastic backbone. In addition to a critical rigidity percolation region and a homogeneously elastic regime we find a novel intermediate scaling regime, where the elasticity is dominated by bending deformations.