Biomolecular Reaction Mechanisms

The kinetics of ligand binding to an antibody usually follows a simple biomolecular reaction mechanism... 

At a first sight this could very well be an elementary biomolecular reaction with two molecules of ammonia combining to yield directly the four product molecules. From this principle, however, the reverse reaction would then also have to be an elementary reaction involving the direct combination of three molecules of hydrogen with one of nitrogen. Because such a process is rejected as improbable, the bimolecular forward mechanism must also be rejected. 

There has been a review of relationships between activation parameters and mechanisms for biomolecular reactions in solution, including both nucleophilic substitutions and additions.5 Several studies have been reported involving substitutions by amine nucleophiles where both electronic and steric effects may be important. Kinetic studies of the reactions of 2,4-dinitrophenyl 2,4,6-trinitrophenyl ether (1) with ring-substituted... 

This cooperation not only takes place between the sinusoidal cells, but also with the hepatocytes .) endothelial and Kupffer cells complement each other through various mechanisms of endocytosis and different pathways of enzymatic clearance (2.) as a double barrier, they protect the liver cells both from toxic and undesired substances, even to the extent of self-sacrifice (i.) they intervene in the metabolism of liver cells with self-produced substances 4.) they send signal substances like cytokines (e.g. interferons) and eicosanoids (e.g. leukotrienes) to the liver cells for independent control of biochemical and biomolecular reaction cascades. 

Recent technological developments of experimental techniques, for example, optical tweezers, atomic force microscope, etc., made it possible to apply a force of the order of pN to manipulate the single biomolecules (Kumar and Li 2010 Rief et al. 1999, 1997 Tskhovrebova et al. 1997). Many interesting results, for example, structural, functional, and elastic properties of biomolecules, information about the kinetics of biomolecular reactions, and detection of molecular intermediates have been obtained (Bustamante et al. 2000 Cecconi et al. 2005 Smith et al. 1992, 1996). Moreover, these experiments also provided a platform to verify theoretical predictions based on the models developed in the framework of statistical mechanics (Bhattacharjee 2000 Giri and Kumar 2006 Kumar 2009 Kumar and Giri 2007 Kumar et al. 2005 Lubensky and Nelson 2000 Marenduzzo et al. 2001a Zhou et al. 2006). 

Kildahl-Andersen G, Anthonsen T, and Liaaen-Jensen S. 2007. Studies on the mechanism of the Carr-Price blue color reaction. Organic Biomolecular Chemistry 5 3027-3033. 

X = 0, CH2, CHCOOH, C(COOH)2, NH, NCH3 N(CH2CH=CH2), N(CHs)2 Cl Bobrowski and Das published a series of papers on the transients in the pulse radiolysis of retinyl polyenes31-37, due to their importance in a variety of biomolecular processes. They studied32 the kinetics and mechanisms of protonation reaction. The protons were released by pulse radiolysis, on a nanosecond time scale, of 2-propanol air-saturated solutions containing, in addition to the retinyl polyenes, also 0.5 M acetone and 0.2 M CCI4. Within less than 300 ns, the electron beam pulse results in formation of HC1. The protonated products of retinyl polyenes were found to absorb optically with Xmax at the range of 475-585 nm and were measured by this absorption. They found that the protonation rate constants of polyene s Schiff bases depend on the polyene chain... 

Deterministic and stochastic processes should be taken into account. The deterministic scenario invokes transfer of the intrinsic chirality of the universe to the biopolymers of life [6,7]. Ab initio theoretical estimates that take into account the chiral electroweak forces indicate that the L-amino acids and the D-sugars are more stable than their corresponding enantiomers [8,9]. The minute energy differences between these enantiomeric pairs, under Darwinian reaction kinetics in a flow reactor, were invoked to account for the biomolecular handedness that arose when fife began [7]. Several reports describing deterministic mechanisms that could have induced mirror sym-... 

Not only does DNA form itself into catenated and knotted structures, it also rotaxanates itself with macrocyclic enzymes. A,-Exonuclease [30, 37] is an enzyme that participates in DNA replication and repair by fully encircling DNA as it sequentially hydrolyzes nucleotides - a biomolecular rotaxane The structure of the enzyme is shown in Fig. 3d. T4 DNA polymerase holoenzyme [38] is an analogous example its protein subunits clamp around a DNA strand to form a toroid in what chemists of the mechanical bond would call a clipping process. It should be noted that chemists have been able to mimic this concept of a topologically linked catalyst on a polymer [39] using traditional organic catalytic reactions. 

In this chapter we provide a review of variational transition state theory with a focus on how quantum mechanical effects are incorporated. We use illustrative examples of H-transfer reactions to assist in the presentation of the concepts and to highlight special considerations or procedures required in different cases. The examples span the range from simple gas-phase hydrogen atom transfer reactions (triatomic to polyatomic systems), to solid-state and liquid-phase reactions, including complex reactions in biomolecular enzyme systems. 

The working principle of the family of biosensors based on nanomechanical transducers, and specifically on microcantilevers, involves the translation of biochemical reactions into a mechanical movement in the nanometer range. In microcantilever sensors, the biochemical receptor layer is directly in contact with one of the cantilever surface. The biomolecular recognition process between the receptor layer and its corresponding analyte induce... 

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