Biomolecular chains

ABSTRACT We present a dynamical scheme for biological systems. We use methods and techniques of quantum field theory since our analysis is at a microscopic molecular level. Davydov solitons on biomolecular chains and coherent electric dipole waves are described as collective dynamical modes. Electric polarization waves predicted by Frohlich are identified with the Goldstone massless modes of the theory with spontaneous breakdown of the dipole-rotational symmetry. Self-organization, dissipativity, and stability of biological systems appear as observable manifestations of the microscopic quantum dynamics. 

Very interesting subdynamics have been investigated by A. S. Davydov,who has shown that metabolic reactions can result in strictly confined bumps traveling along biomolecular chains and carrying energy in an efficient way a long distance away from the point of release. 

Nonlinear dynamical effects on one-dimensional systems such as biomolecular chains, e.g., Davydov solitons, can also be analyzed in terms of boson condensation. " In the Frohlich wave case, the condensation... 

Let us consider first the soliton dynamics on the biomolecular chains. 

A biomolecular chain can be schematized as a one-dimensional chain of weakly bound monomers of mass Af, whose electric dipole moment is aligned along the chain. Consequently the internal dipole quantum number, giving the spatial orientation of the dipole, can be taken as frozen the electric dipole, which would be described by a spinor in the usual three dimensions, is described in this one-dimensional case by a scalar. 

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

An important characteristic of biomolecular motion is that the different types of motion are interdependent and coupled to one another. For example, a large-scale dynamic transition cannot occur without involving several medium-scale motions, such as helix rearrangements. Medium-scale motions cannot occur without involving small-scale motions, such as side-chain movement. Finally, even side-chain motions cannot occur without the presence of the very fast atomic fluctuations, which can be viewed as the lubricant that enables the whole molecular construction to move. From the point of view of dynamic... 

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... 

When a biomolecular system is separated into QM and MM regions one must usually cut amino acid side chains or the protein backbone at covalent bonds (Fig. 5.2 a). The construction of the covalent boundary between the QM and MM parts is key to accurate results from QM/MM calculations. Because there is no unique way to treat the covalent boundary, several different approaches have been described. In the first applications of coupled QM/MM simulations link atoms were used to create the covalent QM/MM boundary (Fig. 5.2b). Link atoms are atoms added to the QM part to fill the broken valences of the boundary QM atoms. These atoms are placed along the broken QM/MM bond at a distance appropriate for the QM bond added. The link atoms have usually been hydrogen atoms but methyl groups and pseudohalogen atoms have also been used [35]. 

CNTs can be functionalized with protein via non-covalent bond (Li et al., 2005 Kim et al., 2003 Mitchell et al., 2002). For example, (beta-lactamase I, that can be immobilized inside or outside CNTs, doesn t change enzyme s activity (Vinuesa and Goodnow, 2002). Taq enzyme can attach to the outside of CNT, and doesn t change its activity (Cui et al., 2004). Peptide with Histidine and Tryptophan can have selective affinity for CNT(Guo et al., 1998). Monoclonal antibody can attach to SWNTs. Protein-modified CNTs can be used to improve its biocompatibility and biomolecular recognition capabilities (Um et al., 2006). For example, CNTs functionalized with PEG and Triton X-100 can prevent nonspecific binding of protein and CNTs. Biotin moiety is attached to the PEG chains Streptavidin can bind specifically with biotin-CNT (Shim et al., 2002). 

Four different aryldiazonium salts have been used to functionalize SWCNTs through electrochemical reduction. By XPS and Raman diffusion measurements, the growth of aryl chains on the sidewalls of the nanotubes was observed [178]. Electrically addressable biomolecular functionalization of SWCNT electrodes and vertically aligned carbon nanofiber electrodes with DNA was achieved by elec-trochemically addressing (reduction) of nitrophenyl substituted nanotubes and nanofibers. Subsequently, the resulting amino functions were covalently linked to DNA forming an array of DNA-CNT hybrid nanostructures (Scheme 1.28) [179],... 

In a subsequent investigation by the author [ 1 ] multivalent glycopolymers with chain-terminating binding groups, (I), were prepared and used in carbohydrate-mediated biomolecular recognition processes. 

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