Biomolecule

Weiss S 1999 Fluorescence spectroscopy of single biomolecules Science 283 1676-83... 

The variety of molecules used to prepare LB films is enonnous. and only a small selection of examples can be presented here. Liquid crystals and biomolecules such as phospholipids, for example, can also be used to prepare LB films. The reader is referred to tire literature for infonnation about individual species. 

Wolynes P G 1996 Symmetry and the energy landscape of biomolecules Proc. Natl Acad. Sci. (USA) 93 14 249-55... 

Apart from the sheer complexity of the static stmctures of biomolecules, they are also rather labile. On the one hand this means that especial consideration must be given to the fact (for example in electron microscopy) that samples have to be dried, possibly stained, and then measured in high vacuum, which may introduce artifacts into the observed images [5]. On the other, apart from the vexing question of whether a protein in a crystal has the same stmcture as one freely diffusing in solution, the static stmcture resulting from an x-ray diffraction experiment gives few clues to the molecular motions on which operation of an enzyme depends [6]. 

The most recently introduced optical teclmique is based on the retardation of light guided in an optical waveguide when biomolecules of a polarizability different from that of the solvent they displace are adsorbed at the waveguide surface (optical waveguide lightmode spectroscopy, OWLS) [H]. It is even more sensitive than ellipsometry, and the mode... 

The reactions of biopolymers at interfaces fonn tire basis of some extremely important industrial processes. The primary process in all cases is tire adsorjDtion of biomolecules, usually proteins. If ultimately living cells are adsorbed, tliis always takes place onto a preadsorbed protein layer (which may be secreted by tire cells themselves [130]). These processes can be classified into tliree categories ... 

A salient feature of natural surfaces is tliat tliey are overwhelmingly electron donors [133]. This is tlie basis for tlie ubiquitous hydrophilic repulsion which ensures tliat a cell can function, since massive protein-protein aggregation and protein-membrane adsorjition is tliereby prevented. In fact, for biomolecule interactions under typical physiological conditions, i.e. aqueous solutions of moderately high ionic strengtli, tlie donor-acceptor energy dominates. 

Peyrard M (ed) 1995 Nonlinear Excitations in Biomolecules Les Ulis Editions de Physique)... 

Newton M D 1999 Electron transfer from isolated molecules to biomolecules Advanced Chemicai Physics vol 106, ed J Jortner and M Bixon (New York Wiley) pp 303-75... 

Wynne K and Hochstrasser R M 1999 Coherence and adiabaticity in ultrafast electron transfer Adv. Chem. Phys. 107 (Electron transfer from isolated molecules to biomolecules) part 2, 263-309... 

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

Miyazawa, T. Conformational aspects and biological functions of biomolecules. J. Mol. Struct. 126 (1985) 493-508... 

Gascoyne, P.R.C., Pethig, R. Experimental and theoretical aspects of hydration isotherms for biomolecules. J. Chem. Soc. Faradey Trans. 1 (1977) 171-180... 

The last part of this account will be devoted to protein kinases and protein phosphatases and some recent results we have obtained for them. Protein kinases and phosphatases are signaling biomolecules that control the level of phosphorylation and dephosphorylation of tyrosine, serine or threonine residues in other proteins, and by this means regulate a variety of fundamental cellular processes including cell growth and proliferation, cell cycle and cytoskeletal integrity. 

Since the stochastic Langevin force mimics collisions among solvent molecules and the biomolecule (the solute), the characteristic vibrational frequencies of a molecule in vacuum are dampened. In particular, the low-frequency vibrational modes are overdamped, and various correlation functions are smoothed (see Case [35] for a review and further references). The magnitude of such disturbances with respect to Newtonian behavior depends on 7, as can be seen from Fig. 8 showing computed spectral densities of the protein BPTI for three 7 values. Overall, this effect can certainly alter the dynamics of a system, and it remains to study these consequences in connection with biomolecular dynamics. 

The IE scheme is nonconservative, with the damping both frequency and timestep dependent [42, 43]. However, IE is unconditionally stable or A-stable, i.e., the stability domain of the model problem y t) = qy t), where q is a complex number (exact solution y t) = exp(gt)), is the set of all qAt satisfying Re (qAt) < 0, or the left-half of the complex plane. The discussion of IE here is only for future reference, since the application of the scheme is faulty for biomolecules. 

The LIN method (described below) was constructed on the premise of filtering out the high-frequency motion by NM analysis and using a large-timestep implicit method to resolve the remaining motion components. This technique turned out to work when properly implemented for up to moderate timesteps (e.g., 15 Is) [73] (each timestep interval is associated with a new linearization model). However, the CPU gain for biomolecules is modest even when substantial work is expanded on sparse matrix techniques, adaptive timestep selection, and fast minimization [73]. Still, LIN can be considered a true long-timestep method. 

In order to apply the techniques discussed above to the MD simulation o biomolecules, one takes the Liouville operator for a macromolecule in vacuo containing N atoms to be... 

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