Model biological macromolecule

This paper describes the development and initial applications of nab, a computer language for modeling biological macromolecules. It was developed to create atomic-level models of nucleic acid structures such as stem-loops, pseudoknots, multi-armed junctions and catalytic RNAs, and to investigate biological processes that involve nucleic acids, such as hybridization, branch migration at junctions, and DNA replication. 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

The final class of methods that we shall consider for calculating the electrostatic compone of the solvation free energy are based upon the Poisson or the Poisson-Boltzmann equatior Ihese methods have been particularly useful for investigating the electrostatic properties biological macromolecules such as proteins and DNA. The solute is treated as a body of co stant low dielectric (usually between 2 and 4), and the solvent is modelled as a continuum high dielectric. The Poisson equation relates the variation in the potential (f> within a mediu of uniform dielectric constant e to the charge density p ... 

Photo 14 Linus Pauling in 1950, showing his still evident enthusiasm for the structures of complex minerals (Chapters 5, 6), in this case possibly beryl. In a typical pose, he holds a specimen of the mineral and stands beside an atomic model. The enthusiasm for minerals continued even though Pauling had by this time largely moved on to studies of biological macromolecules (Part III). 

The total electric field, E, is composed of the external electric field from the permanent charges E° and the contribution from other induced dipoles. This is the basis of most polarizable force fields currently being developed for biomolecular simulations. In the present chapter an overview of the formalisms most commonly used for MM force fields will be presented. It should be emphasized that this chapter is not meant to provide a broad overview of the field but rather focuses on the formalisms of the induced dipole, classical Drude oscillator and fluctuating charge models and their development in the context of providing a practical polarization model for molecular simulations of biological macromolecules [12-21], While references to works in which the different methods have been developed and applied are included throughout the text, the major discussion of the implementation of these models focuses... 

D. Landheer, G. Aers, W.R. Mckinnon, M.J. Deen, and J.C. Ranuarez, Model for the field effect from layers of biological macromolecules on the gates of metal-oxide-semiconductor transistors. J. Appl. Phys. 98, 044701-1-15 (2005). 

Considerable use has been made of the thermodynamic perturbation and thermodynamic integration methods in biochemical modelling, calculating the relative Gibbs energies of binding of inhibitors of biological macromolecules (e.g. proteins) with the aid of suitable thermodynamic cycles. Some applications to materials are described by Alfe et al. [11]. 

Located several kilometres above the Earth s surface is the stratosphere. Here the ozone layer acts as a filter, protecting life on Earth from harmful low-wavelength ultraviolet radiation known as UV-C, which damages biological macromolecules such as proteins and DNA. In order to understand the effects of anthropogenic input into the stratosphere, the production and destruction of the ozone layer has been studied by a variety of photochemical models and experimental methods. 

There has been a noticeable increase in interest in hydrophobic interactions during the last decade. This interest is mostly related to the supposed importance of the hydrophobic interactions as determinants of stability in and interactions between biological macromolecules. A relatively small part of this interest has been focused on the volume changes associated with the interactions. Most of our knowledge about these volume change comes from studies on small molecules serving as model systems for the much larger macromolecules,... 

Lamzin, V. S., Perrakis, A. and Wilson, K. S. (2001). The ARP/wARP suite for automated construction and refinement of protein models. In International Tables for Crystallography. Volume F Crystallography of biological macromolecules, Rossmann, M. G. and Arnold, E. eds., pp. 720-722. Dordrecht, Kluwer Academic Publishers, The Netherlands. 

Mathematical description of the polymerization of biological macromolecules on templates, based on simple models, has been published by Simhaet al Two types of reaction were discussed. The first type of reaction was initiated by polymerization of two monomers on each template. The reaction proceeded throughout the addition of monomer to the growing ends or by the coupling of the growing chains. In the second type of re-... 

The first examples of the so-called supramolecular catalysis are based on bioinspired molecular recognition, which is an essential attribute of biochemical systems. Structures such as receptors, antibodies, and enzymes can all recognize a feature that is important for their specific functions, often in the presence of species of quite similar structure. The ability to discriminate depends exclusively on the structural properties of these biological macromolecules. Recent progress in bioor-ganic chemistry has shown that many of these functions can be incorporated into smaller, synthetically more accessible structures as model systems [27]. 

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