Models of Biological Macromolecules

Rullmann, J.A.C. and Duijnen P.Th. van, Potential energy models of biological macromolecules a case for ab initio quantum chemistry. CRC Reports in Molecular Theory (1990) 1 1—21. 

Models of Biological Macromolecules A Case for Ab Initio Quantum Chemistry. 

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]. 

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-... 

Molecular databases and the associated data banks require the development of a conceptual structure for the information stored about the molecules, descriptive language representing the data, and methods for analysis enabling molecular modeling, similarity searches, classification, visualization, or other uses of the database.320 Currendy, the Protein Data Bank (PDB http 7www.rcsb.org/pdb/) is one of the best known examples of a molecular database. The PDB is a worldwide archive of three-dimensional structural data of biological macromolecules.321 The PDB is a common accentor to many structural databases.322 The success of... 

Actin and tubulin are two important cellular components that are involved in cell shape and movement. Actin is present in all mammalian cells and is involved in cellular transport and phagocytosis (eating of extracellular materials), provides rigidity to cell membranes, and when bonded to tropomyosin and troponin, forms the thin filaments of muscle. Thbulin is the subunit from which microtubules are self-assembled. Microtubules are most commonly known for their role in cell division. The mechanisms of self-assembly of these macromolecules have been well studied and are important models of biological assembly processes. Below we examine each of these processes. 

Michael E. Paulaitis is Professor of Chemical and Biomolecular Engineering and Ohio Eminent Scholar at Ohio State University. He is also Director of the Institute of Multiscale Modeling of Biological Interactions at Johns Hopkins University. His research focuses on molecular thermodynamics of hydration, protein solution thermodynamics, and molecular simulations of biological macromolecules. 

I. Jager, The sticky chain A kinetic model for the deformation of biological macromolecules. Biophys. J. 81, 1897-1906 (2001)... 

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