Biological molecules, design

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

A number of more general force fields for the study of small molecules are available that can be extended to biological molecules. These force fields have been designed with the goal of being able to treat a wide variety of molecules, based on the ability to transfer parameters between chemical systems and the use of additional terms (e.g., cross terms) in their potential energy functions. Typically, these force fields have been optimized to... 

As we have seen above, FRET is a technique that provides precise information about distances between 10 and 100 A which is in the range of the size of biological molecules and proteins. Researchers have taken advantage of this feature and developed different strategies to synthesize FRET sensors that are able to follow in real time and with high sensitivity very diverse processes such as enzymatic activity, conformational change, or molecule-molecule interaction. The design of these FRET sensors is described below. 

Designing High-Throughput HPLC Assays for Small and Biological Molecules... 

Przhonska OV, Webster S, Padilha LA et al (2010) Two-photon absorption in near-IR conjugated molecules design strategy and structure-property relations. In Demchenko AP (ed) Advanced fluorescence reporters in chemistry and biology. I. Springer Ser Fluoresc 8 105-147... 

The purpose of the venom is offensive while that of a poison is defensive, which in turn influences the characteristics of the toxin. Venoms, either large or small molecules, are usually variants of essential biological molecules such as lipids, steroids, histamines or other proteins. They are often mixtures with a specific mechanism of action such as paralyzing the nervous system. Poisons are designed to teach a predator that this is not a good meal. They usually cause more localized pain to discourage a predator, but depending on the dose and sensitivity of the individual, the poison can be deadly. 

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