Biological complexity

C.-K. Cheng, L. B. Kier, and P. G. Seybold, CASim Version 1.0, Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA, 2005. 

Biological Complexity and the Role of Medicine in the Future of the Genome... 

Summarizing, nucleophilic attack by water on GTP in the Cdc42-Cdc42GAP enzymatic complex has been investigated by use of DFT-based MD simulations. The model system enabled consideration of the most relevant physicochemical interactions between GTP, WAT, and the biological complex. In particular, the system seemed to include the atoms forming the pre-organized catalytic site and took into account the major contribution of the electric... 

Several kinetic parameters can be measured on different experimental systems to account for the interaction of a compound with CYPs. For example when studying the metabolic stability of a compound, it could be measured in a recombinant CYP system, in human liver microsomes, in hepatocytes and so on. Each system increases in biological complexity. Although in the recombinant CYP system only the cytochrome under consideration is studied, in the case of the human liver microsomes, there is a pool of enzyme present that includes several CYPs, and finally in the hepatocyte cell system, metabolizing enzymes play an important role in the metabolic compound stability. In addition, transport systems are also present that could involve recirculation or other transport phenomena. The more complex the experimental system, the more difficult it is to extract information on the protein/ligand interaction, albeit it is closer to the in vivo real situation and therefore to the mechanism that is actually working in the body. 

G. N. Stephanopoulos, H. Alper, and J. Moxley, Exploiting biological complexity for strain improvement through systems biology. Nat. Biotechnol. 22, 1261 1267 (2004). 

The number of protein-coding genes in an organism provides a useful indication of its molecular complexity, although there is as yet no firm correlation between the number of genes and biological complexity. 

Another way is the intermediate method to bridge the two approaches above. This method determines biologically multiplexed activity profile data. It integrates biological complexity at multiple levels pathways, signal transductions, and environmental factors. 

Perhaps the most important (and least recognized) aspect of biology fhaf makes if difficulf to understand systemahcally is the fact that biological complexity was not produced by a watch maker or an engineer. 

US-FDA performs premarket review of laboratory, animal, and human clinical testing for new human dmgs and biologies, complex medical devices, food and color additives, and animal dmgs for safety and effectiveness. Infant formulas are reviewed for required nutrient content and safety in manufacturing practices. 

A second obvious line of research for the future must be that related to the development and improvement of computer-based simulation of long-term environmental behaviour of radionuclides. Most currently available models are still comparatively simple compared with the physical, chemical and biological complexity of environments they purport to represent but, as noted in Section 13.5, our ability to construct ever more complex conceptual models for predicting the future behaviour of radionuclides is improving. However, the more complex the model, the more demands it places on the basic thermodynamic data and knowledge of likely speciation. The challenge for the future will therefore be to produce high-quality data for model construction and to devise realistic ways to validate those models once produced. 

Bird AP. Gene number, noise reduction and biological complexity. Trends Genet 1995 11 94-100. 

While the two-dimensional electrophoretic analysis described above is suitable for biological complexes that contain only a few major components (such as the human erythrocyte membrane), it is not feasible to extend its use to more complex systems such as the plasma membranes of many other cell types. Nevertheless, several ways to improve the method may prove useful. Immunoprecipitation of all the crosslinking products... 

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