Biological systems protein function

In biological systems, proteins and nucleic acids perform two major roles metabolism and conversion of materials and the storage and transmission of genetic information. Proteins are synthesized according to programs written in DNA, while nucleic acid replication and repair both require protein functionality. Proteins and nucleic acids needs each other - they are interdependent. 

An enzyme is a protein whose function is to serve as a catalyst for a chemical reaction within a biological system. Some functions that enzymes perform are the synthesis of proteins and other biomolecules, digestion of fats and other molecules, and sometimes they are even put to use in industrial applications outside of their natural biological environment. 

Material characteristics such as size, shape, chemical composition, surface chemistry, roughness, and surface functionalizations profoundly influence the interactions that occur at the interface between nanomaterials and biological systems (proteins, membranes, endocytic vesicles, organelles, DNA, and biological fluids). Evidence from the literature suggests that the biodistribution of nanosized carriers to specific sites is mostly dictated by the physicochemical characteristics of... 

Our work is targeted to biomolecular simulation applications, where the objective is to illuminate the structure and function of biological molecules (proteins, enzymes, etc) ranging in size from dozens of atoms to tens of thousands of atoms today, with the desire to increase this limit to millions of atoms in the near future. Such molecular dynamics (MD) simulations simply apply Newton s law to each atom in the system, with the force on each atom being determined by evaluating the gradient of the potential field at each atom s position. The potential includes contributions from bonding forces. 

Many globular proteins are enzymes They accelerate the rates of chemical reactions m biological systems but the kinds of reactions that take place are the fundamental reactions of organic chemistry One way m which enzymes accelerate these reactions is by bringing reactive func tions together m the presence of catalytically active functions of the protein... 

The use of QM-MD as opposed to QM-MM minimization techniques is computationally intensive and thus precluded the use of an ab initio or density functional method for the quantum region. This study was performed with an AMi Hamiltonian, and the first step of the dephosphorylation reaction was studied (see Fig. 4). Because of the important role that phosphorus has in biological systems [62], phosphatase reactions have been studied extensively [63]. From experimental data it is believed that Cys-i2 and Asp-i29 residues are involved in the first step of the dephosphorylation reaction of BPTP [64,65]. Alaliambra et al. [30] included the side chains of the phosphorylated tyrosine, Cys-i2, and Asp-i 29 in the quantum region, with link atoms used at the quantum/classical boundaries. In this study the protein was not truncated and was surrounded with a 24 A radius sphere of water molecules. Stochastic boundary methods were applied [66]. 

With remarkable accuracy, Democritus in the fifth century B.C. set the stage for modem chemistry. His atomic theory of matter, which he formulated without experimental verification, still stands, more or less intact, and encapsulates the profound truth that nature s stunning wealth boils down to atoms and molecules. As science uncovers the mysteries of the world around us, we stand ever more in awe of nature s ingenious molecular designs and biological systems nucleic acids, saccharides, proteins, and secondary metabolites are four classes of wondrous molecules that nature synthesizes with remarkable ease, and uses with admirable precision in the assembly and function of living systems. 

All biological systems contain aqueous electrolyte solutions. These solutions consist of strong electrolytes (inorganic salts) as well as various organic substances with acidic or basic functional groups which usually behave as weak electrolytes. The solutions are often gel-like in their consistency because of the polyelectrolytes, proteins, and other macromolecules contained in them. The pH values of biological solutions as a rule are between 6.7 and 7.6. 

A) Biological systems any biological entity, from a functional protein to an ecosystem virtual in silica) 3D models mathematical models... 

Proteins are essential to all living systems. Proteins are macromolecules and, like all biological macromolecules, polymers (Alberts et al. 1994). The structural units of proteins (monomers) are about 20 amino acids. Although no clear line exists, proteins are generally considered to have minimal chain lengths of about 50 amino acids, corresponding to molecular masses near 5000 daltons. The most complicated proteins contain several thousand amino acids and have molecular masses of several million daltons. The functional diversity ranges from ... 

Crameri, R., and Suter, M. (1993). Display of biologically active proteins on the surface of filamentous phages a cDNA cloning system for selection of functional gene products linked to the genetic information responsible for their production. Gene 137, 69-75. 

From the atomic to the macroscopic level chirality is a characteristic feature of biological systems and plays an important role in the interplay of structure and function. Originating from small chiral precursors complex macromolecules such as proteins or DNA have developed during evolution. On a supramolecular level chirality is expressed in molecular organization, e.g. in the secondary and tertiary structure of proteins, in membranes, cells or tissues. On a macroscopic level, it appears in the chirality of our hands or in the asymmetric arrangement of our organs, or in the helicity of snail shells. Nature usually displays a preference for one sense of chirality over the other. This leads to specific interactions called chiral recognition. 

Two features of expression profiling make it the most productive approach to study biological systems for the immediate future. First, the present efficiency with which investigators can obtain global and quantitative information with DNA arrays exceeds that of proteomic techniques. Second, RNA expression profiles provide an extremely precise and reproducible signature of the state of the cell that probably reflects albeit indirectly, the functional state of all proteins (Young, 2000, p. 13)-... 

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