Energies protein folding, assembling

Self-organization systems under thermodynamic control (spontaneous processes with a negative free-energy change), such as supramolecular complexes, crystallization, surfactant aggregation, certain nano-structures, protein folding, protein assembly, DNA duplex. 

The Mulliken-Mezey AFDF scheme and the more general AFDF schemes - also serve as the basis for the adjustable density matrix assembler (ADMA) method. The ADMA method generates ab initio quality macromolecular density matrices, which can be used for the computation of a variety of ab initio quality properties for macromolecules. The ADMA method is also suitable for the calculation of ab initio quality electronic densities, however, additional molecular properties, such as forces and energies, can also be calculated. These options of the ADMA method are expected to be useful in macromolecular conformational analysis, geometry optimizations, and in computational studies of protein folding. 

Energy Sources Cause Proteins to Fold, Assemble, and Function... 

C.B. Anfinsen, Principles that Govern the Folding of Protein Chains. Science, 181, 223-230, 1973. The Anfinsen principle is that the sequence of a protein dictates the full three-dimensional structure that it would form, that is, sequence dictates protein folding and assembly. The need for molecular chaperones suggests that the correctly folded protein, the lowest energy structure, is not always the result and that the problem arises out of improper hydrophobic associations. Interestingly, the... 

Another of the successful methods that is based on a reverse approach relies on protein fold recognition by threading (31). This method takes advantage of the fact that the number of folds is limited. Instead of tr5nng to predict the fold of the protein on the basis of the amount of free energy, the method determines whether a given sequence can be fitted to a known fold. As the number of folds (Fig. 3) appears to be finite, it provides a way to look for the structure of new proteins using known folds. Another method for the prediction of three-dimensional structures of proteins is based on the in silico assembly of protein structure from shorter structural elements with more defined structures (32). 

DCC is typically associated with the amplification of the fittest. In fact, nearly all studies discussed in the previous section rely on the self-selection of high-affinity binders from a dynamic library pool. Nonetheless, many processes in chemistry are guided by weak differences in energy. Examples are the interaction of a catalyst with the transition state of a chemical reaction, protein folding, as well as the self-assembly of nanoarchitectures. In all these cases, a few kilojoules of energy can make the difference between success and failure. This section deals with the application of DCC in the realm of weak interactions, using a methodology referred to as dynamic covalent capture The essential... 

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