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Energetics and Thermodynamics of Collagen Self-Assembly
Published in Marcel E. Nimni, Collagen, 1988
The conformational energy of a polypeptide chain can be calculated by means of a welldefined series of computational steps:16 (1) atomic coordinates are computed for a given conformation, i.e., for a given set of dihedral angles; (2) the intramolecular potential energy is calculated as a sum of pairwise interactions, using empirical potential functions; (3) the hydration energy of the molecule is calculated; (4) if one searches for a stable conformation of the molecule, the above steps are linked with a computer algorithm for function optimization, in order to find the conformation of lowest energy (or lowest free energy if the solvent is taken into account68). A widely used computer program, in which steps (1) and (2) have been incorporated, named ECEPP (Empirical Conformational Energy Program for Peptides), was developed in the laboratory of Scheraga.72–74 In this program, the computation of the polypeptide conformation is based on a standard set of bond lengths and bond angles. The empirical potential function contains terms for nonbonded interactions (with a repulsive and an attractive component), electrostatic interactions, hydrogen bonding, and torsional potentials for rotation around bonds.72 The program can be combined with various functionoptimizing algorithms in order to carry out step (4). Several other computational algorithms are in use in polypeptide studies (reviewed, e.g.63,75). Their general principles are usually similar to each other, but they differ mostly in terms of the formulation of the potential function, in the manner of deriving the numerical parameters describing the energy, and in the organization of the programs.
Clay nanoparticles as pharmaceutical carriers in drug delivery systems
Published in Expert Opinion on Drug Delivery, 2021
Jiani Dong, Zeneng Cheng, Songwen Tan, Qubo Zhu
Biological and genetic materials are no exception. Lin et al [46]. inserted the BSA(bovine serum albumin) protein into the layered silicate clay by direct intercalation or step by step intercalation. Assifaoui et al [47]. investigated the hybrid of betalactoglobulin(BLG) and MMT in acidic buffer (pH =3). They concluded that the secondary structure of the protein was affected by the adsorption on MMT. The adsorption of purines, pyrimidines, and nucleosides from aqueous solution to MMT was affected by suspension pH and the exchangeable cations. Perezgasga et al [48]. found that adenine, adenosine, AMP(adenosine monophosphate), ADP(adenosine diphosphate), ATP(adenosine-triphosphate), Poly A, uracil, uridine and Poly U were distributed in the interlaminar channels and at the edges of MMT, which was mainly due to the pH, pKa and van der Waals interactions. Gujjari et al [15]. compared the binding of small RNA, which was similar to those used for RNA interference (RNAi) therapy, between the two major forms of clay: Na+-MMT and Ca2+-MMT. They found that the association between RNA and Na+-MMT was weak. The increase of the Na+ ions concentration did not contribute to the binding, while the Mg2+ strongly increased the association between single-stranded RNAs and Na+-MMT. In contrast to the results with the Na+-MMT, the binding between RNA and Ca2+-MMT was stronger, because the size and hydration energy of Na+ were smaller and the ability to participate in cationic bridging was less.