Theoretical protein models

The PDB is the repository for solved 3-D structures of proteins, peptides, viruses, protein-nucleic acid complexes, nucleic acids, and carbohydrates. Most structures deposited in the PDB are based on X-ray crystallography (approximately 80%) with the remaining structures solved using nuclear magnetic resonance (NMR) techniques. The PDB no longer stores theoretical protein models in the main archive, but it does accept them for storage in a separate theoretical model section where they are neither aimotated nor validated. The PDB staff members annotate and validate the submitted 3-D structures to ensure the information provided to the public is correct. The structures archived at the PDB are provided in two formats, PDB and... 

Theoretical and model analysis based on a nanofluidic approach is needed for this situation. One may ask, is it possible to release proteins loaded in nanotubules We have found that the addition of the polycation PEI in the release solvent resulted in much quicker protein release, as demonstrated in Figure 14.9. In this case, most of the insulin was released in 1 hour instead of 100 hours. 10-40% of glucose oxidase, catalyse, and hemoglobin were released within 4 hours through complexation with PEI. It is unclear, whether the proteins were replaced by the polycation or released in a complex with PEI. 

The result is the electron density map of the protein crystal. The final task for the crystallographer is to build the appropriate protein model, i. e., putting amino acid for amino acid into the electron density. Routinely the theoretical amplitudes and phases are calculated from the model and compared to the experimental data in order to check the correctness of model building. The positions of the protein backbone and the amino acid side chains are well defined by X-ray structures at a... 

In a beautifiil recent work, the groups of K. Pierloot and B. O. Roos have proposed a fairly complete understanding of the relation between the electronic spectra and the stmcture of the mononuclear copper-cysteinate proteins. This theoretical work is based on DFT geometry optimizations of several blue copper protein models from [Cu(NH3)2(SH)(SH2)+] to... 

Amadei A et al (2010) Theoretical-computational modelling of infrared spectra in peptides and proteins anew frontier for combined theoretical-experimental investigations. Curr Opin Struct Biol 20 155-161... 

Because this problem is complex several avenues of attack have been devised in the last fifteen years. A combination of experimental developments (protein engineering, advances in x-ray and nuclear magnetic resonance (NMR), various time-resolved spectroscopies, single molecule manipulation methods) and theoretical approaches (use of statistical mechanics, different computational strategies, use of simple models) [5, 6 and 7] has led to a greater understanding of how polypeptide chains reach the native confonnation. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

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