Confronting the problem of interconnected structural changes in the comparative modeling of proteins
| Autor: | Huai-bei Zhou, Rui Luo, Krzysztof Fidelis, Jan T. Pedersen, Ram Samudrala, John Moult |
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| Rok vydání: | 1995 |
| Předmět: |
Models
Molecular Protein Conformation Receptors Retinoic Acid Molecular Sequence Data Neurotoxins Sequence alignment Eosinophil-Derived Neurotoxin Biology Biochemistry Interconnectedness Ribonucleases Protein structure Bacterial Proteins Chain (algebraic topology) Structural Biology Side chain Computer Simulation Amino Acid Sequence Loop modeling Phosphoenolpyruvate Sugar Phosphotransferase System Molecular Biology Sequence Deletion Sequence (medicine) Structure (mathematical logic) Templates Genetic Crystallography Sequence Alignment Algorithm Software Information Systems |
| Zdroj: | Proteins: Structure, Function, and Genetics. 23:327-336 |
| ISSN: | 1097-0134 0887-3585 |
| Popis: | Comparative models of three proteins have been built using a variety of computational methods, heavily supplemented by visual inspection. We consider the accuracy obtained to be worse than expected. A careful analysis of the models shows that a major reason for the poor results is the interconnectedness of the structural differences between the target proteins and the template structures they were modeled from. Side chain conformations are often determined by details of the structure remote in the sequence, and can be influenced by relatively small main chain changes. Almost all of the regions of substantial main chain conformational change interact with at least one other such region, so that they often cannot be modeled independently. Visual inspection is sometimes effective in correcting errors in sequence alignment and in spotting when an alternative template structure is more appropriate. We expect some improvements in the near future through the development of structure-based sequence alignment tools, side chain interconnectedness rotamer choice algorithms, and a better understanding of the context sensitivity of conformational features. |
| Databáze: | OpenAIRE |
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