Computational design of ligand binding is not a solved problem Export

@article{citeulike:6065286, abstract = {10.1073/pnas.0907950106 Computational design has been very successful in recent years: multiple novel ligand binding proteins as well as enzymes have been reported. We wanted to know in molecular detail how precise the predictions of the interactions of protein and ligands are. Therefore, we performed a structural analysis of a number of published receptors designed onto the periplasmic binding protein scaffold that were reported to bind to the new ligands with nano- to micromolar affinities. It turned out that most of these designed proteins are not suitable for structural studies due to instability and aggregation. However, we were able to solve the crystal structure of an arabinose binding protein designed to bind serotonin to 2.2 \~{A}… resolution. While crystallized in the presence of an excess of serotonin, the protein is in an open conformation with no serotonin bound, although the side-chain conformations in the empty binding pocket are very similar to the conformations predicted. During subsequent characterization using isothermal titration calorimetry, CD, and NMR spectroscopy, no indication of binding could be detected for any of the tested designed receptors, whereas wild-type proteins bound their ligands as expected. We conclude that although the computational prediction of side-chain conformations appears to be working, it does not necessarily confer binding as expected. Hence, the computational design of ligand binding is not a solved problem and needs to be revisited.}, author = {Schreier, Bettina and Stumpp, Christian and Wiesner, Silke and H\~{A}{\P}cker, Birte}, citeulike-article-id = {6065286}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0907950106}, citeulike-linkout-1 = {http://www.pnas.org/content/106/44/18491.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/44/18491.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19833875}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19833875}, day = {3}, doi = {10.1073/pnas.0907950106}, journal = {Proceedings of the National Academy of Sciences}, keywords = {design, protein}, month = {November}, number = {44}, pages = {18491--18496}, posted-at = {2009-11-04 09:16:00}, priority = {2}, title = {Computational design of ligand binding is not a solved problem}, url = {http://dx.doi.org/10.1073/pnas.0907950106}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:6065286 L3 - citeulike-article-id:6065286 N2 - 10.1073/pnas.0907950106 Computational design has been very successful in recent years: multiple novel ligand binding proteins as well as enzymes have been reported. We wanted to know in molecular detail how precise the predictions of the interactions of protein and ligands are. Therefore, we performed a structural analysis of a number of published receptors designed onto the periplasmic binding protein scaffold that were reported to bind to the new ligands with nano- to micromolar affinities. It turned out that most of these designed proteins are not suitable for structural studies due to instability and aggregation. However, we were able to solve the crystal structure of an arabinose binding protein designed to bind serotonin to 2.2 Å resolution. While crystallized in the presence of an excess of serotonin, the protein is in an open conformation with no serotonin bound, although the side-chain conformations in the empty binding pocket are very similar to the conformations predicted. During subsequent characterization using isothermal titration calorimetry, CD, and NMR spectroscopy, no indication of binding could be detected for any of the tested designed receptors, whereas wild-type proteins bound their ligands as expected. We conclude that although the computational prediction of side-chain conformations appears to be working, it does not necessarily confer binding as expected. Hence, the computational design of ligand binding is not a solved problem and needs to be revisited. IS - 44 JF - Proceedings of the National Academy of Sciences EP - 18496 TI - Computational design of ligand binding is not a solved problem VL - 106 SP - 18491 KW - design KW - protein AU - Schreier, Bettina AU - Stumpp, Christian AU - Wiesner, Silke AU - Höcker, Birte PY - 2009/11/03/ UR - http://dx.doi.org/10.1073/pnas.0907950106 ER -