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@article{1299537, author = {Krepl, Miroslav and Havrila, Marek and Stadlbauer, Petr and Banáš, Pavel and Otyepka, Michal and Pasulka, Josef and Štefl, Richard and Šponer, Jiří}, article_location = {WASHINGTON}, article_number = {3}, doi = {http://dx.doi.org/10.1021/ct5008108}, keywords = {MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE MESH EWALD; MECHANICS FORCE-FIELDS; RIBOSOMAL L1 STALK; BINDING PROTEINS; NUCLEIC-ACIDS; CAENORHABDITIS-ELEGANS; CRYSTAL-STRUCTURE; NONCODING RNAS; ANIMAL VIRUS}, language = {eng}, issn = {1549-9618}, journal = {Journal of Chemical Theory and Computation}, title = {Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?}, url = {http://pubs.acs.org/doi/pdf/10.1021/ct5008108}, volume = {11}, year = {2015} }
TY - JOUR ID - 1299537 AU - Krepl, Miroslav - Havrila, Marek - Stadlbauer, Petr - Banáš, Pavel - Otyepka, Michal - Pasulka, Josef - Štefl, Richard - Šponer, Jiří PY - 2015 TI - Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? JF - Journal of Chemical Theory and Computation VL - 11 IS - 3 SP - 1220-1243 EP - 1220-1243 PB - AMER CHEMICAL SOC SN - 15499618 KW - MOLECULAR-DYNAMICS SIMULATIONS KW - PARTICLE MESH EWALD KW - MECHANICS FORCE-FIELDS KW - RIBOSOMAL L1 STALK KW - BINDING PROTEINS KW - NUCLEIC-ACIDS KW - CAENORHABDITIS-ELEGANS KW - CRYSTAL-STRUCTURE KW - NONCODING RNAS KW - ANIMAL VIRUS UR - http://pubs.acs.org/doi/pdf/10.1021/ct5008108 L2 - http://pubs.acs.org/doi/pdf/10.1021/ct5008108 N2 - We report over 30 mu s of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent. We utilize the AMBER ff99bsc0 chi(OL3) RNA force field combined with the ff99SB protein force field and its more recent ff12SB version with reparametrized side-chain dihedrals. The simulations show variable behavior, ranging from systems that are essentially stable to systems with progressive deviations from the experimental structure, which we could not stabilize anywhere close to the starting experimental structure. For some systems, microsecond-scale simulations are necessary to achieve stabilization after initial sizable structural perturbations. The results show that simulations of protein-RNA complexes are challenging and every system should be treated individually. The simulations are affected by numerous factors, including properties of the starting structures (the initially high force field potential energy, resolution limits, conformational averaging, crystal packing, etc.), force field imbalances, and real flexibility of the studied systems. These factors, and thus the simulation behavior, differ from system to system. The structural stability of simulated systems does not correlate with the size of buried interaction surface or experimentally determined binding affinities but reflects the type of protein-RNA recognition. Protein-RNA interfaces involving shape-specific recognition of RNA are more stable than those relying on sequence-specific RNA recognition. The differences between the protein force fields are considerably smaller than the uncertainties caused by sampling and starting structures. The ff12SB improves description of the tyrosine side-chain group, which eliminates some problems associated with tyrosine dynamics. ER -
KREPL, Miroslav, Marek HAVRILA, Petr STADLBAUER, Pavel BANÁŠ, Michal OTYEPKA, Josef PASULKA, Richard ŠTEFL a Jiří ŠPONER. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, roč.~11, č.~3, s.~1220-1243. ISSN~1549-9618. doi:10.1021/ct5008108. 2015.
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