Computational protocol: The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation

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Protocol publication

[…] The TFE WH domain was modeled based on the S. solfataricus TFE N-terminal domain crystal structure (PDB: 1Q1H, resolution 2.9 Å) (), and the TFE ZR domain was modeled based on the human TFIIEα NMR structure ensemble (PDB: 1VD4) (), both using Modeler 9.7 (build 6923) (). Stereochemistry was checked using Procheck V3.4 (). The TM score for the WH domain model is 0.93 and the average rmsd 1.24 Å, and for the ZR domain model 0.62 and 2.09 Å, respectively (). The two domains were connected by an initially coiled linker of 12 aa missing in the templates and energy minimized in a 3 ns unconstrained molecular dynamics simulation (in explicit water with ions) using simulated annealing energy minimization with the force field Amber99 () as implemented in Yasara (). […]

Pipeline specifications

Software tools PROCHECK, YASARA
Applications Drug design, Protein structure analysis
Organisms Methanocaldococcus jannaschii
Chemicals Zinc