Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH
| Autor: | Masahiko Okuda, Tadashi Komatsu, Junichi Higo, Kenji Sugase, Tsuyoshi Konuma, Yoshifumi Nishimura |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Protein subunit Biophysics Molecular Dynamics Simulation 010402 general chemistry Antiparallel (biochemistry) 01 natural sciences Protein Structure Secondary Transcription Factors TFII 03 medical and health sciences Molecular dynamics Protein Domains Humans Amino Acid Sequence Nuclear Magnetic Resonance Biomolecular Alanine Acidic Region Chemistry Proteins 0104 chemical sciences Pleckstrin homology domain Crystallography 030104 developmental biology Mutation Transcription factor II H Transcription factor II E Hydrophobic and Hydrophilic Interactions Transcription Factor TFIIH Algorithms Protein Binding |
| Zdroj: | Biophysical Journal. 111:950-962 |
| ISSN: | 0006-3495 |
| DOI: | 10.1016/j.bpj.2016.07.042 |
| Popis: | General transcription factor II E (TFIIE) contains an acid-rich region (residues 378–393) in its α -subunit, comprising 13 acidic and two hydrophobic (Phe387 and Val390) residues. Upon binding to the p62 subunit of TFIIH, the acidic region adopts an extended string-like structure on the basic groove of the pleckstrin homology domain (PHD) of p62, and inserts Phe387 and Val390 into two shallow pockets in the groove. Here, we have examined the dynamics of this interaction by NMR and molecular dynamics (MD) simulations. Although alanine substitution of Phe387 and/or Val390 greatly reduced binding to PHD, the binding mode of the mutants was similar to that of the wild-type, as judged by the chemical-shift changes of the PHD. NMR relaxation dispersion profiles of the interaction exhibited large amplitudes for residues in the C-terminal half-string in the acidic region (Phe387, Glu388, Val390, Ala391, and Asp392), indicating a two-site binding mode: one corresponding to the final complex structure, and one to an off-pathway minor complex. To probe the off-pathway complex structure, an atomically detailed free-energy landscape of the binding mode was computed by all-atom multicanonical MD. The most thermodynamically stable cluster corresponded to the final complex structure. One of the next stable clusters was the off-pathway structure cluster, showing the reversed orientation of the C-terminal half-string on the PHD groove, as compared with the final structure. MD calculations elucidated that the C-terminal half-acidic-string forms encounter complexes mainly around the positive groove region with nearly two different orientations of the string, parallel and antiparallel to the final structure. Interestingly, the most encountered complexes exhibit a parallel-like orientation, suggesting that the string has a tendency to bind around the groove in the proper orientation with the aid of Phe387 and/or Val390 to proceed smoothly to the final complex structure. |
| Databáze: | OpenAIRE |
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