Comput Math Methods Med - Transcriptional protein-protein cooperativity in POU/HMG/DNA complexes revealed by normal mode analysis.

Tópicos

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Resumo

Biomolecular cooperativity is of great scientific interest due to its role in biological processes. Two transcription factors (TFs), Oct-4 and Sox-2, are crucial in transcriptional regulation of embryonic stem cells. In this paper, we analyze how Oct-1 (a similar POU factor) and Sox-2, interact cooperatively at their enhancer binding sites in collective motions. Normal mode analysis (NMA) is implemented to study the collective motions of two complexes with each involving these TFs and an enhancer. The special structure of Oct proteins is analyzed comprehensively, after which each Oct/Sox group is reassembled into two protein pairs. We subsequently propose a segmentation idea to extract the most correlated segments in each pair, using correlations of motion magnitude curves. The median analysis on these correlation values shows the intimacy of subunit POUS (Oct-1) and Sox-2. Using those larger-than-median correlation values, we conduct statistical studies and propose several protein-protein cooperative modes (S and D) coupled with their subtypes. Additional filters are applied and similar results are obtained. A supplementary study on the rotation angle curves reaches an agreement with these modes. Overall, these proposed cooperative modes provide useful information for us to understand the complicated interaction mechanism in the POU/HMG/DNA complexes.

Resumo Limpo

biomolecular cooper great scientif interest due role biolog process two transcript factor tfs oct sox crucial transcript regul embryon stem cell paper analyz oct similar pou factor sox interact cooper enhanc bind site collect motion normal mode analysi nma implement studi collect motion two complex involv tfs enhanc special structur oct protein analyz comprehens octsox group reassembl two protein pair subsequ propos segment idea extract correl segment pair use correl motion magnitud curv median analysi correl valu show intimaci subunit pous oct sox use largerthanmedian correl valu conduct statist studi propos sever proteinprotein cooper mode s d coupl subtyp addit filter appli similar result obtain supplementari studi rotat angl curv reach agreement mode overal propos cooper mode provid use inform us understand complic interact mechan pouhmgdna complex

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