Mini AuAg Wavy Nanorods Displaying Plasmon-Induced Photothermal and Photocatalytic Properties

Alloyed AuAg wavy nanorods (wNRs) of approximate to 24.0 nm length and 3.5 nm width are formed by the mild decomposition of the organometallic complex [Au2Ag2(C6F5)(4)(OEt2)(2)](n) in tetrahydrofuran (THF) in the presence of oleic acid. Ligand exchange with l-glutathione (GSH) or poly(ethylene glycol) methyl ether thiol (PEG-SH) leads to water-soluble nanostructures. These AuAg wNRs display tunable size-dependent longitudinal localized surface plasmon resonance (l-LSPR) broad absorptions beyond 750 nm in the near-infrared (NIR) I and II regions. These intense plasmonic absorptions lead to interesting photothermal, catalytic, and photocatalytic properties, including the catalytic reduction of 4-nitrophenol, the photocatalytic reduction of 4-nitrostyrene, or the photocatalytic dehydrogenation of ammonia borane for H-2 release

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Unbinding free energy profiles.

<p>(A) POU_S. (B) POU_HD. The black and red curves show the profiles in absence and presence of SOX2 respectively. The dotted vertical lines mark the different bound-unbound thresholds tested (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004287#pcbi.1004287.t001" target="_blank">Table 1</a>.). The shaded lines represent the error calculated as described in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004287#sec010" target="_blank">Methods</a>. See also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004287#pcbi.1004287.s009" target="_blank">S6 Fig</a>.</p

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

<div><p>Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions.</p></div