Malleable Machines in Transcription Regulation: The Mediator Complex

The Mediator complex provides an interface between gene-specific regulatory proteins and the general transcription machinery including RNA polymerase II (RNAP II). The complex has a modular architecture (Head, Middle, and Tail) and cryoelectron microscopy analysis suggested that it undergoes dramatic conformational changes upon interactions with activators and RNAP II. These rearrangements have been proposed to play a role in the assembly of the preinitiation complex and also to contribute to the regulatory mechanism of Mediator. In analogy to many regulatory and transcriptional proteins, we reasoned that Mediator might also utilize intrinsically disordered regions (IDRs) to facilitate structural transitions and transmit transcriptional signals. Indeed, a high prevalence of IDRs was found in various subunits of Mediator from both Saccharomyces cerevisiae and Homo sapiens, especially in the Tail and the Middle modules. The level of disorder increases from yeast to man, although in both organisms it significantly exceeds that of multiprotein complexes of a similar size. IDRs can contribute to Mediator's function in three different ways: they can individually serve as target sites for multiple partners having distinctive structures; they can act as malleable linkers connecting globular domains that impart modular functionality on the complex; and they can also facilitate assembly and disassembly of complexes in response to regulatory signals. Short segments of IDRs, termed molecular recognition features (MoRFs) distinguished by a high protein–protein interaction propensity, were identified in 16 and 19 subunits of the yeast and human Mediator, respectively. In Saccharomyces cerevisiae, the functional roles of 11 MoRFs have been experimentally verified, and those in the Med8/Med18/Med20 and Med7/Med21 complexes were structurally confirmed. Although the Saccharomyces cerevisiae and Homo sapiens Mediator sequences are only weakly conserved, the arrangements of the disordered regions and their embedded interaction sites are quite similar in the two organisms. All of these data suggest an integral role for intrinsic disorder in Mediator's function

Formation of fulvene in the reaction of C2H with 1,3-butadiene

Abstract Products formed in the reaction of C2H radicals with 1,3-butadiene at 4 Torr and 298 K are probed using photoionization time-of-flight mass spectrometry. The reaction takes place in a slow-flow reactor, and products are ionized by tunable vacuum-ultraviolet light from the Advanced Light Source. The principal reaction channel involves addition of the radical to one of the unsaturated sites of 1,3-butadiene, followed by H-loss to give isomers of C6H6. The photoionization spectrum of the C6H6 product indicates that fulvene is formed with a branching fraction of (57 ± 30)%. At least one more isomer is formed, which is likely to be one or more of 3,4-dimethylenecyclobut-1-ene, 3-methylene-1-penten-4-yne or 3-methyl-1,2-pentadien-4-yne. An experimental photoionization spectrum of 3,4-dimethylenecyclobut-1-ene and simulated photoionization spectra of 3-methylene-1-penten-4-yne and 3-methyl-1,2-pentadien-4-yne are used to fit the measured data and obtain maximum branching fractions of 74%, 24% and 31%, respectively, for these isomers. An upper limit of 45% is placed on the branching fraction for the sum of benzene and 1,3-hexadien-5-yne. The reactive potential energy surface is also investigated computationally. Minima and first-order saddle-points on several possible reaction pathways to fulvene + H and 3,4-dimethylenecyclobut-1-ene + H products are calculated