We have recently proposed a phase diagram for mixtures of porcine brain sphingomyelin (BSM), cholesterol (Chol), and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) on the basis of kinetics of carboxyfluorescein efflux induced by the amphipathic peptide δ-lysin. Although that study indicated the existence of domains, phase separations in the micrometer scale have not been observed by fluorescence microscopy in BSM/Chol/POPC mixtures, though they have for some other sphingomyelins (SM). Here we examine the same BSM/Chol/POPC system by a combination of fluorescence resonance energy transfer (FRET) and Monte Carlo simulations. The results clearly demonstrate that domains are formed in this system. Comparison of the FRET experimental data with the computer simulations allows the estimate of lipid-lipid interaction Gibbs energies between SM/Chol, SM/POPC, and Chol/POPC. The latter two interactions are weakly repulsive, but the interaction between SM and Chol is favorable. Furthermore, those three unlike lipid interaction parameters between the three possible lipid pairs are sufficient for the existence of a closed loop in the ternary phase diagram, without the need to involve multibody interactions. The calculations also indicate that the largest POPC domains contain several thousand lipids, corresponding to linear sizes of the order of a few hundred nanometers.
Multidrug-resistant Staphylococcus aureus infections pose a significant threat to human health. Antibiotic resistance is most commonly propagated by conjugative plasmids like pLW1043, the first vancomycin-resistant S. aureus vector identified in humans. We present the molecular basis for resistance transmission by the nicking enzyme in S. aureus (NES), which is essential for conjugative transfer. NES initiates and terminates the transfer of plasmids that variously confer resistance to a range of drugs, including vancomycin, gentamicin, and mupirocin. The NES N-terminal relaxase-DNA complex crystal structure reveals unique protein-DNA contacts essential in vitro and for conjugation in S. aureus. Using this structural information, we designed a DNA minor groove-targeted polyamide that inhibits NES with low micromolar efficacy. The crystal structure of the 341-residue C-terminal region outlines a unique architecture; in vitro and cell-based studies further establish that it is essential for conjugation and regulates the activity of the N-terminal relaxase. This conclusion is supported by a smallangle X-ray scattering structure of a full-length, 665-residue NES-DNA complex. Together, these data reveal the structural basis for antibiotic multiresistance acquisition by S. aureus and suggest novel strategies for therapeutic intervention.A ntibiotic resistance, which arises in bacterial pathogens through conjugative plasmid DNA transfer, is a well-established threat to global health. For example, whereas vancomycin has been essential in treating recalcitrant Staphylococcus aureus infections for decades, vancomycin-resistant S. aureus (VRSA) strains have now appeared in clinical settings worldwide (1-3). VRSA first arose in the United States through the interplay of conjugative DNA transfer and resistance-determinant transposition. The resulting plasmid, pLW1043, has been sequenced and contains not only a vanHAX vancomycin-resistance transposon, but also a cadre of putative DNA transfer genes (4). It was recently shown that the S. aureus plasmid pSK41, which is closely related to pLW1043, mediates the transfer of vancomycin resistance from Enterococcus faecalis into strains of methicillin resistant S. aureus (MRSA) (5). Conjugative bacterial plasmids use almost exclusively plasmid-encoded factors that work in concert to coordinate the cell-to-cell transfer of one strand of the duplex plasmid (6, 7). An element common to all conjugative processes is the plasmid-encoded relaxase enzyme that initiates and terminates transfer by creating a transient single-strand DNA break and covalent protein-DNA intermediate (8,9).The vancomycin-resistance plasmid pLW1043 (4) and related plasmids from S. aureus (10, 11), including pSK41 and pGO1 (12-14) as well as plasmids from streptococcal, lactococcal, and clostridial strains, encode a relaxase enzyme termed nicking enzyme in Staphylococcus (NES) that exhibits a unique fulllength sequence (Fig. S1). It is 665 residues in length, confines its relaxase motifs to its N-terminal ∼220 aa, an...
Protein arginine methyltransferase 10 (PRMT10) is a type-I arginine methyltransferase essential for regulating flowering time in Arabidopsis thaliana (At). We present a 2.6 Å resolution crystal structure of AtPRMT10 in complex with a reaction product, S-adenosylhomocysteine. The structure reveals a dimerization arm 12–20 residues longer than PRMT structures elucidated previously; as a result, the essential AtPRMT10 dimer exhibits a large central cavity and a distinctly accessible active site. We employ molecular dynamics to examine how dimerization facilitates AtPRMT10 motions necessary for activity, and show that these motions are conserved in other PRMT enzymes. Finally, functional data reveal that the N-terminal ten residues of AtPRMT10 influence substrate specificity, and that enzyme activity is dependent on substrate protein sequences distal from the methylation site. Taken together, these data provide insights into the molecular mechanism of Arabidopsis thaliana PRMT10 as well as other members of the PRMT family of enzymes. They highlight differences between AtPRMT10 and other PRMTs, but also indicate that motions are a conserved element of PRMT function.
Nuclear receptor ligand binding domains (LBDs) convert ligand binding events into changes in gene expression by recruiting transcriptional coregulators to a conserved activation function-2 (AF-2) surface. While most nuclear receptor LBDs form homo- or heterodimers, the human nuclear receptor pregnane X receptor (PXR) forms a unique and essential homodimer and is proposed to assemble into a functional heterotetramer with the retinoid X receptor (RXR). How the homodimer interface, which is located 30 Å from the AF-2, would affect function at this critical surface has remained unclear. By using 20- to 30-ns molecular dynamics simulations on PXR in various oligomerization states, we observed a remarkably high degree of correlated motion in the PXR–RXR heterotetramer, most notably in the four helices that create the AF-2 domain. The function of such correlation may be to create “active-capable” receptor complexes that are ready to bind to transcriptional coactivators. Indeed, we found in additional simulations that active-capable receptor complexes involving other orphan or steroid nuclear receptors also exhibit highly correlated AF-2 domain motions. We further propose a mechanism for the transmission of long-range motions through the nuclear receptor LBD to the AF-2 surface. Taken together, our findings indicate that long-range motions within the LBD scaffold are critical to nuclear receptor function by promoting a mobile AF-2 state ready to bind coactivators.
The majority of eukaryotic pre-mRNAs are processed by 3′-end cleavage and polyadenylation, although in metazoa the replication-dependant histone mRNAs are processed by 3′-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the ~1,160-residue protein Symplekin. Secondary structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 Å resolution using SAD phasing methods. The structure exhibits 5 canonical HEAT repeats along with an extended 31 amino acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3′-end processing. Taken together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process.
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