Globin-coupled sensors (GCS) are heme-binding signal transducers in Bacteria and Archaea where an N-terminal globin controls the activity of a variable C-terminal domain. Here we report that BpeGReg, a globin-coupled diguanylate cyclase (GCDC) from the whooping-cough pathogen Bordetella pertussis, synthesizes the second messenger bis-(3’–5’)-cyclic diguanosine monophosphate (c-di-GMP) upon oxygen binding. Expression of BpeGReg in Salmonella typhimurium enhances biofilm formation, while knockout of the BpeGReg gene of B. pertussis results in decreased biofilm formation. These results represent the first identification of a gaseous ligand for any diguanylate cyclase and provide definitive experimental evidence that a globin-coupled sensor regulates c-di-GMP synthesis and biofilm formation. We propose that the synthesis of c-di-GMP by globin sensors is a widespread phenomenon in bacteria.

Hemoglobins are ubiquitous in Eukarya and Bacteria but, until now, have not been found in Archaea. A phylogenetic analysis of the recently revealed microbial family of globin-coupled hemebased sensors suggests that these sensors descended from an ancient globin-only progenitor, or a protoglobin (Pgb). Here, we report the discovery and characterization of two Pgbs from the Archaea: ApPgb from the obligately aerobic hyperthermophile Aeropyrum pernix, and MaPgb from the strictly anaerobic methanogen Methanosarcina acetivorans. Both ApPgb and MaPgb bind molecular oxygen, nitric oxide, and carbon monoxide by means of a heme moiety that is coordinated to the protein through the F8 histidine (histidine 120). We postulate that these archaeal globins are the ancestors of contemporary hemoglobins.globin-coupled sensor ͉ oxygen sensor ͉ NO sensor ͉ myoglobin

The popular MARTINI coarse-grained model is used as a test case to analyze the adherence of top-down coarse-grained molecular dynamics models (i.e., models primarily parametrized to match experimental results) to the known features of statistical mechanics for the underlying all-atom representations. Specifically, the temperature dependence of various pair distribution functions, and hence their underlying potentials of mean force via the reversible work theorem, are compared between MARTINI 2.0, Dry MARTINI, and all-atom simulations mapped onto equivalent coarse-grained sites for certain lipid bilayers. It is found that the MARTINI models do not completely capture the lipid structure seen in atomistic simulations as projected onto the coarse-grained mappings and that issues of accuracy and temperature transferability arise due to an incorrect enthalpy–entropy decomposition of these potentials of mean force. The potential of mean force for the association of two amphipathic helices in a lipid bilayer is also calculated, and especially at shorter ranges, the MARTINI and all-atom projection results differ substantially. The former is much less repulsive and hence will lead to a higher probability of MARTINI helix association in the MARTINI bilayer than occurs in the actual all-atom case. Additionally, the bilayer height fluctuation spectra are calculated for the MARTINI model, and compared to the all-atom results, it is found that the magnitude of thermally averaged amplitudes at intermediate length scales are quite different, pointing to a number of possible consequences for realistic modeling of membrane processes. Taken as a whole, the results presented here show disagreement in the enthalpic and entropic driving forces driving lateral structure in lipid bilayers as well as quantitative differences in association of embedded amphipathic helices, which can help direct future efforts to parametrize CG models with better agreement to the all-atom systems they aspire to represent.