Transcription factor Atf1-dependent degradation of the mitotic cyclin Cdc13 is regulated by multiple factors in Schizosaccharomyces pombe.

The bZIP transcription factor Atf1 is a key player in the transcriptional programme of Schizosaccharomyces pombe cell cycle. It also controls both expression and degradation of mitotic cyclin Cdc13. Temporal regulation of these opposing functions of Atf1 is critical for fidelity of cell division. Our investigations revealed that an increase in the activity of mitogen-activated protein kinase (MAPK) Spc1 during mitotic exit and the consequent phosphorylation of Atf1 along with the prevailing high activity of cyclin-dependent kinase Cdc2 regulate Cdc13 degradation. Our results also indicate the possibility of a complex interplay between Cdc2 inhibitory kinase Wee1, the anaphase-promoting complex and Atf1 during mitotic exit. These observations provide evidence of new regulatory mechanisms of mitotic exit.

Dataset describing the genome wide effects on transcription resulting from alterations in the relative levels of the bZIP transcription factors Atf1 and Pcr1 in Schizosaccharomyces pombe.

Schizosaccharomyces pombe has been used as an excellent model for studying eukaryotic cell cycle regulation and stress responses. The bZIP transcription factors Atf1(ATF2 homolog) and Pcr1(CREB homolog) have been shown to be important for regulating the expression of genes related to both stress response and cell cycle. Pcr1 has in fact been implicated as a determining factor in the segregation of the cell cycle and stress response related functions of Atf1. Interestingly Atf1 and Pcr1 levels are known to vary during the cell cycle thus giving rise to the possibility that their relative levels can influence the periodic transcriptional program of the cell. Here we report our observations on the changes in transcriptome of S. pombe cells which have been genetically manipulated to create relative differences in the levels of Atf1 and Pcr1. These results highlight new information regarding the potential role of Atf1 and Pcr1 in orchestrating the integration of the transcriptional programs of cell cycle and stress response.

Antagonistic regulation of cyclin expression by the bZIP transcription factors Pcr1 and Atf1 during G2/M transition.

The transcription factor Atf1 is known to promote cell survival during various stress conditions in Schizosaccharomyces pombe by activating the expression of appropriate genes. It can also activate transcription of other important genes responsible for cell cycle progression. An Atf1-dependent increase in the expression of cell division promoting genes will oppose activation of checkpoints necessary to ensure repairs and cell survival during stress. Hence, selective inhibition of the cell cycle-related functions of Atf1 would be indispensable for cellular survival during stress. Here we present evidence in favour of selective inhibition of Atf1's ability to activate cdc13+ transcription. We show that the transcription factor Pcr1 can specifically inhibit the recruitment of Atf1 on cdc13 promoter and thereby prevent Atf1-mediated mitotic acceleration. We also show that this opposition of Atf1 functions by Pcr1 extends to the G1-S transition event as well. Altogether these results suggest a previously unknown antagonistic function of Atf1 and Pcr1 in regulating Cdc13 expression during cell cycle progression.

An experimental and computational study to understand the lithium storage mechanism in molybdenum disulfide.

The lithium storage mechanism in molybdenum disulfide (MoS(2)) has been comprehensively investigated as the existing conversion-based storage mechanism is unable to explain the reason behind its high practical capacity, high polarization losses, and the change in the discharge profile after the 1(st) charge-discharge cycle. To resolve these issues and to gain a deeper understanding of MoS(2)-based Li-ion batteries, for the first time, we have studied the reaction mechanism of the MoS(2) anode using various experimental techniques such as XRD, Raman spectroscopy, electrochemical impedance spectroscopy, XANES, and EXAFS, as well as ab initio density functional theory based calculations. On the basis of the results presented here, and in line with some experimental findings, we find that the reaction of MoS(2) with Li is not as simple as with usual metal oxide based conversion reactions, but that the pathway of the conversion reaction changes after the first discharge process. In the first discharge process, lithiation is initiated by a limited intercalation process, followed by a conversion reaction that produces molybdenum nanoparticles (Mo) and lithium sulfide (Li(2)S). Whereas, unlike oxide-based conversion materials, MoS(2) does not transverse back during the delithiation process. Indeed, instead of MoS(2) formation, we identified the presence of polysulfur after the complete cycle. In consecutive cycles, polysulfur reacts with lithium and forms Li(2)S/Li(2)S(2), and this Li-S reaction is found to be highly reversible in nature and the only source of the high practical capacity observed in this electrode. To validate our experimental findings, an atomic scale ab initio computational study was also carried out, which likewise suggests that Li first intercalates between the MoS(2) layers but that after a certain concentration, it reacts with MoS(2) to form Li(2)S. The calculations also support the non-reversibility of the conversion reaction, by showing that Mo + Li(2)S formation is energetically more favorable than the re-formation of MoS(2) + Li.

An in silico method for designing thermostable variant of a dimeric mesophilic protein based on its 3D structure.

Designing proteins with enhanced thermostability has been a major interest of protein engineering because of its potential industrial applications. Here, we have presented a computational method for designing dimeric thermostable protein based on rational mutations on a mesophilic protein. Experimental and structural data indicate that the surface stability of a protein is a major factor controlling denaturation of a protein and ion-pairs are most efficient in enhancing the stability of the surfaces of the monomers and the interface between them. Our mutation based strategy is to first identify several polar or charged residues on the protein surface, interacting weakly with the rest of the protein and then replacing the side-chains of suitable neighboring residues to increase the interaction between these two residues. In stabilizing the interface, mutation is done in the interface for forming an ion pairs between the monomers. Application of this design strategy to a homo-dimeric protein and a hetero-dimeric protein as examples has produced excellent results. In both the cases the designed mutated proteins including the individual monomers and the interfaces were found to be considerably more stable than the respective mesophilic proteins as judged by self-energies and residue-wise interaction patterns. This method is easily applicable to any multi-meric proteins.

Do homologous thermophilic-mesophilic proteins exhibit similar structures and dynamics at optimal growth temperatures? A molecular dynamics simulation study.

Structure and dynamics both are known to be important for the activity of a protein. A fundamental question is whether a thermophilic protein and its mesophilic homologue exhibit similar dynamics at their respective optimal growth temperatures. We have addressed this question by performing molecular dynamics (MD) simulations of a natural mesophilic-thermophilic homologue pair at their respective optimal growth temperatures to compare their structural, dynamical, and solvent properties. The MD simulations were done in explicit aqueous solvent under periodic boundary and constant pressure and temperature (CPT) conditions and continued for 10.0 ns using the same protocol for the two proteins, excepting the temperatures. The trajectories were analyzed to compare the properties of the two proteins. Results indicated that the dynamical behaviors of the two proteins at the respective optimal growth temperatures were remarkably similar. For the common residues in the thermophilic protein, the rms fluctuations have a general trend to be slightly higher compared to that in the mesophilic counterpart. Lindemann parameter values indicated that only a few residues exhibited solid-like dynamics while the protein as a whole appeared as a molten globule in each case. Interestingly, the water-water interaction was found to be strikingly similar in spite of the difference in temperatures while, the protein-water interaction was significantly different in the two simulations.

One-pot thioetherification of aryl halides with thiourea and benzyl bromide in water catalyzed by Cu-grafted furfural imine-functionalized mesoporous SBA-15.

Surface functionalization of SBA-15 followed by its reaction with Cu(OAc)(2) has been carried out to develop a new Cu-grafted functionalized mesoporous material, which catalyzes one-pot three component coupling of different aryl halides with thiourea and benzyl bromide in aqueous medium to produce aryl thioethers in very good yields (80-88%).

Turning a mesophilic protein into a thermophilic one: a computational approach based on 3D structural features.

In spite of considerable improvement of our understanding of factors responsible for protein thermostability, rational designing of thermostable variants of mesophilic proteins is not yet fully established. The present paper describes an effective computational strategy that we have developed to identify the most suitable mutations converting a chosen mesophilic protein into a thermophilic one starting from its 3D structure. The approach is based on the concept that stabilization of several surface residues should enhance the global stability of the protein. The method relies on the estimation of electrostatic and van der Waals interactions in computing the interaction among the side chains of individual residues and the rest of the protein. The polar or charged residues whose side chains interact weakly with the rest of the original protein are identified first. Then, for each such identified residue (A), another residue (B) in its spatial vicinity is identified. The side chain of the residue (B) is then replaced by a suitable conformer of a residue that is electrostatically complementary to the residue (A) to enhance local interactions and hence the stability of the protein. The steric effect is taken care of through van der Waals interactions. We reject the mutations that improve interactions only locally along the sequence as it is unlikely to enhance the global stability of the 3D architecture. We use the difference in self-energies (DeltaEself) as a measure of the stability difference between the original and its mutant variant. This paper presents two test cases with demonstration of the enhanced stability of such mutated proteins and validates the strategy by considering five experimentally known thermophilic-mesophilic protein pairs.