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We present experimental evidence for soft X-ray induced intramolecular hydrogen transfer in the protonated synthetic tri-oligonucleotide d($^{\mbox{\footnotesize{F}}}$UAG) in the gas-phase. The trinucleotide cations were stored in a cryogenic ion trap...

The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5’-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have...

Infrared fluorescent proteins (iRFPs) are potential candidates for deep-tissue in vivo imaging. Here, we provide molecular-level insights into the role of the protein environment in the structural stability of the chromophore within the protein binding pocket through the flexible hydrogen-bonding network using molecular dynamics simulation. Furthermore, we present systematic excited-state analysis to characterize the nature of the first two excited states and the role of the environment in shaping the nature of the chromophore’s excited states within the hybrid quantum mechanics/molecular mechanics framework. Our results reveal that the environment red-shifts the absorption of the chromophore by about 0.32 eV compared to the isolated counterpart, and besides the structural stability, the protein environment does not alter the nature of the excited state of the chromophore significantly. Our study contributes to the fundamental understanding of the excited-state processes of iRFPs in a complex environment and provides a design principle for developing iRFPs with desired spectral properties.

Cyclin-dependent-kinases (CDKs) are essential for cell cycle progression. While dependence of CDK activity on Cyclin levels is established, molecular mechanisms that regulate their binding are less studied. Here, we show that CDKl:Cyclin-B interactions are regulated by acetylation, which was hitherto unknown. We demonstrate that cell cycle dependent acetylation of the evolutionarily conserved catalytic lysine in CDK1 or eliminating its charge state abrogates Cyclin-B binding. Opposing activities of SIRT1 and P300 regulate acetylation, which marks a reserved pool of CDK1. Our high resolution structural analyses into the formation of kinase competent CDK1: Cyclin-B complex have unveiled long-range effects of catalytic lysine in configuring the CDK1 interface for Cyclin-B binding. Cells expressing acetylation mimic mutant of Cdc2 in yeast are arrested in G2 and fail to divide. Thus, by illustrating cell cycle dependent deacetylation as a determinant of CDK1:Cyclin-B interaction, our results redefine the current model of CDK1 activation and cell cycle progression.