Biology subjects

Verma, N.

Publications and source records attributed to Verma, N..

3 recordsLinked to original sources

bioRxiv2026

Structural mechanism governing radiationless energy transfer in Renilla bioluminescence

The nonradiative transport of electronic excitation from one chromophore to another, known as resonance energy transfer, lies at the root of photochemical processes in biology. Unlike photosynthesis, bioluminescence converts chemical energy into light through an enzymatic oxygenation of an energy-rich luciferin. In glowing cnidarians, the energy is relocated from an excited oxyluciferin to a fluorescent protein, shifting the colour and enhancing the quantum yield of a photogenic reaction. How protein-chromophore complexes assemble during this interplay in real space, and what this association entails for function, are unknown. Here, we report co-crystal structures of a 120-kilodalton energy-transfer complex from the luminescent soft coral Renilla reniformis. We find a heterotetrameric 2:2 assembly composed of two coelenteramide-loaded luciferases (RrLuc) docked at opposite sides of a head-to-tail dimer of green fluorescent protein (RrGFP). The edge-to-edge distance between donor and acceptor chromophores is below 3 nm, favouring the Forster-type radiationless energy transfer. Furthermore, RrGFP serves not only as a colour-switchable antenna and luminescence amplifier but also tunes the efficiency of luciferase catalysis by controlling its inherent dynamics. Our results provide detailed spatial information about intermolecular dipole-dipole coupling in Renilla bioluminescence, including the arrangement of donor-acceptor pairs that secure excited-state energy transfer with exquisite precision.

biochemistry↗

bioRxiv2018

Carbonic anhydrase network of genes trigger cytosolic pH enabling differentiation from quiescence

BackgroundCarbonic anhydrase regulates various cellular processes. Intracellular pH flux impacted by carbonic anhydrase alters the enzymes allosteric active site which effects several downstream cellular processes. Earlier, we reported that, the catalytic activity of carbonic anhydrase is independent, but direction of catalysis is affected by cellular pH level. On the other hand carbonic anhydrase alters the cytosolic pH level to facilitate allosteric phosphorylation of proteins which further leads to cellular differentiation through a process being regulated by ncRNAs.\n\nResultsThis study illustrates various ways of cell differentiation/ organ development regulation via carbonic anhydrase interacting network of proteins involved in various cellular processes. It is involved in protein degradation process of other proteins like RPT, 26S proteasome, AT3G15120 and its variant producing ncRNA, etc. Carbonic anhydrase indirectly involved in signaling process along with MAPK in providing innate resistance against biotic and abiotic stresses. It is also indirectly linked to cell membrane transporters like H+-ATPase and V-ATPase B.\n\nConclusionsThough carbonic anhydrase is not directly linked with EMS1 as revealed by network analyses and protein-protein interaction there could be a suitable condition generated by the carbonic anhydrase for EMS1 to be active. Hence, we report that carbonic anhydrase, along with other pH regulating gene complexes plays a major role for making EMS1 functional.

systems biology↗

bioRxiv2018

The cortical dynamics orchestrating skilled prehension

Skillful control of movement is central to our ability to sense and manipulate the world. A large body of work in nonhuman primates has demonstrated that motor cortex provides flexible, time-varying activity patterns that control the arm during reaching and grasping. Previous studies have suggested that these patterns are generated by strong local recurrent dynamics operating autonomously from inputs during movement execution. An alternative possibility is that motor cortex requires coordination with upstream brain regions throughout the entire movement in order to yield these patterns. Here, we developed an experimental preparation in the mouse to directly test these possibilities using optogenetics and electrophysiology during a skilled reach-to-grab-to-eat task. To validate this preparation, we first established that a specific, time-varying pattern of motor cortical activity was required to produce coordinated movement. Next, in order to disentangle the contribution of local recurrent motor cortical dynamics from external input, we optogenetically held the recurrent contribution constant, then observed how motor cortical activity recovered following the end of this perturbation. Both the neural responses and hand trajectory varied from trial to trial, and this variability reflected variability in external inputs. To directly probe the role of these inputs, we used optogenetics to perturb activity in the thalamus. Thalamic perturbation at the start of the trial prevented movement initiation, and perturbation at any stage of the movement prevented progression of the hand to the target; this demonstrates that input is required throughout the movement. By comparing motor cortical activity with and without thalamic perturbation, we were able to estimate the effects of external inputs on motor cortical population activity. Thus, unlike pattern-generating circuits that are local and autonomous, such as those in the spinal cord that generate left-right alternation during locomotion, the pattern generator for reaching and grasping is distributed across multiple, strongly-interacting brain regions.

neuroscience↗