@article {49133, title = {Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of {\textquoteleft}peptidase{\textquoteright} domain of Spt16}, journal = {Journal of Biomolecular Structure and Dynamics}, volume = {41}, year = {2023}, month = {MAR }, pages = {1445-1457}, type = {Article}, abstract = {

Protein function is encoded in its sequence, manifested in its three-dimensional structure, and facilitated by its dynamics. Studies have suggested that protein structures with higher sequence similarity could have more similar patterns of dynamics. However, such studies of protein dynamics within and across protein families typically rely on coarse-grained models, or approximate metrics like crystallographic B-factors. This study uses mu s scale molecular dynamics (MD) simulations to explore the conservation of dynamics among homologs of similar to 50 kDa N-terminal module of Spt16 (Spt16N). Spt16N from Saccharomyces cerevisiae (Sc-Spt16N) and three of its homologs with 30-40\% sequence identities were available in the PDB. To make our data-set more comprehensive, the crystal structure of an additional homolog (62\% sequence identity with Sc-Spt16N) was solved at 1.7 angstrom resolution. Cumulative MD simulations of 6 mu s were carried out on these Spt16N structures and on two additional protein structures with varying degrees of similarity to it. The simulations revealed that correlation in patterns of backbone fluctuations vary linearly with sequence identity. This trend could not be inferred using crystallographic B-factors. Further, normal mode analysis suggested a similar pattern of inter-domain (inter-lobe) motions not only among Spt16N homologs, but also in the M24 peptidase structure. On the other hand, MD simulation results highlighted conserved motions that were found unique for Spt16N protein, this along with electrostatics trends shed light on functional aspects of Spt16N. Communicated by Ramaswamy H. Sarma.

}, keywords = {Backbone fluctuations, FACT complex, histone binding, interdomain motion, M24 peptidase}, issn = {0739-1102}, doi = {10.1080/07391102.2021.2021990}, author = {Gaur, Neeraj K. and Ghosh, Biplab and Goyal, Venuka Durani and Kulkarni, Kiran and Makde, Ravindra D.} } @article {49446, title = {Multifunctional NiO/Ti3+{\textendash}TiO2 for concurrent water reduction and glycerol oxidation to value added products by sunlight driven photocatalysis}, journal = {Journal of Materials Chemistry A}, year = {2024}, month = {SEP}, type = {Article}, abstract = {

The present work describes the synthesis of bifunctional-mesoporous-self-doped Ti3+\ containing NiO/TiO2\ photocatalysts for concurrent utilization of e-\ and h+\ to produce H2\ and value-added products (VAPs), respectively, from aqueous glycerol. UV-vis diffuse reflectance results and band gap analysis revealed an improved light absorption due to integration of Ni2+\ with Ti3+/TiO2. Various electrochemical, PL and TRPL spectral analyses demonstrate p{\textendash}n heterojunction formation between NiO and Ti3+{\textendash}TiO2, which enhances charge separation and helps in achieving improved activity. HRTEM analysis of NiO/Ti3+{\textendash}TiO2\ nanocomposites revealed that NiO is highly dispersed on TiO2\ with interfacial heterojunctions between them. XPS results demonstrate the partial reduction of Ti4+\ to Ti3+\ and Ni{\textendash}Ti synergetic interaction in NiO/TiO2\ to form NiO/Ti3+{\textendash}TiO2\ nanocomposites. EXAFS studies show that the Ni{\textendash}O bond distance is similar to that of NiTiO3\ suggesting electronic integration of components of the photocatalyst by forming a Ni2+{\textendash}O{\textendash}Ti3+/Ti4+\ lattice network. Ni2+/Ti3+{\textendash}TiO2\ nanocomposites as a bifunctional photocatalyst exhibited significantly enhanced activity in H2\ production and conversion of glycerol to VAPs, namely, glycolaldehyde, 1,3-dihydroxyacetone, and formic acid; formation of these products highlights not only oxidation, but also C{\textendash}C cleavage of glycerol. The NiO/Ti3+{\textendash}TiO2\ photocatalysts fabricated in thin film form displayed higher photocatalytic efficiency than their powder counterpart. Among NiO/Ti3+{\textendash}TiO2\ nanocomposites NiT-3 exhibits the highest H2\ yield at 15.62 mmol h-1\ g-1, which is 38 times higher than that of bare TiO2. The enhanced photocatalytic activity is ascribed to the high charge carrier density, the synergistic interaction between Ni2+\ and Ti3+{\textendash}TiO2, formation of a p{\textendash}n heterojunction at the interface between NiO and Ti3+{\textendash}TiO2\ and effective utilization of charge carriers for redox reactions.

}, doi = {https://doi.org/10.1039/D4TA06910B}, author = {Rajendran, Sivaraj and Saju, Simi and Mani, Sunesh S. and Asoka, Anantha Krishnan and Saha, Arindam and Arun, Pushkaran S. and Ghosh, Biplab and Mathew, Thomas and Gopinath, Chinnakonda S.} }