@article { ISI:000320836600009, title = {Effect of different arginine methylations on the thermodynamics of tat peptide binding to HIV-1 TAR RNA}, journal = {Biochimie}, volume = {95}, number = {7}, year = {2013}, month = {JUL}, pages = {1422-1431}, publisher = {ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER}, address = {23 RUE LINOIS, 75724 PARIS, FRANCE}, abstract = {

RNA-binding proteins are an important class of mediators that regulate cell function and differentiation. Methylation of arginine, a post-translational modification (PTM) found in these proteins, can modulate their function. Arginine can be monomethylated or dimethylated, depending on the type of methyl transferases involved. This paper describes a comparative study of the thermodynamics of unmodified and modified Tat peptide interaction with TAR RNA, where the peptide is methylated at epsilon (epsilon) and eta (eta) nitrogen atoms of guanidinium group of arginine side chain at position 52 or 53. The results indicate that monomethylation of arginine at epsilon (epsilon) nitrogen atom enhances binding affinity, owing to a more favourable enthalpy component which overrides the less favourable entropy change. In contrast, monomethylation of arginine residue at eta nitrogen results in reduced binding affinity originating exclusively from a less favourable enthalpy change leaving entropic component unaffected. However, in case of simultaneous methylation at epsilon and eta positions, the binding parameters remain almost unaffected, when compared to the unmodified peptide. In case of symmetric dimethylation at eta position the observed enthalpy change of the binding was found to be smaller than the values obtained for the unmodified peptide. Asymmetric dimethylation at eta position showed the most reduced binding affinities owing to less favourable enthalpy changes. These results provide insights that enable elucidation of the biological outcome of arginine methylation as PTMs that regulate protein function, and will contribute to our understanding of how these PTMs are established in vitro and in vivo. (C) 2013 Elsevier Masson SAS. All rights reserved.

}, keywords = {HIV-1, Post-translational modification, Protein methylation, RNA-protein interaction, Thermodynamics}, issn = {0300-9084}, doi = {10.1016/j.biochi.2013.03.008}, author = {Kumar, Santosh and Maiti, Souvik} } @article {46656, title = {Structure and regulation of SWEET transporters in plants: an update}, journal = {Plant Physiology and Biochemistry}, volume = {156}, year = {2020}, month = {NOV}, pages = {1-6}, type = {Review}, abstract = {

Sugar will eventually be exported transporters (SWEETs), a novel family of sugar transporters found in both eukaryotes and prokaryotes, facilitate sugar flux across the cell membrane. Although these transporters were first discovered in plants, their homologs have been reported in different organisms. SWEETs have critical roles in various developmental processes, including phloem loading, nectar secretion, and pathogen nutrition. The structure of bacterial homologs, called SemiSWEETs, has been well studied thus far. Here, we provide an overview of SWEET protein structure and dynamic function by analyzing the solved crystal structures and predicted models that are available for a few SWEETs in a monocot plant (rice) and dicot plant (Arabidopsis thaliana). Despite the advancement in structure-related studies, the regulation of SWEETs remains unknown. In light of reported regulatory mechanisms of a few other sugar transporters, we propose the regulation of SWEETs at the post-translational level. We then enumerate the potential post-translational modification sites in SWEETs using computational tools. Overall, in this review, we critically analyze SWEET protein structure in plants to predict the post-translational regulation of SWEETs. Such findings have a direct bearing on plant nutrition and defense and targeting the regulation at these levels will be important in crop improvement.

}, keywords = {oligomerization, Phosphorylation, Post-translational modification, Sugar transporters, Sugar will eventually be exported transporters}, issn = {0981-9428}, doi = {10.1016/j.plaphy.2020.08.043}, author = {Anjali, Anjali and Fatima, Urooj and Manu, M. S. and Ramasamy, Sureshkumar and Senthil-Kumar, Muthappa} } @article {47989, title = {Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation}, journal = {International Journal of Biological Macromolecules}, volume = {206}, year = {2022}, month = {MAY }, pages = {812-822}, type = {Article}, abstract = {

The chemokine receptor CXCR4 and its cognate ligand CXCL12 mediate pathways that lead to cell migration and chemotaxis. Although the structural details of related receptor-ligand complexes have been resolved, the roles of the N-terminal domain of the receptor and post-translational sulfation that are determinants of ligand selectivity and affinity remain unclear. Here, we analyze the structural dynamics induced by receptor sulfation by combining molecular dynamics, docking and network analysis. The sulfotyrosine residues, 7YsN-term, 12Ys(N-term) and 21Ys(N-term) allow the N-terminal domain of the apo-sulfated receptor to adopt an {\textquoteleft}{\textquoteleft}open {\textquoteleft}{\textquoteleft} conformation that appears to facilitate ligand binding. The overall topology of the CXCR4-CXCL12 complex is independent of the sulfation state, but an extensive network of protein-protein interactions characterizes the sulfated receptor, in line with its increased ligand affinity. The altered interactions of sulfotyrosine residues, such as 21Ys(N-term)- 47R(CXCL12) replacing the 21Y(N-term)-13F(CXCL12) interaction, propagate via allosteric pathways towards the receptor lumen. In particular, our results suggest that the experimentally-reported receptor-ligand interactions 262D(6.58)- 8R(CXCL12) and 277E(7.28)-12R(CXCL12) could be dependent on the sulfation state of the receptor and need to be carefully analyzed. Our work is an important step in understanding chemokine-receptor interactions and how post-translational modifications could modulate receptor-ligand complexes.

}, keywords = {Allosteric communication pathway, Atomistic molecular dynamics simulations, G protein-coupled receptor, Ligand binding, Post-translational modification, Protein-protein interface}, issn = {0141-8130}, doi = {10.1016/j.ijbiomac.2022.03.078}, author = {Sonawani, Archana and Kharche, Shalmali and Dasgupta, Debjani and Sengupta, Durba} }