Biology subjects

Sundaresan, S.

Publications and source records attributed to Sundaresan, S..

4 recordsLinked to original sources

bioRxiv2024

The entangled world of DNA quadruplex folds

DNA quadruplexes take part in many biological functions. It takes up a variety of folds based on the sequence and environment. Here, a meticulous analysis of experimentally determined 392 quadruplex structures (388 PDB IDs) deposited in PDB is carried out. The analysis reveals the modular representation of the quadruplex folds. 48 unique quadruplex motifs (whose diversity arises out of the propeller, bulge, diagonal, and lateral loops that connect the quartets) are identified, leading to simple to complex inter-/intra-molecular quadruplex folds. These structural two-layered motifs are further classified into 33 continuous and 15 discontinuous motifs. The discontinuous motifs cannot further be classified into parallel, antiparallel, or hybrid as one or more guanines of the adjacent quartets are not connected. While the continuous motifs can be extended to a quadruplex fold, the discontinuous motif requires additional loop(s) to complete a fold, as illustrated here with examples. Similarly, the higher-order quadruplex folds can also be represented by continuous or discontinuous motifs or their combinations. Such a modular representation of the quadruplex folds may assist in custom engineering of quadruplexes, designing motif-based drugs, and the prediction of quadruplex structure. Further, it could facilitate understanding the role of quadruplexes in biological functions and diseases.

biochemistry↗

bioRxiv2024

Molecular Dynamics Trajectory Analysis of Permeation (MDTAP): A tool to analyze permeation events across membrane proteins

Background and ObjectiveMolecular dynamics (MD) simulations are indispensable and versatile in capturing the time-dependent conformational changes of biomolecules to shed light on the concomitant biological processes. MD is used to provide critical mechanistic insights into the transportation of solvent/solute/drug molecules across protein channels embedded in a membrane bilayer. The huge size and volume of the MD trajectories of a membrane-embedded system provide challenges in the analyses of membrane permeation events. Thus, a software, Molecular Dynamics Trajectory Analysis of Permeation (MDTAP), is presented here to analyze the permeation events across membrane-embedded proteins and nucleic acids automatically. MethodsA software is developed here to automatically detect the permeation events across the channels irrespective of their shape and size and the type of solute molecules from the MD trajectories. MDTAP employs bash scripts to fetch information about the permeation, residence time, and diffusion of the molecules of interest in a Linux/Mac-based environment. The source code of MDTAP is freely available to the public, along with installation and usage information on GitHub (attached as supplementary for the review process and will be made accessible to the public through the following link upon acceptance for publication: https://github.com/MBL-lab/MDTAP). ResultsThe efficiency of MDTAP is demonstrated here by considering the MD trajectories of 2 water-conducting channels as test cases: E. coli outer membrane protein Wzi and E. coli Aquaporin Z. The dimensions of the channels and their capacity to accommodate and conduct water, the number of permeating water molecules along with the path traced and time taken to cross the channel is validated. ConclusionIn summary, the graphical representation of the time-dependent behavior of the solute/solvent permeation events corresponding to an MD trajectory in MDTAP allows the user to easily visualize the mechanism of permeation, including the localization of the permeating molecule (if any) and permeating path. Thus, MDTAP immensely reduces the difficult task of manually analyzing solute/solvent permeations from the bulk MD trajectories. Such a simplistic representation of permeation events across the protein transporters helps in the design of drug molecules to treat the associated diseases. Further, MDTAP is also designed to characterize the permeation events across artificial nucleic acid channels, considering their importance in recent times.

biophysics↗

bioRxiv2022

Clinically defined mutations in MEN1 alter its tumor-suppressive function through increased menin turnover

Loss of the tumor suppressor protein menin is a critical event underlying the formation of neuroendocrine tumors (NETs) in hormone-expressing tissues including gastrinomas. While aberrant expression of menin impairs its tumor suppression, few studies explore the structure- function relationship of clinical Multiple Endocrine Neoplasia, type 1 (MEN1) mutations in the absence of a complete loss of heterozygosity at both loci. Here, we determined whether clinical MEN1 mutations render nuclear menin unstable and lead to its functional inactivation. We studied the structural and functional implications of three clinical MEN1 mutations (R516fs, E235K, and A541T) recently identified in a cohort of ten patients with GEP-NETs. We evaluated the subcellular localization and half-lives of these mutated menin variants in Men1-null mouse embryo fibroblast cells and in hormone-expressing human gastric adenocarcinoma and murine enteroendocrine tumor cell lines. Loss of menin function was assessed by cell proliferation and gastrin gene expression assays. Lastly, we evaluated the effect of the small molecule compound MI-503 on stabilizing nuclear menin expression and function in vitro and in a previously reported mouse model of gastric NET development. Both the R516fs and E235K variants exhibited severe defects in total and subcellular expression of menin, and this was consistent with reduced half-lives of these mutants. Mutated menin variants exhibited loss of function in suppressing tumor cell proliferation and gastrin expression. Treatment with MI-503 rescued nuclear menin expression and attenuated hypergastrinemia and gastric hyperplasia in NET-bearing mice. ImplicationClinically defined germline and somatic MEN1 mutations confer pathogenicity by destabilizing nuclear menin expression.

cancer biology↗

bioRxiv2022

Menin-MLL Inhibitor MI-503 Blocks Menin Nuclear Export and Suppresses Hypergastrinemia

Menin is the protein product of the Multiple Endocrine Neoplasia 1 (MEN1) gene locus at 11q13 and is a known tumor suppressor of neuroendocrine neoplasms (NENs). Gastrin-expressing NENs (gastrinomas) comprise the most frequent and malignant of the MEN1-dependent endocrine tumors. When gastrinomas are part of the MEN1 syndrome, they exhibit a greater propensity to develop within the submucosal Brunners glands of the duodenum. Therefore, models to analyze the biology of these intestinal gastrin-expressing NENs should consider their submucosal location. AimThe goal of this study was to determine whether the Menin-MLL inhibitor MI-503 suppressed hypergastrinemia. MethodsA murine model of hypergastrinemia generated by omeprazole treatment of mice carrying a conditional deletion of Men1 bred onto a somatostatin null genetic background (OMS) was treated intraperitoneally with MI-503 for 1 month. Primary enteric glial cells were prepared from these OMS mice and were treated with increasing doses of MI-503. Similarly human AGS and mouse STC-1 gastrin producing cell lines were treated with EGF without or with MI-503. >ResultsWe found that the treatment reduced serum and gastro-duodenal tissue expression of gastrin. Ex vivo MI-503 treatment of glial fibrillary acidic protein (GFAP)+ enteric cells isolated from the OMS mice or gastrin-expressing cell lines revealed that MI-503 blocked the nuclear export of Menin and suppressed gastrin gene expression. RNA-Seq analysis of gastrin-treated GFAP+ enteric cells revealed that they express EGF receptor ligands and that EGF treatment of GFAP+ cells also induced Menin translocation and concurrent induction of gastrin gene expression. ConclusionWe concluded that MI-503 inhibits gastrin gene expression by blocking Menin translocation.

cancer biology↗