Sudip Kundu

Bio: Sudip Kundu is an academic researcher from University of Calcutta. The author has contributed to research in topics: Protein folding & Ribosomal protein. The author has an hindex of 14, co-authored 60 publications receiving 810 citations.

Genome-scale conserved molecular principles of mRNA half-life regulation

Abstract: Precise control of protein and mRNA degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. Here, we report that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5′ terminal, 3′ terminal and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5′ exo- 3′ exo- and endo-ribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation unravels their remarkable mechanistic similarities, and suggests how the intrinsic structural features of the two molecular species regulate their half-lives on genome-scale and during evolution.

Role of physico-chemical properties of amino acids in protein's structural organization: a network perspective

Abstract: The three-dimensional structure of a protein can be described as a graph where nodes represent residues and interactions between them are edges. We have constructed protein contact networks at different length-scales for different interaction strength cutoffs. The largest connected component of short-range networks exhibit a highly cooperative transition, while long- and all-range networks (more similar to each other), have less cooperativity. The hydrophobic subnetworks in all- and long-range networks have similar phase transition behaviours while hydrophilic and charged networks don't. Hydrophobic subclusters in long- and all-range networks exhibit higher occurrence of assortativity and hence higher communication ability in transmitting information within a protein. The highly cliquish hydrophobic nodes in long- and short-range networks play a significant role in bridging and stabilizing distantly placed residues during protein folding. We have also observed a significant dominance of charged residues cliques in short-range networks.

Quercetin@Gd3+ doped Prussian blue nanocubes induce the pyroptotic death of MDA-MB-231 cells: combinational targeted multimodal therapy, dual modal MRI, intuitive modelling of r1-r2 relaxivities.

Abstract: Quercetin (Qu), a potential bioflavonoid has gained considerable interest as a promising chemotherapeutic drug which can inhibit the proliferation of triple-negative breast cancer (TNBC) cells due to its regulation of the expression of tumor-suppressor gene metastasis and antioxidant property. Notably, Qu exhibits a very negligible cytotoxic effect on normal cells, even with high-dose treatment, while it is shows high affinity to TNBC. However, the efficiency of Qu is limited clinically due to its poor bioavailability, caused by its low aqueous solubility (2.15 μg mL-1 at 25 °C), rapid gastrointestinal digestion and chemical instability in alkaline and neutral media. Herein, polydopamine (PDA)-coated, NH2-PEG-NH2 and hyaluronic acid (HA)-functionalized Gd3+-doped Prussian blue nanocubes (GPBNC) are reported as a multifunctional platform for the codelivery of Qu as a chemotherapeutic agent and GPBNC as a photodynamic (PDT) and photothermal (PTT) agent with improved therapeutic efficiency to overcome theses barriers. PDA, NH2-PEG-NH2 and HA stabilize GPBNC@Qu and facilitate bioavailability and active-targeting, while absorption of near infrared (NIR) (808 nm; 1 W cm-2) induces PDT and PTT activities and dual T1-T2-weighted magnetic resonance imaging (MRI) with high relaxometric parameters (r1 10.06 mM-1 s-1 and r2 24.96 mM-1 s-1 at a magnetic field of 3 T). The designed platform shows a pH-responsive Qu release profile and NIR-induced therapeutic efficiency of ∼79% in 20 minutes of irradiation, wherein N-terminal gardermin D (N-GSDMD) and a P2X7-receptor-mediated pyroptosis pathway induces cell death, corroborating the up-regulation of NLRP3, caspase-1, caspase-5, N-GSDMD, IL-1β, cleaved Pannexin-1 and P2X7 proteins. More interestingly, the increasing relaxivity values of Prussian blue nanocubes with Gd3+ doping have been explained on the basis of Solomon-Bloembergen-Morgan theory, considering inner- and outer-sphere relaxivity, wherein crystal defects, coordinated water molecules, tumbling rate, metal to water proton distance, correlation time, magnetisation value etc. play a significant role. In summary, our study suggests that GPBNC could be a beneficial nanocarrier for theranostic purposes against TNBC, while our conceptual study clearly demonstrates the role of various factors in increasing relaxometric parameters.

Protein contact networks at different length scales and role of hydrophobic, hydrophilic and charged residues in protein's structural organisation

Abstract: The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed protein contact networks at different length scales, long and short-range. While long and short-range interactions are determined by the positions of amino acids in primary chain, the contact networks are constructed based on the 3D spatial distances of amino acids. We have further divided these networks into sub-networks of hydrophobic, hydrophilic and charged residues. Our analysis reveals that a significantly higher percentage of assortative sub-clusters of long-range hydrophobic networks helps a protein in communicating the necessary information for protein folding in one hand; on the other hand the higher values of clustering coefficients of hydrophobic sub-clusters play a major role in slowing down the process so that necessary local and global stability can be achieved through intra connectivities of the amino acid residues. Further, higher degrees of hydrophobic long-range interactions suggest their greater role in protein folding and stability. The small-range all amino acids networks have signature of hierarchy. The present analysis with other evidences suggest that in a protein's 3D conformational space, the growth of connectivity is not evolved either through preferential attachment or through random connections; rather, it follows a specific structural necessity based guiding principle - where some of the interactions are primary while the others, generated as a consequence of these primary interactions are secondary.

Random graphs

Abstract: We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Hierarchical Organization of Human Cortical Networks in Health and Schizophrenia

Abstract: The complex organization of connectivity in the human brain is incompletely understood. Recently, topological measures based on graph theory have provided a new approach to quantify large-scale cortical networks. These methods have been applied to anatomical connectivity data on nonhuman species, and cortical networks have been shown to have small-world topology, associated with high local and global efficiency of information transfer. Anatomical networks derived from cortical thickness measurements have shown the same organizational properties of the healthy human brain, consistent with similar results reported in functional networks derived from resting state functional magnetic resonance imaging (MRI) and magnetoencephalographic data. Here we show, using anatomical networks derived from analysis of inter-regional covariation of gray matter volume in MRI data on 259 healthy volunteers, that classical divisions of cortex (multimodal, unimodal, and transmodal) have some distinct topological attributes. Although all cortical divisions shared nonrandom properties of small-worldness and efficient wiring (short mean Euclidean distance between connected regions), the multimodal network had a hierarchical organization, dominated by frontal hubs with low clustering, whereas the transmodal network was assortative. Moreover, in a sample of 203 people with schizophrenia, multimodal network organization was abnormal, as indicated by reduced hierarchy, the loss of frontal and the emergence of nonfrontal hubs, and increased connection distance. We propose that the topological differences between divisions of normal cortex may represent the outcome of different growth processes for multimodal and transmodal networks and that neurodevelopmental abnormalities in schizophrenia specifically impact multimodal cortical organization.

MicroRNAs: Target Recognition and Regulatory Functions

Abstract: MicroRNAs (miRNAs) are endogenous ∼23 nt RNAs that play important gene-regulatory roles in animals and plants by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional repression. This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.