@article {163311, title = {Investigating Enzyme-Substrate Interactions in the Assembly of K48/K63 Heterotypic Ubiquitin Chains.}, journal = {Biochemistry}, year = {2026}, month = {2026 Jan 26}, abstract = {

Ubiquitination, a post-translational modification, regulates numerous cellular processes by attaching ubiquitin molecules to the target proteins, thereby altering their cellular levels and functions. A central aspect of ubiquitin-mediated signaling is the formation of different types of polyubiquitin (polyUb) chains, which can be either homotypic or heterotypic, generating a variety of cellular signals that activate distinct downstream pathways. Homotypic chains are linked via the same lysine on each molecule, whereas heterotypic chains are conjugated via multiple lysines. The synthesis of these diverse polyubiquitin chains is driven by interactions between substrate-conjugated ubiquitin molecules, ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). However, the molecular details of these interactions and how they govern the synthesis of different homotypic and heterotypic chains remain poorly understood. The E2 enzyme E2-25K preferentially extends K48-linked polyubiquitin chains on K63-linked template polyubiquitin chains, creating branched K48/K63 chains. In this study, we investigated the role of dynamic interactions between E2-25K and the K63-linked diubiquitin substrate to assess the molecular mechanism of branched-chain assembly. Our data reveal that E2-25K shows no preference for binding to the proximal or distal ubiquitin of a template chain. However, binding to the distal unit activates the complex; binding to the proximal unit does not. This study highlights the critical role of stereospecificity in enzyme/substrate interactions for branched ubiquitin chain synthesis and provides insights into the mechanisms of ubiquitin signaling.

}, keywords = {Conformation, Genetics, Nuclear magnetic resonance spectroscopy, Peptides and proteins, Titration}, issn = {1520-4995}, doi = {10.1021/acs.biochem.5c00709}, url = {https://pubs.acs.org/doi/10.1021/acs.biochem.5c00709}, author = {Singh, Gajendra and Negi, Hitendra and Ravichandran, Aravind and Yadav, Shalu and Das, Ranabir} } @article {161980, title = {Structure-guided engineering of protein stability through core hydrophobicity.}, journal = {Protein Sci}, volume = {34}, year = {2025}, month = {2025 Dec}, pages = {e70360}, abstract = {

Engineering thermostable proteins is advantageous for industrial and biomedical applications, where improved thermal stability can enhance conformational integrity, prolong functional half-life, and increase catalytic efficiency at elevated temperatures. We explored modifying the length of buried hydrocarbon chains to improve protein thermal stability. By optimizing the hydrophobic core through targeted amino acid substitutions, we aimed to minimize internal voids and improve core packing. To achieve this, we developed an algorithm that replaces buried hydrophobic residues with longer or bulkier hydrophobic side chains. The algorithm calculates the free energy of unfolding (ΔG) for each substitution, selecting only significantly stabilizing configurations. Functionally important residues and contact networks were excluded from mutation to preserve protein function. We applied the method to several proteins from the beta-grasp fold family. For experimental validation, we chose NEDD8, a beta-grasp protein with poor solubility and low thermal stability. Two subtle substitutions predicted by our algorithm increased NEDD8{\textquoteright}s thermal stability by 1.7 kcal/mol and raised its melting point by 17{\textdegree}C. MD simulations and NMR spectroscopy revealed reduced conformational fluctuations and increased stabilizing interactions, such as hydrogen bonding and electrostatic contacts. Functional assays confirmed that the substitutions did not perturb NEDD8{\textquoteright}s global fold or interactions with cofactors and enzymes. These results highlight the effectiveness of tuning buried hydrophobic residues to enhance protein stability without compromising function. This strategy could serve as a general framework for designing robust therapeutic proteins and enzymes for industrial or biomedical applications.

}, keywords = {Algorithms, Amino Acid Substitution, Hydrophobic and Hydrophilic Interactions, Molecular Dynamics Simulation, NEDD8 Protein, Protein Conformation, Protein Engineering, Protein Stability, Thermodynamics}, issn = {1469-896X}, doi = {10.1002/pro.70360}, author = {Ravichandran, Aravind and Puri, Anindita and Bhate, Suhas H and Habibullah, Batul Ismail and Singh, Gajendra and Das, Ranabir} } @article {130549, title = {Decoding the Assembly of Mixed and Branched Heterotypic Ubiquitin Chains.}, journal = {Anal Chem}, volume = {95}, year = {2023}, month = {2023 Jul 04}, pages = {10061-10067}, abstract = {

Ubiquitination is a post-translational modification that regulates cell signaling, immune response, protein processing, molecular trafficking, and DNA repair. Generally, molecular trafficking and DNA repair processes need the attachment of a single ubiquitin on a substrate, known as monoubiquitination. The other functions of ubiquitin require the assembly of polymeric ubiquitin chains on the substrate, known as polyubiquitination. The chains are linked through the lysine residues of ubiquitin, and depending on which lysine is connected, the chains could be heterotypic or homotypic. Heterotypic polyubiquitin chains can be mixed, branched, or combined, generating myriad cellular signals with functions distinct from the homotypic ubiquitin chains. The molecular rules of heterotypic chain assembly are poorly understood due to the lack of techniques to monitor their assembly. New approaches are required to monitor the conjugation site of new ubiquitin molecules on a pre-existing chain. Here, we describe a new method based on isotopic labeling and mass spectrometry to study the assembly of heterotypic chains called isotopically resolved mass spectrometry of peptides (IRMSP). The technique is demonstrated using multiple ubiquitin enzymes and ubiquitin chains as substrates. It causes minimal perturbation to the enzyme/substrate and will be instrumental in studying the assembly of large polymeric ubiquitin chains. Using this technique, it is feasible to monitor how and with what rate branched ubiquitin chains grow in different directions in a single experiment.

}, issn = {1520-6882}, doi = {10.1021/acs.analchem.3c01425}, author = {Singh, Gajendra and Kumar, Sanjeev and Das, Ranabir} } @article {99101, title = {Design, Synthesis and Conformational Studies of Cyclic Tetrapeptides having beta gamma Fused Turns as HDAC Inhibitors}, journal = {CHEMISTRYSELECT}, volume = {6}, year = {2021}, month = {08/2021}, pages = {7887-7893}, abstract = {

Histone deacetylases (HDACs) belong to a class of major targets for the development of anticancer drugs for which cyclic peptide-based molecules are attracting wide attention. Here we show the synthesis, conformational and in silico analysis of tetrahydrofuran amino acid (TAA) based 15-membered cyclic tetrapeptides (CTPs) containing hydroxamic acid side chain as potential HDAC inhibitors. NMR based solution studies in protected and deprotected forms reveal that the macrocycles are stabilized by 10-membered beta-turn as well as a 7-membered gamma-turn. This type of fused structures within the same macrocycle is not frequently sighted. Our initial in silico docking results indicated that the hydroxamic acid protected CTPs show promising binding with the class-1 HDACs. We also noticed that the C-chain with hydroxamic functional group attached on the ornithine sidechain did not affect the core structure of the peptide ring. Moreover, some of these cyclic tetrapeptides with hydroxamic acid side chain exhibited an induction of acetylation of histones on preliminary cell-based experiments. Our initial results provide an insight into the development of HDAC inhibitors based on the CTPs with novel beta gamma fused turns which have not been explored yet.

}, doi = {10.1002/slct.202102417}, author = {Ghosh, Uttam and Basu, Moumita and Pal, Sudip and Meena, Sanjeev and Datta, Dipak and Ampapathi, Ravi Sankar and Kundu, Tapas K. and Singh, Gajendra and Chakraborty, Tushar Kanti} }