Veerendra Kumar

Molecular dynamics (MD) simulation is a fundamental technique for resolving biomolecular structures and functions at atomic resolution. Accelerated by GPU computing and machine learning-integrated force fields (FF), modern MD simulation facilitates the study of large-scale systems and rare biological events, such as protein folding, allosteric transitions, etc. While advanced sampling methods and AI integration have significantly enhanced efficiency in drug discovery and protein engineering, the field still faces challenges regarding FF accuracy, timescale constraints, and quantum effects. Continued development of hybrid quantum and molecular mechanics methods and standardized workflows is essential to further improve the predictive power and reproducibility of MD in biotechnological research. In this review, we attempted to provide the latest developments in the MD simulations.

The voltage gated calcium channels (Cav1 and Cav2) and sodium channels are modulated by calmodulin (CaM) via IQ motifs. But Cav3 (aka T-type) channels lack IQ motif and therefore, they transiently interact with CaM via the gating brake (GB) regions of T-type channels. However, the structural basis of the interactions remains unclear. This study employs molecular dynamics (MD) simulations to investigate the complete binding process of GB peptides (GB3.1 and GB3.2) with CaM at an atomic level, starting from a non-interacting state to a fully formed complex. We provide a detailed analysis of the binding trajectories, identifying how the GB peptides dynamically explore and engage their binding interfaces on CaM. Our results reveal that GB3.1 induces significant conformational rearrangement in CaM, bending its central helix by ∼90° and forming a compact structure. In contrast, GB3.2 binding does not induce such changes, and CaM remains in an extended conformation. Both peptides interact primarily with CaM’s N-lobe. The MM-PBSA analysis yielded negative binding energies indicating a spontaneous and favourable complex formation.

G protein-coupled receptors (GPCRs) are the largest group of receptors involved in various types of signaling. GPCR signaling is regulated via receptor phosphorylation by G protein-coupled receptor kinases 5 (GRK5). Calmodulin (CaM), a universal Ca²⁺ sensor, inhibits receptor phosphorylation by binding to GRK5. However, the inhibitor malbrancheamide (MBC), which binds at CaM C-lobe, allows for receptor phosphorylation. To understand the phosphorylation mechanism by GRK5, we carried out a MD simulation of the CaM/GRK5 complex in the presence and absence of the MBC inhibitor. The lipid binding domain (LBD) of GRK5 adopted different positions in the presence and absence of inhibitor. Furthermore, the inhibitor MBC restricted the movement of the N-lobe tether (NLT) loop, probably blocking the autophosphorylation of GRK5.Communicated by Ramaswamy H. Sarma.

Protein-protein interaction (PPI) is a crucial event for many biological functions. Studying the molecular details of PPI requires structure determination using X-ray crystallography, nuclear magnetic resistance (NMR), and single particle Cryo-EM. However, sometimes it is not easy to solve the complex structure for various reasons. For example, complex may be unstable, not enough protein expression for structural studies, etc. Further, PPI are intricate processes, and its molecular details cannot be fully explained by experimental observations. Here, we describe a quick and simple method to study the PPI using the combinatorial approach of molecular dynamics simulation and biophysical methods. Key words GROMACS Force fields Molecular dynamics simulations Protein-protein interactions Structural biology

Cervical cancer is the fourth leading cause of death in women worldwide, with 99% of cases associated with a human papillomavirus (HPV) infection. Given that HPV prophylactic vaccines do not exert a therapeutic effect in individuals previously infected, have low coverage of all HPV types, and have poor accessibility in developing countries, it is unlikely that HPV-associated cancers will be eradicated in the coming years. Therefore, there is an emerging need for the development of anti-HPV drugs. Considering HPV E6’s oncogenic role, this protein has been proposed as a relevant target for cancer treatment. In the present work, we employed in silico tools to discover potential E6 inhibitors, as well as biochemical and cellular assays to understand the action of selected compounds in HPV-positive cells (Caski and HeLa) vs. HPV-negative (C33A) and non-carcinogenic (NHEK) cell lines. In fact, by molecular docking and molecular dynamics simulations, we found three phenolic compounds able to dock in the E6AP binding pocket of the E6 protein. In particular, lucidin and taxifolin were able to inhibit E6-mediated p53 degradation, selectively reduce the viability, and induce apoptosis in HPV-positive cells. Altogether, our data can be relevant for discovering promising leads for the development of specific anti-HPV drugs.

Calmodulin, a ubiquitous eukaryotic calcium sensor responsible for the regulation of many fundamental cellular processes, is a highly flexible protein and exhibits an unusually wide range of conformations. Furthermore, CaM is known to interact with more than 300 cellular targets. Molecular dynamics (MD) simulation trajectories suggest that EF-hand loops show different magnitudes of flexibility. Therefore, the four EF-hand motifs have different affinities for Ca²⁺ ions, which enables CaM to function on wide range of Ca²⁺ ion concentrations. EF-hand loops are 2–3 times more flexible in apo CaM whereas least flexible in Ca²⁺/CaM-IQ motif complexes. We report a unique intermediate conformation of Ca²⁺/CaM while transitioning from extended to compact form. We also report the complex formation process between Ca²⁺/CaM and IQ CaM-binding motifs. Our results showed how IQ motif recognise its binding site on the CaM and how CaM transforms from extended to compact form upon binding to IQ motif.

The disease COVID-19 has caused heavy socio-economic burden and there is immediate need to control it. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The viral entry into human cell depends on the attachment of spike (S) protein via its receptor binding domain (RBD) to human cell receptor angiotensin-converting enzyme 2 (hACE2). Thus, blocking the virus attachment to hACE2 could serve as potential therapeutics for viral infection. We have designed a peptide inhibitor (ΔABP-α2) targeting the RBD of S protein using in-silico approach. Docking studies and computed affinities suggested that peptide inhibitor binds at the RBD with ∼95-fold higher affinity than hACE2. Molecular dynamics (MD) simulation confirms the stable binding of inhibitor to hACE2. Immunoinformatics studies suggest non-immunogenic and non-toxic nature of peptide. Thus, the proposed peptide could serve as potential blocker for viral attachment. Communicated by Ramaswamy H. Sarma

The disease COVID-19 has caused heavy socio-economic burden and there is urgent need to control the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic. The viral entry into human cell depends on the attachment of spike (S) protein to human cell receptor angiotensin-converting enzyme 2 (ACE2). We have designed a peptide inhibitor (ΔABP- α2) targeting the receptor binding domain (RBD) of S protein using in silico approach. Docking studies and computed affinities suggest peptide inhibitor binds at the RBD with 10-fold higher affinity than hACE2. MD simulation confirm the stable binding of inhibitor to hACE2. Immunoinformatic studies non-immunogenic nature of peptide. Thus, the proposed peptide could serve potential therapeutics for viral infection.

The SARS-CoV-2 virus has caused a pandemic and is public health emergency of international concern. As of now, no registered therapies are available for treatment of coronavirus infection. The viral infection depends on the attachment of spike (S) glycoprotein to human cell receptor angiotensin-converting enzyme 2 (ACE2). We have designed a protein inhibitor (ΔABP-D25Y) targeting S protein using computational approach. The inhibitor consists of two α helical peptides homologues to protease domain (PD) of ACE2. Docking studies and molecular dynamic simulation revealed that the inhibitor binds exclusively at the ACE2 binding site of S protein. The computed binding affinity of the inhibitor is higher than the ACE2 and thus will likely out compete ACE2 for binding to S protein. Hence, the proposed inhibitor ΔABP-D25Y could be a potential blocker of S protein and receptor binding domain (RBD) attachment.

Summary: Dunaliella has been extensively studied due to its intriguing adaptation to high salinity. Its di‐domain glycerol‐3‐phosphate dehydrogenase (GPDH) isoform is likely to underlie the rapid production of the osmoprotectant glycerol. Here, we report the structure of the chimeric Dunaliella salina GPDH (DsGPDH) protein featuring a phosphoserine phosphatase‐like domain fused to the canonical glycerol‐3‐phosphate (G3P) dehydrogenase domain. Biochemical assays confirm that DsGPDH can convert dihydroxyacetone phosphate (DHAP) directly to glycerol, whereas a separate phosphatase protein is required for this conversion process in most organisms. The structure of DsGPDH in complex with its substrate DHAP and co‐factor nicotinamide adenine dinucleotide (NAD) allows the identification of the residues that form the active sites. Furthermore, the structure reveals an intriguing homotetramer form that likely contributes to the rapid biosynthesis of glycerol.