Fungal alkaloid malbrancheamide reorients the lipid binding domain of GRK5.

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 Studies Using Molecular Dynamics Simulation.

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.

Taxifolin and Lucidin as Potential E6 Protein Inhibitors: p53 Function Re-Establishment and Apoptosis Induction in Cervical Cancer Cells.

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.

A potential peptide inhibitor of SARS-CoV-2 S and human ACE2 complex.

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 mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics.

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.