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Lupala, C. S.

Publications and source records attributed to Lupala, C. S..

3 recordsLinked to original sources

Aromatic amino acids in the orthosteric region regulate cannabinoid receptor 1 conformation transitions

Cannabinoid receptor 1 (CB1) is a class A G protein-coupled receptor that exhibits constitutive activity by spontaneously sampling both active and inactive states in the absence of ligand binding. Structural studies have identified a domain of aromatic residues, F2003.36, W3566.48, and W2795.43, that modulates receptor function and ligand engagement; however, their mechanistic roles remain unclear. Here, we use equilibrium and targeted molecular dynamics simulations to investigate how alanine substitutions at these positions alter CB1 dynamics. Our results show that mutations, especially the F200A+W356A combination, enhanced conformational flexibility and shifted the receptor toward inactive-like states. W3566.48 emerged as a structural pivot essential for active-state stability, F2003.36 acted as a late-stage kinetic barrier to inactivation, and W2795.43 modulated orthosteric pocket packing and flexibility, amplifying destabilization when combined with F2003.36 or W3566.48 mutations. Targeted simulations showed that mutation of this aromatic domain lowers energetic barriers and rewires the inactivation pathway. These findings define the structural logic of CB1 toggle-switch control and provide a mechanistic framework for designing modulators that tune basal activity in CB1.

biophysics↗

Mutations in RBD of SARS-CoV-2 Omicron variant result stronger binding to human ACE2 protein

The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have emerged and posed challenges in controlling the pandemic. The recently occurred Omicron variant raised serious concerns about reducing the efficacy of vaccines and neutralization antibodies due to its vast mutations. We have modelled the complex structure of the human ACE2 protein and the receptor binding domain (RBD) of Omicron Spike protein (S-protein), and conducted atomistic molecular dynamics simulations to study the binding interactions. The analysis shows that the Omicron RBD binds more strongly to the human ACE2 protein than the original strain. The mutations at the ACE2-RBD interface enhance the tight binding by increasing hydrogen bonding interaction and enlarging buried solvent accessible surface area.

bioinformatics↗

Computational insights into differential interaction of mamalian ACE2 with the SARS-CoV-2 spike receptor binding domain

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causing agent of the COVID-19 pandemic, has spread globally. Angiotensin-converting enzyme 2 (ACE2) has been identified as the host cell receptor that binds to receptor-binding domain (RBD) of the SARS-COV-2 spike protein and mediates cell entry. Because the ACE2 proteins are widely available in mammals, it is important to investigate the interactions between the RBD and the ACE2 of other mammals. Here we analyzed the sequences of ACE2 proteins from 16 mammals and predicted the structures of ACE2-RBD complexes. Analyses on sequence, structure, and dynamics synergistically provide valuable insights into the interactions between ACE2 and RBD. The comparison results suggest that the ACE2 of bovine, cat and panda form strong binding with RBD, while in the cases of rat, least horseshoe bat, horse, pig, mouse and civet, the ACE2 proteins interact weakly with RBD.

bioinformatics↗