The long unstructured region of Bcl-xl modulates its structural dynamics

Impact of yohimbine on myoglobin stability: insights from molecular spectroscopic, and computational approaches

The prolific role of bioactive ligands in interacting with a variety of proteins has become a focal point of interest in pharmacokinetics and pharmacodynamics, thus sparking substantial enthusiasm within the realm of medicinal chemistry. The reversible binding of small molecules and proteins is a characteristic feature, and it's essential to investigate these interactions to understand their mode and mechanism of action within the human body. Therefore, the primary objective of the present study is to understand the underlying mechanism by which yohimbine (Yoh) interacts with protein myoglobin (Mb), employing both in silico and in vitro methodologies. The emission spectroscopy studies yielded a binding constant of 105 M-1 and a binding site ratio of 1:1. The structural perturbation induced in the protein Mb by Yoh was also illustrated by circular dichroism. The results of the molecular docking investigation resulted in numerous significant interactions between Mb and Yoh, indicating a substantial binding affinity. The accuracy of the docking data was further confirmed through the use of molecular dynamics (MD) simulations, which were then followed by principal component analysis and free energy landscape investigations. The study posited that the stability of the Mb-Yoh complex remains intact throughout the simulated duration, exhibiting little alterations in its structural conformation. Therefore, the association between ligand-protein plays a key role in determining circulatory lifetimes and bioavailability. These factors, in turn, are pivotal in the rational drug design process.

Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-xL

Bcl-x_L is an antiapoptotic mitochondrial trans-membrane protein, which is known to play a crucial role in the survival of tumor cells. The deamidation of Bcl-x_L is a pivotal switch that regulates its biological function. The potential impact of deamidation on the structure and dynamics of Bcl-x_L is directly linked to the intrinsically disordered region (IDR), which is the main site for post-translational modifications (PTMs). In this study, we explored deamidation-induced conformational changes in Bcl-x_L to gain insight into its loss of function by performing microsecond-long molecular dynamics (MD) simulations. MD simulation outcomes showed that the IDR motion and interaction patterns have changed notably upon deamidation. Principal component analysis (PCA) demonstrates significant differences between wild-type and deamidated Bcl-x_L and suggests that deamidation affects the structure and dynamics of Bcl-x_L. The combination of clustering analysis, H-bond analysis, and PCA revealed changes in conformation, interaction, and dynamics upon deamidation. Differences in contact patterns and essential dynamics that lead to a narrowing in the binding groove (BG) are clear indications of deamidation-induced allosteric effects. In line with previous studies, we show that the IDR plays a very important role in the loss of apoptotic functions of Bcl-x_L while providing a unique perspective on the underlying mechanism of Bcl-x_L deamidation-induced cell death.

Coevolutionary forces shaping the fitness of SARS-CoV-2 spike glycoprotein against human receptor ACE2

The current global health problem caused by SARS-CoV-2 has challenged the scientific community in various ways. Therefore, worldwide several scientific groups are exploring SARS-CoV-2 from different aspects including its origin, spread, severe infectivity, and also to find a cure. It is now well known that spike glycoprotein helps SARS-CoV-2 to enter inside the human host through a cellular receptor ACE2. However, the role of coevolutionary forces that makes SARS-CoV-2 spike glycoprotein more fit towards its human host remains unexplored. Therefore, in present bioinformatics study we identify coevolving amino acids in spike glycoprotein. Additionally, the effects of coevolution on the stability of the spike glycoprotein as well as its binding with receptor ACE2 were predicted. The results clearly indicate that coevolutionary forces play a pivotal role in increasing the fitness of spike glycoprotein against ACE2.

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Coevolutionary amino acids increasing the fitness of spike glycoprotein against ACE2 were analysed

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Role of coevolution on the stability of the spike glycoprotein and its binding with receptor ACE2 were predicted

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Findings of present analysis suggest that coevolutionary forces help to increase the infectivity of SARS-CoV-2

Allostery of multidomain proteins with disordered linkers

Intrinsically disordered regions are often involved in allosteric regulation of multidomain proteins. They can act as disordered linkers to connect and interact with domains, resulting in rather complex allosteric mechanism and novel protein behavior. Therefore, it is necessary to analyze the diverse functions of disordered linkers in order to better understand allostery and relevant regulation process. Here we summarize recent advances in understanding the function of linkers and the advantages of adopting mutlidomain architecture with disorder linkers. It was shown that linkers between domains enhance the local domain concentration and make the allosteric regulation of weakly interacting partners possible, while linkers with only one tethered end cause an entropy effect to reduce binding affinity and prevent aggregation.

Impact of lymphoma-linked Asn11Tyr point mutation on the interaction between Bcl-2 and a BH3 mimetic: Insights from molecular dynamics simulation

Frequent mutations in the Bcl-2 anti-apoptotic protein are often implicated in diffuse large B-cell lymphoma (DLBCL), a disease profoundly resistant to drugs. Bcl-2-competitive inhibitors, "BH3 mimetics," activate apoptosis by interfering with the interactions between pro-apoptotic BH3 domains and the hydrophobic groove of Bcl-2. The aim of our research is to determine the potential of DLBCL-linked N11Y mutation to facilitate resistance against a "BH3 mimetic" using molecular dynamics simulation. Binding free energy calculations suggest a significant decrease in the binding affinity in the mutant model. In-depth analysis of the models using residue interaction network, dynamic cross-correlation, and free energy landscape approaches reveal that the mutation modifies the conformations of key residues, thereby altering the shape of the hydrophobic groove. This subsequently changes the ligand orientation and counteracts the phenomenon of LB region unwinding, a crucial event observed in the wild-type model. Lowest frequency motions captured by principal component analysis reflect the stretching of the groove for efficient ligand accommodation in the wild-type complex but not in the mutant model. This is the first in silico study that unravels the mechanism of drug resistance induced by a Bcl-2 mutation, which could be of great relevance while designing and tailoring therapeutics.

BCL-xL, a Mitochondrial Protein Involved in Successful Aging: From C. elegans to Human Centenarians

B-Cell Lymphoma-extra-large (BCL-xL) is involved in longevity and successful aging, which indicates a role for BCL-xL in cell survival pathway regulation. Beyond its well described role as an inhibitor of apoptosis by preventing cytochrome c release, BCL-xL has also been related, indirectly, to autophagy and senescence pathways. Although in these latter cases, BCL-xL has dual roles, either activating or inhibiting, depending on the cell type and the specific conditions. Taken together, all these findings suggest a precise mechanism of action for BCL-xL, able to regulate the crosstalk between apoptosis, autophagy, and senescence, thus promoting cell survival or cell death. All three pathways can be both beneficial or detrimental depending on the circumstances. Thus, targeting BCL-xL would in turn be a "double-edge sword" and therefore, additional studies are needed to better comprehend this dual and apparently contradictory role of BCL-XL in longevity.

Targeting cancer's Achilles’ heel: role of BCL-2 inhibitors in cellular senescence and apoptosis

Members of the antiapoptotic BCL-2 proteins are involved in tumor growth, progression and survival, and are also responsible for chemoresistance to conventional anticancer agents. Early efforts to target these proteins yielded some active compounds; however, newer methodologies involving structure-based drug design, Nuclear Magnetic Resonance (NMR)-based screening and fragment-based screening yielded more potent compounds. Discovery of specific as well as nonspecific inhibitors of this class of proteins has resulted in great advances in targeted chemotherapy and decrease in chemoresistance. Here, we review the history and current progress in direct as well as selective targeting of the BCL-2 proteins for anticancer therapy.

Flexibility enables to discriminate between ligands: Lessons from structural ensembles of Bcl-xl and Mcl-1

The proteins of Bcl-2 family, which are promising anti-cancer-drug targets, have substantial similarity in primary sequence and share homologous domains as well as similar structural folds. In spite of similarities in sequence and structures, the members of its pro- and anti- apoptotic subgroups form complexes with different type of partners with discriminating binding affinities. Understanding the origin of this discrimination is very important for designing ligands that can either selectively target a protein or could be made broad ranged as necessary. Using principal component analysis (PCA) of the available structures and from the analysis of the evolution of the binding pocket residues, the correlation has been investigated considering two important anti-apoptotic protein Bcl-xl and Mcl-1, which serve as two ideal representatives of this family. The flexibility of the receptor enables them to discriminate between the ligands or the binding partners. It has been observed that although Bcl-xl and Mcl-1 are classified as homologous proteins, through the course of evolution the binding pocket residues are highly conserved for Bcl-xl; whereas they have been substituted frequently in Mcl-1. The investigation has revealed that the Bcl-xl can adjust the backbone conformation of the binding pocket residues to a larger extent to complement with the shape of different binding partners whereas the Mcl-1 shows more variation in the side chain conformation of binding pocket residues for the same purpose.

BIM Binding Remotely Regulates BAX Activation: Insights from the Free Energy Landscapes

Activation of the pro-apoptotic BAX protein, a BCL-2 family member, is known to trigger apoptosis by forming pores in the mitochondrial outer membrane (MOM). While in the cytosol, release of its transmembrane C-terminal helix (called α9 helix) from a well-characterized binding pocket (BC groove) and subsequent permeabilization of the MOM are understood to be the initiating events of the activation. Concerning what initiates BAX activation, so far one plausible suggestion has been that the transient attachment of BH3-only peptide at a distal site from the BC groove triggers the activation process. Yet how this pivotal step displaces α9 from the BC groove has remained poorly understood. Using a combination of standard molecular dynamics and enhanced sampling methods, the energy landscape of BIM (BH3-only peptide) induced BAX activation has been computed, and the molecular origin of those events is hereby reported in atomistic detail. The simulated transition pathway of α9 release reveals that BIM subdues the energetic cost of the process by reducing the activation energy barrier to some extent but mostly by minimizing the free energy difference between the active (α9-released) and inactive (α9-bound) states. Interestingly, the flexibility of the α9 helix itself plays a decisive role in this mechanism. The impact of BIM encounter at the distal site is found to propagate to the α9 (BC groove bound) mostly through conserved pathways of residue level interactions. Overall, the thermodynamic basis of the "hit-and-run" mechanism for activation of the BCL-2 family is presented reconciling the available biochemical observations.