A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Inactivated mechanisms of high pressure processing combined with mild temperature on pectin methylesterase and its inhibitor

High pressure processing (HPP) of orange juice faces storage issues due to refrigeration need and cloud loss caused by pectin methylesterase (PME). Our previous research indicated that HPP conjunction with pectin methylesterase inhibitor (PMEI) enhanced juice stability, but not fully inactivated PME. This study explored the effectiveness of HPP with mild temperature treatments to fully inactivate PME and sterilize microorganisms in juice, using experimental analysis and molecular dynamics simulation. The findings revealed that PME activity was reduced by 94 % at 600 MPa and 60 °C, with completely inactivating at 80 °C. Conversely, PMEI exhibited resistance to pressure and temperature. Following processes at 600 MPa and above 60 °C, the tail-end helix structure of PME destabilized, with α-helices converting to β-sheets and disrupting hydrogen bonds within molecular chain. Conversely, the structure of PMEI was stable. Additionally, the combination of HPP and temperature treatment enhanced the binding affinity between PME and PMEI.

Identification of a new small Rho GTPase inhibitor effective in glioblastoma human cells

Glioblastoma (GBM) is the most common and lethal primary brain tumour. The prognosis for GBM patients remains poor due to rapid tumour recurrence and resistance to conventional treatments. Small Rho GTPase proteins, which regulate cell shape and motility, are critical for GBM aggressive growth and infiltration into the surrounding brain parenchyma. Hence, small-molecule inhibitors targeting them represent an appealing opportunity to hinder the infiltration behaviour of GBM. Here, a synergistic experimental and computational approach allowed us to identify an inhibitor that reduces migration in patient-derived GBM cell lines. Computational and in vitro functional assays reveal that this compound inhibits Rho GTPases function by targeting multiple allosteric sites thereby enhancing flexibility of key functional regions and hindering their interaction with protein regulators. Our research unveiled a novel hit molecule targeting Rho GTPases with significant potential to improve the treatment of GBM and other highly aggressive tumours.

Computational methods for modeling protein-protein interactions in the AI era: Current status and future directions

The modeling of protein-protein interactions (PPIs) has been revolutionized by artificial intelligence, with deep learning and end-to-end frameworks such as AlphaFold and its derivatives now dominating the field. This review surveys the current computational landscape for predicting protein complex structures, outlining the role of traditional docking approaches as well as focusing on recent advances in AI-driven methods. We discuss key challenges, including protein flexibility, reliance on co-evolutionary signals, modeling of large assemblies, and interactions involving intrinsically disordered regions (IDRs). Recent innovations aimed at improving sampling diversity, integrating experimental data, and enhancing robustness are also highlighted. Although classical methods remain relevant in specific contexts, the continued evolution of AI-based tools offers transformative potential for structural biology. These advances are poised to deepen our understanding of biomolecular interactions and accelerate the design of therapeutic interventions.

Efficient Design of Affilin® Protein Binders for HER3

Engineered scaffold-based proteins that bind to concrete targets with high affinity offer significant advantages over traditional antibodies in theranostic applications. Their development often relies on display methods, where large libraries of variants are physically contacted with the desired target protein and pools of binding variants can be selected. Herein, we use a novel combined artificial intelligence/physics-based computational framework and phage display approach to obtain ubiquitin based Affilin® proteins targeting the human epidermal growth factor receptor 3 (HER3) extracellular domain, a relevant tumor target. As traditional antibodies against the receptor have failed so far, we sought to provide molecules in a smaller more versatile format to cover the medical need in HER3 related diseases. We demonstrate that the developed in silico pipeline can generate de novo Affilin® proteins binding the biochemical HER3 target using a small training set of <1000 sequences. The classical phage display yielded primary candidates with low nanomolar affinities to the biochemical target and HER3-expressing cells. The latter could be further optimized by phage display and computational maturation alike. These combined efforts resulted in four HER3 ligands with high affinity, cell binding, and serum stability with theranostic potential.

Hesperetin acts as a potent xanthine oxidase inhibitor: New evidence from its reactive oxygen suppression and enzyme binding

Xanthine oxidase (XO) plays a crucial role in purine metabolism, catalyzing the oxidation of hypoxanthine to xanthine and subsequently to uric acid. Elevated uric acid levels can lead to hyperuricemia, a condition linked to gout, kidney stones, and other chronic diseases. Inhibiting XO activity represents a promising strategy for managing hyperuricemia. This study investigated the inhibitory effects of the flavonoid hesperetin enriched in citrus fruits on XO activity, its antioxidant properties against reactive oxygen species (ROS) generated by the XO reaction, and the underlying mechanisms of enzyme inhibition. Enzyme kinetics and spectroscopy revealed that hesperetin competitively inhibited XO at an inhibition constant of (2.15 ± 0.05) × 10-6 mol/L through its binding to the molybdopterin active center of XO, preventing the entry of xanthine and the transfer of electrons, effectively scavenging superoxide radicals by inhibiting uric acid production and oxygen reduction, and inducing conformational changes in XO's structure. Fluorescence quenching indicated that hesperetin interacted with XO through a combination of static and dynamic quenching mechanisms. Molecular docking simulations demonstrated that hesperetin binded tightly to XO's active site, blocking substrate entry. Molecular dynamics confirmed that hesperetin stabilized the XO-hesperetin complex through reinforced hydrophobic and hydrogen-bond interactions. The results suggest that hesperetin can act as a potent natural xanthine oxidase inhibitor or a functional food supplement to alleviate hyperuricemia.

Immunoinformatic strategy for developing multi-epitope subunit vaccine against Helicobacter pylori

Helicobacter pylori is a gram-negative bacterium that persistently infects the human stomach, leading to peptic ulcers, gastritis, and an increased risk of gastric cancer. The extremophilic characteristics of this bacterium make it resistant to current drug treatments, and there are no licensed vaccines available against H. pylori. Computational approaches offer a viable alternative for designing antigenic, stable, and safe vaccines to control infections caused by this pathogen. In this study, we employed an immunoinformatic strategy to design a set of candidate multi-epitope subunit vaccines by combining the most potent B and T cell epitopes from three targeted antigenic proteins (BabA, CagA, and VacA). Out of the 12 hypothetical vaccines generated, two (HP_VaX_V1 and HP_VaX_V2) were found to be strongly immunogenic, non-allergenic, and structurally stable. The proposed vaccine candidates were evaluated based on population coverage, molecular docking, immune simulations, codon adaptation, secondary mRNA structure, and in silico cloning. The vaccine candidates exhibited antigenic scores of 1.19 and 1.01, with 93.5% and 90.4% of the most rama-favored regions, respectively. HP_VaX_V1 and HP_VaX_V2 exhibited the strongest binding affinity towards TLR-7 and TLR-8, as determined by molecular docking simulations (ΔG = -20.3 and -20.9, respectively). Afterward, multi-scale normal mode analysis simulation revealed the structural flexibility and stability of vaccine candidates. Additionally, immune simulations showed elevated levels of cell-mediated immunity, while repeated exposure simulations indicated rapid antigen clearance. Finally, in silico cloning was performed using the expression vector pET28a (+) with optimized restriction sites to develop a viable strategy for large-scale production of the chosen vaccine constructs. These analyses suggest that the proposed vaccines may elicit potent immune responses against H. pylori, but laboratory validation is needed to verify their safety and immunogenicity.

Impact of pH and protein/polysaccharide ratio on phycocyanin-okra polysaccharides complex

Phycocyanin is a natural blue pigment that tends to denature and lose its color in acidic solutions. In response to this problem, the complexes of phycocyanin (PC) with okra polysaccharides (OP) were prepared by ultrasonic processing at different pH conditions, and the molecular interactions of the complexes were characterized. The results showed that there were significant differences in the color, functional groups, and surface morphology of the complexes formed at different pH conditions. By colorimetry and particle size tester, it was demonstrated that the complex solution showed a steady blue color at pH 3.4. The highest fluorescence intensity (1.55 × 107 a.u.) and the significant red-shift of the complexes were observed at 0.4 % m/v polysaccharides addition. Infrared spectroscopy test further demonstrated that OP induced the formation of higher-order trimers of PC, which kept the color stable. Molecular dynamics simulations showed that the binding energy of PC/OP complex was -42.21 ± 2.61 kcal/mol, indicating that the binding affinity was very strong. Overall, this study suggests that this complex stabilizes the structure of PC, which in turn exerts a biological effect and will facilitate the use of PC as an artificial color substitute in food or beverage applications.

Interacting myosin head dynamics and their modification by 2'-deoxy-ADP

The contraction of striated muscle is driven by cycling myosin motor proteins embedded within the thick filaments of sarcomeres. In addition to cross-bridge cycling with actin, these myosin proteins can enter an inactive, sequestered state in which the globular S1 heads rest along the thick filament surface and are inhibited from performing motor activities. Structurally, this state is called the interacting heads motif (IHM) and is a critical conformational state of myosin that regulates muscle contractility and energy expenditure. Structural perturbation of the sequestered state can pathologically disrupt IHM structure and the mechanical performance of muscle tissue. Thus, the IHM state has become a target for therapeutic intervention. An ATP analog called 2'-deoxy-ATP (dATP) is a potent myosin activator that destabilizes the IHM. Here, we use molecular dynamics simulations to study the molecular mechanisms by which dATP modifies the structure and dynamics of myosin in a sequestered state. Simulations of the IHM state containing ADP.Pi in both nucleotide binding pockets revealed dynamic motions of the blocked head-free head interface, light chain binding domain, and S2 in this "inactive" state of myosin. Replacement of ADP.Pi by dADP.Pi triggered a series of structural changes that increased heterogeneity among residue contact pairs at the blocked head-free head interface and a 14% decrease in the interaction energy at the interface. Dynamic changes to this interface were accompanied by dynamics in the light chain binding region. A comparative analysis of these dynamics predicted new structural sites that may affect IHM stability.

A whole-cell platform for discovering synthetic cell adhesion molecules in bacteria

Developing programmable bacterial cell-cell adhesion is of significant interest due to its versatile applications. Current methods that rely on presenting cell adhesion molecules (CAMs) on bacterial surfaces are limited by the lack of a generalizable strategy to identify such molecules targeting bacterial membrane proteins in their natural states. Here, we introduce a whole-cell screening platform designed to discover CAMs targeting bacterial membrane proteins within a synthetic bacteria-displayed nanobody library. Leveraging the potency of the bacterial type IV secretion system-a contact-dependent DNA delivery nanomachine-we have established a positive feedback mechanism to selectively enrich for bacteria displaying nanobodies that target antigen-expressing cells. Our platform successfully identified functional CAMs capable of recognizing three distinct outer membrane proteins (TraN, OmpA, OmpC), demonstrating its efficacy in CAM discovery. This approach holds promise for engineering bacterial cell-cell adhesion, such as directing the antibacterial activity of programmed inhibitor cells toward target bacteria in mixed populations.

Inactivation mechanisms on pectin methylesterase by high pressure processing combined with its recombinant inhibitor

High pressure processing (HPP) juice often experiences cloud loss during storage, caused by the activity of pectin methylesterase (PME). The combination of HPP with natural pectin methylesterase inhibitor (PMEI) could improve juice stability. However, extracting natural PMEI is challenging. Gene recombination technology offers a solution by efficiently expressing recombinant PMEI from Escherichia coli and Pichia pastoris. Experimental and molecular dynamics simulation were conducted to investigate changes in activity, structure, and interaction of PME and recombinant PMEI during HPP. The results showed PME retained high residual activity, while PMEI demonstrated superior pressure resistance. Under HPP, PMEI's structure remained stable, while the N-terminus of PME's α-helix became unstable. Additionally, the helix at the junction with the PME/PMEI complex changed, thereby affecting its binding. Furthermore, PMEI competed with pectin for active sites on PME, elucidating. The potential mechanism of PME inactivation through the synergistic effects of HPP and PMEI.

Exploring the Conformational Ensembles of Protein-Protein Complex with Transformer-Based Generative Model

Protein-protein interactions are the basis of many protein functions, and understanding the contact and conformational changes of protein-protein interactions is crucial for linking the protein structure to biological function. Although difficult to detect experimentally, molecular dynamics (MD) simulations are widely used to study the conformational ensembles and dynamics of protein-protein complexes, but there are significant limitations in sampling efficiency and computational costs. In this study, a generative neural network was trained on protein-protein complex conformations obtained from molecular simulations to directly generate novel conformations with physical realism. We demonstrated the use of a deep learning model based on the transformer architecture to explore the conformational ensembles of protein-protein complexes through MD simulations. The results showed that the learned latent space can be used to generate unsampled conformations of protein-protein complexes for obtaining new conformations complementing pre-existing ones, which can be used as an exploratory tool for the analysis and enhancement of molecular simulations of protein-protein complexes.

An atomistic model of myosin interacting heads motif dynamics and their modification by 2'-deoxy-ADP

The contraction of striated muscle is driven by cycling myosin motor proteins embedded within the thick filaments of sarcomeres. In addition to cross-bridge cycling with actin, these myosin proteins can enter an inactive, sequestered state in which the globular S1 heads rest along the thick filament surface and are unable to perform motor activities. Structurally, this state is called the interacting heads motif (IHM) and is a critical conformational state of myosin that regulates muscle contractility and energy expenditure. Structural perturbation of the sequestered state via missense mutations can pathologically disrupt the mechanical performance of muscle tissue. Thus, the IHM state has become a target for therapeutic intervention. An ATP analogue called 2'-deoxy-ATP (dATP) is a potent myosin activator which destabilizes the IHM. Here we use molecular dynamics simulations to study the molecular mechanisms by which dATP modifies the structure and dynamics of myosin in a sequestered state. Simulations with IHM containing ADP.Pi in both nucleotide binding pockets revealed residual dynamics in an otherwise 'inactive' and 'sequestered' state of a motor protein. Replacement of ADP.Pi by dADP.Pi triggered a series of structural changes that modify the protein-protein interface that stabilizes the sequestered state, and changes to this interface were accompanied by allosteric changes in remote regions of the protein complex. A comparative analysis of these dynamics predicted new structural sites that may affect IHM stability.

Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations

Facing the current challenges posed by human health diseases requires the understanding of cell machinery at a molecular level. The interplay between proteins and RNA is key for any physiological phenomenon, as well protein-RNA interactions. To understand these interactions, many experimental techniques have been developed, spanning a very wide range of spatial and temporal resolutions. In particular, the knowledge of tridimensional structures of protein-RNA complexes provides structural, mechanical, and dynamical pieces of information essential to understand their functions. To get insights into the dynamics of protein-RNA complexes, we carried out all-atom molecular dynamics simulations in explicit solvent on nine different protein-RNA complexes with different functions and interface size by taking into account the bound and unbound forms. First, we characterized structural changes upon binding and, for the RNA part, the change in the puckering. Second, we extensively analyzed the interfaces, their dynamics and structural properties, and the structural waters involved in the binding, as well as the contacts mediated by them. Based on our analysis, the interfaces rearranged during the simulation time showing alternative and stable residue-residue contacts with respect to the experimental structure.

Identifying inflammation-related targets of natural lactones using network pharmacology, molecular modeling and in vitro approaches

Natural lactones have been used in traditional and folklore medicine for centuries owing to their anti-inflammatory properties. The study uses a multifaceted approach to identify lead anti-inflammatory lactones from the SISTEMATX natural products database. The study analyzed the natural lactone database, revealing 18 lactones linked to inflammation targets. The primary targets were PTGES, PTGS1, COX-2, ALOX5 and IL1B. STX 12273 was the best hit, with the lowest binding energy and potential for inhibiting the COX-2 enzyme. The study suggested natural lactone, STX 12273, from the SISTEMATX database with anti-inflammatory potential and postulated its use for inflammation treatment or prevention.

Structural Insights of PD-1/PD-L1 Axis: An In silico Approach

BACKGROUND

Interaction of PD-1 protein (present on immune T-cell) with its ligand PD-L1 (over-expressed on cancerous cell) makes the cancerous cell survive and thrive. The association of PD-1/PD-L1 represents a classical protein-protein interaction (PPI), where receptor and ligand binding through a large flat surface. Blocking the PD-1/PDL-1 complex formation can restore the normal immune mechanism, thereby destroying cancerous cells. However, the PD-1/PDL1 interactions are only partially characterized.

OBJECTIVE

We aim to comprehend the time-dependent behavior of PD-1 upon its binding with PD-L1.

METHODS

The current work focuses on a molecular dynamics simulation (MDs) simulation study of apo and ligand bound PD-1.

RESULTS

Our simulation reveals the flexible nature of the PD-1, both in apo and bound form. Moreover, the current study also differentiates the type of strong and weak interactions which could be targeted to overcome the complex formation.

CONCLUSION

The current article could provide a valuable structural insight about the target protein (PD-1) and its ligand (PD-L1) which could open new opportunities in developing small molecule inhibitors (SMIs) targeting either PD-1 or PD-L1.

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery

Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.