GPCR Allostery: A View from Computational Biology

Abstract: G protein-coupled receptors (GPCRs) represent a large superfamily of cell-surface proteins that mediate cell signaling and regulate virtually various aspects of physiological and pathological processes, therefore serving as a rich source of drug targets. As intrinsically allosteric proteins, numerous functions of GPCRs are regulated via allostery, whereby allosteric modulators binding at a distal site regulate the function of the typical orthosteric site. However, only a few GPCR allosteric ligands have been presently approved as drugs due to the high dynamic structures of GPCRs. Fortunately, the rapid development of computational biology sheds light on understanding the mechanism of GPCR allosteric ligands, which is critical for the discovery of new therapeutic agents. Here, we present a comprehensive overview of the currently available resources and approaches in computational biology related to G protein-coupled receptor allostery and their conformational dynamics. In addition, current limitations and major challenges in the field are also discussed accordingly.

Application of computational approaches in biomembranes: From structure to function

AbstractBiological membranes (biomembranes) are one of the most complicated structures that allow life to exist. Investigating their structure, dynamics, and function is crucial for advancing our knowledge of cellular mechanisms and developing novel therapeutic strategies. However, experimental investigation of many biomembrane phenomena is challenging due to their compositional and structural complexity, as well as the inherently multi‐scalar features. Computational approaches, particularly molecular dynamics (MD) simulations, have emerged as powerful tools for addressing the atomic details of biomembrane systems, driving breakthroughs in our understanding of biomembranes and their roles in cellular function. This review presents an overview of the latest advancements in related computational approaches, from force fields and model construction to MD simulations and trajectory analysis. We also discussed current hot research topics and challenges. Finally, we outline future directions, emphasizing the integration of force field development, enhanced sampling techniques, and data‐driven approaches to accelerate the growth of this field in the years to come. We aim to equip readers with an understanding of the promise and limitations of emerging computational technologies in biomembrane systems and offer valuable recommendations for future research endeavors.This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

Computational Insights into the Allosteric Modulation of a Phthalate-Degrading Hydrolase by Distal Mutations

Phthalate esters (PAEs) are a ubiquitous kind of environmental endocrine-disrupting chemicals, causing environmental and health issues. EstJ6 is an effective phthalate-degrading hydrolase, and its mutant with a combination of three non-conservative distal mutations has an improved activity against PAEs with unknown molecular mechanisms. Herein, we attempt to fill the significant gap between distal mutations and the activity of this enzyme using computational approaches. We find mutations result in a redistribution of enzyme’s preexisting conformational states and dynamics changes of key functional regions, especially the lid over the active site. The outward motion of the lid upon mutations should make it easier for substrates or products to enter or exit. Additionally, the stronger substrate binding affinity and conformational rearrangements of catalytic reaction-associated residues in mutant, accompanied by the strengthened communication within the protein, might contribute to the elevated catalytic efficiency. Finally, an attempt has been done to improve the thermostability of EstJ6 upon introducing a distal disulfide bond between residues A23 and A29, and the simulation results are as expected. Together, our work explored the allosteric effects caused by distal mutations, which could provide insights into the rational design of esterases for industrial applications in the future.

Allosteric inhibition of myosin by phenamacril: a synergistic mechanism revealed by computational and experimental approaches

AbstractBackgroundMyosin plays a crucial role in cellular processes, while its dysfunction can lead to organismal malfunction. Phenamacril (PHA), a highly species‐specific and non‐competitive inhibitor of myosin I (FgMyoI) from Fusarium graminearum, has been identified as an effective fungicide for controlling plant diseases caused by partial Fusarium pathogens, such as wheat scab and rice bakanae. However, the molecular basis of its action is still unclear.ResultsThis study used multiple computational approaches first to elucidate the allosteric inhibition mechanism of FgMyoI by PHA at the atomistic level. The results indicated the increase of adenosine triphosphate (ATP) binding affinity upon PHA binding, which might impede the release of hydrolysis products. Furthermore, simulations revealed a broadened outer cleft and a significantly more flexible interface for actin binding, accompanied by a decrease in signaling transduction from the catalytic center to the actin‐binding interface. These various effects might work together to disrupt the actomyosin cycle and hinder the ability of motor to generate force. Our experimental results further confirmed that PHA reduces the enzymatic activity of myosin and its binding with actin.ConclusionTherefore, our findings demonstrated that PHA might suppress the function of myosin through a synergistic mechanism, providing new insights into myosin allostery and offering new avenues for drug/fungicide discovery targeting myosin. © 2023 Society of Chemical Industry.

Synthetic K⁺ Channels Constructed by Rebuilding the Core Modules of Natural K⁺ Channels in an Artificial System

AbstractDifferent types of natural K+ channels share similar core modules and cation permeability characteristics. In this study, we have developed novel artificial K+ channels by rebuilding the core modules of natural K+ channels in artificial systems. All the channels displayed high selectivity for K+ over Na+ and exhibited a selectivity sequence of K+≈Rb+ during the transport process, which is highly consistent with the cation permeability characteristics of natural K+ channels. More importantly, these artificial channels could be efficiently inserted into cell membranes and mediate the transmembrane transport of K+, disrupting the cellular K+ homeostasis and eventually triggering the apoptosis of cells. These findings demonstrate that, by rebuilding the core modules of natural K+ channels in artificial systems, the structures, transport behaviors, and physiological functions of natural K+ channels can be mimicked in synthetic channels.

Uncovering the Molecular Basis for the Better Gefitinib Sensitivity of EGFR with Complex Mutations over Single Rare Mutation: Insights from Molecular Simulations

Epidermal growth factor receptor (EGFR) is an intensively focused target for anti-tumor compounds used in non-small cell lung cancer (NSCLC) therapy. Compared to the classical activating mutations, there are still many uncommon EGFR mutations associated with poorer responses to EGFR inhibitors. A detailed understanding of the molecular basis for multiple EGFR mutants exhibiting diverse responses to inhibitors is of critical importance for related drug development. Herein, we explored the molecular determinants contributing to the distinct responses of EGFR with a single rare mutation (G719S) or combined mutations (G719S/L858R and G719S/l861Q) to Gefitinib (IRE). Our results indicated that interactions, formed within the tetrad of residues S768 (in the αC-helix), D770 (in the αC-β4 loop), Y827 (in the αE-helix), and R831 (in the catalytic loop), play an important role in the stability of αC-helix and the maintenance of K745–E762 salt bridge in the absence of IRE, which are weakened in the EGFRG719S system and enhanced in the EGFRG719S/L858R system upon IRE binding. Besides, the introduced hydrogen bonds by the co-occurring mutation partner also contribute to the stability of αC-helix. The work done for inhibitor dissociation suggests that IRE exhibits a stronger binding affinity to EGFRG719S/L858R mutant. Together, these findings provide a deeper understanding of minor mutations, which is essential for drug development targeting EGFR with less common mutations.

Understanding the Allosteric Modulation of PTH1R by a Negative Allosteric Modulator

The parathyroid hormone type 1 receptor (PTH1R) acts as a canonical class B G protein-coupled receptor, regulating crucial functions including calcium homeostasis and bone formation. The identification and development of PTH1R non-peptide allosteric modulators have obtained widespread attention. It has been found that a negative allosteric modulator (NAM) could inhibit the activation of PTH1R, but the implied mechanism remains unclear. Herein, extensive molecular dynamics simulations together with multiple analytical approaches are utilized to unravel the mechanism of PTH1R allosteric inhibition. The results suggest that the binding of NAM destabilizes the structure of the PTH1R–PTH–spep/qpep (the C terminus of Gs/Gq proteins) complexes. Moreover, the presence of NAM weakens the binding of PTH/peps (spep and qpep) and PTH1R. The intra- and inter-molecular couplings are also weakened in PTH1R upon NAM binding. Interestingly, compared with our previous study of the positive allosteric effects induced by extracellular Ca2+, the enhanced correlation between the PTH and G-protein binding sites is significantly reduced by the replacement of this negative allosteric regulator. Our findings might contribute to the development of new therapeutic agents for diseases caused by the abnormal activation of PTH1R.

Insights into the negative regulation of EGFR upon the binding of an allosteric inhibitor

AbstractEpidermal growth factor receptor (EGFR) is an intensively focused drug target for non‐small cell lung cancer (NSCLC). JBJ‐04–125–02 is an effective ATP‐noncompetitive and T790M/L858R‐selective inhibitor of EGFR, but the implied negative regulation mechanism is not fully clarified. Here, computational approaches were employed to address this. We find that JBJ‐04–125–02 induces contrary effects on the binding of adenosine and phosphate moieties of ATP. The allosteric inhibitor lowers the stability of the hinge region, affecting the anchor of the adenosine portion of ATP, while a more closed conformation of P‐loop is observed and might be unfavorable for the phosphotransfer and product release. The umbrella sampling simulations further demonstrate that less free energy is needed for the initial dissociation of ATP (the adenosine group) from the inactive EGFR in the presence of JBJ‐04–125–02, but more for the phosphate groups egressing from the active cavity. Together, these findings provide a deeper understanding of the negative regulation of JBJ‐04–125–02. Moreover, the key inter‐molecular interactions contributing to ATP binding are identified. Our work might pave the way for designing allosteric drugs targeting EGFR for lung cancer patients, and also suggests that computational techniques are effective for investigating the allosteric mechanism.

Critical Extracellular Ca²⁺ Dependence of the Binding between PTH1R and a G-Protein Peptide Revealed by MD Simulations

Mechanism of enhanced sensitivity of mutated β‐adrenergic‐like octopamine receptor to amitraz in honeybee <i>Apis mellifera</i>: An insight from <scp>MD</scp> simulations

AbstractBACKGROUNDAmitraz is one of the critical acaricides/insecticides for effective control of pest infestation of Varroa destructor mite, a devastating parasite of Apis mellifera, because of its low toxicity to honeybees. Previous assays verified that a typical G protein‐coupled receptor, β‐adrenergic‐like octopamine receptor (Octβ2R), is the unique target of amitraz, but the honeybee Octβ2R resists to amitraz. However, the underlying molecular mechanism of the enhanced sensitivity or toxicity of amitraz to mutated honeybee Octβ2RE208V/I335T/I350V is not fully understood. Here, molecular dynamics simulations are employed to explore the implied mechanism of the enhanced sensitivity to amitraz in mutant honeybee Octβ2R.RESULTSWe found that amitraz binding stabilized the structure of Octβ2R, particularly the intracellular loop 3 associated with the Octβ2R signaling. Then, it was further demonstrated that both mutations and ligand binding resulted in a more rigid and compact amitraz binding site, as well as the outward movement of the transmembrane helix 6, which was a prerequisite for G protein coupling and activation. Moreover, mutations were found to promote the binding between Octβ2R and amitraz. Finally, community analysis illuminated that mutations and amitraz strengthened the residue–residue communication within the transmembrane domain, which might facilitate the allosteric signal propagation and activation of Octβ2R.CONCLUSIONOur results unveiled structural determinants of improved sensitivity in the Octβ2R‐amitraz complex and may contribute to further structure‐based drug design for safer and less toxic selective insecticides. © 2022 Society of Chemical Industry.

Investigating the Permeation Mechanism of Typical Phthalic Acid Esters (PAEs) and Membrane Response Using Molecular Dynamics Simulations

Phthalic acid esters (PAEs) are typical environmental endocrine disrupters, interfering with the endocrine system of organisms at very low concentrations. The plasma membrane is the first barrier for organic pollutants to enter the organism, so membrane permeability is a key factor affecting their biological toxicity. In this study, based on computational approaches, we investigated the permeation and intramembrane aggregation of typical PAEs (dimethyl phthalate, DMP; dibutyl phthalate, DBP; di-2-ethyl hexyl phthalate, DEHP), as well as their effects on membrane properties, and related molecular mechanisms were uncovered. Our results suggested that PAEs could enter the membrane spontaneously, preferring the headgroup-acyl chain interface of the bilayer, and the longer the side chain (DEHP > DBP > DMP), the deeper the insertion. Compared with the shortest DMP, DEHP apparently increased membrane thickness, order, and rigidity, which might be due to its stronger hydrophobicity. Potential of means force (PMF) analysis revealed the presence of an energy barrier located at the water-membrane interface, with a maximum value of 2.14 kcal mol−1 obtained in the DEHP-system. Therefore, the difficulty of membrane insertion is also positively correlated with the side-chain length or hydrophobicity of PAE molecules. These findings will inspire our understanding of structure-activity relationship between PAEs and their effects on membrane properties, and provide a scientific basis for the formulation of environmental pollution standards and the prevention and control of small molecule pollutants.

Conformational dynamics is critical for the allosteric inhibition of cGAS upon acetyl-mimic mutations

In the present study, the allosteric inhibition mechanism of cGAS upon acetyl-mimic mutations was investigated, and conformational dynamics was found to be especially critical.

Molecular Mechanism of Ca²⁺ in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1

Bacterial lipopolysaccharide core structures mediate effects of butanol ingress

The molecular mechanism of pH‐regulating C3d‐CR2 interactions: Insights from molecular dynamics simulation

AbstractThe interactions of complement receptor 2 (CR2) and the degradation fragment C3d of complement component C3 mediate the innate and adaptive immune systems. Due to the importance of C3d‐CR2 interaction in the design of vaccines, many studies have indicated the interactions are pH‐dependent. Moreover, C3d‐CR2 interactions at pH 5.0 are unknown. To investigate the molecular mechanism of pH‐regulating C3d‐CR2 interaction, molecular dynamics simulations for C3d‐CR2 complex in different pH are performed. Our results revealed that the protonation of His9 in C3d at pH 6.0 slightly weakens C3d‐CR2 association as reducing pH from 7.4 to 6.0, initiated from a key hydrogen bond formed between Gly270 and His9 in C3d at pH 6.0. When reducing pH from 6.0 to 5.0, the protonation of His33 in C3d weakens C3d‐SCR1 association by changing the hydrogen‐bond network of Asp36, Glu37, and Glu39 in C3d with Arg13 in CR2. In addition, the protonation of His90 significantly enhances C3d‐SCR2 association. This is because the enhanced hydrogen‐bond interactions of His90 with Glu63 and Ser69 of the linker change the conformations of the linker, Cys112‐Asn116 and Pro87‐Gly91 regions. This study uncovers the molecular mechanism of the mediation of pH on C3d‐CR2 interaction, which is valuable for vaccine design.

Response of microbial membranes to butanol: interdigitation<i>vs.</i>disorder

Elucidating butanol interactions with lipid bilayers will inform membrane engineering approaches for improving butanol tolerance in industrial fermentations.

How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

Artificial K⁺ Channels Formed by Pillararene‐Cyclodextrin Hybrid Molecules: Tuning Cation Selectivity and Generating Membrane Potential

AbstractA class of artificial K+ channels formed by pillararene‐cyclodextrin hybrid molecules have been designed and synthesized. These channels efficiently inserted into lipid bilayers and displayed high selectivity for K+ over Na+ in fluorescence and electrophysiological experiments. The cation transport selectivity of the artificial channels is tunable by varying the length of the linkers between pillararene and cyclodexrin. The shortest channel showed specific transmembrane transport preference for K+ over all alkali metal ions (selective sequence: K+ > Cs+ > Rb+ > Na+ > Li+), and is rarely observed for artificial K+ channels. The high selectivity of this artificial channel for K+ over Na+ ensures specific transmembrane translocation of K+, and generated stable membrane potential across lipid bilayers.

Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1

The molecular mechanism of two coreceptor binding site antibodies X5 and 17b neutralizing HIV-1: Insights from molecular dynamics simulation

One-pot formation of hydrazide macrocycles with modified cavities: an example of pH-sensitive unimolecular cation channels

The number and position of carboxyls in the channel have a significant impact on the membrane-incorporation ability, ion selectivity and NH4+ transport activity of the macrocyclic channels.

A unimolecular channel formed by dual helical peptide modified pillar[5]arene: correlating transmembrane transport properties with antimicrobial activity and haemolytic toxicity

Five unimolecular channels with different lengths are presented. The varying length of these channels has significant impact on their transport properties.

The solvent at antigen-binding site regulated C3d–CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation

Protein Allostery and Conformational Dynamics

Allosteric activation of SENP1 by SUMO1 β-grasp domain involves a dock-and-coalesce mechanism

Small ubiquitin-related modifiers (SUMOs) are conjugated to proteins to regulate a variety of cellular processes. SENPs are cysteine proteases with a catalytic center located within a channel between two subdomains that catalyzes SUMO C-terminal cleavage for processing of SUMO precursors and de-SUMOylation of target proteins. The β-grasp domain of SUMOs binds to an exosite cleft, and allosterically activates SENPs via an unknown mechanism. Our molecular dynamics simulations showed that binding of the β-grasp domain induces significant conformational and dynamic changes in SENP1, including widening of the exosite cleft and quenching of nanosecond dynamics in all but a distal region. A dock-and-coalesce mechanism emerges for SENP-catalyzed SUMO cleavage: the wedging of the β-grasp domain enables the docking of the proximal portion of the C-terminus and the strengthened cross-channel motional coupling initiates inter-subdomain correlated motions to allow for the distal portion to coalesce around the catalytic center.

Two Pathways Mediate Inter-Domain Allosteric Regulation in Pin1

Dynamically Driven Protein Allostery Exhibits Disparate Responses for Fast and Slow Motions

Two Pathways Mediate Interdomain Allosteric Regulation in Pin1

Exploring the Influence of EGCG on the β-Sheet-Rich Oligomers of Human Islet Amyloid Polypeptide (hIAPP1–37) and Identifying Its Possible Binding Sites from Molecular Dynamics Simulation

The role of Cys179–Cys214 disulfide bond in the stability and folding of prion protein: insights from molecular dynamics simulations

Stabilities and structures of islet amyloid polypeptide (IAPP22–28) oligomers: From dimer to 16-mer

Structural Diversity and Initial Oligomerization of PrP106–126 Studied by Replica-Exchange and Conventional Molecular Dynamics Simulations

The adsorption mechanism and induced conformational changes of three typical proteins with different secondary structural features on graphene

Exploring the Influence of Carbon Nanoparticles on the Formation of β-Sheet-Rich Oligomers of IAPP22–28 Peptide by Molecular Dynamics Simulation

The Evolution of HLA-B*3501 Binding Affinity to Variable Immunodominant NP418-426 Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study

Influence of the pathogenic mutations T188K/R/A on the structural stability and misfolding of human prion protein: Insight from molecular dynamics simulations

Molecular mechanism of the enhanced virulence of 2009 pandemic Influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study

Exploring structural and thermodynamic stabilities of human prion protein pathogenic mutants D202N, E211Q and Q217R

The molecular basis of IGF-II/IGF2R recognition: a combined molecular dynamics simulation, free-energy calculation and computational alanine scanning study