Ligand Conformational Changes Research Articles

Structural Basis for Chemerin Recognition and Signaling Through Its Receptors

Chemerin is a chemotactic adipokine that participates in a multitude of physiological processes, including adipogenesis, leukocyte chemotaxis, and neuroinflammation. Chemerin exerts biological functions through binding to one or more of its G protein-coupled receptors (GPCRs), namely chemokine-like receptor 1 (CMKLR1), G protein-coupled receptor 1 (GPR1), and CC-motif receptor-like 2 (CCRL2). Of these receptors, CMKLR1 and GPR1 have been confirmed as signaling receptors of chemerin, whereas CCRL2 serves as a chemerin-binding protein without transmembrane signaling. High-resolution structures of two chemerin receptors are now available thanks to recent advancements in structure biology. This review focuses on the structural perspectives of the chemerin receptors with an emphasis on the structure–activity correlation, including key components of the two receptors for ligand recognition and conformational changes induced by chemerin and its derivative peptides for G protein activation. There are also comparisons between the two chemerin receptors and selected GPCRs with peptide ligands for better appreciation of the shared and distinct features of the chemerin receptors in ligand recognition and transmembrane signaling, and in the evolution of this subclass of GPCRs.

Design, synthesis, in vitro, and in silico studies of new thiadiazol derivatives as promising VEGFR-2 inhibitors and apoptosis inducers

The presented study reports the synthesis, in silico and in vitro evaluations of a series of novel thiadiazole derivatives designed with the pharmacophoric features of Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) inhibitors. A comprehensive assessment against MCF-7 and HepG2 cancer cell lines revealed promising inhibitors, particularly, N-(4-((E)-1-(((Z)-5-acetyl-3-(2-chlorophenyl)-1,3,4-thiadiazol-2(3H)-ylidene) hydrazono) ethyl) phenyl)-4-chlorobenzamide (compound 22) exhibited a significantly low half-maximal inhibitory concentration (IC50) value against both MCF-7 and HepG2 cells of 0.03 µM and 0.39 µM, respectively. The rest of compounds exhibited also significant IC50 values against MCF-7 and HepG2 cells of (0.07–4.7 µM) and (0.12–8.75 µM), respectively. Furthermore, compound 22 displayed a VEGFR-2 inhibitory activity (VEGFR-2 = 0.042 µM) comparable to the established inhibitor sorafenib (VEGFR-2 = 0.041 µM). Detailed cell cycle analysis demonstrated that compound 22 induced a G0-G1 phase arrest of the MCF-7 cells (71.33 %), indicative of its potential to modulate cell cycle progression. Notably, compound 22 also exhibited a substantial increase in apoptosis in the MCF-7 cells, particularly in early (22.04 %) and late stages (13.94 %), underscoring its remarkable pro-apoptotic effect. Additionally, Compound 22 demonstrated a notable decrease in the migratory ability and wound healing capacity of MCF-7 cells. Computational studies, including molecular docking, revealed high binding affinities. Over a 200 ns MD simulation, the VEGFR-2-compound 22 complex initially displayed a rapid increase in RMSD followed by stability around 3.5 Å due to ligand conformational change while maintaining stable protein binding. This was confirmed by RMSF, SASA, RoG, and hydrogen bonding analysis. MM-GBSA, ProLIF, PCAT and FEL studies confirmed VEGFR-2-compound 22 complex binding at both dynamic and energetic levels. The computational ADMET studies demonstrated favorable pharmacokinetic properties. Furthermore, Density Functional Theory (DFT) studies confirmed the reactivity and stability of compound 22. These comprehensive findings underscore the potential of compound 22 as a lead candidate for further investigation in the development of VEGFR-2-targeted anticancer agents.

Receptor-associated protein impairs ligand binding to megalin and megalin-dependent endocytic flux in proximal tubule cells.

Proximal tubule (PT) cells retrieve albumin and a broad array of other ligands from the glomerular ultrafiltrate. Efficient uptake of albumin requires PT expression of both megalin and cubilin receptors. Although most proteins engage cubilin selectively, megalin is required to maintain robust flux through the apical endocytic pathway. Receptor-associated protein (RAP) is a chaperone that directs megalin to the cell surface, and recombinant RAP dramatically inhibits the uptake of numerous megalin and cubilin ligands. The mechanism by which this occurs has been suggested to involve competitive inhibition of ligand binding and/or conformational changes in megalin that prevent interaction with ligands and/or with cubilin. To discriminate between these possibilities, we determined the effect of RAP on endocytosis of albumin, which binds to cubilin and megalin receptors with high and low affinity, respectively. Uptake was quantified in opossum kidney (OK) cells and in megalin or cubilin (Cubn) knockout (KO) clones. Surprisingly, RAP inhibited fluid-phase uptake in addition to receptor-mediated uptake in OK cells and Cubn KO cells but had no effect on endocytosis when megalin was absent. The apparent Ki for RAP inhibition of albumin uptake was 10-fold higher in Cubn KO cells compared with parental OK cells. We conclude that in addition to its predicted high-affinity competition for ligand binding to megalin, the primary effect of RAP on PT cell endocytosis is to globally dampen megalin-dependent endocytic flux. Our data explain the complex effects of RAP on binding and uptake of filtered proteins and reveal a novel role in modulating endocytosis in PT cells.NEW & NOTEWORTHY Receptor-associated protein inhibits binding and uptake of all known endogenous ligands by megalin and cubilin receptors via unknown mechanism(s). Here, we took advantage of recently generated knockout cell lines to dissect the effect of this protein on megalin- and cubilin-mediated endocytosis. Our study reveals a novel role for receptor-associated protein in blocking megalin-stimulated endocytic uptake of fluid-phase markers and receptor-bound ligands in proximal tubule cells in addition to its direct effect on ligand binding to megalin receptors.

Determining Ligand and Ion-Induced Conformational Changes in Serotonin Transporter with Its Fluorescent Substrates.

Conformational changes are fundamental events in the transport mechanism. The serotonin transporter (SERT) catalyzes reuptake of the neurotransmitter serotonin after its release by serotonergic neurons and is the molecular target for antidepressant drugs and psychostimulants. Despite significant progress in characterizing the structure–function relationship of SERT, its conformational mechanism has not been fully understood. We present here a cell-based method for determining conformational changes in SERT with its fluorescent substrates by fluorescence imaging analysis. This method fluorometrically measures accessibility of strategically positioned cysteine residues in the substrate permeation pathway to calculate the rate constants of reactivity with MTS reagents in live or permeabilized cells. We validated this method by investigating ligand and ion-induced conformational changes in both the extracellular and cytoplasmic pathways of SERT. Furthermore, we applied this method for examining the influence of Cl− binding and vilazodone inhibition on SERT conformation. Our results showed that Cl− ion, in the presence of Na+, facilitates the conformational conversion from outward to inward open states, and that vilazodone binding stabilizes SERT in an outward open and inward-closed conformation. The present work provided insights into the conformational mechanism of SERT and also indicated that the cell-based fluorometric method is robust, straightforward to perform, and potentially applicable to any monoamine transporters in exploring the transport mechanism and mechanism of action of therapeutic agents for the treatment of several psychiatric disorders.

NKG2D discriminates diverse ligands through selectively mechano‐regulated ligand conformational changes

Stimulatory immune receptor NKG2D binds diverse ligands to elicit differential anti‐tumor and anti‐virus immune responses. Two conflicting degeneracy recognition models based on static crystal structures and in‐solution binding affinities have been considered for almost two decades. Whether and how NKG2D recognizes and discriminates diverse ligands still remain unclear. Using live‐cell‐based single‐molecule biomechanical assay, we characterized the in situ binding kinetics of NKG2D interacting with different ligands in the absence or presence of mechanical force. We found that mechanical force application selectively prolonged NKG2D interaction lifetimes with the ligands MICA and MICB, but not with ULBPs, and that force‐strengthened binding is much more pronounced for MICA than for other ligands. We also integrated steered molecular dynamics simulations and mutagenesis to reveal force‐induced rotational conformational changes of MICA, involving formation of additional hydrogen bonds on its binding interface with NKG2D, impeding MICA dissociation under force. We further provided a kinetic triggering model to reveal that force‐dependent affinity determines NKG2D ligand discrimination and its downstream NK cell activation. Together, our results demonstrate that NKG2D has a discrimination power to recognize different ligands, which depends on selective mechanical force‐induced ligand conformational changes.

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine.

Solute-binding proteins (SBPs) have evolved to balance the demands of ligand affinity, thermostability, and conformational change to accomplish diverse functions in small molecule transport, sensing, and chemotaxis. Although the ligand-induced conformational changes that occur in SBPs make them useful components in biosensors, they are challenging targets for protein engineering and design. Here, we have engineered a d-alanine-specific SBP into a fluorescence biosensor with specificity for the signaling molecule d-serine (D-serFS). This was achieved through binding site and remote mutations that improved affinity (KD = 6.7 ± 0.5 μM), specificity (40-fold increase vs glycine), thermostability (Tm = 79 °C), and dynamic range (∼14%). This sensor allowed measurement of physiologically relevant changes in d-serine concentration using two-photon excitation fluorescence microscopy in rat brain hippocampal slices. This work illustrates the functional trade-offs between protein dynamics, ligand affinity, and thermostability and how these must be balanced to achieve desirable activities in the engineering of complex, dynamic proteins.

Neuromechanobiology: An Expanding Field Driven by the Force of Greater Focus.

The brain processes information by transmitting signals through highly connected and dynamic networks of neurons. Neurons use specific cellular structures, including axons, dendrites and synapses, and specific molecules, including cell adhesion molecules, ion channels and chemical receptors to form, maintain and communicate among cells in the networks. These cellular and molecular processes take place in environments rich of mechanical cues, thus offering ample opportunities for mechanical regulation of neural development and function. Recent studies have suggested the importance of mechanical cues and their potential regulatory roles in the development and maintenance of these neuronal structures. Also suggested are the importance of mechanical cues and their potential regulatory roles in the interaction and function of molecules mediating the interneuronal communications. In this review, the current understanding is integrated and promising future directions of neuromechanobiology are suggested at the cellular and molecular levels. Several neuronal processes where mechanics likely plays a role are examined and how forces affect ligand binding, conformational change, and signal induction of molecules key to these neuronal processes are indicated, especially at the synapse. The disease relevance of neuromechanobiology as well as therapies and engineering solutions to neurological disorders stemmed from this emergent field of study are also discussed.

Molecular insight into the outside‐in activation of integrin αvβ3 by 24( S )‐hydroxycholesterol

Objective Oxysterols such as 25-hydroxycholesterol (25HC) are metabolites of cholesterol produced in the human body. Oxysterols are implicated in many physiological and pathological processes and are shown to regulate the immune system. Recently, we demonstrated that during virus infections, 25HC amplifies proinflammatory response by directly binding to αvβ3 and α5β1 integrins and by activating FAK-NFkB signaling pathway, resulting in the production of proinflammatory mediators such as TNFα and IL-6. Surprisingly, our combined in silico and in vitro studies revealed that 25HC binds to integrins at a novel binding site (site 2) that is distinct from the classical ‘RGD’ binding site, where many extracellular matrix proteins with Arg-Gly-Asp motif are known to bind. Integrins are ubiquitous and play an important role in cell adhesion, cell-cell interactions, cell signaling, and extracellular matrix assembly. Given the abundance of both integrins and endogenous oxysterols, we hypothesized that other oxysterols (other than 25HC) might also activate integrins in a similar fashion. In this study, using a combined computational and experimental approach, we show that 24(S)-hydroxycholesterol (24HC) binds to integrin αvβ3 with high-affinity and triggers proinflammatory response via integrin-FAK pathway. Methods Molecular docking and all-atom molecular dynamics (MD) simulations were used to obtain binding poses and to study the ligand stability and conformational changes, respectively. Induced fit docking of 24HC at site 2 of αVβ3 ectodomain (PDB ID 3IIJE) was performed using MOE software. All-atom MD simulations were performed with GROMACS v5.1.2 using CHARMM36 force field and TIP3P water model. MD simulations were run in triplicates each for 200 ns. The proinflammatory response was determined by the production of TNF using ELISA. Results Our studies reveal the preferred binding orientation of 24HC, which is distinct from that of 25HC. Binding of 24HC induced structural changes in the specificity determining loop (SDL) of the βI domain, leading to an increase in solvent-accessible surface area (SASA) of the RGD site, disruption of native SDL-βI and SDL-β-propeller interface contacts, possibly altering the conformation of the RGD binding site. Robust production of TNF analyzed by ELISA indicates activation of the inflammatory response by 24HC. Similar to 25HC, 24HC also requires integrin-FAK pathway for inflammatory response since, FAK inhibitor, PF-431396 abrogated 24HC mediated response. Conclusions: As the primary cholesterol metabolite with exclusive production in the brain, these findings may provide key insight into factors that influence the complexities of brain function. Our study, for the first time, offers useful insight into the structural and mechanistic bases for the potential proinflammatory response mediated by 24HC through integrins and paves the way for drug discovery efforts towards identifying therapeutics in the treatment of infectious, inflammatory, and immune disorders.

A novel approach for studying receptor-ligand interactions on living cells surface by using NUS/T1ρ-NMR methodologies combined with computational techniques: The RGDechi15D-αvβ5 integrin complex

Structural investigations of receptor-ligand interactions on living cells surface by high-resolution Nuclear Magnetic Resonance (NMR) are problematic due to their short lifetime, which often prevents the acquisition of experiments longer than few hours. To overcome these limitations, we developed an on-cell NMR-based approach for exploring the molecular determinants driving the receptor-ligand recognition mechanism under native conditions. Our method relies on the combination of high-resolution structural and dynamics NMR data with Molecular Dynamics simulations and Molecular Docking studies. The key point of our strategy is the use of Non Uniform Sampling (NUS) and T1ρ-NMR techniques to collect atomic-resolution structural and dynamics information on the receptor-ligand interactions with living cells, that can be used as conformational constraints in computational studies. In fact, the application of these two NMR methodologies allows to record spectra with high S/N ratio and resolution within the lifetime of cells. In particular, 2D NUS [1H–1H] trNOESY spectra are used to explore the ligand conformational changes induced by receptor binding; whereas T1ρ-based experiments are applied to characterize the ligand binding epitope by defining two parameters: T1ρ Attenuation factor and T1ρ Binding Effect. This approach has been tested to characterize the molecular determinants regulating the recognition mechanism of αvβ5-integrin by a selective cyclic binder peptide named RGDechi15D. Our data demonstrate that the developed strategy represents an alternative in-cell NMR tool for studying, at atomic resolution, receptor-ligand recognition mechanism on living cells surface. Additionally, our application may be extremely useful for screening of the interaction profiling of drugs with their therapeutic targets in their native cellular environment.

Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics Study.

The histamine H receptor (H2R) plays an important role in the regulation of gastric acid secretion. Therefore, it is a main drug target for the treatment of gastroesophageal reflux or peptic ulcer disease. However, there is as of yet no 3D-structural information available hampering a mechanistic understanding of H2R. Therefore, we created a model of the histamine-H2R-Gs complex based on the structure of the ternary complex of the -adrenoceptor and investigated the conformational stability of this active GPCR conformation. Since the physiologically relevant motions with respect to ligand binding and conformational changes of GPCRs can only partly be assessed on the timescale of conventional MD (cMD) simulations, we also applied metadynamics and Gaussian accelerated molecular dynamics (GaMD) simulations. A multiple walker metadynamics simulation in combination with cMD was applied for the determination of the histamine binding mode. The preferential binding pose detected is in good agreement with previous data from site directed mutagenesis and provides a basis for rational ligand design. Inspection of the H2R-Gs interface reveals a network of polar interactions that may contribute to H2R coupling selectivity. The cMD and GaMD simulations demonstrate that the active conformation is retained on a s-timescale in the ternary histamine-H2R-Gs complex and in a truncated complex that contains only Gs helix 5 instead of the entire G protein. In contrast, histamine alone is unable to stabilize the active conformation, which is in line with previous studies of other GPCRs.

Interplay of Conformational Plasticity and Substrate Polymorphism in Malarial tyrosyl-tRNA Synthetase

Aminoacyl-tRNA catalyze ATP dependent attachment of amino-acids to their cognate tRNAs. Malarial tyrosyl-tRNA synthetase, a validated drug target, exhibits an intricate conformational landscape for the evolutionarily conserved ATP-binding loop. To examine the conformational dynamics, all-atom model for homodimeric holo- tyrosyl-tRNA synthetase was simulated for half microsecond under isochoric-isothermal conditions using AMBER force-fields. Root-mean-square deviation (RMSD), with respect to the crystal structure, for one of the monomers was ∼2Å while for the other monomer it reached upto a maximum of ∼3.5Å. The two monomers also showed markedly different atomic fluctuations during the simulation. In one monomer, loop regions in the N- and C-terminal domains had much higher calculated B-factors compared to the corresponding secondary structure elements in the other monomer. Intriguingly, the monomer with lower overall RMSD had higher atomic fluctuations than the monomer having greater conformational changes. The bound tyrosyl-adenylate sampled discrete conformational sub-states as evident by the distribution of adenosyl dihedral angles. The change in ligand conformation was triggered after 300ns; concomitant with the increased RMSD for the protein. The alpha torsion angle for both the ligands fluctuated between 45° to 90°, however, during 300 to 400ns, for one of the ligands, these angles were in 290° to 340° range. Further, for the same ligand, pairwise distribution for the beta and chi torsions showed presence of three distinct conformations. Interplay between protein and ligand dynamics has also been analyzed by monitoring ligand hydration pattern and variation in the intermolecular interactions. These results insightfully capture the distinct conformational states for the ATP binding loops and guide to dissect the ligand stabilizing interactions within the active site. The observed intermolecular dynamics would prove valuable in astutely designing experiments to discover potential leads against malaria.

Describing Complex Structure-Function Relationships in Biomolecules at Equilibrium

One of the great ambitions of structural biology is to describe structure-function relationships quantitatively. Statistical thermodynamics is a powerful, general tool for computing the behavior of biological macromolecules at equilibrium because it establishes a direct link between structure and function. Complex behavior emerges as equilibria of multiple reactions are coupled. Analytical treatment of linked equilibria scales poorly with increasing numbers of reactions and states as the algebraic constructs rapidly become unwieldy. We therefore developed a generalizable, but straightforward computational method to handle arbitrarily complex systems. To demonstrate this approach, we collected a multidimensional fluorescence landscape of an engineered fluorescent glucose biosensor and showed that its features could be modeled with ten intricately linked ligand-binding and conformational exchange reactions. This protein represents a minimalist model of sufficient complexity to encompass fundamental biomolecular structure-function relationships: two-state and multistate conformational ensembles, conformational hierarchies, osmolytes, coupling between different binding sites and coupling between ligand binding and conformational change. The successful fit of this complex, multifaceted system demonstrates generality of the method.

Computational microscopy: Revealing molecular mechanisms in plants using molecular dynamics simulations.

plantcell;31/12/tpc.119.tt1219/FIG1F1fig1Structural biology has provided valuable insights and high-resolution views of the biophysical processes in plants, such as photosynthesis, hormone signaling, nutrient transport, and toxin efflux. However, structural biology only provides a few "snapshots" of protein structure, whereas in vivo, protein function involves complex dynamical processes such as ligand binding and conformational changes that structures alone are unable to capture in full detail. Here, we present all-atom molecular dynamics (MD) simulations as a "computational microscope" that can be used to capture detailed structural and dynamical information about the molecular machinery in plants and gain high-resolution insights into plant growth and function. In addition to the background information provided here, we have prepared a set of tutorials that allow students to run and explore MD simulations of plant proteins.(Posted December 10, 2019)Click HERE to access Teaching Tools ComponentsRECOMMENDED CITATION STYLE:Feng, J., Chen, J., Selvam, B., and Shukla, D. (December 10, 2019). Computational microscopy: Revealing molecular mechanisms in plants using molecular dynamics simulations. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/ /10.1105/tpc.tt1219.

Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations.

We here report on nonequilibrium targeted molecular dynamics simulations as a tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray crystallography on two small molecule compound libraries bound to the N-terminal domain of the chaperone Hsp90, we show that the mean nonequilibrium work computed in an ensemble of trajectories of enforced ligand unbinding is a promising predictor for ligand unbinding rates. We furthermore investigate the molecular basis determining unbinding rates within the compound libraries. We propose ligand conformational changes and protein-ligand nonbonded interactions to impact on unbinding rates. Ligands may remain longer at the protein if they exhibit strong electrostatic and/or van der Waals interactions with the target. In the case of ligands with a rigid chemical scaffold that exhibit longer residence times, transient electrostatic interactions with the protein appear to facilitate unbinding. Our results imply that understanding the unbinding pathway and the protein-ligand interactions along this path is crucial for the prediction of small molecule ligands with defined unbinding kinetics.

P11.65 Insights into the mechanisms of primary brain tumor invasion

Abstract We have made progress in unravelling the mechanisms of tumor cell invasion by focusing the attention on two molecular pathways including chemokines and extracellular matrix molecules. Chemokines are important mediators of cell signaling that operate both on normal cells and tumor cells and in the immune-cell compartment (Billottet et al, 2013). Among the chemokine receptors, CXCR3 mediate diverse biological functions and comes in two major isoforms the A and B isoform. We found that ligand affinities and conformational changes are very different for the A and B form. We have recently elucidated the role and mechanism of CXCR3A in GBM invasion (Boyé et al, 2017b). We demonstrated that agonist stimulation enhances in vitro cell migration and invasion in GBM cells. A major finding was that CXCR3A forms a complex with the trafficking receptor Lipoprotein-related receptor-1 (LRP1). Silencing of LRP1 leads to an increase in the magnitude of ligand-induced conformational change with CXCR3-A focalized at the cell membrane, leading to sustained receptor activity and increase in the migration. This was also clinically validated. Our study defines LRP1 as a new regulator of CXCR3 and indicates that targeting CXCR3-A in GBM may constitute a promising strategy to halt tumor cell invasion. The extracellular matrix (ECM) has morphogenic roles in tumors. Important ECM components are the matricellular proteins, called thrombospondins(THBS1-5) (Adams and Lawler 2011). We recently elucidated the complex role of THSB1 in GBM invasion (Daubon et al.2019). Global expression analysis revealed that THBS1 is up-regulated in GBMs and associated with a poor prognosis. We, furthermore, demonstrated that THBS1 did not activate TGFβ in GBM but that TGFβ1 induced the expression of THBS1 via SMAD3. Furthermore, GBM invasion is compromised when THBS1 is silenced in tumor cells. Thus, our data clearly show that THBS1 is not only involved in the regulation of angiogenesis in GBM, but also impacts the invasive behaviour of glioma cells by interacting with a molecule called CD47 expressed on the surface of GBM cells. RNA-sequencing after microdissection of central and peripheral tumour areas in a human PDX model demonstrated that THBS1 was the gene with the highest connectivity in the peripheral invasive tumour areas. Taken together, these data indicate that THBS1 plays important role in the infiltrative process in GBM. REFERENCES: Adams JC, Lawler J. Cold Spring Harb Perspect Biol. 2011;3:a009712 Billottet C, Quemener C, Bikfalvi A. Biochim Biophys Acta. 2013;1836:287- Boyé K et al. Sci Rep. 2017;7:10703 Boyé K et al. Nat Commun. 2017;8:1571 Daubon T et al, Nature Communications. Nat Commun. 2019 Mar 8;10(1):1146 Murphy-Ullrich JE, Poczatek M. Cytokine Growth Factor Rev. 2000 11:59

Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites

Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C–H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C–H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups, which break planarity rules. For example, in Src homology 3 (SH3) domains, a conserved bent aromatic residue is observed near the ligand binding site. Fatty acid binding protein (FABP) 3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, the deuteration of protein and/or solvent are promising variables in protein crystal optimization.

Single-Molecule Observation of Ligand Binding and Conformational Changes in FeuA

The specific binding of ligands by proteins and the coupling of this process to conformational changes is fundamental to protein function. We designed a fluorescence-based single-molecule assay and data analysis procedure that allows the simultaneous real-time observation of ligand binding and conformational changes in FeuA. The substrate-binding protein FeuA binds the ligand ferri-bacillibactin and delivers it to the ATP-binding cassette importer FeuBC, which is involved in bacterial iron uptake. The conformational dynamics of FeuA was assessed via Förster resonance energy transfer, whereas the presence of the ligand was probed by fluorophore quenching. We reveal that ligand binding shifts the conformational equilibrium of FeuA from an open to a closed conformation. Ligand binding occurs via an induced-fit mechanism, i.e., the ligand binds to the open state and subsequently triggers a rapid closing of the protein. However, FeuA also rarely samples the closed conformation without the involvement of the ligand. This shows that ligand interactions are not required for conformational changes in FeuA. However, ligand interactions accelerate the conformational change 10,000-fold and temporally stabilize the formed conformation 250-fold.

A Kinetic Study of Ligand Binding and Conformational Changes in Inducible Nitric Oxide Synthase

The mammalian inducible nitric oxide synthase (iNOS) catalyzes the production of nitric oxide (NO) in a two-step monooxygenation of L-arginine (L-Arg) to NO and L-citrulline via the intermediate Nω-hydroxy-L-arginine (NOHA). The reaction starts with the formation of a ternary complex consisting of the enzyme, an O2 ligand bound to the heme iron and the L-Arg substrate residing close to the heme-bound ligand. We have blocked the enzymatic turnover by replacing O2 by carbon monoxide (CO), because it resembles O2 in size and heme binding properties, and then studied CO binding to the iNOS oxygenase domain, iNOSoxy, by using flash photolysis. The P420 and P450 forms of the enzyme, assigned to a protonated and unprotonated proximal cysteine, through which the heme is anchored to the protein, show markedly different CO rebinding properties. Only very few CO ligands can escape from P420. They rebind very slowly, suggesting that P420 has a widely open distal pocket that admits water. CO rebinding to the P450 form strongly depends on the presence of the substrate L-Arg, the intermediate Nω-hydroxy-L-arginine and also the cofactor tetrahydrobiopterin. After adding these small molecules to the enzyme solution, the CO kinetics change slowly over hours. This process can be described as a relaxation from a fast rebinding, metastable P450 species to a slowly rebinding, thermodynamically stable P450 species, which we associate with the enzymatically active form. Our results allow us to determine kinetic parameters of L-Arg binding to ferrous deoxy iNOS protein, the L-Arg dissociation rate coefficient,= 15.4 ± 0.4 s−1, the bimolecular L-Arg association rate coefficient, = 1153 ± 71 mM−1s−1, and by taking the ratio of the two values, the equilibrium dissociation coefficient of L-Arg and ferrous iNOSoxy, KD = 13.4 ± 0.9 μM.

Multimodal Ligand Binding Studies of Human and Mouse G-Coupled Taste Receptors to Correlate Their Species-Specific Sweetness Tasting Properties.

Taste signaling is a complex process that is linked to obesity and its associated metabolic syndromes. The sweet taste is mediated through a heterodimeric G protein coupled receptor (GPCR) in a species-specific manner and at multi-tissue specific levels. The sweet receptor recognizes a large number of ligands with structural and functional diversities to modulate different amplitudes of downstream signaling pathway(s). The human sweet-taste receptor has been extremely difficult to study by biophysical methods due to the difficulty in producing large homogeneous quantities of the taste-receptor protein and the lack of reliable in vitro assays to precisely measure productive ligand binding modes that lead to activation of the receptor protein. We report here a multimodal high throughput assay to monitor ligand binding, receptor stability and conformational changes to model the molecular ligand-receptor interactions. We applied saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR) complemented by differential scanning calorimetry (DSC), circular dichroism (CD) spectroscopy, and intrinsic fluorescence spectroscopy (IF) to characterize binding interactions. Our method using complementary NMR and biophysical analysis is advantageous to study the mechanism of ligand binding and signaling processes in other GPCRs.

Kinetic Study of Ligand Binding and Conformational Changes in Inducible Nitric Oxide Synthase.

Nitric oxide synthases (NOSs) are heme enzymes that generate highly reactive nitric oxide from l-arginine (l-Arg) in a complex mechanism that is still only partially understood. We have studied carbon monoxide (CO) binding to the oxygenase domain of murine inducible NOS (iNOS) by using flash photolysis. The P420 and P450 forms of the enzyme, assigned to a protonated and unprotonated proximal cysteine, through which the heme is anchored to the protein, show markedly different CO rebinding properties. The data suggest that P420 has a widely open distal pocket that admits water. CO rebinding to the P450 form strongly depends on the presence of the substrate l-Arg, the intermediate Nω-hydroxy-l-arginine, and the cofactor tetrahydrobiopterin. After adding these small molecules to the enzyme solution, the CO kinetics change slowly over the hours. This process can be described as a relaxation from a fast rebinding, metastable species to a slowly rebinding, thermodynamically stable species, which we associate with the enzymatically active form. Our results allow us to determine kinetic parameters of l-Arg binding to the ferrous deoxy iNOS protein for the first time and also provide clues regarding the nature of structural differences between the two interconverting species.