Solution Conformation Research Articles

The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery.

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in Mpro that play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of Mpro in an apo state and substrate-bound state. We find that the flexible loops can adopt open, intermediate (partly open), and closed conformations in solution, which differs from the partially closed state observed in crystal structures of Mpro. When the loops are in closed or intermediate states, the catalytic residues are more likely to be in close proximity, which is crucial for catalysis. Additionally, we find that substrate binding to one protomer of the homodimer increases the frequency of intermediate states in the bound protomer while also affecting the structural propensity of the apo protomer's flexible loops. Using dynamic network analysis, we identify multiple allosteric pathways connecting the two active sites of the homodimer. Common to these pathways is an allosteric hotspot involving the N-terminus, a critical region that comprises part of the binding pocket. Taken together, the results of our simulation study provide detailed insight into the relationships between the flexible loops and substrate binding in a prime drug target for COVID-19.

Rheological Behavior of Clay Tailings in the Presence of Divalent Cations and Sodium Polyacrylate: Insights from Molecular Dynamics Simulations.

This study analyzes the behavior of sodium polyacrylate (NaPA) as a rheological modifier for clay-based tailings. Special emphasis is placed on the impact of calcium and magnesium ions in industrial water, which are analyzed through rheograms, zeta potential measurements, and molecular dynamics simulations. The results are interpreted as electrostatic interactions, steric phenomena, and cation solvation. This interpretation integrates experimental studies with microscopic analyses, employing molecular dynamics simulations to elucidate the underlying mechanisms. In all cases, a decrease in the yield stress of synthetic slurries is observed as the dosing of NaPA increases due to greater repulsion between tailings particles through an increase in electrostatic repulsion and larger steric forces that hinder agglomeration. However, efficiency is reduced in the presence of divalent cations as zeta potential measurements suggest a reduction in the electrical charges of the particles and the polymer, making its application more challenging. The differences obtained in the presence of calcium compared to magnesium are explained in terms of the solvation of these ions and their impact on the polymer conformation in solution and adsorption on the mineral surfaces. This explanation is reinforced by molecular dynamics studies, which indicate that polymer adsorption on minerals depends on the type of mineral and type of ion. Particularly for quartz, the highest adsorption of NaPA occurs in the presence of calcium, whereas for a kaolinite surface, the highest polymer adsorption is obtained in the presence of magnesium. The competitive effect of these phenomena leads to the rheological behavior of the tailings being dominated by the effects originating in the clay.

4hJCHOCH Spin Coupling in a Lewisx Trisaccharide as Evidence of Inter-Residue C-H···O Hydrogen Bonding in Aqueous Solution.

Prior studies of the solution conformation of the Lewisx (Lex) trisaccharide, αFuc-(1→3)[βGal-(1→4)]-βGlcNAc, suggest that nonclassical inter-residue C-H···O hydrogen bonding in aqueous solution contributes to the stabilization of its 3D structure and affects its biological properties. Experimental evidence for this hydrogen bond in aqueous solution has been reported in the form of a 4hJCHOCH NMR spin-coupling constant between C5'Fuc and H1″Gal measured by 2D NMR methods in unlabeled samples. A methyl glycoside of Lex (MeβLex) was prepared containing selective 13C-labeling at C5'Fuc, and the H1″Gal signal was examined in high-field 1H NMR spectra for evidence of splitting or line-broadening caused by the 13C at C5'Fuc. High-resolution 1H NMR spectra obtained at high field and at different temperatures using different FID processing parameters showed no resolved splitting of the H1″Gal signal or evidence of line-broadening. Spectral simulation showed that this splitting and/or line-broadening would be observable if the reported J-value (∼1.1 Hz) is correct. DFT calculations on MeβLex and a carbon analog (O5″Gal replaced by a CH2 group) gave very small and nearly identical calculated 4hJC5',H1″ values, suggesting that the coupling is essentially zero. DFT calculations also showed that an alternate inter-residue 3hJH5',H1″ is small. Based on NMR analyses and DFT calculations, we found that 4hJC5',H1″ in MeβLex has an upper limit of ∼0.4 Hz and that the value could be lower, possibly zero, calling into question its value as experimental proof of persistent nonclassical hydrogen bonding in aqueous solutions of MeβLex and related structures.

Effect of ultrasound assisted H2O2 degradation on longan polysaccharide: degradation kinetics, physicochemical properties and prebiotic activity

This study aimed to investigate the effect of ultrasound-assisted H2O2 (US/H2O2) reaction on degradation parameters and kinetics, physicochemical properties and prebiotic activity of longan polysaccharide (LP). Results showed that US/H2O2 had a synergistic effect on the degradation of LP, and its kinetic equation followed to the fist – order model. US/H2O2 degradation did not change the chemical and monosaccharide composition of LP but altered their ratio. Compared with LP, three degraded polysaccharides (DLPs) displayed lower molecular weight, particle size and viscosity, but higher solubility. SEM and AFM revealed that US/H2O2 degradation led to significant differences in the microstructure and solution conformation of LP. Moreover, LP and DLPs showed different proliferation effects on four lactobacilli and bifidobacteria strains, among which DLP-8 (degraded for 8 h) exhibited the strongest prebiotic activity. US/H2O2 could be effectively applied to the degradation of LP to improve its physicochemical properties and bioactivities.

Context Effects on Human Milk Oligosaccharide Linkage Conformation and Dynamics Revealed by MA'AT Analysis.

An emerging NMR method, MA'AT analysis, has been applied to investigate context effects on the conformational properties of several human milk oligosaccharides (HMOs). The MA'AT model of the β-(1→4) linkage in the disaccharide, methyl β-lactoside (MeL), was compared to those obtained for the same linkage in the HMO trisaccharides, methyl 2'-fucosyllactoside (Me2'FL) and methyl 3-fucosyllactoside (Me3FL), and in the tetrasaccharide, methyl 2',3-difucosyllactoside (Me2',3DFL). MA'AT analysis revealed significant context effects on the mean values and circular standard deviations (CSDs) of the psi (ψ) torsion angles in these linkages. α-Fucosylation at both O2'Gal and O3Glc of MeL to give Me2',3DFL significantly constrained librational motion about ψ (70% reduction in the CSD) and shifted its mean value by ∼18°. α-Fucosylation at the O3Glc of MeL to give Me3FL constrained ψ more than α-fucosylation at the O2Gal to give Me2'FL. These effects can be explained by the expected solution conformation of Me3FL, which closely resembles the Lewisx trisaccharide. Comparisons of MA'AT models of ψ to those obtained by 1 μs aqueous molecular dynamics simulation (GLYCAM06) revealed identical trends, that is, MA'AT analysis was able to recapitulate molecular behavior in solution that was heretofore only available from MD simulation. The results highlight the capabilities of MA'AT analysis to determine probability distributions of molecular torsion angles in solution as well as degrees of librational averaging of these angles.

Deciphering the Conformations of Glutathione Oxidized Peptide: A Comparative NMR Study in Solution and Solid-State Environments.

Glutathione (GSH) and its oxidized dimer (GSSG) play an important role in living systems as an antioxidant, balancing the presence of reactive oxygen species (ROS). The central thiol (-S-S-) bond in GSSG can undergo free rotation, providing multiple conformations with respect to the S-S bridge. The six titratable sites of GSSG, which are influenced by pH variations, affect these conformations in solution, whereas in solids, additionally crystal packing effects come into play. In view of differing reports about the structure of GSSG in literature, we have here conducted an extensive reexamination of its conformations using NMR, and contrasting results have been obtained for solution and solid state. In solution, the existence of more than one antiparallel orientation of the monomer unit with different hydrogen bonding schemes has been indicated by NOE and amide temperature coefficient results. On the other hand, in the solid-state, a 1H-1H double-quantum (DQ) to 13C single-quantum (SQ) correlation study has confirmed a parallel orientation, consistent with the reported X-ray crystal structure. Experimentally assigned solid-state NMR resonances have been validated using GIPAW calculations incorporated in the Quantum ESPRESSO package.

NMR Coupling Constants, Karplus Equations, and Adjusted MD Statistics: Detecting Diagnostic Torsion Angles for the Solution Geometry of 6-[α-d-Mannopyranosyl]-d-Mannopyranose (Mannobiose).

The quantitative solution conformations of 2-(hydroxymethyl)-tetrahydropyran, α-methyl-d-mannopyranoside, and 6-[α-d-mannopyranosyl]-d-mannopyranose (mannobiose) are described. Parametrized Karplus equations for redundant spin pairs across the terminal ω-torsion and the glycosidic ω-torsion for mannobiose are developed, including ω/θ-hypersurfaces for the terminal hydroxymethylene group. Experimental NMR data, algorithmic spectral simulation (clustered Hamiltonian method), molecular dynamics (MD) simulations (GLYCAM06), energy minimizations by DFT, and adjusted torsion angle populations weighted over the Karplus-type equations are used. We demonstrate that spectral simulation is a powerful tool in the refinement of initial J values obtained from static GAIO DFT calculations. We also show that only as few as one of multiple redundant torsions can be diagnostic for conformational analysis of the disaccharide.

The evolution of flexibility and function in the Fc domains of IgM, IgY, and IgE.

Antibody Fc regions harbour the binding sites for receptors that mediate effector functions following antigen engagement by the Fab regions. An extended "hinge" region in IgG allows flexibility between Fab and Fc, but in both the most primitive antibody, IgM, and in the evolutionarily more recent IgE, the hinge is replaced by an additional domain pair in the homodimeric six-domain Fc region. This permits additional flexibility within the Fc region, which has been exploited by nature to modulate antibody effector functions. Thus, in pentameric or hexameric IgM, the Fc regions appear to adopt a planar conformation in solution until antigen binding causes a conformational change and exposes the complement binding sites. In contrast, IgE-Fc principally adopts an acutely bent conformation in solution, but the binding of different receptors is controlled by the degree of bending, and there is allosteric communication between receptor binding sites. We sought to trace the evolution of Fc conformational diversity from IgM to IgE via the intermediate avian IgY by studying the solution conformations of their Fc regions by small-angle X-ray scattering. We compared four extant proteins: human IgM-Fc homodimer, chicken IgY-Fc, platypus IgE-Fc, and human IgE-Fc. These are examples of proteins that first appeared in the jawed fish [425 million years ago (mya)], tetrapod (310 mya), monotreme (166 mya), and hominid (2.5 mya) clades, respectively. We analysed the scattering curves in terms of contributions from a pool of variously bent models chosen by a non-negative linear least-squares algorithm and found that the four proteins form a series in which the proportion of acutely bent material increases: IgM-Fc < IgY-Fc < plIgE-Fc < huIgE-Fc. This follows their order of appearance in evolution. For the huIgM-Fc homodimer, although none are acutely bent, and a significant fraction of the protein is sufficiently bent to expose the C1q-binding site, it predominantly adopts a fully extended conformation. In contrast, huIgE-Fc is found principally to be acutely bent, as expected from earlier studies. IgY-Fc, in this first structural analysis of the complete Fc region, exhibits an ensemble of conformations from acutely bent to fully extended, reflecting IgY's position as an evolutionary intermediate between IgM and IgE.

Acid resistance of different polysaccharide hydrocolloids: pH effects

The acid resistance of polysaccharide hydrocolloids is very important for its application in food industry. In this study, the acid resistance of tamarind seed polysaccharide (TSP), xanthan gum (XG), and locust bean gum (LBG) at different pH was investigated. Results showed that the shear viscosity of TSP and LBG was significantly decreased at pH 1. Structural analyses showed that molecular degradation on the side chain of TSP and LBG occurred at pH 1, whereas the composition of the monosaccharides of XG showed no significant difference. Molecular degradation led to a decrease in the molecular weight of TSP and LBG with the gradual decrease of pH, accompanied by a shift in solution conformation, i.e., from semi-flexible chain to rigid rod for TSP and LBG, whereas XG did not undergo significant structural changes with the gradual decrease of pH. In addition, the SEM results showed that with the gradual decrease of molecular weight, the structures of TSP and LBG were gradually broken and showed fragmentation, while XG only showed slight cracks. These results show that the structure of the polysaccharides changes with the gradual decrease of pH, resulting in a change in the solution conformation and a decrease in viscosity. This study provides a new theoretical basis for the application of these polysaccharide hydrocolloids in food processing.

Synthesis and structural analysis of 1,4′-pyrazolo[3,4-e][1,4]thiazepin-7′(6H)ones: An example of conformational chirality in seven-membered heterocycles

A series of five new N-alkylspiro[1,4]thiazepin-2-ones was obtained in good yields using a two-step synthesis strategy involving the preparation of the spirothiazepinone core, followed by the N-alkylation using alkyl halides in alkaline conditions. The latter N-alkylation reaction gave rise to conformational chirality, evidenced in NMR spectra, polarimetry, chiral HPLC, and X-ray diffraction analysis. X-ray studies revealed the presence of enantiomorphic boat-type conformers in centrosymmetric unit cells interacting by van der Waals forces, in contrast to a predominant conformer in solution supported by the chiral properties of the N-alkylated derivatives. The present work makes an important contribution to the study of the structural properties of 1,4-thiazepinone systems and the phenomenon of conformational chirality in seven-membered N-heterocycles.

Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.

Small molecule ligands exhibit a diverse range of conformations in solution. Upon binding to a target protein, this conformational diversity is generally reduced. However, ligands can retain some degree of conformational flexibility even when bound to a receptor. In the Protein Data Bank (PDB), a small number of ligands have been modeled with distinct alternative conformations that are supported by X-ray crystallography density maps. However, the vast majority of structural models are fit to a single ligand conformation, potentially ignoring the underlying conformational heterogeneity present in the sample. We previously developed qFit-ligand to sample diverse ligand conformations and to select a parsimonious ensemble consistent with the density. While this approach indicated that many ligands populate alternative conformations, limitations in our sampling procedures often resulted in non-physical conformations and could not model complex ligands like macrocycles. Here, we introduce several improvements to qFit-ligand, including the use of routines within RDKit for stochastic conformational sampling. This new sampling method greatly enriches low energy conformations of small molecules and macrocycles. We further extended qFit-ligand to identify alternative conformations in PanDDA-modified density maps from high throughput X-ray fragment screening experiments. The new version of qFit-ligand improves fit to electron density and reduces torsional strain relative to deposited single conformer models and our previous version of qFit-ligand. These advances enhance the analysis of residual conformational heterogeneity present in ligand-bound structures, which can provide important insights for the rational design of therapeutic agents.

A naturally occurring 22-amino acid fragment of human hemoglobin A inhibits autophagy and HIV-1

Autophagy is an evolutionarily ancient catabolic pathway and has recently emerged as an integral part of the innate immune system. While the core machinery of autophagy is well defined, the physiological regulation of autophagy is less understood. Here, we identify a C-terminal fragment of human hemoglobin A (HBA1, amino acids 111–132) in human bone marrow as a fast-acting non-inflammatory inhibitor of autophagy initiation. It is proteolytically released from full-length HBA1 by cathepsin E, trypsin or pepsin. Biochemical characterization revealed that HBA1(111–132) has an in vitro stability of 52 min in human plasma and adopts a flexible monomeric conformation in solution. Structure–activity relationship studies revealed that the C-terminal 13 amino acids of HBA1(120–132) are sufficient to inhibit autophagy, two charged amino acids (D127, K128) mediate solubility, and two serines (S125, S132) are required for function. Successful viruses like human immunodeficiency virus 1 (HIV-1) evolved strategies to subvert autophagy for virion production. Our results show that HBA1(120–132) reduced virus yields of lab-adapted and primary HIV-1. Summarizing, our data identifies naturally occurring HBA1(111–132) as a physiological, non-inflammatory antagonist of autophagy. Optimized derivatives of HBA1(111–132) may offer perspectives to restrict autophagy-dependent viruses.

Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery

Peptide therapeutics have emerged as an appealing modality in the pharmaceutical industry. Understanding peptide conformation in solution remains one of the most critical areas for peptide drug development. Circular dichroism (CD) spectroscopy is a useful technique to study the secondary structure of proteins and peptides, but the current approaches are limited to protein-focused models to predict high-order structures of peptides, and the models were built based on X-ray crystallography instead of solution-based technique, as a result, such models may have poor predictions for peptides. In this study, we present a novel CD deconvolution model to determine peptide conformation in solution. To quantitatively obtain secondary structure information using CD, a calibration model is needed beforehand to establish the relationship between each secondary structure feature and the corresponding CD response. A reference set containing the majority of cyclic peptides with known structures from solution-state NMR spectroscopy was used to build the calibration model for CD deconvolution. Improved prediction accuracy on the secondary structure determination for cyclic peptides was achieved by this model compared to the commercial standard model using commercially available platforms. This new CD deconvolution method is crucial for peptide conformational analysis in solution, and has the potential to greatly accelerate peptide drug candidate optimization in the pharmaceutical drug discovery field.

Toward Reliable Conformational Energies of Amino Acids and Dipeptides─The DipCONFS Benchmark and DipCONL Datasets.

Simulating peptides and proteins is becoming increasingly important, leading to a growing need for efficient computational methods. These are typically semiempirical quantum mechanical (SQM) methods, force fields (FFs), or machine-learned interatomic potentials (MLIPs), all of which require a large amount of accurate data for robust training and evaluation. To assess potential reference methods and complement the available data, we introduce two sets, DipCONFL and DipCONFS, which cover large parts of the conformational space of 17 amino acids and their 289 possible dipeptides in aqueous solution. The conformers were selected from the exhaustive PeptideCS dataset by Andris et al. [ J. Phys. Chem. B 2022, 126, 5949-5958]. The structures, originally generated with GFN2-xTB, were reoptimized using the accurate r2SCAN-3c density functional theory (DFT) composite method including the implicit CPCM water solvation model. The DipCONFS benchmark set contains 918 conformers and is one of the largest sets with highly accurate coupled cluster conformational energies so far. It is employed to evaluate various DFT and wave function theory (WFT) methods, especially regarding whether they are accurate enough to be used as reliable reference methods for larger datasets intended for training and testing more approximated SQM, FF, and MLIP methods. The results reveal that the originally provided BP86-D3(BJ)/DGauss-DZVP conformational energies are not sufficiently accurate. Among the DFT methods tested as an alternative reference level, the revDSD-PBEP86-D4 double hybrid performs best with a mean absolute error (MAD) of 0.2 kcal mol-1 compared with the PNO-LCCSD(T)-F12b reference. The very efficient r2SCAN-3c composite method also shows excellent results, with an MAD of 0.3 kcal mol-1, similar to the best-tested hybrid ωB97M-D4. With these findings, we compiled the large DipCONFL set, which includes over 29,000 realistic conformers in solution with reasonably accurate r2SCAN-3c reference conformational energies, gradients, and further properties potentially relevant for training MLIP methods. This set, also in comparison to DipCONFS, is used to assess the performance of various SQM, FF, and MLIP methods robustly and can complement training sets for those.

Rapid Aminations of Functionalized Aryl Fluorosulfates in Water

AbstractAryl fluorosulfates of varying complexities have been used in amination reactions in water using a new Pd oxidative addition complex (OAC‐1) developed specifically to match the needs of the fine chemicals industry, not only in terms of functional group tolerance, but also reflecting time considerations associated with these important C−N couplings. Also especially noteworthy is that they replace both PFAS‐related triflates and nonaflates, which are today out of favor due to recent government regulations. The new complex based on the BippyPhos ligand is used at low loadings and under aqueous micellar conditions. Moreover, it is easily prepared and stable to long term storage. DFT calculations on the OAC precatalyst compare well with the X‐ray structure of the crystals with π‐complexation to the aromatic system of the ligand and also confirm the NMR data showing a mixture of conformers in solution that differ from the X‐ray structure in rotation of the phenyl and t‐butyl ligand substituents. An extensive variety of coupling partners, including pharmaceutically relevant APIs, readily participate under mild and environmentally responsible reaction conditions.

Mechanism of two styryl BODIPYs as fluorescent probes and protective agents in lipid bilayers against aqueous ClO.

Two styryl BODIPY derivatives, BOH and BOE, with different hydrophilic properties, were investigated for their reaction mechanisms in lipid bilayers against aqueous ClO-, by both experimental and theoretical methods. Density functional theory (DFT) calculations confirmed their identical conformations in solution. Fluorescence spectra and high-resolution mass spectra corroborated the central vinyl group as a common antioxidation moiety against ClO- oxidation. In giant unilamellar vesicles (GUVs), distinct reaction kinetics with ClO- suggested that BOE provided superior protective effects compared to BOH on lipids. Molecular dynamics simulations indicated that the lipophilic octyloxy group in BOE led to its deeper localization within the lipid phase, bringing it closer to the corresponding lipid target group. This study establishes the two styryl BODIPYs as promising fluorescent probes for detecting aqueous ClO- in lipid-water polyphasic systems.

Structural basis for CCR6 modulation by allosteric antagonists

The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.

Effect of cationic surfactants on titration behavior of isotactic and atactic poly(methacrylic acid)

By forming strong complexes with oppositely charged polyelectrolytes, cationic surfactants significantly affect their solution properties. We investigated the effect of bound surfactant on the titration behavior of two isomer forms of poly(methacrylic acid), PMA, atactic and isotactic PMA, aPMA and iPMA, respectively, which are known for the cooperative change in chain conformation in water. The bound surfactant micelles increase the initial degree of ionization, α, of carboxyl groups on PMA, shift the conformational transition to higher α and make it narrower, and exclude the complexed chains from the solution. The titration curves were analyzed in the framework of the Henderson-Hasselbalch theory and the Gibbs free energy change of the conformational transition was calculated. The results were discussed in the context of a complex influence of surfactant on the PMA chain conformation in solution. It is proposed that the PMA-surfactant interaction changes from a so-called hydrophobic mode, which is responsible for the solubilization of the unionized and water-insoluble iPMA at low α, to a predominantly electrostatic one at high α, which leads to the precipitation of both aPMA and iPMA from solution. Constant pH simulations using simple coarse-grained models for the PMA polymers and individual surfactants were performed to rationalize the titration behavior of PMAs in the absence and presence of surfactant. By inducing an attractive interaction between PMA monomers, an excellent agreement between the experimental and numerical titration curves was obtained. Such agreement becomes poorer upon the addition of surfactant; however, the main features of the PMA titration curves are preserved, which supports the role of hydrophobic interactions in PMA-surfactant association at low pH values and that of electrostatics at higher pH.

Mapping of the Lipid-Binding Regions of the Antifungal Protein NFAP2 by Exploiting Model Membranes.

Fungal infections with high mortality rates represent an increasing health risk. The Neosartorya (Aspergillus) fischeri antifungal protein 2 (NFAP2) is a small, cysteine-rich, cationic protein exhibiting potent anti-Candida activity. As the underlying mechanism, pore formation has been demonstrated; however, molecular level details on its membrane disruption action are lacking. Herein, we addressed the lipid binding of NFAP2 using a combined computational and experimental approach to simple lipid compositions with various surface charge properties. Simulation results revealed binding preferences for negatively charged model membranes, where selectivity is mediated by anionic lipid components enriched at the protein binding site but also assisted by zwitterionic lipid species. Several potential binding routes initiated by various anchoring contacts were observed, which resulted in one main binding mode and a few variants, with NFAP2 residing on the membrane surface. Region 10NCPNNCKHKKG20 of the flexible N-terminal part of the protein showed potency to insert into the lipid bilayer, where the disulfide bond-stabilized short motif 11CPNNC15 could play a key role. In addition, several areas, including the beginning of the N-terminal (residues 1-8), played roles in facilitating initial membrane contacts. Besides, individual roles of residues such as Lys24, Lys32, Lys34, and Trp42 were also revealed by the simulations. Combined data demonstrated that the solution conformation was not perturbed markedly upon membrane interaction, and the folded part of the protein also contributed to stabilizing the bound state. Data also highlighted that the binding of NFAP2 to lipid vesicles is sensitively affected by environmental factors such as ionic strength. Electrostatic interactions driven by anionic lipids were found pivotal, explaining the reduced membrane activity observed under high salt conditions. Experimental data supported the lipid-selective binding mechanisms and pointed to salt-dependent effects, particularly to protein-assisted vesicle aggregation at low ionic strength. Our findings can contribute to the development of NFAP2-based anti-Candida agents and studies aiming at future medical use of peptide-based natural antifungal compounds.

The Influence of Disulfide, Thioacetal and Lanthionine-Bridges on the Conformation of a Macrocyclic Peptide.

Cyclisation of peptides by forming thioether (lanthionine), disulfide (cystine) or methylene thioacetal bridges between side chains is established as an important tool to stabilise a given structure, enhance metabolic stability and optimise both potency and selectivity. However, a systematic comparative study of the effects of differing bridging modalities on peptide conformation has not previously been carried out. In this paper, we have used the NMR deconvolution algorithm, NAMFIS, to determine the conformational ensembles, in aqueous solution, of three cyclic analogues of angiotensin(1-7), incorporating either disulfide, or non-reducible thioether or methylene thioacetal bridges. We demonstrate that the major solution conformations are conserved between the different bridged peptides, but the distribution of conformations differs appreciably. This suggests that subtle differences in ring size and bridging structure can be exploited to fine-tune the conformational properties of cyclic peptides, which may modulate their bioactivities.