Conformational Dynamics of apo‐GlnBP Revealed by Experimental and Computational Analysis

The glutamine binding protein (GlnBP) binds l ‐glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo‐ and holo‐GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single‐molecule FRET techniques to decipher the conformational dynamics of apo‐GlnBP. The NMR residual dipolar couplings of apo‐GlnBP were in good agreement with a MD‐derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four‐state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP.     

(Thermo)dynamic Role of Receptor Flexibility,Entropy, and Motional Correlation in Protein–Ligand Binding

The binding of 2‐amino‐5‐methylthiazole to the W191G cavity mutant of cytochrome c peroxidase is an ideal test case to investigate the entropic contribution to the binding free energy due to changes in receptor flexibility. The dynamic and thermodynamic role of receptor flexibility are studied by 50 ns‐long explicit‐solvent molecular dynamics simulations of three separate receptor ensembles: W191G binding a K⁺ ion, W191G–2a5mt complex with a closed 190–195 gating loop, and apo with an open loop. We employ a method recently proposed to estimate accurate absolute single‐molecule configurational entropies and their differences for systems undergoing conformational transitions. We find that receptor flexibility plays a generally underestimated role in protein–ligand binding (thermo)dynamics and that changes of receptor motional correlation determine such large entropy contributions.     

High Relaxivity Supramolecular Adducts Between Human‐Liver Fatty‐Acid‐Binding Protein and Amphiphilic GdIII Complexes: Structural Basis for the Design of Intracellular Targeting MRI Probes

Gadolinium complexes linked to an apolar fragment are known to be efficiently internalized into various cell types, including hepatocytes. Two lipid‐functionalized gadolinium chelates have been investigated for the targeting of the human liver fatty acid binding protein (hL‐FABP) as a means of increasing the sensitivity and specificity of intracellular‐directed MRI probes. hL‐FABP, the most abundant cytosolic lipid binding protein in hepatocytes, displays the ability to interact with multiple ligands involved in lipid signaling and is believed to be an obligate carrier to escort lipidic drugs across the cell. The interaction modes of a fatty acid and a bile acid based gadolinium complex with hL‐FABP have been characterized by relaxometric and NMR experiments in solution with close‐to‐physiological protein concentrations. We have introduced the analysis of paramagnetic‐induced protein NMR signal intensity changes as a quantitative tool for the determination of binding stoichiometry and of precise metal‐ion‐center positioning in protein–ligand supramolecular adducts. A few additional NMR‐derived restraints were then sufficient to locate the ligand molecules in the protein binding sites by using a rapid data‐driven docking method. Relaxometric and ¹³C NMR competition experiments with oleate and the gadolinium complexes revealed the formation of heterotypic adducts, which indicates that the amphiphilic compounds may co‐exist in the protein cavity with physiological ligands. The differences in adduct formation between fatty acid and bile acid based complexes provide the basis for an improved molecular design of intracellular targeted probes.     

Monitoring Conformational Changes in the NDM‐1 Metallo‐β‐lactamase by 19F NMR Spectroscopy

The New Delhi metallo‐β‐lactamase (NDM‐1) is involved in the emerging antibiotic resistance problem. Development of metallo‐β‐lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site‐selective labeling of NDM‐1 with 1,1,1‐trifluoro‐3‐bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using ¹⁹F NMR spectroscopy. The results demonstrate different modes of binding of known NDM‐1 inhibitors, including L ‐ and D ‐captopril by monitoring the changing chemical environment of the active‐site loop of NDM‐1. The method described will be applicable to other MBLs and more generally to monitoring ligand‐induced conformational changes.     

A Disulfide Bridge Allows for Site‐Selective Binding in Liver Bile Acid Binding Protein Thereby Stabilising the Orientation of Key Amino Acid Side Chains

The presence of a disulfide bridge in liver bile acid binding protein (L‐BABP/S‐S) allows for site‐selective binding of two bile acids, glycochenodeoxycholic (GCDA) and glycocholic acid (GCA), differing only in the presence of a hydroxyl group. The protein form devoid of the disulfide bridge (L‐BABP) binds both bile salts without discriminating ability. We investigate the determinants of the molecular recognition process in the formation of the heterotypic L‐BABP/S‐S complex with GCA and GCDA located in the superficial and inner protein sites, respectively. The comparison of the NMR spectroscopy structure of heterotypic holo L‐BABP/S‐S, the first reported for this protein family, with that of the homotypic L‐BABP complex demonstrates that the introduction of a S–S link between adjacent strands changes the conformation of three key residues, which function as hot‐spot mediators of molecular discrimination. The favoured χ₁ rotameric states (t, g⁺ and g^? for E99, Q100 and E109 residues, respectively) allow the onset of an extended intramolecular hydrogen‐bond network and the consequent stabilisation of the side‐chain orientation of a buried histidine, which is capable of anchoring a specific ligand.     

Segmental,Domain‐Selective Perdeuteration and Small‐Angle Neutron Scattering for Structural Analysis of Multi‐Domain Proteins

Multi‐domain proteins play critical roles in fine‐tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic rearrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi‐domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA‐1 using Sortase A mediated protein ligation. We show that domain‐selective perdeuteration combined with contrast‐matched small‐angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi‐domain proteins and changes induced by ligand binding.     

Segmental,Domain‐Selective Perdeuteration and Small‐Angle Neutron Scattering for Structural Analysis of Multi‐Domain Proteins

Multi‐domain proteins play critical roles in fine‐tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic rearrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi‐domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA‐1 using Sortase A mediated protein ligation. We show that domain‐selective perdeuteration combined with contrast‐matched small‐angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi‐domain proteins and changes induced by ligand binding.     

Blind docking method combining search of low‐resolution binding sites with ligand pose refinement by molecular dynamics‐based global optimization

This study describes the development of a new blind hierarchical docking method, bhDock, its implementation, and accuracy assessment. The bhDock method uses two‐step algorithm. First, a comprehensive set of low‐resolution binding sites is determined by analyzing entire protein surface and ranked by a simple score function. Second, ligand position is determined via a molecular dynamics‐based method of global optimization starting from a small set of high ranked low‐resolution binding sites. The refinement of the ligand binding pose starts from uniformly distributed multiple initial ligand orientations and uses simulated annealing molecular dynamics coupled with guided force‐field deformation of protein–ligand interactions to find the global minimum. Assessment of the bhDock method on the set of 37 protein–ligand complexes has shown the success rate of predictions of 78%, which is better than the rate reported for the most cited docking methods, such as AutoDock, DOCK, GOLD, and FlexX, on the same set of complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Fluorescence Sensing and Selective Binding of a Novel 4,4′‐Sulfonyldianiline‐Bridged Bis(β‐cyclodextrin) for Bile Salts

A novel 4,4′‐sulfonyldianiline‐bridged bis(β‐cyclodextrin (CD)) 2 was synthesized, and its complex stability constants (K_s) for the 1 : 1 inclusion complexation with bile salts, i.e., cholate (CA), deoxycholate (DCA), glycocholate (GCA), and taurocholate (TCA) have been determined in phosphate buffer (pH 7.2) at 25° by fluorescence spectroscopy. The result indicated that 2 can act as efficient fluorescent sensor and display remarkable fluorescence enhancement upon addition of optically inert bile salts. Structures of the inclusion complexes between bile salts and 2 were elucidated by 2D‐NMR experiments, indicating that the anionic tail group and the D ring of bile salts penetrate into one CD cavity of 2 from the wide opening deeply, while the phenyl moiety of the CD linker is partially self‐included in the other CD cavity to form a host–linker–guest binding mode. As compared with native β‐CD 1 upon complexation with bile salts, bis(β‐CD) 2 enhances the binding ability and molecular selectivity. Typically, 2 gives the highest K_s value of 26200 M ^?1 for the complexation with CA, which may be ascribed to the simultaneous contributions of hydrophobic, H‐bond, and electrostatic interactions. These phenomena are discussed from the viewpoints of multiple recognition and induce‐fit interactions between host and guest.     

HMGB1–Carbenoxolone Interactions: Dynamics Insights from Combined Nuclear Magnetic Resonance and Molecular Dynamics

The interplay of protein dynamics and molecular recognition is of fundamental importance in biological processes. Atomic‐resolution insights into these phenomena may provide new opportunities for drug discovery. Herein, we have combined NMR relaxation experiments and residual dipolar coupling (RDC) measurements with molecular dynamics (MD) simulations to study the effects of the anti‐inflammatory drug carbenoxolone (CBNX) on the conformational properties and on the internal dynamics of a subdomain (box A) of high‐mobility group B protein (HMGB1). ¹⁵N relaxation data show that CBNX binding enhances the fast pico‐ to nanosecond motions of a loop and partially removes the internal motional anisotropy of the first two helices of box A. Dipolar wave analysis of amide RDC data shows that ligand binding induces helical distortions. In parallel, increased mobility of the loop upon ligand binding is highlighted by the essential dynamics analysis (EDA) of MD simulations. Moreover, simulations detect two possible orientations for CBNX, which induces two possible conformations of helix H3, one being similar to the free form and the second one causing a partial helical distortion. Finally, we introduce a new approach for the analysis of the internal coordination of protein residues that is consistent with experimental data and allows us to pinpoint which substructures of box A are dynamically affected by CBNX. The observations reported here may be useful for understanding the role of protein dynamics in binding at atomic resolution.     

An Asymmetric Anion‐Pillared Metal–Organic Framework as a Multisite Adsorbent Enables Simultaneous Removal of Propyne and Propadiene from Propylene

The one‐step removal of multi‐component gases based on a single material will significantly improve the efficiency of separation processes but it is challenging, owing to the difficulty to precisely fabricate porous materials with multiple binding sites tailored for different guest molecules. Now a niobium oxide–fluoride anion‐pillared interpenetrated material ZU‐62 (NbOFFIVE‐2‐Cu‐i, NbOFFIVE=NbOF₅^2?) is presented. It features asymmetric O/F node coordination for the simultaneous removal of trace propyne and propadiene from propylene. The narrow distribution nanospace (aperture of Site I 6.75 Å, Site II 6.94 Å, Site III 7.20 Å) derived from the special coordination geometry within ZU‐62 customized the corresponding energy‐favorable binding sites for the propyne and propadiene that enable propadiene uptake (1.74 mmol g^?1) as well as excellent propyne uptake (1.87 mmol g^?1) under ultra‐low pressure (5000 ppm). The multisite capture mechanism was revealed by modeling studies.     

Two‐Dimensional Crowding Uncovers a Hidden Conformation of α‐Synuclein

The intrinsically disordered protein (IDP), α‐synuclein (αS), is well‐known for phospholipid membrane binding‐coupled folding into tunable helical conformers. Here, using single‐molecule experiments in conjunction with ensemble assays and a theoretical model, we present a unique case demonstrating that the interaction–folding landscape of αS can be tuned by two‐dimensional (2D) crowding through simultaneous binding of a second protein on the bilayer surface. Unexpectedly, the experimental data show a clear deviation from a simple competitive inhibition model, but are consistent with a bimodal inhibition mechanism wherein membrane binding of a second protein (a membrane interacting chaperone, Hsp27, in this case) differentially inhibits two distinct modules of αS–membrane interaction. As a consequence, αS molecules are forced to access a hidden conformational state on the phospholipid bilayer in which only the higher‐affinity module remains membrane‐bound. Our results demonstrate that macromolecular crowding in two dimensions can play a significant role in shaping the conformational landscape of membrane‐binding IDPs with multiple binding modes.     

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT‐ID, was used to identify relevant ligand‐modulated structural variations in the β₂‐adrenergic (β₂AR) G‐protein coupled receptor. Micro‐second MD simulations of the β₂AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI‐167107 (agonist), epinephrine (agonist), salbutamol (long‐acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of β₂AR differently and DIRECT‐ID analysis of the inverse‐agonist vs. agonist‐modulated β₂AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand‐specific microswitches across the GPCR. This study demonstrates the utility of DIRECT‐ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems. © 2015 Wiley Periodicals, Inc.     

Mechanostability of the Single‐Electron‐Transfer Complexes of Anabaena Ferredoxin–NADP+ Reductase

The complexes formed between the flavoenzyme ferredoxin–NADP⁺ reductase (FNR; NADP⁺=nicotinamide adenine dinucleotide phosphate) and its redox protein partners, ferredoxin (Fd) and flavodoxin (Fld), have been analysed by using dynamic force spectroscopy through AFM. A strategy is developed to immobilise proteins on a substrate and AFM tip to optimise the recognition ability. The differences in the recognition efficiency regarding a random attachment procedure, together with nanomechanical results, show two binding models for these systems. The interaction of the reductase with the natural electron donor, Fd, is threefold stronger and its lifetime is longer and more specific than that with the substitute under iron‐deficient conditions, Fld. The higher bond probability and two possible dissociation pathways in Fld binding to FNR are probably due to the nature of this complex, which is closer to a dynamic ensemble model. This is in contrast with the one‐step dissociation kinetics that has been observed and a specific interaction described for the FNR:Fd complex.     

Janus‐Like Squaramide‐Based Hosts: Dual Mode of Binding and Conformational Transitions Driven by Ion‐Pair Recognition

New tripodal squaramide‐based hosts have been synthesised and structurally characterised by spectroscopic methods. In 2.5 % (v/v) [D₆]DMSO in CDCl₃, compound 4 formed dimeric assemblies [log K_dim=3.68(8)] as demonstrated by ¹H NMR spectroscopy and UV dilution experiments. AFM and SEM analyses revealed the formation of a network of bundled fibres, which indicates a preferential mechanism for aggregation. These C₃‐symmetric tripodal hosts exhibited two different and mutually exclusive modes of binding, each one easily accessible by simultaneous reorientation of the squaramide groups. In the first, a convergent disposition of the NH squaramide protons allowed the formation of an array of N? H???X^? hydrogen bonds with anions. In the second mode, reorientation of carbonyl squaramide groups allowed multiple C?O???H interactions with ammonium cations. The titration of 4 with different tetraalkylammonium iodides persistently showed the formation of 1:1 complexes, as well as 1:2 and 1:3 complexes. The corresponding stoichiometries and binding affinities of the complexes were evaluated by multi‐regression analysis. The formation of high‐order complexes, supported by ROESY, NOESY and mass spectrometry experiments, has been attributed to the insertion of NR₄I ion pairs between the carbonyl and NH protons of the squaramide groups located in adjacent arms of 4 . The observed effects reflect the induction of significant conformational changes in the hosts, mainly in relation to the relative orientation of the squaramide groups adapting their geometries to incoming ion‐pair complementary substrates. The results presented herein identify and fully describe two different modes of ion‐pair recognition aimed at directing conformational transitions in the host, therefore establishing a base for controlling more elaborate movements of molecular devices through ion‐pair recognition.     

Coarse‐grained molecular dynamics simulations of protein–ligand binding

Coarse‐grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. We chose two protein–ligand systems, the levansucrase–sugar (glucose or sucrose), and LinB–1,2‐dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand‐binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse‐grained (CG) ligand molecules revealed potential ligand‐binding sites on the protein surfaces other than the real ligand‐binding sites. The ligands bound most strongly to the real ligand‐binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase–sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand‐binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein–ligand binding processes. © 2014 Wiley Periodicals, Inc.     

Chloride‐Anion‐Templated Synthesis of a Strapped‐Porphyrin‐Containing Catenane Host System

The synthesis, structure and anion‐recognition properties of a new strapped‐porphyrin‐containing [2]catenane anion host system are described. The assembly of the catenane is directed by discrete chloride anion templation acting in synergy with secondary aromatic donor–acceptor and coordinative pyridine–zinc interactions. The [2]catenane incorporates a three‐dimensional, hydrogen‐bond‐donating anion‐binding pocket; solid‐state structural analysis of the catenane?chloride complex reveals that the chloride anion is encapsulated within the catenane’s interlocked binding cavity through six convergent CH????Cl and NH???Cl hydrogen‐bonding interactions and solution‐phase ¹H NMR titration experiments demonstrate that this complementary hydrogen‐bonding arrangement facilitates the selective recognition of chloride over larger halide anions in DMSO solution.     

Structure‐based ligand design by a build‐up approach and genetic algorithm search in conformational space

Program to engineer peptides (PEP) is a build‐up approach for ligand docking and design with implicit solvation. It requires the knowledge of a seed from which it iteratively grows polymeric ligands consisting of any type of amino acid, i.e., natural and/or nonnatural from a user‐defined library. At every growing step, a genetic algorithm is used for conformational optimization of the last added monomer in the rigid binding site. Pruning is performed at every growing step by selecting sequences according to binding energy with electrostatic solvation. PEP is applied to three members of the caspase family of cysteine proteases using Asp at P₁ as seed. The optimal P₄–P₂ peptide recognition motifs and variants thereof are docked correctly in the active site (backbone root‐mean‐square deviation < 0.9 Å). Moreover, for each caspase, the P₄–P₂ sequences of potent aldehyde inhibitors are ranked among the 15 hits with the most favorable PEP energy. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1956–1970, 2001