Conformational Requirements of Acetylcholine Analogues and Local Anaesthetics

ATTEMPTS have been made to view the roles of acetylcholine and of cholinergic agonists as triggering permeability changes in excitable membranes through attachment to acetylcholine receptor biopolymers^1,2. Similarly, it has been proposed that local anaesthetics might block nerve conduction through attachment to axonal acetylcholine receptors^3,4. These considerations raise a number of questions. Are certain specific conformations essential for molecules related to acetylcholine either to “trigger” or to “block” depolarization of excitable membranes ? Are the conformations of such molecules identical in the crystal and in solution ? What are the rotational barriers to conformational alteration of such molecules ?     

On the link between conformational changes,ligand binding and heat capacity

BackgroundConformational changes coupled to ligand binding constitute the structural and energetics basis underlying cooperativity, allostery and, in general, protein regulation. These conformational rearrangements are associated with heat capacity changes. ITC is a unique technique for studying binding interactions because of the simultaneous determination of the binding affinity and enthalpy, and for providing the best estimates of binding heat capacity changes.Scope of reviewStill controversial issues in ligand binding are the discrimination between the “conformational selection model” and the “induced fit model”, and whether or not conformational changes lead to temperature dependent apparent binding heat capacities. The assessment of conformational changes associated with ligand binding by ITC is discussed. In addition, the “conformational selection” and “induced fit” models are reconciled, and discussed within the context of intrinsically (partially) unstructured proteins.Major conclusionsConformational equilibrium is a major contribution to binding heat capacity changes. A simple model may explain both conformational selection and induced fit scenarios. A temperature-independent binding heat capacity does not necessarily indicate absence of conformational changes upon ligand binding. ITC provides information on the energetics of conformational changes associated with ligand binding (and other possible additional coupled equilibria).General significancePreferential ligand binding to certain protein states leads to an equilibrium shift that is reflected in the coupling between ligand binding and additional equilibria. This represents the structural/energetic basis of the widespread dependence of ligand binding parameters on temperature, as well as pH, ionic strength and the concentration of other chemical species. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

The solvent polarity dependent conformational equilibrium of the carboxylic ionophore narasin: A proton NMR study

Two dimensional homonuclear (¹H-¹H) chemical shift correlation, double resonance and nuclear Overhauser effect difference spectroscopy were used to determine spectral parameters of narasin acid in different solvents approximating the range of polarities encountered within a biological membrane. The observed chemical shift and coupling constant changes were consistent with a polarity mediated shift between two conformational states, with the major conformational adjustments occurring in two specific backbone regions of the molecule previously described as “hinges” (1,2). Evidence suggests that the conformational equilibrium is not only mediated by solvent polarity but may in part be determined by the intrinsic propensity of narasin to form inclusion complexes with H⁺.     

Biological effects of oscillating electric fields: Role of voltage-sensitive ion channels

An alternating component of potential across the membrane of an excitable cell may change the membrane conductance by interacting with the voltagesensing charged groups of the protein macromolecules that form voltage-sensitive ion channels. Because the probability that a voltage sensor is in a given state is a highly nonlinear function of the applied electric field, the average occupancy of a particular state will change in an oscillating electric field of sufficient magnitude. This “rectification” at the level of the voltage sensors could result in conformational changes (gating) that would modify channel conductance. A simplified two-state model is examined where the relaxation time of the voltage sensor is assumed to be considerably faster than the fastest changes of ionic conductance. Significant changes in the occupancy of voltage sensor states in response to an applied oscillating electric field are predicted by the model.     

Internal perfusion of crayfish, giant axons: action of tannic acid, DDT, and TEA

Crayfish giant axons remain viable following internal perfusion with a mixture of fluoride and citrate salts. The relative favorability of various internal anions, and the dependence of resting and action potentials on internal cations are both similar to results on internally perfused squid axons. TEA widens the falling phase of the spike only from inside the axon, while DDT is active from either side of the membrane. Records of impedance changes show that effects of TEA and DDT on components of ionic conductances are similar to those found in other axons by voltage clamp measurements. Tannic acid perfused internally at a concentration of the order of 10 μM produces spontaneous activity, and a progressive increase in spike width. After 30 minutes, action potentials are “cardiac” type and are up to several minutes in duration. Records of impedance changes, and data from rapid changes in external ionic concentrations, suggest that the plateau phase of the spike is due to a maintained increase in sodium conductance. Since tannic acid is capable of crosslinking proteins and “rigidifying” protein monolayers, it is suggested that its effects on the axon may be the result of an interference with a conformational change in a membrane protein or protein-phospholipid complex during excitation.     

Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca2+‐ATPase

Sarco(endo)plasmic reticulum Ca²⁺‐ATPase transports two Ca²⁺ per ATP‐hydrolyzed across biological membranes against a large concentration gradient by undergoing large conformational changes. Structural studies with X‐ray crystallography revealed functional roles of coupled motions between the cytoplasmic domains and the transmembrane helices in individual reaction steps. Here, we employed “Motion Tree (MT),” a tree diagram that describes a conformational change between two structures, and applied it to representative Ca²⁺‐ATPase structures. MT provides information of coupled rigid‐body motions of the ATPase in individual reaction steps. Fourteen rigid structural units, “common rigid domains (CRDs)” are identified from seven MTs throughout the whole enzymatic reaction cycle. CRDs likely act as not only the structural units, but also the functional units. Some of the functional importance has been newly revealed by the analysis. Stability of each CRD is examined on the morphing trajectories that cover seven conformational transitions. We confirmed that the large conformational changes are realized by the motions only in the flexible regions that connect CRDs. The Ca²⁺‐ATPase efficiently utilizes its intrinsic flexibility and rigidity to response different switches like ligand binding/dissociation or ATP hydrolysis. The analysis detects functional motions without extensive biological knowledge of experts, suggesting its general applicability to domain movements in other membrane proteins to deepen the understanding of protein structure and function. Proteins 2015; 83:746–756. © 2015 Wiley Periodicals, Inc.     

Direct binding studies of 125I-α-bungarotoxin and 3H-quinuclidinyl benzilate interaction with axon plasma membrane fragments. Evidence for nicotinic and muscarinic binding sites

The attachment of ¹²⁵I-α-bungarotoxin (BgTx) which is reportedly bound exclusively to “nicotinic” acetylcholine receptors, as well as ³H-atropine and ³H-3-quinuclidinyl benzilate (QNB), which reportedly bind exclusively to “muscarinic” receptors, was measured in isolated lobster axon plasma membrane fragments and in the soluble axonal protein fraction. ¹²⁵I-α-BgTx binding was also measured in lysolecithin-solubilized fragments. Binding assays were adapted for these studies and are described in detail. High affinity, saturable binding of all three ligands to membrane fragments was observed, as well as binding of BgTx to a macromolecule present in both the soluble fraction and the membrane fragments. These experiments provide the first evidence for the very tight binding of both “nicotinic” and “muscarinic” ligands in peripheral nerve.     

Immunocytochemical identification of synaptotagmin 1, syntaxin 1, Ca2+ channel of the N-type, and nicotinic cholinoreceptor in motor neuromuscular junctions of somatic muscle of the earthworm Lumbricus terrestris

The earthworm somatic muscle contains myoneural synapses forming clusters of “synaptic buttons” in which the proteins syntaxin 1, synaptotagmin 1, and alpha 1B subunit of the Ca²⁺ channel of the N-type were identified. It is supposed that “synaptic buttons” contain a limited number of active zones, which is due to their small size (1–2 μm) and the pattern of distribution of proteins of the exoendocytotic cycle. The postsynaptic membrane of cholinergic synapses contains nicotinic acetylcholine receptors able to bind alpha-bungarotoxin. The area of the position of receptors on postsynaptic membrane is strongly restricted to the synaptic contact region.     

A fully nonequilibrium concerted model for enzymes

The concerted model of Monod, Wyman, and Changeux is generalized so that all effects of interactions for an enzyme operating at a nonequilibrium stationary state are considered. In contrast to the original model, which is based on an analogy to equilibrium ligand binding, the generalization may show both “positive” and “negative cooperativity” in both catalytic binding and conformational processes. Furthermore, in contrast to any equilibrium binding model, the Hill coefficients may be greater than the number of sites n. For catalysis, the maximum value is 2n, and for conformational changes, n + 1. These points are illustrated by two cases that yield simpler analytic expressions. The first obtains when catalysis occurs on a much faster time scale than the conformational changes, and the second, when this situation is reversed.     

Inactivation of yeast enolase with tetranitromethane

Yeast enolase is inactivated by tetranitromethane with production of 1.2 moles of nitrotyrosine per subunit. Protection is afforded by “conformational” metal ion alone. Enzyme thus inactivated no longer appears to bind “conformational” metal ion. There is evidence against direct coordination of the tyrosine to “conformational” metal ion, suggesting modification of the tyrosyl may obstruct the binding site.     

Intrinsically Disordered Proteins and Their Environment: Effects of Strong Denaturants, Temperature, pH, Counter Ions, Membranes, Binding Partners, Osmolytes, and Macromolecular Crowding

Intrinsically disordered proteins (IDPs) differ from “normal” ordered proteins at several levels, structural, functional and conformational. Amino acid biases characteristic for IDPs determine their structural variability and lack of rigid well-folded structure. This structural plasticity is necessary for the unique functional repertoire of IDPs, which is complementary to the catalytic activities of ordered proteins. Amino acid biases also drive atypical responses of IDPs to changes in their environment. The conformational behavior of IDPs is characterized by the low cooperativity (or the complete lack thereof) of the denaturant-induced unfolding, lack of the measurable excess heat absorption peak(s) characteristic for the melting of ordered proteins, “turned out” response to heat and changes in pH, the ability to gain structure in the presence of various counter ions, osmolytes, membranes and binding partners, and by the unique response to macromolecular crowding. This review describes some of the most characteristic features of the IDP conformational behavior and the unique response of IDPs to changes in their environment.     

Structural basis for binding and transfer of heme in bacterial heme‐acquisition systems

Periplasmic heme‐binding proteins (PBPs) in Gram‐negative bacteria are components of the heme acquisition system. These proteins shuttle heme across the periplasmic space from outer membrane receptors to ATP‐binding cassette (ABC) heme importers located in the inner‐membrane. In the present study, we characterized the structures of PBPs found in the pathogen Burkholderia cenocepacia (BhuT) and in the thermophile Roseiflexus sp. RS‐1 (RhuT) in the heme‐free and heme‐bound forms. The conserved motif, in which a well‐conserved Tyr interacts with the nearby Arg coordinates on heme iron, was observed in both PBPs. The heme was recognized by its surroundings in a variety of manners including hydrophobic interactions and hydrogen bonds, which was confirmed by isothermal titration calorimetry. Furthermore, this study of 3 forms of BhuT allowed the first structural comparison and showed that the heme‐binding cleft of BhuT adopts an “open” state in the heme‐free and 2‐heme‐bound forms, and a “closed” state in the one‐heme‐bound form with unique conformational changes. Such a conformational change might adjust the interaction of the heme(s) with the residues in PBP and facilitate the transfer of the heme into the translocation channel of the importer.     

Intensity and motion responses of giant vertical neurons of the fly eye

There are nine “giant vertical” neurons in the lobula plate of the fly optic lobe. Intracellular recordings were obtained from the three most peripheral of these cells. These cells respond to a light flash with graded changes in the membrane potential. The response consists of an “on” transient, a sustained depolarization, an increase in membrane potential fluctuations, and an “off” transient. Signal averaging showed that only the “on” and “off” transients are correlated to the stimulus. A pattern of horizontally oriented stripes moving in the vertical direction evokes a response larger than the response to a stationary pattern. The response is most sensitive to vertical movement; motion in the downward direction evokes a net membrane potential depolarization, and upward motion results in a net hyperpolarization. We conclude that the giant vertical cells function primarily as vertical motion detectors and that the direction of the motion is encoded in the polarity of the shift in the membrane potential.     

Acetylcholine receptor. Binding properties and ion permeability response after covalent attachment of the local anaesthetic quinacrine.

Membrane vesicles rich in nicotinic acetylcholine receptor prepared from Torpedo californica electric tissue have been irreversibly modified with quinacrine mustard, an alkylating derivative of the local anaesthetic quinacrine. The reaction blocked the ion channel regulated by the acetylcholine receptor. Acetylcholine still bound to the modified membrane vesicles with KD approx. 10(-8). The number of binding sites was reduced by up to 50%. Stopped-flow experiments showed that in contrast to what had been found with the reversibly binding quinacrine no fluorescence changes caused by energy transfer from the irradiated protein to the fluorescent local anaesthetic occurred after addition of agonist. This indicates that the conformational changes associated with the activation of the ion channel are blocked by the covalent reaction with quinacrine mustard. Analysis of the membrane vesicles by SDS-polyacrylamide gel electrophoresis showed that all polypeptide chains assumed to be part of the receptor complex had reacted with the mustard. Even small components, probably lipids, migrating with the dye front, showed fluorescence.     

Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a challenge, especially when the extent and direction of the conformational changes taking place upon binding is unknown. Estimating whether the binding of a biomolecule to its partner(s) occurs in a conformational state accessible to its unbound form (“conformational selection”) and/or the binding process induces conformational changes (“induced-fit”) is another challenge. We propose here a method combining conformational sampling using ClustENM—an elastic network-based modeling procedure—with docking using HADDOCK, in a framework that incorporates conformational selection and induced-fit effects upon binding. The extent of the applied deformation is estimated from its energetical costs, inspired from mechanical tensile testing on materials. We applied our pre- and post-docking sampling of conformational changes to the flexible multidomain protein-protein docking benchmark and a subset of the protein-DNA docking benchmark. Our ClustENM-HADDOCK approach produced acceptable to medium quality models in 7/11 and 5/6 cases for the protein-protein and protein-DNA complexes, respectively. The conformational selection (sampling prior to docking) has the highest impact on the quality of the docked models for the protein-protein complexes. The induced-fit stage of the pipeline (post-sampling), however, improved the quality of the final models for the protein-DNA complexes. Compared to previously described strategies to handle conformational changes, ClustENM-HADDOCK performs better than two-body docking in protein-protein cases but worse than a flexible multidomain docking approach. However, it does show a better or similar performance compared to previous protein-DNA docking approaches, which makes it a suitable alternative.     

Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study

Peb4 from Campylobacter jejuni is an intertwined dimeric, periplasmic holdase, which also exhibits peptidyl prolyl cis/trans isomerase (PPIase) activity. Peb4 gene deletion alters the outer membrane protein profile and impairs cellular adhesion and biofilm formation for C. jejuni. Earlier crystallographic study has proposed that the PPIase domains are flexible and might form a cradle for holding the substrate and these aspects of Peb4 were explored using sub-microsecond molecular dynamics simulations in solution environment. Our simulations have revealed that PPIase domains are highly flexible and undergo a large structural change where they move apart from each other by 8 nm starting at .5 nm. Further, this large conformational change renders Peb4 as a compact protein with crossed-over conformation, forms a central cavity, which can “cradle” the target substrate. As reported for other chaperone proteins, flexibility of linker region connecting the chaperone and PPIase domains is key to forming the “crossed-over” conformation. The conformational transition of the Peb4 protein from the X-ray structure to the crossed-over conformation follows the “mother’s arms” chain model proposed for the FkpA chaperone protein. Our results offer insights into how Peb4 and similar chaperones can use the conformational heterogeneity at their disposal to perform its much-revered biological function.     

Cholesterol-dependent conformational changes of P-glycoprotein are detected by the 15D3 monoclonal antibody

The 15D3 mouse monoclonal antibody (mAb) binds an uncharacterized extracellular epitope of the ATP Binding Cassette (ABC) transporter human P-glycoprotein (Pgp). Depletion of cell plasma membrane cholesterol by using methyl-β-cyclodextrin or other chemically modified β-cyclodextrins decreased the Pgp binding affinity of 15D3 mAb. UIC2 mAb, which is known to distinguish two conformers of this ABC transporter, binds only a fraction of cell surface Pgps. UIC2 mAb non-reactive pools of Pgp can be identified with other extracellular mAbs such as 15D3. Cyclosporin A (CsA) can shift non-reactive Pgps into their UIC2-reactive conformation: a phenomenon called the “UIC2 shift”. Competition studies proposed these two mAbs share overlapping epitopes and can reveal conformational changes of Pgp that correlate (r = 0.97) with the cholesterol content of cells. An apparent increase in competition of these mAbs suggested a conformational change similar to those found in the presence of CsA. However, the reason turned out not to be the UIC2-shift because cholesterol removal from the plasma membrane (PM) reduced the amount of detectable Pgps by 15D3 mAb. This study showed that 15D3 mAb bound to a conformation sensitive epitope of Pgp that was responsive to PM cholesterol levels. These conformational changes were gradual and not as great as the changes observed between the two conformers recognized by the UIC2 mAb.     

Driving Protein Conformational Cycles in Physiology and Disease: “Frustrated” Amino Acid Interaction Networks Define Dynamic Energy Landscapes

A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or “conformational cycle,” required for function is proposed. It is suggested that the free-energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free-energy landscape. Some network connections are consistent in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states.     

Aggregation-induced conformation changes dictate islet amyloid polypeptide (IAPP) membrane affinity

Islet amyloid polypeptide (IAPP) is a 37 residue intrinsically disordered protein whose aggregation is associated with Type II diabetes. Like most amyloids, it appears that the intermediate aggregates (“oligomers”) of IAPP are more toxic than the mature fibrils, and interaction with the cell membrane is likely to be an integral component of the toxicity. Here we probe the membrane affinity and the conformation of the peptide as a function of its aggregation state. We find that the affinity of the peptide for artificial lipid bilayers is more than 15 times higher in the small oligomeric state (hydrodynamic radius ~ 1.6 nm) compared to the monomeric state (hydrodynamic radius ~ 0.7 nm). Binding with RIN-m5F cell membranes also shows qualitatively similar behavior. The monomeric state, as determined by Forster Resonance Energy Transfer, has a much larger end to end distance than the oligomeric state, suggesting conformational change between the monomers and the oligomers. Raman and Infrared spectroscopic measurements show the presence of considerable alpha helical content in the oligomers, whereas the larger aggregates have largely beta sheet character. Therefore, the conformation of the small oligomers is distinct from both the smaller monomers and the larger oligomers, and this is associated with an enhanced membrane affinity. This provides a possible structural basis for the enhanced toxicity of amyloid oligomers. Such change is also reminiscent of amyloid beta, another aggregation prone amyloidogenic peptide, though the nature of the conformational change is quite different in the two cases. We infer that conformational change underlying oligomer formation is a key factor in determining the enhanced membrane affinity of disease causing oligomers, but the toxic “oligomer fold” may not be universal.     

1H, 15N and 13C Backbone resonance assignments of a conformational mutant of the adhesion protein ∆-Bd37 from Babesia divergens

We report here the resonance assignment of EDK-?-Bd37, conformational mutant potentially displaying the “open” conformation of Bd37, a 25 kDa surface protein from the Apicomplexa parasite Babesia divergens that could undergo drastic conformational changes during erythrocyte invasion.