A dye-binding induced conformational transition of poly-(methacrylic acid) by Auramine O in aqueous solutions. II. Theoretical interpretation and discussion of the experimental results

The binding of Auramine O to poly-(methacrylic acid) (PMA) is explained using a two-state model for the polyelectrolyte and preferential binding of the dye to the hypercoiled conformational state of PMA predominantly present for the dye-free polyelectrolyte at low degrees of neutralization. Bound-dye interactions were neglected leading to a binding isotherm as given by Monod et al. to which the experimental dialysis results could be fitted. It is shown that this model predicts a conformational transition from the more extended conformational state of PMA to the hyper-coiled one upon progressive binding of the dye. The experimental results obtained by potentiometric and viscosimetric titrations as well as the fluorcsence intensity measurements of the AuO—PMA system arc consistent with the conclusions based on this model.     

Local water bridges and protein conformational stability.

Recent studies have pointed out the important role of local water structures in protein conformational stability. Here, we present an accurate and computationally effective way to estimate the free energy contribution of the simplest water structure motif--the water bridge. Based on the combination of empirical parameters for accessible protein surface area and the explicit consideration of all possible water bridges with the protein, we introduce an improved protein solvation model. We find that accounting for water bridge formation in our model is essential to understand the conformational behavior of polypeptides in water. The model formulation, in fact, does not depend on the polypeptide nature of the solute and is therefore applicable to other flexible biomolecules (i.e., DNAs, RNAs, polysaccharides, etc.).     

Conformational transmission in condensed lipid model compounds. Chain packing modification by head-group-induced conformational changes in the glyceryl backbone

On changing the phosphorus coordination from four to five via a trigonal bipyramidal geometry in phospholipid model systems, a conformational change is initiated around the C2-C3 linkage caused by enhanced electrostatic repulsion between the atoms O3 and O2, situated in the axis of the trigonal bipyramid. This is supported by the absence of conformational change upon substitution of O2 by methylene. With solid-state cross-polarization and magic-angle spinning 13C-NMR it is shown that such a conformational transmission leads to an increased packing density of the lipid chains. It seems to us that changes in lipid packing caused by conformational transmission may also occur when pentacoordination is present transiently, as under biological conditions, thereby inducing an activation of the transport proteins that are embedded in the membrane.     

Explicit and implicit water simulations of a beta-hairpin peptide.

The conformational properties of a beta-hairpin peptide (YITNSDGTWT) were studied by using both explicit and implicit water simulations. The conformational space of the peptide was scanned by using a restricted hydrogen-bonding search method. The search method used generated the conformational space with enough diversity and good representation of beta-hairpin structures. By using a total surface area-based treatment of hydrophobic interactions, implicit water simulations failed to discriminate between experimental beta-hairpin structures from the rest of the conformers present in the authors' conformation library. However, with inclusion of vibrational free energy and accounting separately for polar and nonpolar surface areas, the nuclear magnetic resonance structure was ranked successfully as the most stable conformation. There is a loose correlation between the conformational energies by the continuum model and the conformational energies by explicit water simulation for conformers with similar structures. However, in terms of solvation energy, both approaches have a much better correlation. By using proper treatment of surface effect (partition of the surface area into polar and nonpolar areas) and including vibrational free-energy contribution, the continuum models should be reliable. Furthermore, the authors found that, for this peptide, beta-hairpin structures have large vibrational entropy that contributes decisively to the stability of folded beta-hairpin structures. Proteins 1999;37:73-87.     

Continuum model of voltage-dependent gating. Macroscopic conductance, gating current, and single-channel behavior.

It is assumed that the conformational change of the voltage-gated channel is continuous, characterized by movement along a generalized one-dimensional reaction coordinate, x, varying from 0 to 1. This large conformational change is coupled to the movement of most of the gating charge. Superimposed on this large movement is a smaller, very fast conformational change that opens or closes the channel. The large conformational change perturbs the channel so that opening is favored near x = 1 and closing is favored near x = 0. The movement along the x axis is described by a generalized Nernst-Planck equation, whereas the open-close transition is modeled as a discrete reaction-rate process. The macroscopic conductance, gating current, and single-channel behavior of a simple, linearized version of the model is described. Although the model has only seven adjustable constants (about the same as would be required for a conventional three-state model), it can mimic the behavior of the delayed rectified K+ channel with 12 or more closed states. The single-channel behavior of the model can have bursts of rapid openings and closings, separated by long closed times. If the conformational change is assumed to correspond to the rotation and translation of charged helices, then this model can be used to estimate the effective rotational diffusion coefficient of the helix. Such calculations for the delayed rectifier K+ channel indicate that the motion must be very restricted.     

Conformation of liquid N-alkanes.

The conformations of liquid n-alkanes have been studied using neutron scattering techniques to better understand the conformational forces present in membrane lipid interiors. We have studied hydrocarbon chains having lengths comparable to those found for esterified membrane lipid fatty acids, and find that the steric constraints of packing in the liquid state do not change the conformational distributions of hydrocarbon chains from those imposed by the intrachain forces present in the gas phase. It follows that the central region of membranes containing lipids in the disordered state should contain hydrocarbon chain conformations determined primarily by intrachain forces.     

Molecular dynamics simulations of the whey protein beta-lactoglobulin.

Molecular dynamics simulations have been used to model the motions and conformational behavior of the whey protein bovine beta-lactoglobulin. Simulations were performed for the protein by itself and complexed to a single retinol ligand located in a putative interior binding pocket. In the absence of the retinol ligand, the backbone loops around the opening of this interior pocket shifted inward to partially close off this cavity, similar to the shifts observed in previously reported molecular dynamics simulations of the uncomplexed form of the homologous retinol binding protein. The protein complexed with retinol does not exhibit the same conformational shifts. Conformational changes of this type could serve as a recognition signal allowing in vivo discrimination between the free and retinol complexed forms of the beta-lactoglobulin molecule. The unusual bending of the single alpha-helix observed in the simulations of retinol binding protein were not observed in the present calculations.     

ATP-induced conformational transition of denatured proteins.

Although the conformational change occurring in proteins upon ATP binding is important in many biological reactions, the mechanism by which ATP binding induces the conformational change is unknown. We found that ATP induces acid-unfolded (pH 2) ferricytochrome c or apomyoglobin to adopt a compact structure with a significant amount of alpha-helix and increased hydrophobicity. A very similar conformational transition was observed at neutral pH for an amphiphilic model polypeptide. The effectiveness of various adenine nucleotides in inducing the conformational transition was found to be proportional to their phosphate group contents, i.e., adenosine tetraphosphate greater than ATP greater than ADP greater than AMP. These results should be important when considering the mechanism of the ATP-induced conformational change in proteins during various biological reactions.     

A channel model with fluctuating barrier structures.

Following the theory 'Fluctuations of barrier structure in ionic channels' (L?uger, P., Stephan, W. and Frehland, E. (1980) Biochim. Biophys. Acta 602, 167-180), we constructed a model of a channels with several conformational states. The origin of these conformational states and the source for the transitions from one to the other are given explicitly for the presented model. In this work the effect of multiple conformational states on the ion transport process is analyzed. We considered a channel protein with two main barriers and one binding site. The site is surrounded by dipolar groups. The dipole moment of these groups can be reoriented by thermal activity and also by electrical interaction with the transported ions. Differently polarized states generate different activation energy barriers for the ions. The set of conformational states of the channel is constituted by all the possible polarized states of the binding site. Using the rate-theory analysis of ion transport (Gl?sstone, S., Laider, K.J. and Eyring, H. (1941) The theory of rate processes, McGraw-Hill, New York), the possible coupling between ion flux and the channel conformational transitions has been incorporated into the model by considering the dependence of the rate constants on the heights of the energy barriers. The resulting multistate kinetic equations have been solved numerically. It was shown that the simple saturation characteristic of the flux-concentration curve was obtained. For certain values of the model parameters, the channel shows a strongly different conductance for anions compared to cations. In fact, the model contains an interesting mechanism that exhibits selectivity with respect to the charge of the ions.     

Comparison of protein structure in crystals and in solution by laser raman scattering. I. Lysozyme

The laser Raman-scattering technique was employed to examine the question of whether the structure of a globular protein is the same in crystals as in solution. Lysozyme was selected as a model system for this study. In the amide I and amide III regions we found a good agreement between the Raman spectra of lysozyme chloride crystals (in 100% relative humidity) and lysozyme solution (at pH 4.50), indicating that the main-chain conformation is the same between two phases. However, small but definite spectral differences were observed near 464, 622, 644, 934, 960, 978, 1032, 1129, and 1196 cm^?1. Some of these spectral differences may be interpreted in terms of side-chain conformational changes. Additionally, we present Raman spectrum of lysozyme in the lyophilized form and compare it to those of crystals and solution. It was concluded that lyophilization caused conformational changes appreciably, both in the main chain and side chain.     

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution.     

Conformational study of a nine residue fragment of the antigenic loop of foot-and-mouth disease virus.

The nine-residue peptide Ac-TASARGDLA-NHMe was selected as model peptide in order to understand the conformational features of the antigenic loop of foot-and-mouth disease virus (FMDV). A throughout exploration of the conformational space has been carried out by means of molecular dynamics (MD) and energy minimization. The calculations have been carried out using the AMBER force field. Solvent effects have been included by an effective dielectric constant of epsilon = 4r. The lowest energy conformation presents a secondary structure constituted by an alpha-helix at the N-terminal end followed by two gamma-turns in the central region. The rest of the accessible minima found present also a high tendency to form gamma-turns. Finally, a 100 ps MD trajectory calculation at 298 K suggest a stability of the secondary structure elements of the lowest energy conformation.     

Computational study of the conformational profiles of model bis-cystine cyclic peptides

Bis-cystine cyclic peptides are a new kind of molecules with potential use as cavitands, transporters or antagonists of target ligands. Studies aimed at establishing their conformational profiles may prove useful in understanding their characteristics and potentiate their use in molecular design. The present investigation reports the results of a computational study devoted to establishing the conformational preferences of model bis-cystine cyclic peptides and the properties in common with their linear analogs. For this purpose a study of four model compounds: (Ac-Cys-X-Cys-NHMe)₂ and (Ac-Cys-X-X-Cys-NHMe)₂ with X = Ala, Val, was performed. The goal of the study was to explore the importance of the conformational nature of the central residues, the effect of the number of them, and the loss of conformational freedom after cyclization on model molecules. Accordingly, the conformational space and the dynamic behaviour of the four cyclic peptides as well as the corresponding linear analogs was carefully explored. The results indicate the existence of structural patterns that might be useful for the use of this kind of molecule in de novo molecular design     

The conformation of glucagon: predictions and consequences.

It is proposed that glucagon, a polypeptide hormone, is delicately balanced between two major conformational states. Utilizing a new predictive model [Chou, P.Y., and Fasman, G.D. (1974), Biochemistry 13, 222] which considers all the conformational states in proteins (helix, beta sheet, random coil, and beta turns), the secondary structural regions of glucagon are computed herein. The conformational sensitivity of glucagon may be due to residues 19-27 which have both alpha-helical potential (mean value of Palpha = 1.19) as well as beta-sheet potential (mean value of Pbeta = 1.25). Two conformational states are predicted for glucagon. In predicted form (a), residues 5-10 form a beta-sheet region while residues 19-27 form an alpha-helical region (31% alpha, 21% beta) agreeing well with the circular dichroism (CD) spectra of glucagon. The similarity in the CD spectra of glucagon and insulin further suggests the presence of beta structure in glucagon, since X-ray analysis of insulin showed 24% beta sheet. In predicted form (b), both regions, residues 5-10 and residues 19-27, are beta sheets sheets (0% alpha, 52% beta) in agreement with the infrared spectral evidence that glucagon gels and fibrils have a predominant beta-sheet conformation. Since three reverse beta turns are predicted at residues 2-5, 10-13, and 15-18, glucagon may possess tertiary structure in agreement with viscosity and tritium-hydrogen exchange experiments. A proposal is offered concerning an induced alpha yields beta transition at residues 22-27 in glucagon during receptor site binding. Amino acid substitutions are proposed which should disrupt the beta sheets of glucagon with concomitant loss of biological activity. The experimental findings that glucagon aggregates to form dimers, trimers, and hexamers can be explained in terms of beta-sheet interactions as outlined in the present predictive model. Thus the conflicting conclusions of previous workers, concerning the conformation of glucagon in different environments, can be rationalized by the suggested conformational transition occurring within the molecule.     

The structure of active serpin 1K from Manduca sexta.

BACKGROUND: The reactive center loops (RCL) of serpins undergo large conformational changes triggered by the interaction with their target protease. Available crystallographic data suggest that the serpin RCL is polymorphic, but the relevance of the observed conformations to the competent active structure and the conformational changes that occur on binding target protease has remained obscure. New high-resolution data on an active serpin, serpin 1K from the moth hornworm Manduca sexta, provide insights into how active serpins are stabilized and how conformational changes are induced by protease binding. RESULTS: The 2.1 A structure shows that the RCL of serpin 1K, like that of active alpha1-antitrypsin, is canonical, complimentary and ready to bind to the target protease between P3 and P3 (where P refers to standard protease nomenclature),. In the hinge region (P17-P13), however, the RCL of serpin 1K, like ovalbumin and alpha1-antichymotrypsin, forms tight interactions that stabilize the five-stranded closed form of betasheet A. These interactions are not present in, and are not compatible with, the observed structure of active alpha1-antitrypsin. CONCLUSIONS: Serpin 1K may represent the best resting conformation for serpins - canonical near P1, but stabilized in the closed conformation of betasheet A. By comparison with other active serpins, especially alpha1-antitrypsin, a model is proposed in which interaction with the target protease near P1 leads to conformational changes in betasheet A of the serpin.     

Additivity and non-additivity effects in the conformational changes of 1,2-ethanediol diformatein vacuo and in solution.Ab-initio and molecular mechanics descriptions

The performances of MM2 andab-initio SCF STO-3G calculations to describe conformational changes in (CH₂OCHO)₂ in vacuo and in solution are examined. We present and justify a simple procedure to add solvent effects to the MM2 conformational energies. The analysis is focused on the detection of non-additive effects in simultaneous conformational changes. We have found that the -CH₂-CH₂-group is generally effective in decoupling simultaneous conformational changes. The non-additive effects, actually present in specific classes of conformational changes, are reduced by a solvent contribution when full SCF calculations are employed, and emphasized when MM2 + solvent calculations are employed. A rationale of this finding is presented, and some suggestions are made for the correction of this artifact, due to the use of rigid charges.     

Global conformational changes control the reactivity of methane monooxygenase.

We present here X-ray scattering data that yield new structural information on the multicomponent enzyme methane monooxygenase and its components: a hydroxylase dimer, and two copies each of a reductase and regulatory protein B. Upon formation of the enzyme complex, the hydroxylase undergoes a dramatic conformational change that is observed in the scattering data as a fundamental change in shape of the scattering particle such that one dimension is narrowed (by 25% or 24 A) while the longest dimension increases (by 20% or 25 A). These changes also are reflected in a 13% increase in radius of gyration upon complex formation. Both the reductase and protein B are required for inducing the conformational change. We have modeled the scattering data for the complex by systematically modifying the crystal structure of the hydroxylase and using ellipsoids to represent the reductase and protein B components. Our model indicates that protein B plays a role in optimizing the interaction between the active centers of the reductase and hydroxylase components, thus, facilitating electron transfer between them. In addition, the model suggests reasons why the hydroxylase exists as a dimer and that a possible role for the outlying gamma-subunit may be to stabilize the complex through its interaction with the other components. We further show that proteolysis of protein B to form the inactive B' results in a conformational change and B' does not bind to the hydroxylase. The truncation thus could represent a regulatory mechanism for controlling the enzyme activity.     

Lipid conformational nomenclature: a general method.

We propose a conformational nomenclature for amphiphilic lipid molecules that is general and compatible with the stereospecific numbering scheme, in contrast to earlier methods in which discrepancies with the sn-scheme lead to contradictory assignments of the absolute configuration of the system. The present method can be rationally extended to different classes of lipids, both natural and synthetic. It is simple and provides a convenient framework for conformational studies on widely varying classes of lipids.