Salt-specific stability and denaturation of a short salt-bridge-forming alpha-helix

The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using approximately 1 mus molecular dynamics (MD) computer simulations. The peptide displays 71% alpha-helical structure without salt and destabilizes with the addition of NaCl in agreement with experiments of a somewhat longer version. It is mainly stabilized by direct and indirect (" i + 4")EK salt bridges between the Lys and Glu side chains and a concomitant backbone shielding mechanism. NaI is found to be a stronger denaturant than NaCl, while the potassium salts hardly show influence. Investigation of the molecular structures reveals that consistent with recent experiments Na (+) has a much stronger affinity to side chain carboxylates and backbone carbonyls than K (+), thereby weakening salt bridges and secondary structure hydrogen bonds. At the same time, the large I (-) has a considerable affinity to the nonpolar alanine in line with recent observations of a large propensity of I (-) to adsorb to simple hydrophobes, and thereby "assists" Na (+) in its destabilizing action. In the denatured states of the peptide, novel long-lived (10-20 ns) "loop" configurations are observed in which single Na (+) ions and water molecules are hydrogen-bonded to multiple backbone carbonyls. In an attempt to analyze the denaturation behavior within the preferential interaction formalism, we find indeed that for the strongest denaturant, NaI, the protein is least hydrated. Additionally, a possible indication for protein denaturation might be a preferential solvation of the peptide backbone by the destabilizing cosolute (sodium). The mechanisms found in this work may be of general importance to understand salt effects on protein secondary structure stability.     

Extreme stability of an unsolvated alpha-helix

High-temperature ion mobility measurements have been performed for alpha-helical Ac-A15K+H+ and globular Ac-KA15+H+ peptides. The alpha-helical and globular conformations do not melt into random coils as the temperature is raised. Instead, both conformations survive to the point where the peptide signals vanishes due to fragmentation. This occurs at 600 K for the globular Ac-KA15+H+ peptide and at 725 K for the alpha-helical Ac-A15K+H+. For the helical Ac-A15K+H+ peptide it appears that fragmentation is triggered by disruption of the helical conformation.     

Contribution of aromatic interactions to alpha-helix stability

The influence of natural and unnatural i, i + 4 aromatic side chain-side chain interactions on alpha-helix stability was determined in Ala-Lys host peptides by circular dichroism (CD). All interactions investigated provided some stability to the helix; however, phenylalanine-phenylalanine (F-F) and phenylalanine-pentafluorophenylalanine (F-f5F) interactions resulted in the greatest enhancement in helicity, doubling the helical content over i, i + 5 control peptides at internal positions. Quantification of these interactions using AGADIR multistate helix-coil algorithm revealed that the F-F and F-f5F interaction energies are equivalent at internal positions in the sequence (deltaGF-F = deltaGF-f5F = -0.27 kcal/mol), despite the differences in their expected geometries. As the strength of a face-to-face stacked phenyl-pentafluorophenyl interaction should surpass an edge-to-face or offset-stacked phenyl-phenyl interaction, we believe this result reflects the inability of the side chains in F-f5F to attain a fully stacked geometry within the context of an alpha-helix. Positioning the interactions at the C-terminus led to much stronger interactions (deltaGF-F = -0.8 kcal/mol; deltaGF-f5F = -0.55 kcal/mol) likely because of favorable chi(1) rotameric preferences for aromatic residues at C-capping regions of alpha-helices, suggesting that aromatic side chain-side chain interactions are an effective alpha-helix C-capping method.     

Effect of thioxopeptide bonds on alpha-helix structure and stability

Thioxoamide (thioamide) bonds are nearly isosteric substitutions for amides but have altered hydrogen-bonding and photophysical properties. They are thus well-suited backbone modifications for physicochemical studies on peptides and proteins. The effect of thioxoamides on protein structure and stability has not been subject to detailed experimental investigations up to date. We used alanine-based model peptides to test the influence of single thioxoamide bonds on alpha-helix structure and stability. The results from circular dichroism measurements show that thioxoamides are strongly helix-destabilizing. The effect of an oxo-to-thioxoamide backbone substitution is of similar magnitude as an alanine-to-glycine substitution resulting in a helix destabilization of about 7 kJ/mol. NMR characterization of a helical peptide with a thioxopeptide bond near the N-terminus indicates that the thioxopeptide moiety is tolerated in helical structures. The thioxoamide group is engaged in an i, i+4 hydrogen bond, arguing against the formation of a 3(10)-helical structure as suggested for the N-termini of alpha-helices in general and for thioxopeptides in particular.     

Direct detection of structurally resolved dynamics in a multiconformation receptor-ligand complex

Structure-based drug design relies on static protein structures despite significant evidence for the need to include protein dynamics as a serious consideration. In practice, dynamic motions are neglected because they are not understood well enough to model, a situation resulting from a lack of explicit experimental examples of dynamic receptor-ligand complexes. Here, we report high-resolution details of pronounced ~1 ms time scale motions of a receptor-small molecule complex using a combination of NMR and X-ray crystallography. Large conformational dynamics in Escherichia coli dihydrofolate reductase are driven by internal switching motions of the drug-like, nanomolar-affinity inhibitor. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments and NOEs revealed the crystal structure to contain critical elements of the high energy protein-ligand conformation. The availability of accurate, structurally resolved dynamics in a protein-ligand complex should serve as a valuable benchmark for modeling dynamics in other receptor-ligand complexes and prediction of binding affinities.     

Factors contributing to the stability of conjugated heterocycles containing a single heteroatom

Algebraic analysis indicates that the stability of conjugated heterocyclics containing a single heteroatom is dependent on the same topological factors which determine the stability of the parent hydrocarbon. However, there is an additional term contributing to their stability which is related to the hydrocarbon skeleton of the heterocycle system.     

Multi-analyte sensing: a chemometrics approach to understanding the merits of electrode arrays versus single electrodes

A peptide-modified electrode array with a different peptide on each electrode is compared with a single electrode modified with many peptides for the voltammetric measurement of concentrations of Cu(2+), Cd(2+) and Pb(2+) in solution. The single gold electrode was modified simultaneously with peptides Gly-Gly-His, glutathione and angiotensin I each coupled to thioctic acid, and thioctic acid itself, and the calibration of mixtures of ions was compared with previously published data from an array of four sensors each with an individual modification. Calibration at the multi-peptide single-electrode sensor was by two-way partial least squares (voltammetric current measured with variables 'sample' x 'potential') and for the electrode array by three-way NPLS1 ('sample' x 'potential' x 'electrode'). The advantage of designing experiments to yield multi-way data is demonstrated and discussed.     

On a new FeOF polymorph: Synthesis and stability

A new polymorph of FeOF (up to now only known in its rutile type structure) was prepared by using a new synthesis approach formally based on anionic exchange using the well-known layered FeOCl as precursor. The synthesis was achieved using [CH₃C(CH₂O–)₂(COO–)B] to vehicle fluorine through the formation of soluble (CH₃)₄N⁺ [CH₃C(CH₂O–)₂(COO–)BF]⁻ and using N,N-dimethylformamide (DMF) as the reacting medium. The XRD pattern of layered FeOF can be indexed with an orthorhombic cell which doubles along the b axis (which is the direction perpendicular to the layers) with respect to that of pristine FeOCl (a = 3.792(1) Å, b = 12.699(1) Å, c = 3.321(1) Å). Both thermal analysis and diffraction indicate similar stability for the layered and rutile polymorphs. Such findings are rationalized through Density Functional Theory calculations. It is found that the energy difference between the more stable rutile and layered polymorphs is practically nul. The origin of the similar stability lies in the fact that although the number of Fe–F and Fe–O bonds is different in the two structures, the strength of both the total number of Fe–O as well as Fe–F bonds are found to be almost identical. Even if the crystal and electronic structures are considerably different, the total bonding and thus, the stability of the two polymorphs, is comparable. The stability of different FeOF rutile type structures is also analyzed.     

A multifaceted approach to the interpretation of NMR order parameters: a case study of a dynamic alpha-helix

The model-free approach (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546-4559; 4559-4570) is the standard method for the analysis of NMR relaxation data from proteins. The method assigns to each interaction vector a generalized order parameter S(2), which is a measure of the spatial restriction that the vector experiences in a molecular reference frame. A variety of techniques for the interpretation of S(2) values and their underlying assumptions are tested here for a dynamic alpha-helix represented by an ensemble of peptide structures that satisfies a set of predefined constraints. A self-consistent picture is developed that characterizes the influence of major determinants, including backbone dihedral angle fluctuations and their correlations, separability of internal and overall motion, the preservation of hydrogen bonds, restricted end-to-end distance fluctuations, locally anisotropic dynamics, and local contacts between interaction vector atoms and their environment. Many of the features parallel experimental NMR and computational observations of helices in proteins. The understanding gained from this model system is expected to contribute toward the ever more detailed interpretation of experimental order parameter profiles.     

Current through single conjugated molecules: calculations versus measurements

We use density functional theory based nonequilibrium Green's function to calculate the current through the different rodlike molecules at the finite temperatures self-consistently, which was compared to the experimental measurements presented by Reichert et al. [Phys. Rev. Lett. 88, 176804 (2002)] and by Mayor et al. [Angew. Chem. Int. Ed. 42, 5834 (2003)], respectively. Our results agree with the measurements very well, especially for the bias around +/-1.0 V. The investigation of the topological effect for the symmetrical molecule reveals the fact that the para position compound provides a considerably larger conductance than the meta one.     

On the photo-dynamics of single ions in a trap

Early this century, atomic beams were the closest approach tofree atomic particles. Nowadays, individual ions are stored in traps for, in principle, unlimited times of experimentation. The recoil of absorbed or scattered light permits us to manipulate the ion kinetics: Cooling and heating the ion reveals novel types of nonlinear light forces, one of which results from an all-stimulated parametric process similar to the action of a free-electron laser. — The amplitude of the vibration of a single ion in the potential well of the trap locks to metastable levels of excitation. Few ions form crystals or rotating quasi-molecules. Random exchange of sites is demonstrated by a quasi-molecule composed of a fluorescing and a dark ion.     

Universal properties of a single polymer chain in slit: Scaling versus molecular dynamics simulations

We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyze their range of validity by means of comprehensive molecular dynamics simulations using a coarse-grained bead-spring model of a flexible polymer chain. The normal and parallel components of the average end-to-end distance, mean radius of gyration and their distributions, the density profile, the force exerted on the slit walls, and the local bond orientation characteristics are obtained in slits of width D=4/10 (in units of the bead diameter) and for chain lengths N=50/300. We demonstrate that a wide range of static chain properties in normal direction can be described quantitatively by analytic model-independent expressions in perfect agreement with computer experiment. In particular, the observed profile of confinement-induced bond orientation is shown to closely match theory predictions. The anisotropy of confinement is found to be manifested most dramatically in the dynamic behavior of the polymer chain. We examine the relation between characteristic times for translational diffusion and lateral relaxation. It is demonstrated that the scaling predictions for lateral and normal relaxation times are in good agreement with our observations. A novel feature is the observed coupling of normal and lateral modes with two vastly different relaxation times. We show that the impact of grafting on lateral relaxation is equivalent to doubling the chain length.     

On the symmetry-stability problem

Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 6, pp. 1156–1157, November–December, 1995.     

Motion associated with a single rouse segment versus the alpha relaxation. 2

The dynamics in polystyrene melt and concentrated solution as probed by depolarized photon-correlation spectroscopy has been shown to reflect the motion associated with a single Rouse segment. In the concentrated solution case (entanglement-free), the analysis using the frictional factor K (=zetab2/kTpi2m2) extracted from the viscosity data in terms of the Rouse theory and aided by the Monte Carlo simulation based on the Langevin equation of the Rouse model confirms the conclusion in a precise manner. In the melt case (entangled), the Rouse-segmental motion as observed by depolarized photon-correlation spectroscopy is compared with the alpha relaxation and the highest Rouse-Mooney normal mode extracted from analyzing the creep compliance Jt of sample A reported in the companion paper. Another well-justified way of defining the structural (alpha-) relaxation time is shown basically to be physically equivalent to the one used previously. On the basis of the analysis, an optimum choice tauS = 18tauG (tauG being the average glassy-relaxation time) is made, reflecting both the temperature dependence of tauG and the effect on the bulk mechanical property by the glassy-relaxation process. In terms of thus defined tauS, two traditional ways of defining the alpha-relaxation time are compared and evaluated. It is shown that as the temperature approaches the calorimetric Tg, two modes of temperaturedependence are followed by the dynamic quantities concerning this study: One includes the time constant of the highest Rouse-Mooney normal mode, tauv; the temperature dependence of the viscosity corrected for the changes in density and temperature, eta/rhoT; and the average correlation time obtained by depolarized photon-correlation spectroscopy, tauc. The other, being steeper, is followed by the alpha-relaxation time tauS derived from the glassy-relaxation process and the temperature dependence of the recoverable compliance Jr(t) as obtained by Plazek. The comparison of the dynamic quantities clearly differentiates the motion associated with a single Rouse segment as characterized by tauv or tauc from the alpha-relaxation as characterized by tauS; due to the lack of clear definition of these two types of motion in the past and the proximity of one to the other in the time scale-actually the two crossing over each other-as the temperature is approaching Tg, the two modes could be easily confused. Below approximately 110 degrees C, the rate of tauc changing with temperature lags behind that of tauv is explained as due to the loss of effective ergodicity taking place in the system.     

On a general system-partitioning in the many-electron correlation problem

General system partitioning in the many-electron correlation problem for atomic and molecular systems is addressed within the spinshift formalism. The conventional method of the unitary group subduction coefficient expansion is reconsidered in the latter framework and an orbital-level factorization of the coefficients is obtained. “Group-spinshifts” are introduced and exploited to propose an alternative method of generating states adapted to arbitrary subduction chains. © 1996 John Wiley & Sons, Inc.     

Metal clips induce folding of a short unstructured peptide into an alpha-helix via turn conformations in water. Kinetic versus thermodynamic products

Short peptides corresponding to two to four alpha-helical turns of proteins are not thermodynamically stable helices in water. Unstructured octapeptide Ac-His1-Ala2-Ala3-His4-His5-Glu6-Leu7-His8-NH(2) (1) reacts with two [Pd((15)NH(2)(CH(2))(2)(15)NH(2))(NO(3))(2)] in water to form a kinetically stable intermediate, [[Pden](2)[(1,4)(5,8)-peptide]](2), in which two 19-membered metallocyclic rings stabilize two peptide turns. Slow subsequent folding to a thermodynamically more stable two-turn alpha-helix drives the equilibrium to [[Pden](2)[(1,5)(4,8)-peptide]] (3), featuring two 22-membered rings. This transformation from unstructured peptide via turns to an alpha-helix suggests that metal clips might be useful probes for investigating peptide folding.