Conformations and dynamics of surfactants in micelles and liquid crystals by nuclear magnetic relaxation

The order parameters as well as the rates of overall and internal motions of aggregated surfactants can be obtained from deuteron and carbon-13 nuclear relaxation experiments. The main contribution to the relaxation is generally the quadrupolar coupling (²H) or the short range dipolar interaction with protons (¹³C). In some cases it is convenient to derive the same information from the¹³C relaxation induced by long range dipolar interactions with a paramagnetic probe exchanging rapidly among the polar heads of surfactant molecules. This paper outlines the methods of interpretation of relaxation data by means of a rotational jump model of internal motions, taking into account most of the accessible conformers. The conformational and dynamical parameters are obtained from the magnetic field dependence of the longitudinal relaxation rates (micelles) or from the simultaneous fit of these rates and of the dipolar or quadrupolar splittings (liquid crystals). Some examples of application of these methods are given from recent works on single and double detailed surfactants.     

Structure of the histone tetramer (H3-H4)2: 2. Position of λmax in the tyrosyl fluorescence spectra and tyrosyl accessibility to quenchers

It was shown that the histone tetramer (H3-H4)₂ fluorescence spectra were shifted by about 2 nm towards the long-wave region and had a larger halfwidth than the free tyrosine fluorescence spectra. Denaturation with 8 m urea resulted in a shift towards the short-wave region and a decrease in the halfwidth of the histone tetramer (H3-H4)₂ tyrosine fluorescence spectra. Fluorescence quenching of the histone tetramer (H3-H4)₂ by iodine ions was analysed by the Stern-Volmer equation. It was estimated that at 0.1 m NaCl and 0.3–0.8 m NaCl, 45% and 60% tyrosyl fluorescence, respectively, was quenched by I^? ions. The results obtained suggests that histone tetramer (H3-H4)₂ may have several structural forms distinguished by the amount of ‘exposed’ and ‘buried’ tyrosyls depending upon the conditions of the medium.     

Evidence for conformeric states of Rhodopsin

Spectrophotometric measurements of metarhodopsin II appearance are made on five different kinds of rhodopsin preparations. Although the preparations differ greatly in their rhodopsin: phospholipid ratio, the meta II kinetics in all of them are strikingly similar in certain respects. Meta II appearance kinetics in all of the preparations are best described by two and only two exponentials. The ratio of these two rates is always about 5. The fast fraction: slow fraction ratio depends upon temperature. These fractions are reversibly convertible in the dark, and are interconverted on a time-scale which is long compared to the meta II appearance rate. It is shown that the kinetics of the earlier step in the bleaching sequence, viz., lumi- meta I, is also described by double exponentials. Again the ratio of rates is ca. 5 and the fast-slow fractions correspond to those found in the meta I meta II step. It is proposed that these facts support an hypothesis for the existence of two conformeric states of rhodopsin which are in thermal equilibrium. Thermodynamic parameters associated with this proposed equilibrium are presented.     

Conformational differences in protein disulfide linkages between normal hair and hair from subjects with trichothiodystrophy: a quantitative analysis by Raman microspectroscopy

Raman spectra of normal hair shafts and hair shafts from patients exhibiting trichothiodystrophy (TTD) were obtained using line focus laser illumination. Because hair from TTD patients has a significant decrease in the content of the sulfur-containing amino acids in comparison to normal hair, the 550-500 cm(-1) disulfide stretching mode region of the Raman spectrum was examined in detail. A quantitative spectral analysis demonstrates significant increases in the two energetically less favored gauche-gauche-trans (g-g-t) and trans-gauche-trans (t-g-t) forms. These observations suggest that the increased amounts of these less stable disulfide conformers are contributing factors to or associated with the hair brittleness observed for this congenital disorder. Structure-spectra correlations for the three dominant disulfide conformers are confirmed by quantum chemical calculations using modern density functional theory (DFT).     

A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES

The molecular chaperone, GroEL, essential for correct protein folding in E. coli, is composed of 14 identical subunits organized in two interacting rings, each providing a folding chamber for non‐native substrate proteins. The oligomeric assembly shows positive cooperativity within each ring and negative cooperativity between the rings. Although it is well known that ATP and long‐range allosteric interactions drive the functional cycle of GroEL, an atomic resolution view of how ligand binding modulates conformational adaptations over long distances remains a major challenge. Moreover, little is known on the relation between equilibrium dynamics at physiological temperatures and the allosteric transitions in GroEL. Here we present multiple all‐atom molecular dynamics simulations of the GroEL‐GroES assemblies at different stages of the functional cycle. Combined with an extensive analysis of the complete set of experimentally available structures, principal component analysis and conformer plots, we provide an explicit evaluation of the accessible conformational space of unliganded GroEL. Our results suggest the presence of pre‐existing conformers at the equatorial domain level, and a shift of the conformational ensemble upon ATP‐binding. At the inter‐ring interface the simulations capture a remarkable offset motion of helix D triggered by ATP‐binding to the folding active ring. The reorientation of helix D, previously only observed upon GroES association, correlates with a change of the internal dynamics in the opposite ring. This work contributes to the understanding of the molecular mechanisms in GroEL and highlights the ability of all‐atom MD simulations to model long‐range structural changes and allosteric events in large systems. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

(R)‐Metacycloprodigiosin‐HCl: Chiroptical properties and structure

(R)‐Metacycloprodigiosin can exist in three different tautomeric forms, each with hydrogens at C9′ and C12 in syn or anti orientation. With the addition of HCl, this structural diversity reduces to syn‐(R)‐metacycloprodigiosin‐HCl ( 1a ) and anti‐(R)‐metacycloprodigiosin‐HCl ( 1b ), each with multiple conformers. Energetics and chiroptical properties, namely, electronic circular dichroism (ECD) and specific optical rotation (SOR), of (R)‐metacycloprodigiosin‐HCl have been investigated at B3LYP/6‐311++G(2d,2p) level. The experimental ECD spectra of (R)‐metacycloprodigiosin‐HCl have also been measured. Calculations indicated that the lowest energy conformer of 1b is approximately 2.7 kcal/mol lower in energy than that of 1a , and the energy barrier for anti to syn conversion is approximately 13 kcal/mol. The population weighted calculated SORs of 1a and 1b are, respectively, positive and negative. The respective calculated ECD spectra of these pseudoenantiomers show an almost mirror image relationship between them. The experimental SOR and ECD compare well with those predicted for 1b . Thus, 1b is expected to be predominant, a situation confirmed also by nuclear Overhauser effect (NOE) data, with a similar conclusion reached for prodigiosin R1.     

Synthesis and spectroscopic characterization of protected N-phosphonomethylglycine dipeptides.

A series of terminally blocked dipeptides containing C-terminal N-phosphonomethylglycine (glyphosate, an extremely effective non-selective post-emergence herbicide) have been synthesized by a solution method. The presence of their two conformers, cis (syn) and trans (anti), was shown in solutions by NMR spectroscopy. Molecular structures of the peptides were also determined in the solid state by X-ray diffraction. The attempts for the selective and total removal of the groups protecting amino, carboxylic and phosphonate functions were in many cases unsuccessful due to the formation of cyclic structures and breakage of the phosphorus-to-carbon bond.     

Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme

Methods developed originally to analyze domain motions from simulation [Proteins 27:425–437, 1997] are adapted and extended for the analysis of X-ray conformers and for proteins with more than two domains. The method can be applied as an automatic procedure to any case where more than one conformation is available. The basis of the methodology is that domains can be recognized from the difference in the parameters governing their quasi-rigid body motion, and in particular their rotation vectors. A clustering algorithm is used to determine clusters of rotation vectors corresponding to main-chain segments that form possible dynamic domains. Domains are accepted for further analysis on the basis of a ratio of interdomain to intradomain fluctuation, and Chasles' theorem is used to determine interdomain screw axes. Finally residues involved in the interdomain motion are identified. The methodology is tested on citrate synthase and the M6I mutant of T4 lysozyme. In both cases new aspects to their conformational change are revealed, as are individual residues intimately involved in their dynamics. For citrate synthase the beta sheet is identified to be part of the hinging mechanism. In the case of T4 lysozyme, one of the four transitions in the pathway from the closed to the open conformation, furnished four dynamic domains rather than the expected two. This result indicates that the number of dynamic domains a protein possesses may not be a constant of the motion. Proteins 30:144–154, 1998. © 1998 Wiley-Liss, Inc.     

Prolylproline unit in model peptides and in fragments from databases

The prolylproline sequence unit is found in several naturally occurring linear and cyclic peptides with immunosuppressive and toxic activity. Furthermore, Pro-Pro units are abundant in collagen, in ligand motifs binding to SH3 or WW domains, as well as in vital enzymes such as DNA glycosylase and thrombin. In all these sequence units a special role is dedicated to conformation in order to successfully fulfill the appropriate biological function. Therefore, a detailed analysis of the basic conformational properties of Pro-Pro is expected to reveal the versatile structural role of this sequence. PCM (polarizable continuum model) calculations on the basis of ab initio and density functional theory investigations using the model peptide HCO-L-Pro-L-Pro-NH2 are presented. Cis-trans isomerism, backbone conformation and ring puckering are studied. A systematic comparison is made to experimental data gained on L-prolyl-L-proline sequence units retrieved from the Protein Data Bank as well as from the Cambridge Structural Database. PCM data are in good agreement with high-resolution X-ray crystallography. Population data derived from energy calculations and those gained directly from statistics predict that 87% of the Pro-Pro sequence units adopt elongated structures, while 13% form beta-turns. Both approaches prefer the same 6 out of the 36 ideally possible backbone folds. Polyproline II unit (t epsilonL t epsilonL), other elongated structures (c epsilonL t epsilonL, t epsilonL t alphaL and t epsilonL t gammaL), type VIa (t epsilonL c alphaL) and type I or III beta-turns (t alphaL t alphaL) altogether describe 96% of the prolylproline sequences. In disordered proteins or domains, Pro-Pro sequence units may sample the various conformers and contribute to the segmental motions.     

The (α-1,6) glycosidic bond of isomaltose: a tricky system for theoretical conformational studies

Stable conformations of β-isomaltose (α-d-glucopyranosyl-(1→6)-β-d-glucose) in gas-phase and aqueous solution are investigated in this study using quantum mechanical calculations. Conformational maps are calculated at HF/6-31G(d,p) level and lower energy structures are sampled in the most stable regions. Entropic and thermal corrections are considered and the Boltzmann population is obtained for conformers that are representative of the 18 most stable regions found on the potential energy surface. B3LYP/6-31+G(d,p) and B3LYP/6-311+G(2d,2p) calculations are used in conformational samplings. Solvation effects are considered through the polarizable continuum model approach. Hydroxymethyl group orientations are investigated for the most stable conformers. The influence of electronic correlation and solvation on the glycosidic linkage preference (TG, GT, and GG) and hydroxymethyl group orientation (tg, gt, and gg) are discussed. Heteronuclear spin coupling constants (³J_C,H) along the glycosidic linkage are calculated and comparison with other theoretical results and experiments is used to validate the obtained structures.