Intermolecular Constraints Research Articles

Penetrant shape effects on activated dynamics and selectivity in polymer melts and networks based on self-consistent cooperative hopping theory.

We generalize and apply the microscopic self-consistent cooperative hopping theory for activated penetrant dynamics in polymer melts and crosslinked networks to address the role of highly variable non-spherical molecular shape. The focus is on vastly different shaped penetrants that have identical space filling volume in order to isolate how non-spherical shape explicitly modifies dynamics over a wide range of temperature down to the kinetic glass transition temperature. The theory relates intramolecular and intermolecular structure and kinetic constraints, and reveals how different solvation packing of polymer monomers around variable shaped penetrants impact penetrant hopping. A highly shape-dependent penetrant activated relaxation, including alpha time decoupling and trajectory level cooperativity of the hopping process, is predicted in the deeply supercooled regime for relatively larger penetrants which is sensitive to whether the polymer matrix is a melt or heavily crosslinked network. In contrast, for smaller size penetrants or at high/medium temperatures the effect of isochoric penetrant shape is relatively weak. We propose an aspect ratio variable that organizes how penetrant shape influences the activated relaxation times, leading to a (near) collapse or master curve. The relative absolute values of the penetrant relaxation time (inverse hopping rate) in polymer melts versus in crosslinked networks are found to be opposite when compared at a common absolute temperature versus when they are compared at a fixed value of distance from the glass transition based on the variable Tg/T with Tg the glass transition temperature. Quantitative comparison with recent diffusion experiments on chemically complex molecular penetrants of variable shape but fixed volume in crosslinked networks reveals good agreement, and testable new predictions are made. Extension of the theoretical approach to more complex systems of high experimental interest are discussed, including applications to realize selective transport in membrane separation applications.

Design and synthesis of an azobenzene–betaine surfactant for photo-rheological fluids

HypothesisMorphology of surfactant self-assemblies are governed by the intermolecular interactions and packing constraints of the constituent molecules. Therefore, rational design of surfactant structure should allow targeting of the specific self-assembly modes, such as wormlike micelles (WLMs). By inclusion of an appropriate photo-responsive functionality to a surfactant molecule, light-based control of formulation properties without the need for additives can be achieved. ExperimentsA novel azobenzene-containing surfactant was synthesised with the intention of producing photo-responsive wormlike micelles. Aggregation of the molecule in its cis and trans isomers, and its concomitant flow properties, were characterised using UV–vis spectroscopy, small-angle neutron scattering, and rheological measurements. Finally, the fluids capacity for mediating particle diffusion was assessed using dynamic light scattering. FindingsThe trans isomer of the novel azo-surfactant was found to form a viscoelastic WLM network, which transitioned to inviscid ellipsoidal aggregates upon photo-switching to the cis isomer. This was accompanied by changes in zero-shear viscosity up to 16,000×. UV–vis spectroscopic and rheo-SANS analysis revealed π-π interactions of the trans azobenzene chromophore within the micelles, influencing aggregate structure and contributing to micellar rigidity. Particles dispersed in a 1 wt% surfactant solution showed a fivefold increase in apparent diffusion coefficient after UV-irradiation of the mixture.

Stereoselective On-Surface Cyclodehydrofluorization of a Tetraphenylporphyrin and Homochiral Self-Assembly.

The thermally induced cyclodehydrofluorization of iron tetrakis(pentafluorophenyl)porphyrin proceeded highly stereoselectively to give a prochiral product on a gold surface in an ultrahigh vacuum, whereas dehydrocyclization of the respective iron tetrakisphenylporphyrin did not show such selectivity. Stereoselectivity was predominantly observed for closely packed layers, which is an indication of intermolecular cooperativity and steric constraints induced by adjacent species. Density functional theory identified intermolecular packing constraints as the origin of such selectivity during the reaction. Scanning tunneling microscopy revealed the formation of an enantiomerically pure two-dimensional self-assembly as a conglomerate of mirror domains. On-surface two-dimensional topochemistry, as reported herein, may open new routes for stereoselective synthesis.

Stereoselective On‐Surface Cyclodehydrofluorization of a Tetraphenylporphyrin and Homochiral Self‐Assembly

AbstractThe thermally induced cyclodehydrofluorization of iron tetrakis(pentafluorophenyl)porphyrin proceeded highly stereoselectively to give a prochiral product on a gold surface in an ultrahigh vacuum, whereas dehydrocyclization of the respective iron tetrakisphenylporphyrin did not show such selectivity. Stereoselectivity was predominantly observed for closely packed layers, which is an indication of intermolecular cooperativity and steric constraints induced by adjacent species. Density functional theory identified intermolecular packing constraints as the origin of such selectivity during the reaction. Scanning tunneling microscopy revealed the formation of an enantiomerically pure two‐dimensional self‐assembly as a conglomerate of mirror domains. On‐surface two‐dimensional topochemistry, as reported herein, may open new routes for stereoselective synthesis.

NMR Methods for Structural Characterization of Protein-Protein Complexes.

Protein-protein interactions and the complexes thus formed are critical elements in a wide variety of cellular events that require an atomic-level description to understand them in detail. Such complexes typically constitute challenging systems to characterize and drive the development of innovative biophysical methods. NMR spectroscopy techniques can be applied to extract atomic resolution information on the binding interfaces, intermolecular affinity, and binding-induced conformational changes in protein-protein complexes formed in solution, in the cell membrane, and in large macromolecular assemblies. Here we discuss experimental techniques for the characterization of protein-protein complexes in both solution NMR and solid-state NMR spectroscopy. The approaches include solvent paramagnetic relaxation enhancement and chemical shift perturbations (CSPs) for the identification of binding interfaces, and the application of intermolecular nuclear Overhauser effect spectroscopy and residual dipolar couplings to obtain structural constraints of protein-protein complexes in solution. Complementary methods in solid-state NMR are described, with emphasis on the versatility provided by heteronuclear dipolar recoupling to extract intermolecular constraints in differentially labeled protein complexes. The methods described are of particular relevance to the analysis of membrane proteins, such as those involved in signal transduction pathways, since they can potentially be characterized by both solution and solid-state NMR techniques, and thus outline key developments in this frontier of structural biology.

Unraveling the Molecular Mechanisms of Thermo-responsive Properties of Silk-Elastin-Like Proteins by Integrating Multiscale Modeling and Experiment.

Adaptive hydrogels tailor-made from silk-elastin-like proteins (SELPs) possess excellent biocompatibility and biodegradability with properties that are tunable and responsive to multiple simultaneous external stimuli. To unravel the molecular mechanisms of their physical response to external stimuli in tandem with experiments, here we predict and measure the variation in structural properties as a function of temperature through coarse-grained (CG) modeling of individual and crosslinked SE8Y and S4E8Y molecules, which have ratios of 1:8 and 4:8 of silk to elastin blocks respectively. Extensive structural reshuffling in single SE8Y molecules led to the increased compactness of the structure, whereas S4E8Y molecules did not experience any significant changes as they already adopted very compact structures at low temperatures. Crosslinking of SE8Y molecules at high concentrations impeded their structural transition at high temperatures that drastically reduced the degree of deswelling through extensive suppression of the structural shuffling and the trapping of the molecules in high potential energy states due to inter-molecular constraints. This integrative experimental and computational understanding of the thermal response in single molecules of SELPs and their crosslinked networks should lead to further improvements in the properties of SELP hydrogels through predictive designs and their wider applications in biomaterials and tissue engineering.

Genetically Encoded Chemical Probes in Cells Reveal the Binding Path of Urocortin-I to CRF Class B GPCR

Molecular determinants regulating the activation of class B G-protein-coupled receptors (GPCRs) by native peptide agonists are largely unknown. We have investigated here the interaction between the corticotropin releasing factor receptor type 1 (CRF1R) and its native 40-mer peptide ligand Urocortin-I directly in mammalian cells. By incorporating unnatural amino acid photochemical and new click-chemical probes into the intact receptor expressed in the native membrane of live cells, 44 intermolecular spatial constraints have been derived for the ligand-receptor interaction. The data were analyzed in the context of the recently resolved crystal structure of CRF1R transmembrane domain and existing extracellular domain structures, yielding a complete conformational model for the peptide-receptor complex. Structural features of the receptor-ligand complex yield molecular insights on the mechanism of receptor activation and the basis for discrimination between agonist and antagonist function.

Intermolecular Structure Determination of Amyloid Fibrils with Magic-Angle Spinning and Dynamic Nuclear Polarization NMR

We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range (13)C-(13)C correlation spectra and the third based on the identification of intermolecular interactions in (13)C-(15)N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3 or PI3K-SH3), that efficient (13)C-(13)C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The (13)C-(13)C experiments are corroborated by (15)N-(13)C correlation spectra obtained from a mixed [(15)N,(12)C]/[(14)N,(13)C] sample which directly quantify interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular (15)N-(13)C constraints detectable in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total, the experiments provide 111 intermolecular (13)C-(13)C and (15)N-(13)C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril.

Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction

Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized.

Functional Divergence of Glycoprotein Hormone Receptors

Two lamprey glycoprotein hormone receptors (lGpH-R I and II) highly similar with gnathostome GpH-Rs were cloned from sea lamprey testes and thyroid, respectively. Vertebrate glycoprotein protein receptors have a large extracellular domain (ED) containing a leu rich domain (LRD) linked to a rhodopsin-like transmembrane domain (TMD) through a highly divergent linker region (signal specificity domain, SSD or 'hinge' region) and a third major segment, the intracellular domain. To determine the potential roles of the different domains in the activation of the receptor following ligand-receptor binding, functional assays were performed on lGpH-R I/rat luteinizing hormone (LH)-R domain swapped chimeric receptors. These results show that the functional roles of the lamprey glycoprotein-receptor I (lGpH-R I) domains are conserved compared with its Gnathostome homologs. The ability of different glycoprotein hormones to activate chimeric lamprey/rat receptors suggests that the selectivity of the GpH-Rs in respect to their ligands is not controlled exclusively by a single domain but is the result of specific interactions between domains. We hypothesize that these interactions were refined during millions of years of co-evolution of the receptors with their cognate ligands under particular intramolecular, intermolecular and physiological constraints.

Random packing of model polymers: local structure, topological hindrance and universal scaling

The random packing of rigid objects has not only engrossed mathematicians since biblical times but is receiving attention for numerous applications and processes involving microgels, granular media, colloids, glasses, liquids, synthetic polymers and biomolecules. While dense random assemblies of single hard spheres have been extensively investigated both experimentally and theoretically over the past 50 years, it was only recently that analogous problems for chains of hard spheres have been addressed. We highlight the relevance of these recent advances, and describe the most salient characteristics of the “maximally random jammed” state for hard sphere chains. Particular emphasis is placed on the scaling behavior of chain dimensions and topology with packing density. We also discuss the potentially far-reaching implications of an unexpected connection that has been found between entanglements (intermolecular constraints) and knots (of intramolecular origin) regarding their dependence on volume fraction.

Universal Scaling, Entanglements, and Knots of Model Chain Molecules

By identifying the maximally random jammed state of freely jointed chains of tangent hard spheres we are able to determine the distinct scaling regimes characterizing the dependence of chain dimensions and topology on volume fraction. Calculated distributions of (i) the contour length of the primitive paths and (ii) the number of entanglements per chain agree remarkably well with recent theoretical predictions in all scaling regimes. Furthermore, our simulations reveal a hitherto unsuspected connection between purely intramolecular (knots) and intermolecular (entanglements) topological constraints.

Critical Issues of Current Research on the Dynamics Leading to Glass Transition

Glass transition is still an unsolved problem in condensed matter physics and chemistry. In this paper, we critically reexamine experimental data and theoretical interpretations of dynamic properties of various processes seen over a wide time range from picoseconds to laboratory time scales. In order of increasing time, the ubiquitous processes considered include (i) the dynamics of caged molecular units with motion confined within the anharmonic intermolecular potential and where no genuine relaxation has yet taken place; (ii) the onset of the Johari-Goldstein secondary relaxation involving rotation or translation of the entire molecular unit and causing the decay of the cages, to be followed by the cooperative and dynamically heterogeneous motions participated by increasing number of molecules or length scale; and (iii) the terminal primary alpha-relaxation with the maximum cooperative length-scale allowed by the intermolecular interaction and constraints of the glass former. Some general and important properties found in each of these processes are shown to be interrelated, indicating that the processes are connected, with one being the precursor of the other following it. Thus, a theory of glass transition is neither complete nor fundamental unless all of these processes and their inter-relations have been accounted. In addition to published data, new experimental data are reported here to provide a limited collection of critical experimental facts having an impact on current issues of glass transition research and servingas a guide for the construction of a complete and successful theory in the future.

Excess wing and Johari–Goldstein relaxation in binary mixtures of glass formers

Dielectric loss spectra of pure quinaldine and tert-butylpyridine and their mixtures with tristyrene are presented. The pure systems present an excess wing and no secondary peaks in the temperature interval from above to well below the glass transition. However, when mixed in low concentration with tristyrene the excess wing is replaced by a distinct secondary peak. This distinct process can be identified as a Johari–Goldstein relaxation within the coupling model interpretation. In the frame of the coupling model the transition from the relaxation scenario with the excess wing to that with a distinct secondary peak is related to the increase of intermolecular constraints. In our case this increase of constraints is due to the low mobility component of the mixture (tristyrene).

The Holo-form of the Nucleotide Binding Domain of the KdpFABC Complex from Escherichia coli Reveals a New Binding Mode

P-type ATPases are ubiquitously abundant enzymes involved in active transport of charged residues across biological membranes. The KdpB subunit of the prokaryotic Kdp-ATPase (KdpFABC complex) shares characteristic regions of homology with class II-IV P-type ATPases and has been shown previously to be misgrouped as a class IA P-type ATPase. Here, we present the NMR structure of the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli Kdp-ATPase at high resolution. The aromatic moiety of the nucleotide is clipped into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a cation-pi interaction, respectively. Charged residues at the outer rim of the binding pocket (Arg(317), Arg(382), Asp(399), and Glu(348)) stabilize and direct the triphosphate group via electrostatic attraction and repulsion toward the phosphorylation domain. The nucleotide binding mode was corroborated by the replacement of critical residues. The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. We present a schematic model of the nucleotide binding mode that allows for both high selectivity and a low nucleotide binding constant, necessary for the fast and effective turnover rate realized in the reaction cycle of the Kdp-ATPase.

High-Resolution X-ray Structure of the Unexpectedly Stable Dimer of the [Lys(-2)-Arg(-1)-des(17−21)]Endothelin-1 Peptide

Previous structural studies on the [Lys((-2))-Arg((-1))]endothelin-1 peptide (KR-ET-1), 540-fold less potent than ET-1, strongly suggested the presence of an intramolecular Arg(-1)-Asp(8) (R(-1)-D(8)) salt bridge that was also observed in the shorter [Lys((-2))-Arg((-1))-des(17-21)]endothelin-1 derivative (KR-CSH-ET). In addition, for these two analogues, we have shown that the Lys-Arg dipeptide, which belongs to the prosequence, significantly improves the formation of the native disulfide bonds (>or=96% instead of approximately 70% for ET-1). In contrast to what was inferred from NMR data, molecular dynamics simulations suggested that such an intramolecular salt bridge would be unstable. The KR-CSH-ET peptide has now been crystallized at pH 5.0 and its high-resolution structure determined ab initio at 1.13 A using direct methods. Unexpectedly, KR-CSH-ET was shown to be a head-to-tail symmetric dimer, and the overall interface involves two intermolecular R(-1)-D(8) salt bridges, a two-stranded antiparallel beta-sheet, and hydrophobic contacts. Molecular dynamics simulations carried out on this dimer clearly showed that the two intermolecular salt bridges were in this case very stable. Sedimentation equilibrium experiments unambiguously confirmed that KR-ET-1 and KR-CSH-ET also exist as dimers in solution at pH 5.0. On the basis of the new dimeric structure, previous NMR data were reinterpreted. Structure calculations were performed using 484 intramolecular and 38 intermolecular NMR-derived constraints. The solution and the X-ray structures of the dimer are very similar (mean rmsd of 0.85 A). Since the KR dipeptide at the N-terminus of KR-CSH-ET is present in the prosequence, it can be hypothesized that similar intermolecular salt bridges could be involved in the in vivo formation of the native disulfide bonds of ET-1. Therefore, it appears to be likely that the prosequence does assist the ET-1 folding in a chaperone-like manner before successive cleavages that yield the bioactive ET-1 hormone.

A novel approach for characterizing protein ligand complexes: molecular basis for specificity of small-molecule Bcl-2 inhibitors.

The increasing diversity of small molecule libraries has been an important source for the development of new drugs and, more recently, for unraveling the mechanisms of cellular events-a process termed chemical genetics.(1) Unfortunately, the majority of currently available compounds are mechanism-based enzyme inhibitors, whereas most of cellular activity regulation proceeds on the level of protein-protein interactions. Hence, the development of small molecule inhibitors of protein-protein interactions is important. When screening compound libraries, low-micromolar inhibitors of protein interactions can be routinely found. The enhancement of affinities and rationalization of the binding mechanism require structural information about the protein-ligand complexes. Crystallization of low-affinity complexes is difficult, and their NMR analysis suffers from exchange broadening, which limits the number of obtainable intermolecular constraints. Here we present a novel method of ligand validation and optimization, which is based on the combination of structural and computational approaches. We successfully used this method to analyze the basis for structure-activity relationships of previously selected (2) small molecule inhibitors of the antiapoptotic protein Bcl-xL and identified new members of this inhibitor family.

Chiroporphyrines froncées à distorsion adjustable

We have synthesized a series of chiroporphyrins in which the ester functions on adjacent meso substituents are linked by a bridle of adjustable length. The ruffled distortion induced by the α, β, α, β alternation of the porphyrin meso substituents can be controlled by the length of the bridles. X-ray structure determinations show that intermolecular constraints within the crystalline network can stabilize conformers that considerably differ from the mean conformation observed in solution by 1H–NMR. To cite this article: S. Gazeau et al., C. R. Chimie 5 (2002) 27–31

Computer Simulation of Biphenyl-Phenyl Ester Liquid Crystals

Molecular orbital (MO) calculation and molecular dynamics (MD) simulation were carried out for a set of smectic liquid crystalline molecules, 8O-O8 (4-octyloxyphenyl-4′-octyloxybi-phenyl-4-carboxylate) and 8O-8 (4-octylphenyl-4′-octyloxybiphenyl-4-carboxylate), to understand the molecular origin of different crystalline structure formation and to predict their conformational property in liquid crystalline phases. The results of MO and MD analyses indicate that the structure of 8O-O8 and 8O-8 in crystalline phase is essentially determined by intramolecular interactions and the experimentally observed structure is chosen as a consequence of intermolecular packing constraints. This paper also reports the first application of two-molecular ab-initio calculation to liquid crystalline systems.

Structure prediction of protein complexes by an NMR-based protein docking algorithm.

Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the protein-protein docking problem, where the input consists of the tertiary structures of proteins A and B plus an unassigned one-dimensional 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a 'theoretical' 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental one. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. [Morelli et al. (2000) Biochemistry, 39, 2530-2537]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with four protein complexes whose three-dimensional structures are stored in the PDB data bank (Bernstein et al., 1977) and whose 1H-NMR shift assignments are available from the BMRB database. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives.