Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity.

The cyclin-dependent kinase (Cdk) inhibitor p21Waf1/Cip1/Sdi1, important for p53-dependent cell cycle control, mediates G1/S arrest through inhibition of Cdks and possibly through inhibition of DNA replication. Cdk inhibition requires a sequence of approximately 60 amino acids within the p21 NH2 terminus. We show, using proteolytic mapping, circular dichroism spectropolarimetry, and nuclear magnetic resonance spectroscopy, that p21 and NH2-terminal fragments that are active as Cdk inhibitors lack stable secondary or tertiary structure in the free solution state. In sharp contrast to the disordered free state, however, the p21 NH2 terminus adopts an ordered stable conformation when bound to Cdk2, as shown directly by NMR spectroscopy. We have, thus, identified a striking disorder-order transition for p21 upon binding to one of its biological targets, Cdk2. This structural transition has profound implications in light of the ability of p21 to bind and inhibit a diverse family of cyclin-Cdk complexes, including cyclin A-Cdk2, cyclin E-Cdk2, and cyclin D-Cdk4. Our findings suggest that the flexibility, or disorder, of free p21 is associated with binding diversity and offer insights into the role for structural disorder in mediating binding specificity in biological systems. Further, these observations challenge the generally accepted view of proteins that stable secondary and tertiary structure are prerequisites for biological activity and suggest that a broader view of protein structure should be considered in the context of structure-activity relationships.

Melting of an Anchored Bilayer: Phase Transitions in the Organic-Inorganic Hybrid Pervoskite (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n=11, 13, 15, 17)

The conformation, organization, and phase transitions of alkyl chains in organic-inorganic hybrids based on the double pervoskite-slab lead iodides, (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n = 11, 13, 15, 17) have been investigated by X-ray diffraction, calorimetry, and infrared vibrational spectroscopy. In these hybrid solids, double pervoskite (CH3NH3)Pb2I7 slabs are interleaved with alkyl ammonium chains with the anchored alkyl chains arranged as tilted bilayers and adopting a planar all-trans conformation at room temperature. The (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 compounds exhibit a single reversible phase transition above room temperature with the associated enthalpy change varying linearly with alkyl chain length. This transition corresponds to the melting in two-dimensions of the alkyl chains of the anchored bilayer and is characterized by increased conformational disorder of the methylene units of the chain and loss of tilt angle coherence leading to an increase in the interslab spacing. By monitoring features in the infrared spectra that are characteristic of the global conformation of the alkyl chains, a quantitative relation between conformational disorder and melting of the anchored bilayer is established. It is found that, irrespective of the alkyl chain length, melting occurs when at least 60% of the chains in the anchored bilayer of (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 have one or more gauche defects. This concentration is determined by the underlying lattice to which the alkyl chains are anchored.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Phase transitions in the anchored organic bilayers of long-chain alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4; n=12, 16, 18

The single perovskite slab alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4, n = 12, 16, 18, display two phase transitions, just above room temperature, associated with changes in the alkylammonium chains. We have followed these two phase transitions using scanning calorimetry, X-ray powder diffraction, and IR and Raman spectroscopies. We find the first phase transition to be associated with symmetry changes arising from a dynamic rotational disordering of the ammonium headgroup of the chain whereas the second transition, the melting of the chains in two dimensions, is characterized by an increased conformational disorder of the methylene units of the alkyl chains. We examine these phase transitions in light of the interesting optical properties of these materials, as well as the relevance of these systems as models for phase transitions in lipid bilayers.

AN INFRARED SPECTROSCOPIC CHARACTERIZATION OF THE SOLID SOLID BEHAVIOR OF DODECYLAMMONIUM CHLORIDE

The infrared spectra of the bilayer system dodecylammonium chloride has been studied as a function of temperature. Unusual splitting of some vibrational modes helps us to characterize the structure of different solid states. This study provided the evidence for the occurrence of an order-disorder phase transition whose onset occurs at 327 K and its completion ends at 339 K. In the low temperature phase below 327 K, the virgin crystals form a well-ordered phase with all-transhydrocarbon chains. In the intermediate state between 327 and 339 K, the data demonstrate the introduction of intramolecular as well as intermolecular disorder. The coexistence of solid and liquid-crystal-like states is shown by the persistence of factor group splittings together with the existence of defect bands in the wide intermediate temperature range. In the high temperature phase over 339 K the crystals convert to a liquid-crystal-like system with extensive motional and conformational disorder, but still show characteristics in their infrared spectra which indicate the presence of ordered segments in the hexagonal solid phase.

THERMAL ANALYSIS AND INFRARED SPECTRA OF DIALKYLAMMONIUM TETRAC HLOROCUPRATE

The thermal stability and the solid solid phase transitions in Ills compounds with n = 7-12 have been studied by DSC and TG methods. Comparision with CnZn compounds want made. The nature of three phases of CnCu has been discussed in terms of infrared spectroscopy and the assignment of the phase transitions has been given. The thermal stability of CnCu is lower than that of CnZn and presents an obvious odd even effect. All of these compounds exhibit two solid solid phase transitions in the temperature range of 248-337 K. The peak tempe nature of phase transitions changes regularly. The peak temperature or the main phase transition increases with the chain length. The total transition enthalpies and entropies increase with increasing chain length. When n <= 9, the high temperature phase exists in a partial disorder state. When n >= 10, the high temperature phase exists in a conformational disorder state. The main phase transition and the phase transition at 307.7 K of CnCu may mainly are from the change of the packing structure and the change of the partial conformational order-disorder of alkyl chain, respectively.

Anisotropic refinement of the structure of Thermoascus aurantiacusxylanase I

The isotropic crystallographic model of the structure of xylanase I from Thermoascus aurantiacus (TAXI) has now been refined anisotropically at 1.14 Å resolution to a standard residual of R = 11.1% for all data. TAXI is amongst the five largest proteins deposited in the Protein Data Bank to have been refined with anisotropic displacement parameters (ADPs) at this level of resolution. The anisotropy analysis revealed a more isotropic distribution of anisotropy than usually observed previously. Adding ADPs resulted in high-quality electron-density maps which revealed discrepancies from the previously suggested primary sequences for this enzyme. Side-chain conformational disorder was modelled for 16 residues, including Trp275, a bulky residue at the active site. An unrestrained refinement was consistent with the protonation of the catalytic acid/base glutamate and the deprotonation of the nucleophile glutamate, as required for catalysis. The thermal stability of TAXI is reinterpreted in the light of the new refined model.

Excited-state dynamics of polyfluorene derivatives in solution

The excited-state dynamics of two polyfluorene copolymers, one fully conjugated containing phenylene vinylene units alternated with 9,9`-dihexylfluorenyl groups and the other segmented by -(CH2)(8)- spacer, were studied in dilute solution of different solvents using a picosecond single-photon timing technique. The excited-state dynamics of the segmented copolymer follows the Forster resonant energy-transfer model which describes intrachain energy-transfer kinetics among random oriented chromophores. Energy transfer is confirmed by analysis of fluorescence anisotropy relaxation with the measurement of a short decay component of about 60 ps. The fluorescence decay surface of the fully conjugated copolymer is biexponential with decay times of about 470 and 900 ps, ascribed to deactivation of chain moieties containing trans and cis isomers already in a photostationary condition. Thus, energy transfer is very fast due to the conjugated nature and rigid-rod-like structure of this copolymer chain.

Disordered distribution of defects in polythiophene

In this work we study the electronic structure associated to a disordered distribution of bipolarons in polythiophene. The polymer chain is modelled by a tight-binding Hamiltonian with explicit treatment of electron-phonon coupling and the elastic energy of the sigma framework. The model also includes the electrostatic interaction due to the counterions. The density of states of the disordered system is obtained by the use of the Negative Factor Counting technique. Our results show that ion-induced conformational disorder can account for the closure of the gap and that the states around the Fermi level are extended. © 1993.

Charge-transport simulations in organic semiconductors

In this thesis we have extended the methods for microscopic charge-transport simulations for organic semiconductors. In these materials the weak intermolecular interactions lead to spatially localized charge carriers, and the charge transport occurs as an activated hopping process between diabatic states. In addition to weak electronic couplings between these states, different electrostatic environments in the organic material lead to a broadening of the density of states for the charge energies which limits carrier mobilities.rnThe contributions to the method development includern(i) the derivation of a bimolecular charge-transfer rate,rn(ii) the efficient evaluation of intermolecular (outer-sphere) reorganization energies,rn(iii) the investigation of effects of conformational disorder on intramolecular reorganization energies or internal site energiesrnand (iv) the inclusion of self-consistent polarization interactions for calculation of charge energies.These methods were applied to study charge transport in amorphous phases of small molecules used in the emission layer of organic light emitting diodes (OLED).rnWhen bulky substituents are attached to an aromatic core in order to adjust energy levels or prevent crystallization, a small amount of delocalization of the frontier orbital to the substituents can increase electronic couplings between neighboring molecules. This leads to improved charge-transfer rates and, hence, larger charge-mobility. We therefore suggest using the mesomeric effect (as opposed to the inductive effect) when attaching substituents to aromatic cores, which is necessary for example in deep blue OLEDs, where the energy levels of a host molecule have to be adjusted to those of the emitter.rnFurthermore, the energy landscape for charges in an amorphous phase cannot be predicted by mesoscopic models because they approximate the realistic morphology by a lattice and represent molecular charge distributions in a multipole expansion. The microscopic approach shows that a polarization-induced stabilization of a molecule in its charged and neutral states can lead to large shifts, broadening, and traps in the distribution of charge energies. These results are especially important for multi-component systems (the emission layer of an OLED or the donor-acceptor interface of an organic solar cell), if the change in polarizability upon charging (or excitation in case of energy transport) is different for the components. Thus, the polarizability change upon charging or excitation should be added to the set of molecular parameters essential for understanding charge and energy transport in organic semiconductors.rnWe also studied charge transport in self-assembled systems, where intermolecular packing motives induced by side chains can increase electronic couplings between molecules. This leads to larger charge mobility, which is essential to improve devices such as organic field effect transistors, where low carrier mobilities limit the switching frequency.rnHowever, it is not sufficient to match the average local molecular order induced by the sidernchains (such as the pitch angle between consecutive molecules in a discotic mesophase) with maxima of the electronic couplings.rnIt is also important to make the corresponding distributions as narrow as possible compared to the window determined by the closest minima of thernelectronic couplings. This is especially important in one-dimensional systems, where charge transport is limited by the smallest electronic couplings.rnThe immediate implication for compound design is that the side chains should assist the self-assemblingrnprocess not only via soft entropic interactions, but also via stronger specific interactions, such as hydrogen bonding.rnrnrnrn

Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study

Molecular dynamics (MD) simulations are reported for an anchored bilayer formed by the intercalation of cetyl trimethyl ammonium (CTA) and CH3(CH2)15N+(CH3) ions in a layered solid, CdPS3. The intercalated CTA ions are organized with the cationic headgroups tethered to the inorganic sheet and the hydrocarbon tails arranged as bilayers. Simulations were performed at three temperatures, 65, 180, and 298 K, using an isothermal−isobaric ensemble that was subsequently switched once macroscopic parameters had converged to a canonical isothermal−isochoric ensemble. The simulations are able to reproduce the experimental features of this system, including the formation of the bilayer and layer-to-layer separation distance. An analysis of the conformation of the chains showed that at all three temperatures a fraction of the alkyl chains retained a planar all-trans conformation, and that gauche bonds occurred as part of a “kink” (gauche+−trans−gauche−) sequence and not as isolated gauche bonds. Trans−gauche isomerization rates for the alkyl chains in the anchored bilayer are slower than those in lipid bilayers at the same temperature and show a progressive increase as the torsion numbers approach the tail. A two-dimensional periodic Voronoi tessellation analysis was performed to obtain the single-molecular area of an alkyl chain in the bilayer. The single-molecular area relaxation times are an order of magnitude longer than the trans−gauche isomerization times. The results indicate that the trans−gauche isomerization is associated with the creation and annihilation of a kink defect sequence. The results of the present MD simulation explain the apparent conflicting estimates of the gauche disorder in this system as obtained from infrared and 13C nuclear magnetic resonance measurements.

Intrinsically disordered proteins and conformational noise Implications in cancer

Intrinsically disordered proteins, IDPs, are proteins that lack a rigid 3D structure under physiological conditions, at least in vitro. Despite the lack of structure, IDPs play important roles in biological processes and transition from disorder to order upon binding to their targets. With multiple conformational states and rapid conformational dynamics, they engage in myriad and often ``promiscuous'' interactions. These stochastic interactions between IDPs and their partners, defined here as conformational noise, is an inherent characteristic of IDP interactions. The collective effect of conformational noise is an ensemble of protein network configurations, from which the most suitable can be explored in response to perturbations, conferring protein networks with remarkable flexibility and resilience. Moreover, the ubiquitous presence of IDPs as transcriptional factors and, more generally, as hubs in protein networks, is indicative of their role in propagation of transcriptional (genetic) noise. As effectors of transcriptional and conformational noise, IDPs rewire protein networks and unmask latent interactions in response to perturbations. Thus, noise-driven activation of latent pathways could underlie state-switching events such as cellular transformation in cancer. To test this hypothesis, we created a model of a protein network with the topological characteristics of a cancer protein network and tested its response to a perturbation in presence of IDP hubs and conformational noise. Because numerous IDPs are found to be epigenetic modifiers and chromatin remodelers, we hypothesize that they could further channel noise into stable, heritable genotypic changes.

Alpha-1 antitrypsin deficiency: A conformational disease associated with lung and liver manifestations

Alpha-1 antitrypsin (A1AT) is a serine anti-protease produced chiefly by the liver. A1AT deficiency is a genetic disorder characterized by serum levels of less than 11 μmol/L and is associated with liver and lung manifestations. The liver disease, which occurs in up to 15% of A1AT-deficient individuals, is a result of toxic gain-of-function mutations in the A1AT gene, which cause the A1AT protein to fold aberrantly and accumulate in the endoplasmic reticulum of hepatocytes. The lung disease is associated with loss-of-function, specifically decreased anti-protease protection on the airway epithelial surface. The so-called 'Z' mutation in A1AT deficiency encodes a glutamic acid-to-lysine substitution at position 342 in A1AT and is the most common A1AT allele associated with disease. Here we review the current understanding of the molecular pathogenesis of A1AT deficiency and the best clinical management protocols. © Springer Science+Business Media B.V. 2008.

Conformational polymorphism of the molecular complex of 3-fluorobenzoic acid with 4-acetylpyridine

Two polymorphs of the molecular complex formed between 3-fluorobenzoic acid with 4-acetylpyridine are described and found to be based upon the same dimeric supramolecular construct. The conformational freedom around the hydrogen bond results in a 180 degrees rotation about this intermolecular link, distinguishing the polymorphs and affecting the packing of the dimeric units. The two polymorphs are fully characterised by single crystal X-ray and neutron diffraction and quantum mechanical calculations. There is evidence of structured crystal growth defects in both polymorphic crystals via observation of diffuse scattering and a disorder model for the average structure of Form I, which can be interpreted as a mixing of the two dimer conformations. The similarity of energy of the distinct dimeric units, supporting their likely co-existence, has been verified by periodic quantum chemical calculations.

Order-Disorder Transitions Govern Kinetic Cooperativity and Allostery of Monomeric Human Glucokinase

Glucokinase (GCK) catalyzes the rate-limiting step of glucose catabolism in the pancreas, where it functions as the body's principal glucose sensor. GCK dysfunction leads to several potentially fatal diseases including maturity-onset diabetes of the young type II (MODY-II) and persistent hypoglycemic hyperinsulinemia of infancy (PHHI). GCK maintains glucose homeostasis by displaying a sigmoidal kinetic response to increasing blood glucose levels. This positive cooperativity is unique because the enzyme functions exclusively as a monomer and possesses only a single glucose binding site. Despite nearly a half century of research, the mechanistic basis for GCK's homotropic allostery remains unresolved. Here we explain GCK cooperativity in terms of large-scale, glucose-mediated disorder-order transitions using 17 isotopically labeled isoleucine methyl groups and three tryptophan side chains as sensitive nuclear magnetic resonance (NMR) probes. We find that the small domain of unliganded GCK is intrinsically disordered and samples a broad conformational ensemble. We also demonstrate that small-molecule diabetes therapeutic agents and hyperinsulinemia-associated GCK mutations share a strikingly similar activation mechanism, characterized by a population shift toward a more narrow, well-ordered ensemble resembling the glucose-bound conformation. Our results support a model in which GCK generates its cooperative kinetic response at low glucose concentrations by using a millisecond disorder-order cycle of the small domain as a "time-delay loop," which is bypassed at high glucose concentrations, providing a unique mechanism to allosterically regulate the activity of human GCK under physiological conditions.