Globular Conformation Research Articles

The Structure of an Interdomain Complex That Regulates Talin Activity

Talin is a large flexible rod-shaped protein that activates the integrin family of cell adhesion molecules and couples them to cytoskeletal actin. It exists in both globular and extended conformations, and an intramolecular interaction between the N-terminal F3 FERM subdomain and the C-terminal part of the talin rod contributes to an autoinhibited form of the molecule. Here, we report the solution structure of the primary F3 binding domain within the C-terminal region of the talin rod and use intermolecular nuclear Overhauser effects to determine the structure of the complex. The rod domain (residues 1655–1822) is an amphipathic five-helix bundle; Tyr-377 of F3 docks into a hydrophobic pocket at one end of the bundle, whereas a basic loop in F3 (residues 316–326) interacts with a cluster of acidic residues in the middle of helix 4. Mutation of Glu-1770 abolishes binding. The rod domain competes with β3-integrin tails for binding to F3, and the structure of the complex suggests that the rod is also likely to sterically inhibit binding of the FERM domain to the membrane.

Architecture of the PKA RIIβ Holoenzyme

How the dimeric PKA regulatory (RI and RII) subunits assemble into an inactive tetrameric complex with the catalytic subunits is very isoform specific. By solving structures of holoenzyme complexes, we now appreciate the global conformational changes that take place in each regulatory subunit as they release cAMP and wrap themselves around the catalytic subunit. By using monomeric deletion mutants we can map the novel isoform‐specific interactions of the inhibition sites in the RI and RII subunits. In parallel we have used small angle X‐ray scattering (SAXS) and small angle neutron scattering (SANS) to map the global architectures of the different conformational states. To define the shape and conformational dynamics of the RIIβ subunit, we have engineered a dimeric mutant, RIIβ(1‐280), that lacks the second cAMP binding domain. In contrast to the RIIα subunit, which forms a highly asymmetric complex, and RIα, where the tetramer is Y‐shaped, RIIβ undergoes a major conformational change. While the free RIIβ subunit forms an extended dimer, the RIIβ holoenzyme folds into a compact, globular conformation. Based on SAXS data, the properties required for this change are included within the RIIβ(1‐280) deletion mutant, and most likely relate to the linker that is disordered in the free RIIβ dimer. [Supported by NIH GM34921 to SST]

Conformational studies of the capsular polysaccharide produced by Neisseria meningitidis group A

The effect of different cations on the conformational and morphological properties of the capsular polysaccharide produced by Neisseria meningitidis group A was investigated. Circular dichroism studies showed that the presence of Na +, NH 4 + or Ca 2+ ions induced different local conformations of the polysaccharide chain through interactions with the phosphodiester group bridging the saccharide residues in the polymer chain. Atomic force microscopy experiments confirmed that the morphology of the polysaccharide chains was different depending on the nature of the counterion. Ammonium ions were associated with the presence of single polymer chains in an elongated conformation, whereas sodium ions favored the folding of the chains into a globular conformation. The addition of calcium ions produced the aggregation of a limited number of globular polysaccharide chains to form a ‘toroidal-like’ structure.

Conformational Mechanics of Polymer Adsorption Transitions at Attractive Substrates

Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as monomers and the substrate interact via attractive van der Waals forces. To characterize conformational phases of this hybrid system, we analyze thermal fluctuations of energetic and structural quantities, as well as adequate docking parameters. Introducing a solvent parameter related to the strength of the surface attraction, we construct and discuss the complete solubility-temperature phase diagram. Apart from the main phases of adsorbed and desorbed conformations, we identify several other phase transitions such as the freezing transition between energy-dominated crystalline low-temperature structures and globular entropy-dominated conformations.

Single molecule spectroscopy of red- and green-emitting fluorene-based copolymers

Single molecule fluorescence spectroscopy is used to study the optical properties of two polymers: a fluorene-based statistical copolymer that contains a low fraction (10%) of a red-emitting thiophene group, and the green-emitting polymer poly(9,9-dioctylfluorene-alt-benzothiadiazole). These polymers were studied when isolated at a low concentration in a polymer matrix (either polynorbornene or polystyrene). For the red-emitting polymer, we compare the relative emission intensity from the green-emitting benzothiadiazole groups with the red-emitting thiophene. We find that red emission from the thiophenes is significantly suppressed in the single molecule regime, suggesting that interchain energy transfer dominates intrachain processes in such polyfluorene copolymers. We then use fluorescence spectroscopy and polarization anisotropy measurements to show that the conformations of both polymers are dependent on their host matrix, adopting a more collapsed, globular conformation in polystyrene and a more extended chain conformation in polynorbornene.

Hyperbranched and viologen-functionalized polyglycerols: preparation, photo- and electrochromic performance

Covalently bonding viologen groups at the chain-ends of hyperbranched polyglycerol would enhance the performance of viologen chromophores to external photo- and potential stimuli, because the amorphous, soft and hyperbranched polyether in globular conformation inhibits the aggregation or crystallization of the highly concentrated and ionic viologen chromophores, and also stabilizes the viologen cation radicals. Hyperbranched and functional polyglycerol containing viologen chromophores (HPG-V2+) are prepared by firstly capping the terminal hydroxyl groups of hyperbranched polyglycidol (HPG) with chloroacetyl, and then with the chloroacetyl groups and 4,4′-bipyridine to form the viologen chromophores on the chain-ends of HPG. The evolution of chemical structures from glycidols to HPG-V2+ is carefully characterized. The HPG-V2+ exhibits both photo- and electrochromism with high color contrast, short response time, and well stability: upon UV irradiation, the HPG-V2+ film changes its color from pale yellow to purple, while optical transmittance at 540 nm decreases from ≥90% to <10%; to the stimuli of pulsed 2.5 V electrical potential, the solution type electrochromic cell based on HPG-V2+ responds with reversible color changes from transparent to violet within about 0.52 s, much faster than the previously reported viologen-containing electrochromic polymers. The photochromism of HPG-V2+ is effective even in atmosphere by sunshine: when exposing to sunshine for several minutes the color of the HPG-V2+ film turned to purple, while low molecular weight viologen analogue exhibits only electrochromism.

Pathogenic Mutations Shift the Equilibria of α‐Synuclein Single Molecules towards Structured Conformers

Alpha-synuclein (alpha-Syn) is an abundant brain protein whose mutations have been linked to early-onset Parkinson's disease (PD). We recently demonstrated, by means of a single-molecule force spectroscopy (SMFS) methodology, that the conformational equilibrium of monomeric wild-type (WT) alpha-Syn shifts toward beta-containing structures in several unrelated conditions linked to PD pathogenicity. Herein, we follow the same methodology previously employed for WT alpha-Syn to characterize the conformational heterogeneity of pathological alpha-Syn mutants A30P, A53T, and E46K. Contrary to the bulk ensemble-averaged spectroscopies so far employed to this end by different authors, our single-molecule methodology monitored marked differences in the conformational behaviors of the mutants with respect to the WT sequence. We found that all the mutants have a much higher propensity than the WT to adopt a monomeric compact conformation that is compatible with the acquiring of beta structure. Mutants A30P and A53T show a similar conformational equilibrium that is significantly different from that of E46K. Another class of conformations, stabilized by mechanically weak interactions (MWI), shows a higher variety in the mutants than in the WT protein. In the A30P mutant these interactions are relatively stronger, and therefore the corresponding conformations are possibly more structured. The more structured and globular conformations of the mutants can explain their higher propensity to aggregate with respect to the WT.

Synthesis and characterization of star and brush grafted polysiloxanes, obtained by atom transfer radical polymerization

AbstractStar- and brush-polysiloxanes were synthesized via living radical polymerization using two different catalytic systems. The new compounds were characterized by 1H-NMR, gel permeation chromatography (GPC) and differential scanning calorimetry (DSC) techniques. CuCl and 2,2’-bipyridyl proved to be the most efficient catalytic system. The type of catalytic system and the reaction conditions control the number of arms for star polymers or the grafted-chain density for brush polymers. The use of chloromethyl styrene as monomer or co-monomer yields homogeneous star- or brush-polysiloxanes, although chloromethyl styrene is an inimer system. The homogeneity of materials was verified by GPC and DSC (TOPEM) methods. For linear grafted polysiloxanes the molecular simulations reflect a tendency of chains to adopt globular conformation for high values of the branching density. The polysiloxanes grafted with styrene/chloromethyl styrene were modified with azobenzene in order to obtain systems able to react to the light stimuli. Rheological behavior of the polymer solutions were evaluated before and after irradiation with UV light. After the UV irradiation a significant viscosity increase was evidenced

Structural Instabilities in Lamellar Diblock Copolymer Thin Films During Solvent Vapor Uptake

We have studied the structural rearrangements in a lamellae-forming poly(styrene-b-butadiene) film during exposure to toluene vapor. Real-time, in situ grazing-incidence small-angle X-ray scattering allowed us to identify distinct kinetic regimes: First, the lamellae swell linearly, and the blocks stretch uniaxially. Then, the blocks relax to a more globular molecular conformation, and the lamellar thickness abruptly shrinks again. The increased interfacial area culminates in a dramatic instability causing a major rearrangement of the lamellar stack and the formation of new lamellae. Finally, the lamellar thickness levels off, and the interfaces flatten again.

Synchrotron Small-Angle X-ray Scattering Studies of the Structure of Porcine Pepsin under Various pH Conditions

Structural characteristics of various conformational states of porcine pepsin in solution under different pH conditions were investigated in terms of size and shape by small-angle X-ray scattering (SAXS). Low-resolution structural models of porcine pepsin were reconstructed from SAXS data, which were made inside the search volume of maximum dimension (Dmax), calculated from the pair distance distribution function p(r). The reconstructed structural models were obtained without imposing any restrictions on the symmetry or anisometry of the pepsin molecule. Under conditions emulating those for physiological activity of the enzyme, the reconstructed structural models exhibited a more extended C-terminal domain compared to the crystal structure. The differences between the solution and crystal structures of pepsin can be explained by inherent conformations of the flexible subdomain in the C-terminal domain under the solution pH conditions. Under mild acidic conditions where the enzyme is inactive, the reconstructed structural models revealed a compact globular conformation similar in overall shape to the crystal structure. These results indicate that the changes in fluorescence and circular dichroism curves observed under acidic conditions could also arise from the inherent conformation of the flexible subdomain, which has a tendency to roll into a sphere in the overall structure, but without affecting the stability of internal structure. Furthermore, the conformational changes in the subdomain might explain the inactivity of pepsin under mildly acidic conditions. Finally, compared to neutral denaturing conditions, pepsin under alkaline denaturing conditions had a larger expanded vertical conformation in the reconstructed model, as a consequence of alkaline denaturation of the N-terminal domain and a fully extended conformation of the C-terminal domain. The structural evidence presented here may have important implications for understanding the relationship between the structure of porcine pepsin and enzymatic function.

Differential binding of factor XII and activated factor XII to soluble and immobilized fibronectin – localization of the Hep‐1/Fib‐1 binding site for activated factor XII

Fibronectins (FNs) are dimeric glycoproteins that adopt a globular conformation when present in plasma and solution and an extended conformation in the extracellular matrix. Factor XII (FXII) is a zymogen of the proteolytically active FXIIa that plays a role in thrombus stabilization by enhancing clot formation and in inflammation by enhancing bradykinin formation. To investigate whether the extracellular matrix could play a role in these events, we have recently shown that FXIIa, but not FXII, binds to the extracellular matrix (ECM), and suggested that FN may be the target for the binding. Immunofluorescence microscopy has in the present investigation confirmed that FXIIa added to the ECM colocalizes with FN deposited during growth of human umbilical vein endothelial cells. The aim of the present study, therefore, was to further elucidate the interaction between FXIIa and FN by the use of a solid face binding assay. This showed, like the binding to the ECM, that FXIIa, but not FXII, binds in a Zn2+-independent manner to immobilized FN. The K(D) for the binding was 8.5 +/- 0.9 nM (n = 3). The binding was specific for the immobilized FN, as the binding could not be inhibited by soluble FN. Furthermore, soluble FN did not bind to immobilized FXIIa. However, soluble FN could bind to FXII, and this binding inhibited the surface-induced autoactivation of FXII and subsequent binding of the generated FXIIa to immobilized FN. The presence of FXII in an anti-FN immunoprecipitate of plasma indicated that some FXII in plasma circulates bound to FN. The binding of FXIIa to FN was inhibited by gelatine and fibrin but not by heparin, indicating that FXIIa binds to immobilized FN through the type I repeat modules. Accordingly, FXIIa was found to bind to immobilized fragments of FN containing the type I repeat modules in the N-terminal domain to which fibrin and gelatine bind.

A Novel β-Defensin Structure: A Potential Strategy of Big Defensin for Overcoming Resistance by Gram-Positive Bacteria

Big defensin is a 79-residue peptide derived from hemocytes of the Japanese horseshoe crab. It has antimicrobial activities against Gram-positive and -negative bacteria. The amino acid sequence of big defensin can be divided into an N-terminal hydrophobic half and a C-terminal cationic half. Interestingly, the trypsin cleaves big defensin into two fragments, the N-terminal and C-terminal fragments, which are responsible for antimicrobial activity against Gram-positive and -negative bacteria, respectively. To explore the antimicrobial mechanism of big defensin, we determined the solution structure of mature big defensin and performed a titration experiment with DPC micelles. Big defensin has a novel defensin structure; the C-terminal domain adopts a beta-defensin structure, and the N-terminal domain forms a unique globular conformation. It is noteworthy that the hydrophobic N-terminal domain undergoes a conformational change in micelle solution, while the C-terminal domain remains unchanged. Here, we propose that the N-terminal domain achieves its antimicrobial activity in a novel fashion and explain that big defensin has developed a strategy different from those of other beta-defensins to suppress the growth of Gram-positive bacteria.

Two-Stage pH Response of Poly(4-vinylpyridine) Grafted Gold Nanoparticles

ReceiVed April 22, 2008 ReVised Manuscript ReceiVed July 24, 2008 Polymer brushes have attracted much attention because the polymer tailored surface has desirable energetic, mechanical, and electrical functionalities. Many dense polymer brushes are covalently attached on various surfaces by the “grafting-from” strategy, and recently the surface-initiated atom-transfer radical polymerization (ATRP) has become a popular method in the fabrication of various polymer brushes on planar and spherical surfaces. In polymer physics, the responsive polymer chains will undergo a reversible conformational transition from a good solvent to a bad solvent at the “so-called” cloud point. For example, water below 32 °C is a good solvent for the thermosensitive poly(N-isopropylacrylamide); the polymer chains under this condition are hydrated and adopt a random coiled conformation. However, water becomes a poor solvent above 32 °C, where the polymer chains are dehydrated and turn into a globular conformation. Therefore, when the polymer chains are tethered on a solid surface as a polymer brush, the conformational transition will result in an adjustable property of the solid surface, which can be used to construct intelligent microor nanodevices.

AFM study of the structuration of an ionic surfactant and phenylalanine with κ-carrageenan

Local networks of κ-carrageenan adsorbed in the presence of an ionic surfactant and phenylalanine were examined by atomic force microscopy (AFM). Polymer chains of adsorbed carrageenan are aligned with crystallographic axes. The helical and globular conformations of carrageenan effectively bind the surfactant. Phenylalanine is not involved in the structuration of the carrageenan gel.

Spherical aggregates obtained from N-carboxymethylation and acetylation of chitosan

Chitosan is a biopolymer with great industrial potential. However, solubility in aqueous solutions limits some applications. In this paper, the N-carboxymethylation (CM) of chitosan generated five derivatives namely, N-carboxymethylchitosan (NCMC) 1, NCMC2, NCMC3, NCMC4, and NCMC5, from 10.1% to 80% of CM. Afterwards, a new NCMC6 (∼60% of CM) was acetylated to produce the NCMCAc derivate. The modifications were confirmed by 13C nuclear magnetic resonance. A globular conformation to NCMC derivatives was confirmed by association of static and dynamic light scattering in which the form factor (ρ) is ∼1.3 in phosphate buffer (pH 7.4). The NCMCAc showed a ρ of 0.75, which is characteristic of dense spheres. Topographical analyses were performed by atomic force microscopy images in which dense spheres were observed. The critical aggregation concentration (CAC) was determined using pyrene as a hydrophobic fluorescent probe. For NCMC1–6 and NCMCAc, a CAC of 1.0 and 0.1 mg mL−1 were, respectively, observed. NCMC1–6 and NCMCAc showed a globular and dense spherical conformation, respectively.

PEG attachment to osteoblasts enhances mechanosensitivity

Fluid flow induces proliferation and differentiation of osteoblasts, and fibrous structure like a primary cilium on a cell surface contributes to flow sensing and flow-driven gene regulation. We address a question: Does attachment of synthetic polymers on a cell surface enhance mechanosensitivity of osteoblasts? Using MC3T3 osteoblast cells (C4 clone) and a PEG polymer, one of whose termini was covalently linked to a succinimidyl succinate group (functionalized PEG–PEGSS), we examined attachment of PEGSS to osteoblasts and evaluated its effects on the mRNA expression of stress-responsive genes. AFM images exhibited globular PEGSS conformation of ∼100 nm in size, and SEM images confirmed the attachment of a cluster of pancake-like PEGSS molecules on the osteoblast surface. Compared to control cells incubated with unfunctionalized PEG, real-time PCR revealed that RNA upregulation of c-fos, egr1, ATF3 and Cox2 genes was magnified in the cells incubated with PEGSS. These results support a PEG-induced increase in mechanosensitivity of osteoblasts and indicate that the described approach would be useful to accelerate growth and development of osteoblasts for bone repair and tissue engineering.

Cortactin Adopts a Globular Conformation and Bundles Actin into Sheets

Cortactin is a filamentous actin-binding protein that plays a pivotal role in translating environmental signals into coordinated rearrangement of the cytoskeleton. The dynamic reorganization of actin in the cytoskeleton drives processes including changes in cell morphology, cell migration, and phagocytosis. In general, structural proteins of the cytoskeleton bind in the N-terminal region of cortactin and regulatory proteins in the C-terminal region. Previous structural studies have reported an extended conformation for cortactin. It is therefore unclear how cortactin facilitates cross-talk between structural proteins and their regulators. In the study presented here, circular dichroism, chemical cross-linking, and small angle x-ray scattering are used to demonstrate that cortactin adopts a globular conformation, thereby bringing distant parts of the molecule into close proximity. In addition, the actin bundling activity of cortactin is characterized, showing that fully polymerized actin filaments are bundled into sheet-like structures. We present a low resolution structure that suggests how the various domains of cortactin interact to coordinate its array of binding partners at sites of actin branching.

Vibrational Spectroscopy and Conformational Structure of Protonated Polyalanine Peptides Isolated in the Gas Phase

The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.

Three-dimensional Architecture of Hair-bundle Linkages Revealed by Electron-microscopic Tomography

The senses of hearing and balance rest upon mechanoelectrical transduction by the hair bundles of hair cells in the inner ear. Located at the apical cellular surface, each hair bundle comprises several tens of stereocilia and a single kinocilium that are interconnected by extracellular proteinaceous links. Using electron-microscopic tomography of bullfrog saccular sensory epithelia, we examined the three-dimensional structures of basal links, kinociliary links, and tip links. We observed significant differences in the appearances and dimensions of these three structures and found two distinct populations of tip links suggestive of the involvement of different proteins, splice variants, or protein-protein interactions. We noted auxiliary links connecting the upper portions of tip links to the taller stereocilia. Tip links and auxiliary links show a tendency to adopt a globular conformation when disconnected from the membrane surface.

Kinetics of Loop Formation in Polymer Chains

We investigate the kinetics of loop formation in ideal flexible polymer chains (the Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is tau(c) approximately tau(0)N(2) (where tau(0) is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that when a < b, tau(c) approximately N(alpha)(tau), where 1.5 < alpha(tau) < or = 2 in the range 7 < N < 200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a < b), which captures the two-stage mechanism by which looping occurs when a < b, we obtain an analytic expression for tauc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of tau(c) decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for tau(c) to a power law in N (tau(c) approximately N(alpha)(tau)) show that alpha(tau) varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent alpha(tau) decreases as the strength of the attractive monomer-monomer interactions increases. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined.