ResearchPad - Materials Chemistry Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters]]>


Dimerization is a common feature among the members of the neurotransmitter:sodium symporter (NSS) family of membrane proteins. Yet, the effect of dimerization on the mechanism of action of NSS members is not fully understood. In this study, we examined the collective dynamics of two members of the family, leucine transporter (LeuT) and dopamine transporter (DAT), to assess the significance of dimerization in modulating the functional motions of the monomers. We used to this aim the anisotropic network model (ANM), an efficient and robust method for modeling the intrinsic motions of proteins and their complexes. Transporters belonging to the NSS family are known to alternate between outward-facing (OF) and inward-facing (IF) states, which enables the uptake and release of their substrate (neurotransmitter) respectively, as the substrate is transported from the exterior to the interior of the cell. In both LeuT and DAT, dimerization is found to alter the collective motions intrinsically accessible to the individual monomers in favor of the functional transitions (OF IF), suggesting that dimerization may play a role in facilitating transport.

<![CDATA[Computation of Hemagglutinin Free Energy Difference by the Confinement Method]]>


Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs.

<![CDATA[Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase η]]> <![CDATA[pH Responsive and Oxidation Resistant Wet Adhesive based on Reversible Catechol–Boronate Complexation]]> <![CDATA[Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA]]>


An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results.

<![CDATA[Transition-metal-nitride-based thin films as novel energy harvesting materials]]> <![CDATA[Decorin Mimic Regulates Platelet-Derived Growth Factor and Interferon-γ Stimulation of Vascular Smooth Muscle Cells]]>


Following balloon injury, smooth muscle cells (SMCs) serve as targets for many of the pro-inflammatory and pro-fibrotic factors, including platelet-derived growth factor (PDGF) and interferon-γ (IFN-γ) released from activated inflammatory cells and platelets. Previously, our lab designed a mimic of the proteoglycan decorin, termed DS-SILY20, that suppressed vascular SMC proliferation, migration, and protein synthesis in vitro, and injured vessels treated with DS-SILY20 demonstrated reduced hyperplasia in vivo. Here we characterize the effects of DS-SILY20 on modulating PDGF and IFN-γ stimulation in both proliferative and quiescent human SMCs to further evaluate the potential impact of DS-SILY20-SMC interaction on restenosis. Nanomolar dissociation constants were observed between DS-SILY20 and both PDGF and IFN-γ. PDGF significantly increased migration, proliferation, and protein and cytokine expression, as well as increased ERK-1/2 and p38 MAPK phosphorylation in both quiescent and proliferative cultures. However, DS-SILY20 inhibited these increases, presumably through sequestration of the PDGF. Consistent with the complex responses seen with IFN-γ in SMC physiology in the literature, the response of SMC cultures to IFN-γ was variable and complex. However, where increased activity was seen with IFN-γ, DS-SILY20 attenuated this activity. Overall, the results suggest that DS-SILY20 would be an ideal alternative to traditional therapeutics used and may be an effective therapy for the prevention of intimal hyperplasia after balloon angioplasty.

<![CDATA[Protein–Protein Interactions in Dilute to Concentrated Solutions: α-Chymotrypsinogen in Acidic Conditions]]>


Protein–protein interactions were investigated for α-chymotrypsinogen by static and dynamic light scattering (SLS and DLS, respectively), as well as small-angle neutron scattering (SANS), as a function of protein and salt concentration at acidic conditions. Net protein–protein interactions were probed via the Kirkwood–Buff integral G22 and the static structure factor S(q) from SLS and SANS data. G22 was obtained by regressing the Rayleigh ratio versus protein concentration with a local Taylor series approach, which does not require one to assume the underlying form or nature of intermolecular interactions. In addition, G22 and S(q) were further analyzed by traditional methods involving fits to effective interaction potentials. Although the fitted model parameters were not always physically realistic, the numerical values for G22 and S(q → 0) were in good agreement from SLS and SANS as a function of protein concentration. In the dilute regime, fitted G22 values agreed with those obtained via the osmotic second virial coefficient B22 and showed that electrostatic interactions are the dominant contribution for colloidal interactions in α-chymotrypsinogen solutions. However, as protein concentration increases, the strength of protein–protein interactions decreases, with a more pronounced decrease at low salt concentrations. The results are consistent with an effective “crowding” or excluded volume contribution to G22 due to the long-ranged electrostatic repulsions that are prominent even at the moderate range of protein concentrations used here (<40 g/L). These apparent crowding effects were confirmed and quantified by assessing the hydrodynamic factor H(q → 0), which is obtained by combining measurements of the collective diffusion coefficient from DLS data with measurements of S(q → 0). H(q → 0) was significantly less than that for a corresponding hard-sphere system and showed that hydrodynamic nonidealities can lead to qualitatively incorrect conclusions regarding B22, G22, and static protein–protein interactions if one uses only DLS to assess protein interactions.

<![CDATA[Pyroglutamylated Amyloid-β Peptide Reverses Cross β-Sheets by a Prion-Like Mechanism]]>


The amyloid hypothesis causatively relates the fibrillar deposits of amyloid β peptide (Aβ) to Alzheimer’s disease (AD). More recent data, however, identify the soluble oligomers as the major cytotoxic entities. Pyroglutamylated Aβ (pE-Aβ) is present in AD brains and exerts augmented neurotoxicity, which is believed to result from its higher β-sheet propensity and faster fibrillization. While this concept is based on a set of experimental results, others have reported similar β-sheet contents in unmodified and pyroglutamylated Aβ, and slower aggregation of pE-Aβ as compared to unmodified Aβ, leaving the issue unresolved. Here, we assess the structural differences between Aβ and pE-Aβ peptides that may underlie their distinct cytotoxicities. Transmission electron microscopy identifies a larger number of prefibrillar aggregates of pE-Aβ at early stages of aggregation and suggests that pE-Aβ affects the fibrillogenesis even at low molar fractions. Circular dichroism and FTIR data indicate that while the unmodified Aβ readily forms β-sheet fibrils in aqueous media, pE-Aβ displays increased α-helical and decreased β-sheet propensity. Moreover, isotope-edited FTIR spectroscopy shows that pE-Aβ reverses β-sheet formation and hence fibrillogenesis of the unmodified Aβ peptide via a prion-like mechanism. These data provide a novel structural mechanism for pE-Aβ hypertoxicity; pE-Aβ undergoes faster formation of prefibrillar aggregates due to its increased hydrophobicity, thus shifting the initial stages of fibrillogenesis toward smaller, hypertoxic oligomers of partial α-helical structure.

<![CDATA[Proton Transfer Induced SOMO-to-HOMO Level Switching in One-Electron Oxidized A-T and G-C Base Pairs: A Density Functional Theory Study]]>


In the present study, we show that for one-electron oxidized A-T or G-C base pairs the singly occupied molecular orbital (SOMO) is located on A or G and is lower in energy than the doubly occupied highest-occupied molecular orbital (HOMO) localized to the pyrimidines, T or C. This directs second ionizations to the pyrimidine bases resulting in triplet state diradical dications, (A•+-T•+) and (G•+-C•+). On interbase proton transfer, the SOMO and HOMO levels switch and the second oxidation is redirected to G and A. For G-C, the doubly oxidized singlet G(-H)+-C(H+) is more stable than its triplet (G•+-C•+); however, for A-T, the triplet (A•+-T•+) lies lowest in energy. The study demonstrates that double ionization of the A-T base pair results in a triplet dication diradical, which is more stable than the proton-transferred triplet or singlet species; whereas, double ionization of the G-C base pair, the proton transferred doubly oxidized singlet, G(-H)+-C(H+), is more stable and has both oxidations on guanine. In DNA, with both A-T and G-C, multiple oxidations would transfer to the guanine base alone.

<![CDATA[Intramolecular N–H⋯Cl hydrogen bonds in the outer coordination sphere of a bipyridyl bisurea-based ligand stabilize a tetrahedral FeLCl2 complex]]>

A bipyridyl-bisurea ligand coordinates a tetrahedral FeCl2 complex and demonstrates secondary coordination sphere influence through intramolecular hydrogen bonding to the chloride ligands.

<![CDATA[A complete series of halocarbonyl molybdenum PNP pincer complexes – Unexpected differences between NH and NMe spacers]]>

In the present study a complete series of seven-coordinate neutral halocarbonyl Mo(II) complexes of the type [Mo(PNPMe-Ph)(CO)2X2] (X = I, Br, Cl, F), featuring the new PNP pincer ligand N,N′-bis(diphenylphosphino)-N,N′-methyl-2,6-diaminopyridine (PNPMe-Ph), were prepared and fully characterized. The synthesis of these complexes was accomplished by different methodologies depending on the halide ligands. For X = I and Br, [Mo(PNPMe-Ph)(CO)2I2] and [Mo(PNPMe-Ph)(CO)2Br2] were obtained by reacting [Mo(PNPMe-Ph)(CO)3] with stoichiometric amounts of I2 and Br2, respectively. Alternatively, these complexes were obtained upon treatment of [MoX2(CO)3(CH3CN)2] (X = I, Br) with 1 equiv. of PNPMe-Ph. On the other hand, in the case of X = Cl, [Mo(PNPMe-Ph)(CO)2Cl2] was afforded by the reaction of [Mo(CO)4(μ-Cl)Cl]2 with 1 equiv. of PNPMe-Ph. The equivalent procedure also worked for X = Br. Finally, addition of 1 equiv. of 1-fluoro-2,4,6-trimethylpyridinium tetrafluoroborate to [Mo(PNPMe-Ph)(CO)3] yielded the analogous fluorine complex [Mo(PNPMe-Ph)(CO)2F2]. The modification of the ligand scaffold by introducing a Me group instead of H changed the properties of the PNP-Ph ligand significantly. While in the present case exclusively neutral seven-coordinate complexes of the type [Mo(PNPMe-Ph)(CO)2X2] were obtained, with the parent PNP-Ph ligand, i.e., featuring NH spacers, cationic seven-coordinate complexes of the type [Mo(PNP-Ph)(CO)3X]X were afforded. DFT calculations indicated that the reactions are under thermodynamic control. The structures of representative complexes were determined by X-ray single crystal analyses.

<![CDATA[Structural Properties and Phase Behavior of Crosslinked Networks in Polymer Solutions]]>


Structural properties and phase behavior of crosslinked networks embedded in polymer solutions are theoretically investigated. The partial structure factor of the network is calculated using a matrix formulation of the random phase approximation and the forward scattering limit is correlated with the phase behavior. Swelling and deswelling processes are analyzed in terms of the polymer concentration, the mismatch of solvent quality with respect to polymer and network, the polymers incompatibility and their characteristic sizes. Most studies reported so far in the literature have focussed on the swelling of crosslinked networks and gels in pure solvents but the correlation of the structural properties with the phase behavior in the presence of high molecular weight polymers in solution has not been given sufficient attention. The present work is intended to fill this gap in view of the current efforts to develop novel drug encapsulating and targeted delivery devices.

<![CDATA[Thermodynamic Presynthetic Considerations for Ring-Opening Polymerization]]>


The need for polymers for high-end applications, coupled with the desire to mimic nature’s macromolecular machinery fuels the development of innovative synthetic strategies every year. The recently acquired macromolecular-synthetic tools increase the precision and enable the synthesis of polymers with high control and low dispersity. However, regardless of the specificity, the polymerization behavior is highly dependent on the monomeric structure. This is particularly true for the ring-opening polymerization of lactones, in which the ring size and degree of substitution highly influence the polymer formation properties. In other words, there are two important factors to contemplate when considering the particular polymerization behavior of a specific monomer: catalytic specificity and thermodynamic equilibrium behavior. This perspective focuses on the latter and undertakes a holistic approach among the different lactones with regard to the equilibrium thermodynamic polymerization behavior and its relation to polymer synthesis. This is summarized in a monomeric overview diagram that acts as a presynthetic directional cursor for synthesizing highly specific macromolecules; the means by which monomer equilibrium conversion relates to starting temperature, concentration, ring size, degree of substitution, and its implications for polymerization behavior are discussed. These discussions emphasize the importance of considering not only the catalytic system but also the monomer size and structure relations to thermodynamic equilibrium behavior. The thermodynamic equilibrium behavior relation with a monomer structure offers an additional layer of complexity to our molecular toolbox and, if it is harnessed accordingly, enables a powerful route to both monomer formation and intentional macromolecular design.

<![CDATA[What is the Etiology of Dysarthria and Ataxia in a Woman With Cancer?]]> ]]> <![CDATA[The effect of polymers on the phase behavior of balanced microemulsions: diblock-copolymer and comb-polymers]]>

The effect of some amphipilic diblock-copolymers and comb-polymers on a balanced Winsor III microemulsion system is investigated with the quaternary system n-octyl-β-d-glucoside/1-octanol/n-octane/D2O as basis system. The diblock-copolymers are polyethyleneoxide-co-polydodecenoxide (PEOxPEDODOy) and polyethyleneoxide-co-polybutyleneoxide (PEOxPEBUy), constituted of a straight chain hydrophilic part and a bulky hydrophobic part. Addition of the diblock-copolymer leads to an enhancement of the swelling of the middle phase by uptake of water and oil; a maximum boosting factor of 6 was obtained for PEO111PEDODO25. Nuclear magnetic resonance diffusometry yields the self-diffusion coefficients of all the components in the system. The diffusion experiments provide information on how the microstructure of the bicontinuous microemulsion changes upon addition of the polymers. The reduced self-diffusion coefficients of water and oil are sensitive to the type of polymer that is incorporated in the film. For the diblock-copolymers, as mainly used here, the reduced self-diffusion coefficient of oil and water will respond to how the polymer bends the film. When the film bends away from water, the reduced self-diffusion of the water will increase, whereas the oil diffusion will decrease due to the film acting as a barrier, hindering free diffusion. The self-diffusion coefficient of the polymer and surfactant are similar in magnitude and both decrease slightly with increasing polymer concentration.

<![CDATA[Solid-State NMR Characterization of Autofluorescent Fibrils Formed by the Elastin-Derived Peptide GVGVAGVG]]>


The characterization of the molecular structure and physical properties of self-assembling peptides is an important aspect of optimizing their utility as scaffolds for biomaterials and other applications. Here we report the formation of autofluorescent fibrils by an octapeptide (GVGVAGVG) derived via a single amino acid substitution in one of the hydrophobic repeat elements of human elastin. This is the shortest and most well-defined peptide so far reported to exhibit intrinsic fluorescence in the absence of a discrete fluorophore. Structural characterization by FTIR and solid-state NMR reveals a predominantly β-sheet conformation for the peptide in the fibrils, which are likely assembled in an amyloid-like cross-β structure. Investigation of dynamics and the effects of hydration on the peptide are consistent with a rigid, water excluded structure, which has implications for the likely mechanism of intrinsic fibril fluorescence.