Interchain Hydrodynamic Interaction and Internal Friction of Polyelectrolytes.

Polyelectrolytes (PE) are polymeric macromolecules in aqueous solutions characterized by their chain topology and intrinsic charge in a neutralizing fluid. Structure and dynamics are related to several characteristic screening length scales determined by electrostatic, excluded volume, and hydrodynamic interactions. We examine PE dynamics in dilute to semidilute conditions using dynamic light scattering, neutron spinecho spectroscopy, and pulse field gradient NMR spectroscopy. We connect macroscopic diffusion to segmental chain dynamics, revealing a decoupling of local chain dynamics from interchain interactions. Collective diffusion is described within a colloidal picture, including electrostatic and hydrodynamic interactions. Chain dynamics is characterized by the classical Zimm model of a neutral chain retarded by internal friction. We observe that hydrodynamic interactions are not fully screened between chains and that the internal friction within the chain increases with an increase in ion condensation on the chain.

Stacking Interactions and Flexibility of Human Telomeric Multimers.

G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions, G4s undergo multimerization. Here, we investigate the stacking interactions and structural features of telomeric G4 multimers by means of a novel low-resolution structural approach that combines small-angle X-ray scattering (SAXS) with extremely coarse-grained (ECG) simulations. The degree of multimerization and the strength of the stacking interaction are quantitatively determined in G4 self-assembled multimers. We show that self-assembly induces a significant polydispersity of the G4 multimers with an exponential distribution of contour lengths, consistent with a step-growth polymerization. On increasing DNA concentration, the strength of the stacking interaction between G4 monomers increases, as well as the average number of units in the aggregates. We utilized the same approach to explore the conformational flexibility of a model single-stranded long telomeric sequence. Our findings indicate that its G4 units frequently adopt a beads-on-a-string configuration. We also observe that the interaction between G4 units can be significantly affected by complexation with benchmark ligands. The proposed methodology, which identifies the determinants that govern the formation and structural flexibility of G4 multimers, may be an affordable tool aiding in the selection and design of drugs that target G4s under physiological conditions.

Integrative dynamic structural biology unveils conformers essential for the oligomerization of a large GTPase.

Guanylate binding proteins (GBPs) are soluble dynamin-like proteins that undergo a conformational transition for GTP-controlled oligomerization and disrupt membranes of intracellular parasites to exert their function as part of the innate immune system of mammalian cells. We apply neutron spin echo, X-ray scattering, fluorescence, and EPR spectroscopy as techniques for integrative dynamic structural biology to study the structural basis and mechanism of conformational transitions in the human GBP1 (hGBP1). We mapped hGBP1's essential dynamics from nanoseconds to milliseconds by motional spectra of sub-domains. We find a GTP-independent flexibility of the C-terminal effector domain in the µs-regime and resolve structures of two distinct conformers essential for an opening of hGBP1 like a pocket knife and for oligomerization. Our results on hGBP1's conformational heterogeneity and dynamics (intrinsic flexibility) deepen our molecular understanding relevant for its reversible oligomerization, GTP-triggered association of the GTPase-domains and assembly-dependent GTP-hydrolysis.

Intrinsic Disorder of the Neuronal SNARE Protein SNAP25a in its Pre-fusion Conformation.

The neuronal SNARE protein SNAP25a (isoform 2) forms part of the SNARE complex eliciting synaptic vesicle fusion during neuronal exocytosis. While the post-fusion cis-SNARE complex has been studied extensively, little is known about the pre-fusion conformation of SNAP25a. Here we analyze monomeric SNAP25a by NMR spectroscopy, further supported by small-angle X-ray scattering (SAXS) experiments. SAXS data indicate that monomeric SNAP25 is more compact than a Gaussian chain but still a random coil. NMR shows that for monomeric SNAP25a, before SNAP25a interacts with its SNARE partners to drive membrane fusion, only the N-terminal part (region A5 to V36) of the first SNARE motif, SN1 (L11 - L81), is helical, comprising two α-helices (ranging from A5 to Q20 and S25 toV36). From E37 onwards, SNAP25a is mostly disordered and displays high internal flexibility, including the C-terminal part of SN1, almost the entire second SNARE motif (SN2, N144-A199), and the connecting loop region. Apart from the N-terminal helices, only the C-termini of both SN1 (E73 - K79) and SN2 (region T190 - A199), as well as two short regions in the connecting loop (D99 - K102 and E123 - M127) show a weak α-helical propensity (α-helical population < 25%). We speculate that the N-terminal helices (A5 to Q20 and S25 to V36) which constitute the N-terminus of SN1 act as a nucleation site for initiating SNARE zippering.

Passive Macromolecular Translocation Mechanism through Lipid Membranes.

The translocation of biologically active macromolecules through cell membranes is of vital importance for cells and is a key process for drug delivery. Proteins exploit specific conformational changes in their secondary structure to facilitate membrane translocation. For the large class of biological and synthetic macromolecules, where such conformational adaptions are not possible, guidelines to tailor the structure of monomers and macromolecules to aid membrane translocation and cross-membrane drug delivery would be highly desirable. Here, we use alternating amphiphilic macromolecules to systematically investigate the relation between polarity, polymer chain length, lipid chain length, polymer concentration, and temperature on membrane partition and translocation rate. We employed pulse field gradient NMR and confocal fluorescence microscopy to determine membrane adsorption and desorption rate constants and partitioning coefficients. We find that translocation is a two-step process involving a fast adsorption and membrane insertion process and a slower desorption process. Membrane insertion is a key step that determines the molecular weight, concentration, and temperature dependences. Passive translocation is possible on time scales from minutes to hours. Macromolecules with different adapted hydrophilic/hydrophobic comonomer sequences show the same translocation rate, indicating that common optimized translocation conditions can be realized with a variety of monomer chemical structures. The investigated copolymers are biocompatible, biodegradable, and capable of transporting a hydrophobic payload through the lipid membrane. This detailed understanding of the macromolecular translocation mechanism enables to better tailor the delivery of active agents using macromolecular carriers.

Variation of Structural and Dynamical Flexibility of Myelin Basic Protein in Response to Guanidinium Chloride.

Myelin basic protein (MBP) is intrinsically disordered in solution and is considered as a conformationally flexible biomacromolecule. Here, we present a study on perturbation of MBP structure and dynamics by the denaturant guanidinium chloride (GndCl) using small-angle scattering and neutron spin-echo spectroscopy (NSE). A concentration of 0.2 M GndCl causes charge screening in MBP resulting in a compact, but still disordered protein conformation, while GndCl concentrations above 1 M lead to structural expansion and swelling of MBP. NSE data of MBP were analyzed using the Zimm model with internal friction (ZIF) and normal mode (NM) analysis. A significant contribution of internal friction was found in compact states of MBP that approaches a non-vanishing internal friction relaxation time of approximately 40 ns at high GndCl concentrations. NM analysis demonstrates that the relaxation rates of internal modes of MBP remain unaffected by GndCl, while structural expansion due to GndCl results in increased amplitudes of internal motions. Within the model of the Brownian oscillator our observations can be rationalized by a loss of friction within the protein due to structural expansion. Our study highlights the intimate coupling of structural and dynamical plasticity of MBP, and its fundamental difference to the behavior of ideal polymers in solution.

Self assembling cluster crystals from DNA based dendritic nanostructures.

Cluster crystals are periodic structures with lattice sites occupied by several, overlapping building blocks, featuring fluctuating site occupancy, whose expectation value depends on thermodynamic conditions. Their assembly from atomic or mesoscopic units is long-sought-after, but its experimental realization still remains elusive. Here, we show the existence of well-controlled soft matter cluster crystals. We fabricate dendritic-linear-dendritic triblock composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons of the first and second generation. Conclusive small-angle X-ray scattering (SAXS) evidence reveals that solutions of these triblock at sufficiently high concentrations undergo a reversible phase transition from a cluster fluid to a body-centered cubic (BCC) cluster crystal with density-independent lattice spacing, through alteration of temperature. Moreover, a rich concentration-temperature phase diagram demonstrates the emergence of various ordered nanostructures, including BCC cluster crystals, birefringent cluster crystals, as well as hexagonal phases and cluster glass-like kinetically arrested states at high densities.

Spectroscopic and Small-angle X-ray scattering analysis of binding between Copper(II) -1-allylimidazole complex, a potential anti-tumor agent, and bovine serum albumin.

Interactions between transport proteins and compounds with therapeutic potential are pharmacologically important. In this study, using fluorescence, circular dichroism (CD), and small-angle X-ray Scattering (SAXS), we investigated the interaction between bovine serum albumin (BSA) and a copper(II)-1-allylimidazole complex with potential anti-cancer properties. The results revealed dynamic fluorescence quenching of the model carrier protein BSA by the copper(II) complex. The enthalpy change (ΔH), free energy (ΔG), and entropy change (ΔS) were calculated to be 108 kJ/mol, -16.47 kJ/mol, and 419 J/mol K, respectively, according to the Van't Hoff equation. The reaction was an endothermic and spontaneous process, and hydrophobic interactions played a major role in binding. The results indicate a much lower affinity (Kb âˆ¼ 102-103) for the metal complex compared with similar compounds (Kb âˆ¼ 103-105). CD showed that the studied copper(II) complex does not change the secondary structure of the protein, while SAXS showed that the this compound may attach to the protein surface and stimulate interactions between proteins. The results suggest that the copper(II) complex with 1-allylimidazole binds weakly to BSA, leading to aggregation of albumin in solution, thereby altering its pharmacokinetic properties. The findings are pertinent to drug design.

Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model.

Disordered regions as found in intrinsically disordered proteins (IDP) or during protein folding define response time to stimuli and protein folding times. Neutron spin-echo spectroscopy is a powerful tool to directly access the collective motions of the unfolded chain to enlighten the physical origin of basic conformational relaxation. During the thermal unfolding of native ribonuclease A, we examine the structure and dynamics of the disordered state within a two-state transition model using polymer models, including internal friction, to describe the chain dynamics. The presence of four disulfide bonds alters the disordered configuration to a more compact configuration compared to a Gaussian chain that is defined by the additional links, as demonstrated by coarse-grained simulation. The dynamics of the disordered chain is described by Zimm dynamics with internal friction (ZIF) between neighboring amino acids. Relaxation times are dominated by mode-independent internal friction. Internal friction relaxation times show an Arrhenius-like behavior with an activation energy of 33 kJ/mol. The Zimm dynamics is dominated by internal friction and suggest that the characteristic motions correspond to overdamped elastic modes similar to the motions observed for folded proteins but within a pool of disordered configurations spanning the configurational space. For IDP, internal friction dominates while solvent friction and hydrodynamic interactions are smaller corrections.

Investigation of Cytotoxicity, Oxidative Stress, and Inflammatory Responses of Tantalum Nanoparticles in THP-1-Derived Macrophages.

Tantalum (Ta) is gaining attention as a biomaterial in bone tissue engineering. Although the clinical advantage of Ta-based implants for primary and revision total joint replacement (TJA) has been well documented, few studies investigated the effect of wear products of Ta implants on peri-implant cells, and their potential contribution to aseptic implant loosening. This study is aimed at examining the cytotoxicity, oxidative stress, and proinflammatory potential of Ta and TiO2 nanoparticles (NPs) on macrophages in vitro. NPs were characterized using scanning electron microscopy, dynamic light scattering, and energy-dispersive X-ray. To test the NP-mediated cellular response in macrophages, THP-1-derived macrophages were challenged with both NPs, and cytotoxicity was analyzed using CCK-8 and LDH assays. Flow cytometry was used to investigate particle uptake and their internalization routes. NP-mediated oxidative stress was investigated by measuring the production of reactive oxygen species, and their proinflammatory potential was determined by quantifying the production of TNFα and IL-1ß in cell culture supernatants using ELISA. We found that both Ta and TiO2 NPs were taken up through actin-dependent phagocytosis, although TiO2 NPs did also show some involvement of macropinocytosis and clathrin-mediated endocytosis. Ta NPs caused no apparent toxicity, while TiO2 NPs demonstrated significant cytotoxicity at a concentration of over 100µg/mL at 24 h. Ta NPs induced negligible ROS generation and proinflammatory cytokines (TNFα, IL-1ß) in macrophages. In contrast, TiO2 NPs markedly induced these effects in a dose-dependent manner. Our findings indicate that Ta NPs are inert, nontoxic, and noninflammatory. Therefore, Ta could be considered an excellent biomaterial in primary and revision joint arthroplasty implants.

Poly(propylene imine) dendrimers can bind to PEGylated albumin at PEG and albumin surface: Biophysical examination of a PEGylated platform to transport cationic dendritic nanoparticles.

Cationic dendrimers are considered one of the best drug transporters in the body. However, in order to improve their biocompatibility, modification of them is required to reduce toxicity. In this way, many dendrimers may lose their original properties, for example, anticancer. To improve biocompatibility of dendrimers, it is possible to complex them with albumin, as is done very often in drug delivery. However, the interaction of dendrimers with albumin can lead to protein structure disruption or no complexation at all. Therefore, the investigation of the interaction between cationic poly-(propylene imine) dendrimers and polyethylene glycol (PEG)-albumin by fluorescence, circular dichroism, small angle X-ray scattering (SAXS), and transmission electron microscopy was carried out. Results show that cationic dendrimers bind to PEGylated albumin at PEG and albumin surfaces. The obtained results for 5k-PEG indicate a preferential binding of the dendrimers to PEG. For 20k-PEG binding of dendrimers to PEG and protein could induce a collapse of the PEG chain onto the protein surface. This opens up new possibilities to the use of PEGylated albumin as a platform to carry dendrimers without changing the albumin structure and improve the pharmacokinetic properties of dendrimers without further modification.

Expanding crystallization tools for nucleic acid complexes using U1A protein variants.

The major bottlenecks in structure elucidation of nucleic acids are crystallization and phasing. Co-crystallization with proteins is a straight forward approach to overcome these challenges. The human RNA-binding protein U1A has previously been established as crystallization module, however, the absence of UV-active residues and the predetermined architecture in the asymmetric unit constitute clear limitations of the U1A system. Here, we report three crystal structures of tryptophan-containing U1A variants, which expand the crystallization toolbox for nucleic acids. Analysis of the structures complemented by SAXS, NMR spectroscopy, and optical spectroscopy allow for insights into the potential of the U1A variants to serve as crystallization modules for nucleic acids. In addition, we report a fast and efficient protocol for crystallization of RNA by soaking and present a fluorescence-based approach for detecting RNA-binding in crystallo. Our results provide a new tool set for the crystallization of RNA and RNA:DNA complexes.

Reduced Internal Friction by Osmolyte Interaction in Intrinsically Disordered Myelin Basic Protein.

Urea is a strong denaturing osmolyte that disrupts noncovalent bonds in proteins. Here, we present a small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE) study on the structure and dynamics of the intrinsically disordered myelin basic protein (MBP) denatured by urea. SANS results show that urea-denatured MBP is more compact than ideal polymers, while its secondary structure content is entirely lost. NSE experiments reveal concomitantly an increase of the relaxation time and of the amplitude of internal motions in urea-denatured MBP as compared to native MBP. If interpreted in terms of the Zimm model including internal friction (ZIF), the internal friction parameter decreased by a factor of 6.5. Urea seems to not only smooth local energy barriers, reducing internal friction on a local scale, but also significantly reduces the overall depth of the global energy landscape. This leads to a nearly complete loss of restoring forces beyond entropic forces and in turn allows for larger motional amplitudes. Obviously, the noncovalent H-bonds are largely eliminated, driving the unfolded protein to be more similar to a synthetic polymer.

Jscatter, a program for evaluation and analysis of experimental data.

The aim of Jscatter is the processing of experimental data and physical models with the focus to enable the user to develop/modify their own models and use them within experimental data evaluation. The basic structures dataArray and dataList contain matrix-like data of different size including attributes to store corresponding metadata. The attributes are used in fit routines as parameters allowing multidimensional attribute dependent fitting. Several modules provide models mainly applied in neutron and X- ray scattering for small angle scattering (form factors and structure factors) and inelastic neutron scattering. The intention is to provide an environment with fit routines, data handling routines (based on NumPy arrays) and a model library to allow the user to focus onto user-written models for data analysis with the benefit of convenient documentation of scientific data evaluation in a scripting environment.

Localised contacts lead to nanosecond hinge motions in dimeric bovine serum albumin.

Domain motions in proteins are crucial for biological function. In the present manuscript, we present a neutron spin-echo spectroscopy (NSE) study of native bovine serum albumin (BSA) in solution. NSE allows to probe both global and internal dynamics of the BSA monomer and dimer equilibrium that is formed in solution. Using a model independent approach, we were able to identify an internal dynamic process in BSA that is visible in addition to global rigid-body diffusion of the BSA monomer and dimer mixture. The observed internal protein motion is characterised by a relaxation time of 43 ns. The overdamped Brownian oscillator was considered as an alternative analytical theory that was able to describe the internal process as first-order approximation. More detailed information on the physical nature of the internal protein motion was extracted from the q-dependent internal diffusion coefficients ΔDeff(q) that were detected by NSE in addition to global rigid-body translational and rotational diffusion. The ΔDeff(q) were interpreted using normal mode analysis based on the available crystal structures of the BSA monomer and dimer as structural test models. Normal mode analysis demonstrates that the observed internal dynamic process can be attributed to bending motion of the BSA dimer. The native BSA monomer does not show any internal dynamics on the time- and length-scales probed by NSE. An intermolecular disulphide bridge or a direct structural contact between the BSA monomers forms a localised link acting as a molecular hinge in the BSA dimer. The effect of that hinge on the observed motion of BSA in the used dimeric structural model is discussed in terms of normal modes in a molecular picture.

Creating a synthetic platform for the encapsulation of nanocrystals with covalently bound polymer shells.

We present a platform for the encapsulation of superparamagnetic iron oxide nanocrystals (SPIONs) with a highly stable diblock copolymer shell allowing a homogeneous dispersion of the nanocrystals into a polymer matrix in the resulting nanocomposites. High polymer shell stability was achieved by crosslinking the inner polydiene shell for example in a persulfate based redox process. The advantage of this crosslinking reaction is the avoidance of heat and UV light for the initiation, making it suitable for heat or UV sensitive systems. In addition, we were able to minimize the ligand excess needed for the encapsulation and showcased a variation of molecular weight and composition as well as different ligands which lead to stable micelles. The encapsulated nanocrystals as well as the nanocomposite materials were characterized by transmission electron microscopy (TEM) and small angle scattering (SAXS and SANS).

Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway.

A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.

Confinement Facilitated Protein Stabilization As Investigated by Small-Angle Neutron Scattering.

While mesoporous silicas have been shown to be a compelling candidate for drug delivery and the implementation of biotechnological applications requiring protein confinement and immobilization, the understanding of protein behavior upon physical adsorption into silica pores is limited. Many indirect methods are available to assess general adsorbed protein stability, such as Fourier-transform infrared spectroscopy and activity assays. However, the limitation of these methods is that spatial protein arrangement within the pores cannot be assessed. Mesoporous silicas pose a distinct challenge to direct methods, such as transmission electron microscopy, which lacks the contrast and resolution required to adequately observe immobilized protein structure, and nuclear magnetic resonance, which is computationally intensive and requires knowledge of the primary structure a priori. Small-angle neutron scattering can surmount these limitations and observe spatial protein arrangement within pores. Hereby, we observe the stabilization of fluid-like protein arrangement, facilitated by geometry-dependent crowding effects in cylindrical pores of ordered mesoporous silica, SBA-15. Stabilization is induced from a fluid-like structure factor, which is observed for samples at maximum protein loading in SBA-15 with pore diameters of 6.4 and 8.1 nm. Application of this effect for prevention of irreversible aggregation in high concentration environments is proposed.

Influence of PEGylation on Domain Dynamics of Phosphoglycerate Kinase: PEG Acts Like Entropic Spring for the Protein.

Protein-polymer conjugation is a widely used technique to develop protein therapeutics with improved pharmacokinetic properties as prolonged half-life, higher stability, water solubility, lower immunogenicity, and antigenicity. Combining biochemical methods, small angle scattering (SAXS/SANS), and neutron spin-echo spectroscopy, here we examine the impact of PEGylation (i.e., the covalent conjugation with poly(ethylene glycol) or PEG) on structure and internal domain dynamics of phosphoglycerate kinase (PGK) to elucidate the reason for reduced activity that is connected to PEGylation. PGK is a protein with a hinge motion between the two main domains that is directly related to function. We find that secondary structure and ligand access to the binding sites are not affected. The ligand induced cleft closing is unchanged. We observe an additional internal motion between covalent bonded PEG and the protein compatible with Brownian motion of PGK in a harmonic potential. Entropic interaction with the full PEG chain leads to a force constant of about 8 pN/nm independent of PEG chain length. This additional force preserves protein structure and has negligible effects on the functional domain dynamics of the protein. PEGylation seems to reduce activity just by acting as a local crowder for the ligands. The newly identified interaction mechanism might open possibilities to improve rational design of protein-polymer conjugates.

Bioactivity and properties of a dental adhesive functionalized with polyhedral oligomeric silsesquioxanes (POSS) and bioactive glass.

OBJECTIVES: This study aimed to analyze the effect of infiltrating a commercial adhesive with nanosized bioactive glass (BG-Bi) particles or methacryl-functionalized polyhedral oligomeric silsesquioxanes (POSS) on material properties and bioactivity. METHODS: An acetone-based dental adhesive (Solobond Plus adhesive, VOCO GmbH, Cuxhaven, Germany) was infiltrated with nanosized bioactive glass particles (0.1 or 1wt%), or with monofunctional or multifunctional POSS particles (10 or 20wt%). Unfilled adhesive served as control. Dispersion and hydrodynamic radius of the nanoparticles were studied by dynamic light scattering. Set specimens were immersed for 28days in artificial saliva at 37°C, and surfaces were mapped for the formation of calcium phospate (Ca/P) precipitates (scanning electron microscopy/energy-dispersive X-ray spectroscopy). Viscosity (rheometry) and the structural characteristic of the networks were studied, such as degree of conversion (FTIR spectroscopy), sol fraction and water sorption. RESULTS: POSS particles showed a good dispersion of the particles for both types of particles being smaller than 3nm, while the bioactive glass particles had a strong tendency to agglomerate. All nanoparticles induced the formation of Ca/P precipitates. The viscosity of the adhesive was not or only slightly increased by POSS particle addition but strongly increased by the bioactive glass particles. The degree of conversion, water sorption and sol fraction showed a maintained or improved network structure and properties when filled with BG-Bi and multifunctional POSS, however, less polymerization was found when loading a monofunctional POSS. SIGNIFICANCE: Multifunctional POSS may be incorporated into dental adhesives to provide a bioactive potential without changing material properties adversely.