Hemoglobin dynamics in red blood cells: correlation to body temperature

Both hemoglobin and hemin cause damage to retinal pigment epithelium through the iron ion accumulation

Subretinal hemorrhages result in poor vision and visual field defects. During hemorrhage, several potentially toxic substances are released from iron-based hemoglobin and hemin, inducing cellular damage, the detailed mechanisms of which remain unknown. We examined the effects of excess intracellular iron on retinal pigment epithelial (RPE) cells. A Fe2+ probe, SiRhoNox-1 was used to investigate Fe2+ accumulation after treatment with hemoglobin or hemin in the human RPE cell line ARPE-19. We also evaluated the production of reactive oxygen species (ROS) and lipid peroxidation. Furthermore, the protective effect of-an iron chelator, 2,2'-bipyridyl (BP), and ferrostatin-1 (Fer-1) on the cell damage, was evaluated. Fe2+ accumulation increased in the hemoglobin- or hemin-treated groups, as well as intracellular ROS production and lipid peroxidation. In contrast, BP treatment suppressed RPE cell death, ROS production, and lipid peroxidation. Pretreatment with Fer-1 ameliorated cell death in a concentration-dependent manner and suppressed ROS production and lipid peroxidation. Taken together, these findings indicate that hemoglobin and hemin, as well as subretinal hemorrhage, may induce RPE cell damage and visual dysfunction via intracellular iron accumulation.

Observation of non-equilibrium fluctuation in the shear-stress-driven hemoglobin aggregates

Non-equilibrium fluctuations caused by the rearrangement of hemoglobin molecules into an aggregate state under shear stress have been investigated experimentally. The flow response under the shear stress (σ) corroborates the presence of contrasting aggregate and rejuvenation states governed by entropy production and consumption events. From the time-dependent shear rate fluctuation studies of aggregate states, the probability distribution function (PDF) of the rate of work done is observed to be spread from negative to positive values with a net positive mean. The PDFs follow the steady-state fluctuation theorem, even at a smaller timescale than that desired by the theorem. The behavior of the effective temperature (Teff) that emerges from a non-equilibrium fluctuation and interconnects with the structural restrictions of the aggregate state of our driven system is observed to be within the boundary of the thermodynamic uncertainty. The increase in Teff with the applied σ illustrates a phenomenal nonlinear power flux-dependent aggregating behavior in a classic bio-molecular-driven system.

Elemental and molecular characterization of degrading blood pools

Blood is a commonly encountered type of biological evidence and can provide critical information about the crime that occurred. The ability to accurately and precisely determine the time since deposition (TSD) of a bloodstain is highly sought after in the field of forensic science. Current spectral methods for determining TSD are typically developed using small volume bloodstains, we investigate the applicability to larger volume blood pools where drying and degradation mechanics are different. We explored the differences that exist between the surface and bulk of dried segments from fragments collected from 15 mL dried blood pools and identified heterogeneity using RGB colour analysis and hierarchical cluster analysis (HCA). The physical, molecular, and atomic differences between the layers were further investigated using scanning electron microscopy (SEM), X-Ray photoelectron spectroscopy (XPS), attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, and Raman spectroscopy. SEM identified different morphology on the surface and the bulk indicative of density-dependant cellular settling. XPS revealed that iron was not present on the surface but rather was present in the bulk where the red blood cells had settled. The oxidation state of the iron was quantified over three weeks in which it transitioned from entirely Fe2+ to primarily Fe3+, as expected for ex vivo degradation of hemoglobin. Further, indications of amide saponification occurring at the blood-air interface were identified in the increased quantity of the C-O moiety relative to CO, and the formation of free amines and OC-ONa groups over time. ATR-FTIR and Raman spectroscopy provided insights into differences in the molecular composition of the layers, suggesting that the surface consists of more nucleic acids, lipids, and glycoproteins than the bulk, which was dominated by proteins (p < 0.001% using principal component analysis (PCA)). Additionally, spectral band trends previously reported to have applicability to the estimation of TSD were observed for the bulk portion of the blood pool as the Hb underwent predictable time dependant changes from oxyHb to metHb. PCA was performed based on all spectral data which demonstrated statistically significant differences between the surface and bulk, as well as proof-of-concept for linear TSD estimation models.

Effect of crowding, compartmentalization and nanodomains on protein modification and redox signaling - current state and future challenges

Biological milieus are highly crowded and heterogeneous systems where organization of macromolecules within nanodomains (e.g. membraneless compartments) is vital to the regulation of metabolic processes. There is an increasing interest in understanding the effects that such packed environments have on different biochemical and biological processes. In this context, the redox biochemistry and redox signaling fields are moving towards investigating oxidative processes under conditions that exhibit these key features of biological systems in order to solve existing paradigms including those related to the generation and transmission of specific redox signals within and between cells in both normal physiology and under conditions of oxidative stress. This review outlines the effects that crowding, nanodomain formation and altered local viscosities can have on biochemical processes involving proteins, and then discusses some of the reactions and pathways involving proteins and oxidants that may, or are known to, be modulated by these factors. We postulate that knowledge of protein modification processes (e.g. kinetics, pathways and product formation) under conditions that mimic biological milieus, will provide a better understanding of the response of cells to endogenous and exogenous stressors, and their role in ageing, signaling, health and disease.

Water dynamics around T0 vs R4 of hemoglobin from local hydrophobicity analysis

The local hydration around tetrameric hemoglobin (Hb) in its T₀ and R₄ conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the α₁β₂ and α₂β₁ interfaces, responsible for the quaternary T → R transition, which is encoded in the Monod-Wyman-Changeux model, as well as comparison with earlier computations of the solvent accessible surface area, makes clear that the two quantities measure different aspects of hydration. Local hydrophobicity quantifies the presence and structure of water molecules at the interface, whereas "buried surface" reports on the available space for solvent. For simulations with Hb frozen in its T₀ and R₄ states, the correlation coefficient between LH and buried surface is 0.36 and 0.44, respectively, but it increases considerably if the 95% confidence interval is used. The LH with Hb frozen and flexible changes little for most residues at the interfaces but is significantly altered for a few select ones: Thr41α, Tyr42α, Tyr140α, Trp37β, Glu101β (for T₀) and Thr38α, Tyr42α, Tyr140α (for R₄). The number of water molecules at the interface is found to increase by ∼25% for T₀ → R₄, which is consistent with earlier measurements. Since hydration is found to be essential to protein function, it is clear that hydration also plays an essential role in allostery.

Sulfhemoglobin under the spotlight - Detection and characterization of SHb and HbFeIII-SH

Sulfhemoglobinemia is an incurable disease caused by an overdose of sulfur-containing drugs with oxidizing properties. Its diagnosis remains hindered due to the similarity of symptoms to other pathological state - methemoglobinemia, as well as contradictory information on the structure and characteristics of sulfhemoglobin. Herein, we present sulfhemoglobinemia model on living functional human erythrocytes, designed to recreate processes which could take place in a patient body in order to complement missing information and highlight distinctiveness of two hemoglobin (Hb) adducts formed after interaction with sulfur donors. Employed techniques, UV-Vis absorption, Raman, Fourier transformed infrared (FT-IR) and electronic circular dichroism (ECD) spectroscopies, allowed to distinguish and characterize Hb adduct with sulfur atom bounded directly to the iron ion (HbFe^III-SH), and irreversibly connected to the porphyrin ring (SHb - sulfhemoglobin). Presented herein results provided also new evidence on formation of both these hemoglobin adducts inside functional erythrocytes under oxidative conditions and during sulfur-containing drug presence, what can be further translated into future physiological studies. Moreover, we found that sulfur attachment to the porphyrin ring altered Hb structure and lead to changes in protein packing inside RBCs, eventually. Interestingly, measurement of blood drop smear by Raman spectroscopy occurred the most accurate method to differentiate HbFe^III-SH and SHb, indicating potential of this technique in sulfhemoglobinemia diagnosis.

The alternative proteome in neurobiology

Translation involves the biosynthesis of a protein sequence following the decoding of the genetic information embedded in a messenger RNA (mRNA). Typically, the eukaryotic mRNA was considered to be inherently monocistronic, but this paradigm is not in agreement with the translational landscape of cells, tissues, and organs. Recent ribosome sequencing (Ribo-seq) and proteomics studies show that, in addition to currently annotated reference proteins (RefProt), other proteins termed alternative proteins (AltProts), and microproteins are encoded in regions of mRNAs thought to be untranslated or in transcripts annotated as non-coding. This experimental evidence expands the repertoire of functional proteins within a cell and potentially provides important information on biological processes. This review explores the hitherto overlooked alternative proteome in neurobiology and considers the role of AltProts in pathological and healthy neuromolecular processes.

Molecular rotors in haemoglobin and bovine serum albumin proteins

Molecular rotors are fluorescent viscosity probes and their response in simple fluids is known to be a Förster-Hoffman power law, allowing the viscosity of the medium to be quantified by its fluorescence intensity. They are attractive probes in biological media, usually consisting of proteins, but how does a molecular rotor behave in a protein solution? The response of the DASPI molecular rotor is compared in two globular protein solutions of similar size, haemoglobin (Hb) and bovine serum albumin, one absorbent, the other not. In absorbent Hb, a model validated by experiments in triangular geometry allows one to correct the absorbing effect and to compare the rotor response in both proteins. With concomitant microrheology measurements, we investigate the relation between the DASPI fluorescence intensity and solution viscosity. In protein solutions, we show that viscosity is no longer the parameter determining the rotor response in contrast to simple fluids. Varying the viscosity by concentration or temperature is not equivalent, and the Förster-Hoffmann power laws do not apply when the solution concentration varies. We show that the concentration regime of the protein solution, semi-dilute or concentrated, determines the sensitivity of the rotor to its environment.

Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture

The crowded environment of biological systems such as the interior of living cells is occupied by macromolecules with a broad size distribution. This situation of polydispersity might influence the dependence of the diffusive dynamics of a given tracer macromolecule in a monodisperse solution on its hydrodynamic size and on the volume fraction. The resulting size dependence of diffusive transport crucially influences the function of a living cell. Here, we investigate a simplified model system consisting of two constituents in aqueous solution, namely, of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin (Ig), systematically depending on the total volume fraction and ratio of these constituents. From high-resolution quasi-elastic neutron spectroscopy, the separate apparent short-time diffusion coefficients for BSA and Ig in the mixture are extracted, which show substantial deviations from the diffusion coefficients measured in monodisperse solutions at the same total volume fraction. These deviations can be modeled quantitatively using results from the short-time rotational and translational diffusion in a two-component hard sphere system with two distinct, effective hydrodynamic radii. Thus, we find that a simple colloid picture well describes short-time diffusion in binary mixtures as a function of the mixing ratio and the total volume fraction. Notably, the self-diffusion of the smaller protein BSA in the mixture is faster than the diffusion in a pure BSA solution, whereas the self-diffusion of Ig in the mixture is slower than in the pure Ig solution.

Exploring the Limits of Biological Complexity Amenable to Studies by Incoherent Neutron Spectroscopy

The wavelengths of neutrons available at neutron scattering facilities are comparable with intra- and inter-molecular distances, while their energies are comparable with molecular vibrational energies, making such neutrons highly suitable for studies of molecular-level dynamics. The unmistakable trend in neutron spectroscopy has been towards measurements of systems of greater complexity. Several decades of studies of dynamics using neutron scattering have witnessed a progression from measurements of solids to liquids to protein complexes and biomembranes, which may exhibit properties characteristic of both solids and liquids. Over the last two decades, the frontier of complexity amenable to neutron spectroscopy studies has reached the level of cells. Considering this a baseline for neutron spectroscopy of systems of the utmost biological complexity, we briefly review what has been learned to date from neutron scattering studies at the cellular level and then discuss in more detail the recent strides into neutron spectroscopy of tissues and whole multicellular organisms.

The functional role of the hemoglobin-water interface

The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from in vitro, in vivo, and computational experiments (molecular dynamics simulations) are summarized and put into perspective. One of the main findings from the computations is that the stability of the deoxy, ligand-free T-state (T₀) can be stabilized relative to the deoxy R-state (R₀) only in sufficiently large simulation boxes for the hydrophobic effect to manifest itself. This effect directly influences protein stability and is operative also under physiological conditions. Furthermore, molecular simulations provide a dynamical interpretation of the Perutz model for Hb function. Results from experiments using higher protein concentrations and realistic cellular environments are also discussed. One of the next great challenges for computational studies, which as we show is likely to be taken up in the near future, is to provide a molecular-level understanding of the dynamics of proteins in such crowded environments.

Temperature and salt controlled tuning of protein clusters

The formation of molecular assemblies in protein solutions is of strong interest both from a fundamental viewpoint and for biomedical applications. While ordered and desired protein assemblies are indispensable for some biological functions, undesired protein condensation can induce serious diseases. As a common cofactor, the presence of salt ions is essential for some biological processes involving proteins, and in aqueous suspensions of proteins can also give rise to complex phase diagrams including homogeneous solutions, large aggregates, and dissolution regimes. Here, we systematically study the cluster formation approaching the phase separation in aqueous solutions of the globular protein BSA as a function of temperature (T), the protein concentration (c_p) and the concentrations of the trivalent salts YCl₃ and LaCl₃ (c_s). As an important complement to structural, i.e. time-averaged, techniques we employ a dynamical technique that can detect clusters even when they are transient on the order of a few nanoseconds. By employing incoherent neutron spectroscopy, we unambiguously determine the short-time self-diffusion of the protein clusters depending on c_p, c_s and T. We determine the cluster size in terms of effective hydrodynamic radii as manifested by the cluster center-of-mass diffusion coefficients D. For both salts, we find a simple functional form D(c_p, c_s, T) in the parameter range explored. The calculated inter-particle attraction strength, determined from the microscopic and short-time diffusive properties of the samples, increases with salt concentration and temperature in the regime investigated and can be linked to the macroscopic behavior of the samples.

Effect of Temperature and Flow Rate on the Cell-Free Area in the Microfluidic Channel

Blood cell manipulation in microdevices is an interesting task for the separation of particles, by their size, density, or to remove them from the buffer, in which they are suspended, for further analysis, and more. This study highlights the cell-free area (CFA) widening based on experimental results of red blood cell (RBC) flow, suspended in a microfluidic device, while temperature and flow rate incrementally modify RBC response within the microflow. Studies of human red blood cell flow, at a concentration of 20%, suspended in its autologous plasma and phosphate-buffered saline (PBS) buffer, were carried out at a wide flow rate, varying between 10 and 230 μL/min and a temperature range of 23 °C to 50 °C. The plotted measures show an increment in a CFA near the channel wall due to cell flow inertia after a constricted channel, which becomes more significant as temperature and flow rate increase. The temperature increment widened the CFA up to three times. In comparison, flow rate increment increased the CFA up to 20 times in PBS and 11 times in plasma.

Dynamics of proteins with different molecular structures under solution condition

Incoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, low flux of neutron beam, low signal to noise ratio of QENS spectrometers and unavailability of well-established analyzing method have been obstacles for studying internal dynamics under physiological condition (in solution). The recent progress of neutron source and spectrometer provide the fine iQENS profile with high statistics and as well the progress of computational technique enable us to quantitatively reveal the internal dynamic from the obtained iQENS profile. The internal dynamics of two proteins, globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution, were measured with the state-of-the art QENS spectrometer and then revealed with the newly developed analyzing method. It was clarified that the average relaxation rate of IDP was larger than that of GDP and the fraction of mobile H atoms of IDP was also much higher than that of GDP. Combined with the structural analysis and the calculation of solvent accessible surface area of amino acid residue, it was concluded that the internal dynamics were related to the highly solvent exposed amino acid residues depending upon protein's structure.

The Effect of an Intramembrane Light-Actuator on the Dynamics of Phospholipids in Model Membranes and Intact Cells

The noncovalent intercalation of amphiphilic molecules in the lipid membrane can be exploited to modulate efficiently the physical status of the membrane. Such effects are largely employed in a range of applications, spanning from drug-delivery to therapeutics. In this context, we have very recently developed an intramembrane photo-actuator consisting of an amphiphilic azobenzene molecule, namely ZIAPIN2. The selective photo-isomerization occurring in the lipid bilayer induces a photo-triggered change in the membrane thickness and capacitance, eventually permitting to evoke light-induced neuronal firing both in vitro and in vivo. Here, we present a study on the dynamical perturbation in the lipid membrane caused by ZIAPIN2 and its vehicle solvent, dimethyl sulfoxide. Effects on the dynamics occurring in the picosecond time range and at the molecular level are probed using quasi-elastic neutron scattering. By coupling experiments carried out both on model membranes and intact cells, we found that DMSO leads to a general retardation of the dynamics within a more dynamically ordered landscape, a result that we attribute to the dehydration at the interface. On the other hand, ZIAPIN2 partitioning produces a general softening of the bilayer owing to its interaction with the lipids. These data are in agreement with our recent studies, which indicate that the efficacy of ZIAPIN2 in triggering cellular signalling stems from its ability to mechanically perturb the bilayer as a whole, by forming light-sensitive membrane spanning dimers.

Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study

By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein-protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and Å length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na⁺-selective ionophore monensin and the K⁺-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.

Segmental Motions of Proteins under Non-native States Evaluated Using Quasielastic Neutron Scattering

Characterization of the dynamics of disordered polypeptide chains is required to elucidate the behavior of intrinsically disordered proteins and proteins under non-native states related to the folding process. Here we develop a method using quasielastic neutron scattering, combined with small-angle X-ray scattering and dynamic light scattering, to evaluate segmental motions of proteins as well as diffusion of the entire molecules and local side-chain motions. We apply this method to RNase A under the unfolded and molten-globule (MG) states. The diffusion coefficients arising from the segmental motions are evaluated and found to be different between the unfolded and MG states. The values obtained here are consistent with those obtained using the fluorescence-based techniques. These results demonstrate not only feasibility of this method but also usefulness to characterize the behavior of proteins under various disordered states.

Strong Adverse Contribution of Conformational Dynamics to Streptavidin-Biotin Binding

Molecular dynamics plays an important role for the biological function of proteins. For protein ligand interactions, changes of conformational entropy of protein and hydration layer are relevant for the binding process. Quasielastic neutron scattering (QENS) was used to investigate differences in protein dynamics and conformational entropy of ligand-bound and ligand-free streptavidin. Protein dynamics were probed both on the fast picosecond time scale using neutron time-of-flight spectroscopy and on the slower nanosecond time scale using high-resolution neutron backscattering spectroscopy. We found the internal equilibrium motions of streptavidin and the corresponding mean square displacements (MSDs) to be greatly reduced upon biotin binding. On the basis of the observed MSDs, we calculated the difference of conformational entropy ΔS_conf of the protein component between ligand-bound and ligand-free streptavidin. The rather large negative ΔS_conf value (-2 kJ mol^-1 K^-1 on the nanosecond time scale) obtained for the streptavidin tetramer seems to be counterintuitive, given the exceptionally high affinity of streptavidin-biotin binding. Literature data on the total entropy change ΔS observed upon biotin binding to streptavidin, which includes contributions from both the protein and the hydration water, suggest partial compensation of the unfavorable ΔS_conf by a large positive entropy gain of the surrounding hydration layer and water molecules that are displaced during ligand binding.

Interaction of blood plasma proteins with superhemophobic titania nanotube surfaces

The need to improve blood biocompatibility of medical devices is urgent. As soon as blood encounters a biomaterial implant, proteins adsorb on its surfaces, often leading to several complications such as thrombosis and failure of the device. Therefore, controlling protein adsorption plays a major role in developing hemocompatible materials. In this study, the interaction of key blood plasma proteins with superhemophobic titania nanotube substrates and the blood clotting responses was investigated. The substrate stability was evaluated and fibrinogen adsorption and thrombin formation from plasma were assessed using ELISA. Whole blood clotting kinetics was also investigated, and Factor XII activation on the substrates was characterized by an in vitro plasma coagulation time assay. The results show that superhemophobic titania nanotubes are stable and considerably decrease surface protein adsorption/Factor XII activation as well as delay the whole blood clotting, and thus can be a promising approach for designing blood contacting medical devices.

Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics

The interplay between protein dynamics and catalysis remains a fundamental question in enzymology. We here investigate the ns-timescale dynamics of a light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR), a photoenzyme crucial for chlorophyll synthesis. LPORs catalyze the light-triggered trans addition of a hydride and a proton across the C17═C18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). Because of the lack of an LPOR structure, the global structural and dynamic consequences of LPOR/Pchlide/NADPH ternary complex formation remain elusive. Moreover, photoactivation of LPORs by low-light preillumination is controversially discussed as unequivocal proof for this phenomenon is lacking. By employing quasielastic neutron spectroscopy (QENS), we show that the formation of the ternary holoprotein complex as well as photoactivation lead to progressive rigidification of the protein. These findings are supported by thermostability measurements, which reveal different melting behavior and thermostabilities for the apo- and holoprotein ternary complexes. Molecular dynamics simulations in good agreement with the experimental QENS results suggest that the increased flexibility observed for the apoprotein stems from structural fluctuations of the NADPH and Pchlide substrate binding sites of the enzyme. On the basis of our results, in conjunction with activity and stability measurements, we provide independent proof for LPOR photoactivation, defined as a process that modifies the protein structure and dynamics, resulting in an increased substrate turnover. Our findings advance the structural and dynamic understanding of LPORs and provide a first link between protein dynamics and catalysis for this enzyme class.

Temperature dependence of nanoscale dynamic processes measured in living millipedes by high resolution inelastic and elastic neutron scattering

We have used high energy-resolution neutron scattering to probe nanoscale dynamic processes in living millipedes (Narceus americanus). We have measured the temperature dependence of the intensity of scattered neutrons that do not exchange energy with the living samples on the 1.5 ns time scale, thereby excluding the signal from the highly mobile intra- and extra-cellular bulk-like aqueous constituents in the sample. This measured “elastic” scattering intensity exhibits a non-monotonic temperature dependence, with a noticeable systematic decrease detected between 295 and 303 K on warming up from 283 to 310 K. This decrease demonstrates an excellent inverse correlation with the non-monotonic, as a function of temperature, increase in the slow diffusivity previously observed in planarian flatworms and housefly larvae. This correlation suggests the existence of a biological mechanism, possibly common between different classes (Insects and Myriapods) and even phyla (Arthropods and Platyhelminthes), that dampens the slow nanoscopic dynamics in ectothermic organisms in response to the temperature of the environment exceeding the physiologically optimal range.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

Deep UV dispersion and absorption spectroscopy of biomolecules

Owing to the high precision and sensitivity of optical systems, there is an increasing demand for optical methods that quantitatively characterize the physical and chemical properties of biological samples. Information extracted from such quantitative methods, through phase and/or amplitude variations of light, can be crucial in the diagnosis, treatment and study of disease. In this work we apply a recently developed quantitative method, called ultraviolet hyperspectral interferometry (UHI), to characterize the dispersion and absorbing properties of various important biomolecules. Our system consists of (1) a broadband light source that spans from the deep-UV to the visible region of the spectrum, and (2) a Mach-Zehnder interferometer to gain access to complex optical properties. We apply this method to characterize (and tabulate) the dispersive and absorptive properties of hemoglobin, beta nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), elastin, collagen, cytochrome c, tryptophan and DNA. Our results shed new light on the complex properties of important biomolecules.

Recent and prominent examples of nano- and microarchitectures as hemoglobin-based oxygen carriers

Blood transfusions, which usually consist in the administration of isolated red blood cells (RBCs), are crucial in traumatic injuries, pre-surgical conditions and anemias. Although RBCs transfusion from donors is a safe procedure, donor RBCs can only be stored for a maximum of 42 days under refrigerated conditions and, therefore, stockpiles of RBCs for use in acute disasters do not exist. With a worldwide shortage of donor blood that is expected to increase over time, the creation of oxygen-carriers with long storage life and compatibility without typing and cross-matching, persists as one of the foremost important challenges in biomedicine. However, research has so far failed to produce FDA approved RBCs substitutes (RBCSs) for human usage. As such, due to unacceptable toxicities, the first generation of oxygen-carriers has been withdrawn from the market. Being hemoglobin (Hb) the main component of RBCs, a lot of effort is being devoted in assembling semi-synthetic RBCS utilizing Hb as the oxygen-carrier component, the so-called Hb-based oxygen carriers (HBOCs). However, a native RBC also contains a multi-enzyme system to prevent the conversion of Hb into non-functional methemoglobin (metHb). Thus, the challenge for the fabrication of next-generation HBOCs relies in creating a system that takes advantage of the excellent oxygen-carrying capabilities of Hb, while preserving the redox environment of native RBCs that prevents or reverts the conversion of Hb into metHb. In this review, we feature the most recent advances in the assembly of the new generation of HBOCs with emphasis in two main approaches: the chemical modification of Hb either by cross-linking strategies or by conjugation to other polymers, and the Hb encapsulation strategies, usually in the form of lipidic or polymeric capsules. The applications of the aforementioned HBOCs as blood substitutes or for oxygen-delivery in tissue engineering are highlighted, followed by a discussion of successes, challenges and future trends in this field.

Microscopic diffusion processes measured in living planarians

Living planarian flatworms were probed using quasielastic neutron scattering to measure, on the pico-to-nanosecond time scale and nanometer length scale, microscopic diffusion of water and cell constituents in the planarians. Measurable microscopic diffusivities were surprisingly well defined in such a complex system as living animals. The overall variation in the microscopic diffusivity of cell constituents was found to be far lower than the variation in the microscopic diffusivity of water in planarians in a temperature range of 284.5 to 304.1 K.

In Vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale

Selectively labeled GroEL protein was produced in living deuterated bacterial cells to enhance its neutron scattering signal above that of the intracellular milieu. Quasi-elastic neutron scattering shows that the in-cell diffusion coefficient of GroEL was (4.7 ± 0.3) × 10^-12 m²/s, a factor of 4 slower than its diffusion coefficient in buffer solution. Internal protein dynamics showed a relaxation time of (65 ± 6) ps, a factor of 2 slower compared to the protein in solution. Comparison to the literature suggests that the effective diffusivity of proteins depends on the length and time scale being probed. Retardation of in-cell diffusion compared to the buffer becomes more significant with the increasing probe length scale, suggesting that intracellular diffusion of biomolecules is nonuniform over the cellular volume. The approach outlined here enables investigation of protein dynamics within living cells to open up new lines of research using "in-cell neutron scattering" to study the dynamics of complex biomolecular systems.

Photoactivation Reduces Side-Chain Dynamics of a LOV Photoreceptor

We used neutron-scattering experiments to probe the conformational dynamics of the light, oxygen, voltage (LOV) photoreceptor PpSB1-LOV from Pseudomonas putida in both the dark and light states. Global protein diffusion and internal macromolecular dynamics were measured using incoherent neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond timescales. Global protein diffusion of PpSB1-LOV is not influenced by photoactivation. Observation-time-dependent global diffusion coefficients were found, which converge on the nanosecond timescale toward diffusion coefficients determined by dynamic light scattering. Mean-square displacements of localized internal motions and effective force constants, <k'>, describing the resilience of the proteins were determined on the respective timescales. Photoactivation significantly modifies the flexibility and the resilience of PpSB1-LOV. On the fast, picosecond timescale, small changes in the mean-square displacement and <k'> are observed, which are enhanced on the slower, nanosecond timescale. Photoactivation results in a slightly larger resilience of the photoreceptor on the fast, picosecond timescale, whereas in the nanosecond range, a significantly less resilient structure of the light-state protein is observed. For a residue-resolved interpretation of the experimental neutron-scattering data, we analyzed molecular dynamics simulations of the PpSB1-LOV X-ray structure. Based on these data, it is tempting to speculate that light-induced changes in the protein result in altered side-chain mobility mostly for residues on the protruding Jα helix and on the LOV-LOV dimer interface. Our results provide strong experimental evidence that side-chain dynamics play a crucial role in photoactivation and signaling of PpSB1-LOV via modulation of conformational entropy.

Dynamical Behavior of Human α-Synuclein Studied by Quasielastic Neutron Scattering

α-synuclein (αSyn) is a protein consisting of 140 amino acid residues and is abundant in the presynaptic nerve terminals in the brain. Although its precise function is unknown, the filamentous aggregates (amyloid fibrils) of αSyn have been shown to be involved in the pathogenesis of Parkinson's disease, which is a progressive neurodegenerative disorder. To understand the pathogenesis mechanism of this disease, the mechanism of the amyloid fibril formation of αSyn must be elucidated. Purified αSyn from bacterial expression is monomeric but intrinsically disordered in solution and forms amyloid fibrils under various conditions. As a first step toward elucidating the mechanism of the fibril formation of αSyn, we investigated dynamical behavior of the purified αSyn in the monomeric state and the fibril state using quasielastic neutron scattering (QENS). We prepared the solution sample of 9.5 mg/ml purified αSyn, and that of 46 mg/ml αSyn in the fibril state, both at pD 7.4 in D2O. The QENS experiments on these samples were performed using the near-backscattering spectrometer, BL02 (DNA), at the Materials and Life Science Facility at the Japan Accelerator Research Complex, Japan. Analysis of the QENS spectra obtained shows that diffusive global motions are observed in the monomeric state but largely suppressed in the fibril state. However, the amplitude of the side chain motion is shown to be larger in the fibril state than in the monomeric state. This implies that significant solvent space exists within the fibrils, which is attributed to the αSyn molecules within the fibrils having a distribution of conformations. The larger amplitude of the side chain motion in the fibril state than in the monomeric state implies that the fibril state is entropically favorable.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions.

Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution

The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs = 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.

Correlation of the dynamics of native human acetylcholinesterase and its inhibited huperzine A counterpart from sub-picoseconds to nanoseconds

It is a long debated question whether catalytic activities of enzymes, which lie on the millisecond timescale, are possibly already reflected in variations in atomic thermal fluctuations on the pico- to nanosecond timescale. To shed light on this puzzle, the enzyme human acetylcholinesterase in its wild-type form and complexed with the inhibitor huperzine A were investigated by various neutron scattering techniques and molecular dynamics simulations. Previous results on elastic neutron scattering at various timescales and simulations suggest that dynamical processes are not affected on average by the presence of the ligand within the considered time ranges between 10 ps and 1 ns. In the work presented here, the focus was laid on quasi-elastic (QENS) and inelastic neutron scattering (INS). These techniques give access to different kinds of individual diffusive motions and to the density of states of collective motions at the sub-picoseconds timescale. Hence, they permit going beyond the first approach of looking at mean square displacements. For both samples, the autocorrelation function was well described by a stretched-exponential function indicating a linkage between the timescales of fast and slow functional relaxation dynamics. The findings of the QENS and INS investigation are discussed in relation to the results of our earlier elastic incoherent neutron scattering and molecular dynamics simulations.

Correlation between supercoiling and conformational motions of the bacterial flagellar filament

The bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. Various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. We investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. Thermal fluctuations in the straight L- and R-type filaments were measured and compared to the resting state of the wild-type filament. Amplitudes of motion on the picosecond timescale were found to be similar in the different conformational states. Mean-square displacements and protein resilience on the 0.1 ns timescale demonstrate that the L-type state is more flexible and less resilient than the R-type, whereas the wild-type state lies in between. Our results provide strong support that supercoiling of the protofilaments in the flagellar filament is determined by the strength of molecular forces in and between the flagellin subunits.

Small-angle neutron scattering studies of hemoglobin confined inside silica tubes of varying sizes

In addition to the chemical nature of the surface, the dimensions of the confining host exert a significant influence on confined protein structures; this results in immense biological implications, especially those concerning the enzymatic activities of the protein. This study probes the structure of hemoglobin (Hb), a model protein, confined inside silica tubes with pore diameters that vary by one order of magnitude (≈20-200 nm). The effect of confinement on the protein structure is probed by comparison with the structure of the protein in solution. Small-angle neutron scattering (SANS), which provides information on protein tertiary and quaternary structures, is employed to study the influence of the tube pore diameter on the structure and configuration of the confined protein in detail. Confinement significantly influences the structural stability of Hb and the structure depends on the Si-tube pore diameter. The high radius of gyration (Rg) and polydispersity of Hb in the 20 nm diameter Si-tube indicates that Hb undergoes a significant amount of aggregation. However, for Si-tube diameters greater or equal to 100 nm, the Rg of Hb is found to be in very close proximity to that obtained from the protein data bank (PDB) reported structure (Rg of native Hb=23.8 Å). This strongly indicates that the protein has a preference for the more native-like non-aggregated state if confined inside tubes of diameter greater or equal to 100 nm. Further insight into the Hb structure is obtained from the distance distribution function, p(r), and ab initio models calculated from the SANS patterns. These also suggest that the Si-tube size is a key parameter for protein stability and structure.

SERS reveals the specific interaction of silver and gold nanoparticles with hemoglobin and red blood cell components

The interaction of nanoparticles with hemoglobin (Hb), a major constituent of red blood cells, is important in nanotoxicity research. We report SERS spectra of Hb using gold and silver nanoparticles at very small nanoparticle : Hb molecule ratios, that is, under conditions relevant for SERS-based nanotoxicity experiments with red blood cells at high sensitivity. We show that the structural information obtained from the experiment is highly dependent on the type of SERS substrate and the conditions under which the interaction of nanoparticles with Hb molecules takes place. In experiments with isolated red blood cells, we demonstrate that the dependence of the spectra on the type of nanoparticle used as the SERS substrate extends to whole red blood cells and red blood cell components. Regarding the applicability of SERS to red blood cells in vivo, evidence is provided that the molecular information contained in the spectra is highly dependent on the material and size of the nanoparticles. The results indicate specific interactions of gold and silver nanoparticles with Hb and the red blood cell membrane, and reflect the hemolytic activity of silver nanoparticles. The results of this study help improve our understanding of the interactions of silver and gold nanoparticles with red blood cells.

Effects of spermine NONOate and ATP on protein aggregation: light scattering evidences

BACKGROUND AND OBJECTIVE

Regulating protein function in the cell by small molecules, provide a rapid, reversible and tunable tool of metabolic control. However, due to its complexity the issue is poorly studied so far. The effects of small solutes on protein behavior can be studied by examining changes of protein secondary structure, in its hydrodynamic radius as well as its thermal aggregation. The study aim was to investigate effects of adenosine-5'-triphosphate (ATP), spermine NONOate (NO donor) as well as sodium/potassium ions on thermal aggregation of albumin and hemoglobin. To follow aggregation of the proteins, their diffusion coefficients were measured by quasi-elastic light scattering (QELS) at constant pH (7.4) in the presence of solutes over a temperature range from 25°C to 80°C.

RESULTS AND DISCUSSION

1) Spermine NONOate persistently decreased the hemoglobin aggregation temperature Tairrespectively of the Na+/K+ environment, 2) ATP alone had no effect on the protein's thermal stability but it facilitated protein's destabilization in the presence of spermine NONOate and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions.

CONCLUSION

The ATP effect on protein aggregation was ambiguous: ATP alone had no effect on the protein's thermal stability but it facilitated protein's destabilization in the presence of nitric oxide. The magnitude and direction of the observed effects strongly depended on concentrations of K+ and Na+ in the solution.

Effects of spermine NONOate and ATP on the thermal stability of hemoglobin

Background

Minor changes in protein structure induced by small organic and inorganic molecules can result in significant metabolic effects. The effects can be even more profound if the molecular players are chemically active and present in the cell in considerable amounts. The aim of our study was to investigate effects of a nitric oxide donor (spermine NONOate), ATP and sodium/potassium environment on the dynamics of thermal unfolding of human hemoglobin (Hb). The effect of these molecules was examined by means of circular dichroism spectrometry (CD) in the temperature range between 25°C and 70°C. The alpha-helical content of buffered hemoglobin samples (0.1 mg/ml) was estimated via ellipticity change measurements at a heating rate of 1°C/min.

Results

Major results were: 1) spermine NONOate persistently decreased the hemoglobin unfolding temperature _Tuirrespectively of the ^{Na +} /^{K +} environment, 2) ATP instead increased the unfolding temperature by 3°C in both sodium-based and potassium-based buffers and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions. Moreover, the presence of potassium facilitated a partial unfolding of alpha-helical structures even at room temperature.

Conclusion

The obtained data might shed more light on molecular mechanisms and biophysics involved in the regulation of protein activity by small solutes in the cell.

Dynamic behavior of oligomeric inorganic pyrophosphatase explored by quasielastic neutron scattering

The purpose of this investigation is to determine whether a large oligomeric protein, inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens with quaternary structural complexity, would have distinguishable dynamic characteristics compared to those of the small simple monomeric model protein, lysozyme. In this study, the β-relaxational dynamics of the two proteins, IPPase and lysozyme, are compared in the 10 ps to 0.5 ns time interval using quasi-elastic neutron scattering (QENS). Both of the protein dynamics show a characteristic logarithmic-like decay in the intermediate scattering function (ISF) of the hydrogen atoms. Distinguishable dynamical behavior found between two proteins reveals local flexibility and conformational substates unique to oligomeric structures. Moreover, the temperature dependence of the mean square displacement (MSD) of the hydrogen atoms in protein molecules, which is a traditional way to determine the "softness" of the protein molecule, is measured and shows no difference for the two proteins.

Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.

Dynamics-stability relationships in apo- and holomyoglobin: a combined neutron scattering and molecular dynamics simulations study

The removal of the heme group from myoglobin (Mb) results in a destabilization of the protein structure. The dynamic basis of the destabilization was followed by comparative measurements on holo- (holo-Mb) and apomyoglobin (apo-Mb). Mean-squared displacements (MSD) and protein resilience on the picosecond-to-nanosecond timescale were measured by elastic incoherent neutron scattering. Differences in thermodynamic parameters, MSD, and resilience were observed for both proteins. The resilience of holo-Mb was significantly lower than that of apo-Mb, indicating entropic stabilization by a higher degree of conformational sampling in the heme-bound folded protein. Molecular dynamics simulations provided site-specific information. Averaged over the whole structure, the molecular dynamics simulations yielded similar MSD and resilience values for the two proteins. The mobility of residues around the heme group in holo-Mb showed a smaller MSD and higher resilience compared to the same residue group in apo-Mb. It is of interest that in holo-Mb, higher MSD values are observed for the residues outside the heme pocket, indicating an entropic contribution to protein stabilization by heme binding, which is in agreement with experimental results.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Reaction of hemoglobin with HOCl: mechanism of heme destruction and free iron release

Hypochlorous acid (HOCl) is generated by myeloperoxidase using chloride and hydrogen peroxide as substrates. HOCl and its conjugate base (OCl(-)) bind to the heme moiety of hemoglobin (Hb) and generate a transient ferric species whose formation and decay kinetics indicate it can participate in protein aggregation and heme destruction along with subsequent free iron release. The oxidation of the Hb heme moiety by OCl(-) was accompanied by marked heme destruction as judged by the decrease in and subsequent flattening of the Soret absorbance peak at 405 nm. HOCl-mediated Hb heme depletion was confirmed by HPLC analysis and in-gel heme staining. Exposure of Hb to increasing concentrations of HOCl produced a number of porphyrin degradation products resulting from oxidative cleavage of one or more of the carbon-methene bridges of the tetrapyrrole ring, as identified by their characteristic HPLC fluorescence and LC-MS. A nonreducing denaturing SDS-PAGE showed several degrees of protein aggregation. Similarly, porphyrin degradation products were identified after exposure of red blood cells to increasing concentrations of HOCl, indicating biological relevance of this finding. This work provides a direct link between Hb heme destruction and subsequent free iron accumulation, as occurs under inflammatory conditions where HOCl is formed in substantial amounts.

Protein self-diffusion in crowded solutions

Macromolecular crowding in biological media is an essential factor for cellular function. The interplay of intermolecular interactions at multiple time and length scales governs a fine-tuned system of reaction and transport processes, including particularly protein diffusion as a limiting or driving factor. Using quasielastic neutron backscattering, we probe the protein self-diffusion in crowded aqueous solutions of bovine serum albumin on nanosecond time and nanometer length scales employing the same protein as crowding agent. The measured diffusion coefficient D(ϕ) strongly decreases with increasing protein volume fraction ϕ explored within 7% ≤ ϕ ≤ 30%. With an ellipsoidal protein model and an analytical framework involving colloid diffusion theory, we separate the rotational D(r)(ϕ) and translational D(t)(ϕ) contributions to D(ϕ). The resulting D(t)(ϕ) is described by short-time self-diffusion of effective spheres. Protein self-diffusion at biological volume fractions is found to be slowed down to 20% of the dilute limit solely due to hydrodynamic interactions.