Hydration, slaving and protein function

Biological Surface Layer Formation on Bioceramic Particles for Protein Adsorption

In the biomedical fields of bone regenerative therapy, the immobilization of proteins on the bioceramic particles to maintain their highly ordered structures is significantly important. In this review, we comprehensively discussed the importance of the specific surface layer, which can be called "non-apatitic layer", affecting the immobilization of proteins on particles such as hydroxyapatite and amorphous silica. It was suggested that the water molecules and ions contained in the non-apatitic layer can determine and control the protein immobilization states. In amorphous silica particles, the direct interactions between proteins and silanol groups make it difficult to immobilize the proteins and maintain their highly ordered structures. Thus, the importance of the formation of a surface layer consisting of water molecules and ions (i.e., a non-apatitic layer) on the particle surfaces for immobilizing proteins and maintaining their highly ordered structures was suggested and described. In particular, chlorine-containing amorphous silica particles were also described, which can effectively form the surface layer of protein immobilization carriers. The design of the bio-interactive and bio-compatible surfaces for protein immobilization while maintaining the highly ordered structures will improve cell adhesion and tissue formation, thereby contributing to the construction of social infrastructures to support super-aged society.

Control of Biological Surface States on Chlorine-Doped Amorphous Silica Particles and Their Effective Absorptive Ability for Antibody Protein

Amorphous silica particles (ASPs) have low biotoxicity and are used in foodstuffs; however, the adsorption states of proteins on their surfaces have not yet been clarified. If the adsorption states can be clarified and controlled, then a wide range of biological and medical applications can be expected. The conventional amorphous silica particles have the problem of protein adsorption due to the strong interaction with their dense silanol groups and denaturation. In this study, the surfaces of amorphous silica particles with a lower silanol group density were modified with a small amount of chlorine during the synthesis process to form a specific surface layer by adsorbing water molecules and ions in the biological fluid, thereby controlling the protein adsorption state. Specifically, the hydration state on the surface of the amorphous silica particles containing trace amounts of chlorine was evaluated, and the surface layer (especially the hydration state) for the adsorption of antibody proteins while maintaining their steric structures was evaluated and discussed. The results showed that the inclusion of trace amounts of chlorine increased the silanol groups and Si-Cl bonds in the topmost surface layer of the particles, thereby inducing the adsorption of ions and water molecules in the biological fluid. Then, it was found that a novel surface layer was formed by the effective adsorption of Na and phosphate ions, which would change the proportion of the components in the hydration layer. In particular, the proportion of the free water component increased by 21% with the doping of chlorine. Antibody proteins were effectively adsorbed on the particles doped with trace amounts of chlorine, and their steric adsorption states were evaluated. It was found that the proteins were clearly adsorbed and maintained the steric state of their secondary structure. In the immunoreactivity tests using streptavidin and biotin, biotin bound to the chlorine-doped particles showed efficient reactivity. In conclusion, this study is the first to discover the surface layer of the amorphous silica particles to maintain the steric structures of adsorbed proteins, which is expected to be used as a carrier particle for antibody test kits and immunochromatography.

Investigation of Surface Layers on Biological and Synthetic Hydroxyapatites Based on Bone Mineralization Process

In this review, the current status of the influence of added ions (i.e., SiO₄^4-, CO₃^2-, etc.) and surface states (i.e., hydrated and non-apatite layers) on the biocompatibility nature of hydroxyapatite (HA, Ca₁₀(PO₄)₆(OH)₂) is discussed. It is well known that HA is a type of calcium phosphate with high biocompatibility that is present in biological hard tissues such as bones and enamel. This biomedical material has been extensively studied due to its osteogenic properties. The chemical composition and crystalline structure of HA change depending on the synthetic method and the addition of other ions, thereby affecting the surface properties related to biocompatibility. This review illustrates the structural and surface properties of HA substituted with ions such as silicate, carbonate, and other elemental ions. The importance of the surface characteristics of HA and its components, the hydration layers, and the non-apatite layers for the effective control of biomedical function, as well as their relationship at the interface to improve biocompatibility, has been highlighted. Since the interfacial properties will affect protein adsorption and cell adhesion, the analysis of their properties may provide ideas for effective bone formation and regeneration mechanisms.

Surface modification of hydroxyapatite nanoparticles for bone regeneration by controlling their surface hydration and protein adsorption states

Autogenous bone and metallic implant grafting has been used to repair and regenerate bone defects. However, there are still many unresolved problems. It is suggested that bioceramic nanoparticles should be developed and designed to promote effective bone regeneration. In addition, it is necessary to synthesize bioceramic nanoparticles that can support proteins related to bone repair and regeneration such as collagen and albumin. As the protein-interactive bioceramic, hydroxyapatite (HA) deserves to be mentioned and has several attractive properties that are useful in biomedical fields (e.g., biocompatibility, protein adsorption capacity and stability in the physiological environment). In order to prepare novel HA nanoparticles with high biocompatibility, it can be considered that human bones are mainly composed of HA and contain a small amount of silicate, and therefore, the design of coexistence of HA with silicate can be focused. Moreover, it is proposed that the state of the hydration layer on the nanoparticle surfaces can be controlled by introducing heteroelements and polymer chains, which have a great influence on the subsequent protein adsorption and cell adhesion. In this perspective, in order to develop novel bioceramic nanoparticles for the treatment of bone defect, the design of highly biocompatible HA nanoparticles and the control of the hydration layer and protein adsorption states on the surfaces were systematically discussed based on their surface modification techniques, which are very important for the proper understanding of the interface between cells and bioceramics, leading to the further application in biomedical fields.

PEG functionalization effect of silicate-containing hydroxyapatite particles on effective collagen fibrillation with hydration layer state change

Silicate-containing hydroxyapatite (SiHA) particles were synthesized and functionalized with polyethylene glycol-silane (PEG-silane) for clarifying the effect of the bioceramic surface hydration layer states on the collagen (Col) fibrillation degree. Plate-like SiHA particles were obtained containing the SiO₄^4- ion inside and/or outside the particles. PEG-silane was successfully functionalized on SiHA particles, and the hydration layer and Col adlayer states on the particles were precisely investigated for exemplifying the importance of the water molecular states at the interface. The ratio of free to intermediate water in the hydration layers of the particles decreased when containing silicate components, and it significantly increased with increasing PEG-silane molecular occupancy, where the asymmetric stretching vibration component ratio in the free water clearly increased. In a quartz crystal microbalance with dissipation (QCM-D) measurement, the frequency change (Δf) and the energy dissipation change (ΔD) values increased with Col adsorption on the particles for 32-34 min and then Δf slightly increased (or stopped increasing) and ΔD dramatically increased, indicating the effective water mobility and state changes with the Col fibrillation at the interface. The Col fibrillation degree evaluated by tan δ and the protein secondary structure of the adlayers clearly increased due to the PEG-silane functionalization, and the tendency was supported by the increase in the fibril density under SEM observation. Surprisingly, it was found that the fibrillation degree based on the protein secondary structure was significantly correlated with the asymmetric stretching vibration component ratio in the free water molecules of the hydration layer on the particles, suggesting the importance of the hydration layer states on bioceramics for controlling Col fibrillation.

Impact of macromolecular crowding on the mesomorphic behavior of lipid self-assemblies

Using LAURDAN fluorescence we observed that water dynamics measured at the interface of DOPC bilayers can be differentially regulated by the presence of crowded suspensions of different proteins (HSA, IgG, Gelatin) and PEG, under conditions where the polymers are not in direct molecular contact with the lipid interface. Specifically, we found that the decrease in water dipolar relaxation at the membrane interface correlates with an increased fraction of randomly oriented (or random coil) configurations in the polymers, as Gelatin > PEG > IgG > HSA. By using the same experimental strategy, we also demonstrated that structural transitions from globular to extended conformations in proteins can induce transitions between lamellar and non-lamellar phases in mixtures of DOPC and monoolein. Independent experiments using Raman spectroscopy showed that aqueous suspensions of polymers exhibiting high proportions of randomly oriented conformations display increased fractions of tetracoordinated water, a configuration that is dominant in ice. This indicates a greater capacity of this type of structure for polarizing water and consequently reducing its chemical activity. This effect is in line with one of the tenets of the Association Induction Hypothesis, which predicts a long-range dynamic structuring of water molecules via their interactions with proteins (or other polymers) showing extended conformations. Overall, our results suggest a crucial role of water in promoting couplings between structural changes in macromolecules and supramolecular arrangements of lipids. This mechanism may be of relevance to cell structure/function when the crowded nature of the intracellular milieu is considered.

Dynamics of aqueous peptide solutions in folded and disordered states examined by dynamic light scattering and dielectric spectroscopy

Characterizing the segmental dynamics of proteins, and intrinsically disordered proteins in particular, is a challenge in biophysics. In this study, by combining data from broadband dielectric spectroscopy (BDS) and both depolarized (DDLS) and polarized (PDLS) dynamic light scattering, we were able to determine the dynamics of a small peptide [ε-poly(lysine)] in water solutions in two different conformations (pure β-sheet at pH = 10 and a more disordered conformation at pH = 7). We found that the segmental (α-) relaxation, as probed by DDLS, is faster in the disordered state than in the folded conformation. The water dynamics, as detected by BDS, is also faster in the disordered state. In addition, the combination of BDS and DDLS results allows us to confirm the molecular origin of water-related processes observed by BDS. Finally, we discuss the origin of two slow processes (A and B processes) detected by DDLS and PDLS in both conformations and usually observed in other types of water solutions. For fully homogeneous ε-PLL solutions at pH = 10, the A-DLS process is assigned to the diffusion of individual β-sheets. The combination of both techniques opens a route for understanding the dynamics of peptides and other biological solutions.

Lipids, membranes, colloids and cells: A long view

This paper revisits long-standing ideas about biological membranes in the context of an equally long-standing, but hitherto largely unappreciated, perspective of the cell based on concepts derived from the physics and chemistry of colloids. Specifically, we discuss important biophysical aspects of lipid supramolecular structure to understand how the intracellular milieu may constrain lipid self-assembly. To this end we will develop four lines of thought: first, we will look at the historical development of the current view of cellular structure and physiology, considering also the plurality of approaches that influenced its formative period. Second, we will review recent basic research on the structural and dynamical properties of lipid aggregates as well as the role of phase transitions in biophysical chemistry and cell biology. Third, we will present a general overview of contemporary studies into cellular compartmentalization in the context of a very rich and mostly forgotten general theory of cell physiology called the Association-Induction Hypothesis, which was developed around the time that the current view of cells congealed into its present form. Fourth, we will examine some recent developments in cellular studies, mostly from our laboratory, that raise interesting issues about the dynamical aspects of cell structure and compartmentalization. We will conclude by suggesting what we consider are relevant questions about the nature of cellular processes as emergent phenomena.

Origin of subdiffusions in proteins: Insight from peptide systems

Subdiffusive kinetics are popular in proteins and peptides as observed in experiments and simulations. For protein systems with diverse interactions, are there multiple mechanisms to produce the common subdiffusion behavior? To approach this problem, long trajectories of two model peptides are simulated to study the mechanism of subdiffusion and the relations with their interactions. The free-energy profiles and the subdiffusive kinetics are observed for these two peptides. A hierarchical plateau analysis is employed to extract the features of the landscape from the mean square of displacement. The mechanism of subdiffusions can be postulated by comparing the exponents by simulations with those based on various models. The results indicate that the mechanisms of these two peptides are different and are related to the characteristics of their energy landscapes. The subdiffusion of the flexible peptide is mainly caused by depth distribution of traps on the energy landscape, while the subdiffusion of the helical peptide is attributed to the fractal topology of local minima on the landscape. The emergence of these different mechanisms reflects different kinetic scenarios in peptide systems though the peptides behave in a similar way of diffusion. To confirm these ideas, the transition networks between various conformations of these peptides are generated. Based on the network description, the controlled kinetics based only on the topology of the networks are calculated and compared with the results based on simulations. For the flexible peptide, the feature of controlled diffusion is distinct from that of simulation, and for the helical peptide, two kinds of kinetics have a similar exponent of subdiffusion. These results further exemplify the importance of the landscape topology in the kinetics of structural proteins and the effect of depth distribution of traps for the subdiffusion of disordered peptides.

Templated folding of intrinsically disordered proteins

Much of our current knowledge of biological chemistry is founded in the structure-function relationship, whereby sequence determines structure that determines function. Thus, the discovery that a large fraction of the proteome is intrinsically disordered, while being functional, has revolutionized our understanding of proteins and raised new and interesting questions. Many intrinsically disordered proteins (IDPs) have been determined to undergo a disorder-to-order transition when recognizing their physiological partners, suggesting that their mechanisms of folding are intrinsically different from those observed in globular proteins. However, IDPs also follow some of the classic paradigms established for globular proteins, pointing to important similarities in their behavior. In this review, we compare and contrast the folding mechanisms of globular proteins with the emerging features of binding-induced folding of intrinsically disordered proteins. Specifically, whereas disorder-to-order transitions of intrinsically disordered proteins appear to follow rules of globular protein folding, such as the cooperative nature of the reaction, their folding pathways are remarkably more malleable, due to the heterogeneous nature of their folding nuclei, as probed by analysis of linear free-energy relationship plots. These insights have led to a new model for the disorder-to-order transition in IDPs termed "templated folding," whereby the binding partner dictates distinct structural transitions en route to product, while ensuring a cooperative folding.

Synthesis of nanostructured silica/hydroxyapatite hybrid particles containing amphiphilic triblock copolymer for effectively controlling hydration layer structures with cytocompatibility

We synthesized nanostructured mesoporous silica (MS)/hydroxyapatite (HA) hybrid particles in the presence of amphiphilic poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO₂₀PPO₇₀PEO₂₀) triblock copolymer (P123). The particles exhibited slit-shaped mesostructures and underwent hybridization reaction between the MS and HA phases containing P123. Furthermore, the aggregated form of the particles exhibited dispersion stability in water in the monodispersed state (average particle size: 145 nm and coefficient of variation: 4.3% in the case of the maximum added amount of P123). Then, the structures of the hydration layer and the adsorbed protein on the particles were investigated to understand the effect of the hydration layer structures on the protein secondary structures. The ratio of the bonding water (intermediate and nonfreezing water) to free water increased upon hybridization, and it decreased with increasing P123 concentration. Upon hybridization, the component ratio of the asymmetric O-H stretching vibration between free water molecules decreased, and that of the symmetric O-H stretching vibration of intermediate water molecules increased. With increasing P123 concentration, the asymmetric O-H stretching vibration between free water molecules increased and the symmetric O-H stretching vibration of intermediate water molecules decreased. It was found that the protein native state component ratios of α-helix and β-sheet increased with increasing symmetric O-H stretching vibration between intermediate water molecules, and they decreased with decreasing asymmetric O-H stretching vibration between free water molecules. Moreover, the cytotoxicity against osteoblasts (MC3T3-E1) was evaluated and the hybrid particles exhibited a high cell density, indicating their bioactivity. On the hybrid particles interacting with P123, the cells were three-dimensionally assembled and uniaxially grown with the culture. Therefore, this is the first successful report of the synthesis of nanostructured MS/HA hybrid particles interacting with P123, and the controlled hydration layer structures on the particle surfaces were found to contribute to the protein secondary structures, promoting cytocompatibility.

Motions of water and solutes-Slaving versus plasticization phenomena

It is well-accepted that hydration water is crucial for the structure, dynamics, and function of proteins. However, the exact role of water for the motions and functions of proteins is still debated. Experiments have shown that protein and water dynamics are strongly coupled but with water motions occurring on a considerably faster time scale (the so-called slaving behavior). On the other hand, water also reduces the conformational entropy of proteins and thereby acts as a plasticizer of them. In this work, we analyze the dynamics (using broadband dielectric spectroscopy) of some specific non-biological water solutions in a broad concentration range to elucidate the role of water in the dynamics of the solutes. Our results demonstrate that at low water concentrations (less than 5 wt. %), the plasticization phenomenon prevails for all the materials analyzed. However, at higher water concentrations, two different scenarios can be observed: the slaving phenomenon or plasticization, depending on the solute analyzed. These results generalize the slaving phenomenon to some, but not all, non-biological solutions and allow us to analyze the key factors for observing the slaving behavior in protein solutions as well as to reshaping the slaving concept.

Modulating Enzyme Activity by Altering Protein Dynamics with Solvent

Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ∼3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent k_hydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzyme's ability to access its functionally relevant conformational substates, explaining the decreased k_hydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.

Atomistic Simulation of Adiabatic Reactive Processes Based on Multi-State Potential Energy Surfaces

The adiabatic reactive molecular dynamics (ARMD) method provides a framework to study chemical reactions using molecular dynamics simulations with minimal computational overhead. Here, ARMD is generalized to an arbitrary reactive process between two states in which reactants and products can be treated by an atomistic force field. The implementation is described, and the method is applied to two systems: the kinetics of NO rebinding to myoglobin (Mb) as a validation system and the conformational transition in neuroglobin (Ngb) which explores the full functionality of ARMD. For MbNO, the nonexponential kinetics observed both in experiment and earlier ARMD studies is reproduced. Furthermore, the sensitivity of the results with respect to the asymptotic separation between the two potential energy surfaces (NO bound and unbound) is studied.

Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state

The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray- and terahertz- based time-resolved spectroscopic tools to study protein-water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme-substrate-water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme-collagen system. The long-lasting changes in protein-water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.

The dark recovery rate in the photocycle of the bacterial photoreceptor YtvA is affected by the cellular environment and by hydration

We report thermal recovery kinetics of the lit state into the parental dark state, measured for the blue light-sensing photoreceptor YtvA inside overexpressing E. coli and B. subtilis bacterial cells, performed for the wild type and several mutated proteins. Recovery was followed as a recovery of the fluorescence, as this property is only found for the parental but not for the photochemically generated lit state. When cells were deposited onto a microscope glass plate, the observed thermal recovery rate in the photocycle was found ca. ten times faster in comparison to purified YtvA in solution. When the E. coli or B. subtilis colonies were soaked in an isotonic buffer, the dark relaxation became again much slower and was very similar to that observed for YtvA in solution. The observed effects show that rate constants can be tuned by the cellular environment through factors such as hydration.

The importance of individual protein molecule dynamics in developing and assessing solid state protein preparations

Processing protein solutions into the solid state is a common approach for generating stable amorphous protein mixtures that are suitable for long-term storage. Great care is typically given to protecting the protein native structure during the various drying steps that render it into the amorphous solid state. However, many studies illustrate that chemical and physical degradations still occur in spite of this amorphous material having good glassy properties and it being stored at temperatures below its glass transition temperature (Tg). Because of these persistent issues and recent biophysical studies that have refined the debate ascribing meaning to the molecular dynamical transition temperature and Tg of protein molecules, we provide an updated discussion on the impact of assessing and managing localized, individual protein molecule nondiffusive motions in the context of proteins being prepared into bulk amorphous mixtures. Our aim is to bridge the pharmaceutical studies addressing bulk amorphous preparations and their glassy behavior, with the biophysical studies historically focused on the nondiffusive internal protein dynamics and a protein's activity, along with their combined efforts in assessing the impact of solvent hydrogen-bonding networks on local stability. We also provide recommendations for future research efforts in solid-state formulation approaches.

NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions

Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.

Catalytic activity and stability of glucose oxidase/horseradish peroxidase co-confined in macroporous silica foam

Investigation of the catalytic activity and stability of enzymes in confined nano/microspace provides valuable contributions to the fundamental understanding of biological reactions taking place on a mesoscopic scale within confined spaces. In this paper, macroporous silica foam (MSF) is used as a nanoreactor to co-confine glucose oxidase (GOD) and horseradish peroxidase (HRP). Then, the enzymatic cascade reactions, which act in tandem inside nanoreactors, for oxidation of glucose and 3,3',5,5'-tetramethylbenzidine (TMB) were studied. The catalytic kinetic parameters of apparent Michaelis constant (K(m)(app)) and maximum rate (V(max)) were obtained from Lineweaver-Burk plot by UV-vis spectrometry. Results showed that the catalytic activity of the co-confined enzymes is reduced compared to that of free enzymes in solution at room temperature. The stabilities of co-confined enzymes in denaturing agents, such as guanidinium chloride (GdmCl) and urea, were higher than those of free enzymes in solution. When employing a co-confined bienzyme system as a biosensor for the detection of glucose, a wider linear range of glucose was obtained for the co-confined bienzyme system than for free enzymes in solution.

Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin

Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations

The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.

The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures

We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically, we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen-bonding characteristics and dynamic behavior at different length scales.

Ultrafast red light activation of Synechocystis phytochrome Cph1 triggers major structural change to form the Pfr signalling-competent state

Phytochromes are dimeric photoreceptors that regulate a range of responses in plants and microorganisms through interconversion of red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Photoconversion between these states is initiated by light-driven isomerization of a bilin cofactor, which triggers protein structural change. The extent of this change, and how light-driven structural changes in the N-terminal photosensory region are transmitted to the C-terminal regulatory domain to initiate the signalling cascade, is unknown. We have used pulsed electron-electron double resonance (PELDOR) spectroscopy to identify multiple structural transitions in a phytochrome from Synechocystis sp. PCC6803 (Cph1) by measuring distances between nitroxide labels introduced into the protein. We show that monomers in the Cph1 dimer are aligned in a parallel ‘head-to-head’ arrangement and that photoconversion between the Pr and Pfr forms involves conformational change in both the N- and C-terminal domains of the protein. Cryo-trapping and kinetic measurements were used to probe the extent and temporal properties of protein motions for individual steps during photoconversion of Cph1. Formation of the primary photoproduct Lumi-R is not affected by changes in solvent viscosity and dielectric constant. Lumi-R formation occurs at cryogenic temperatures, consistent with their being no major structural reorganization of Cph1 during primary photoproduct formation. All remaining steps in the formation of the Pfr state are affected by solvent viscosity and dielectric constant and occur only at elevated temperatures, implying involvement of a series of long-range solvent-coupled conformational changes in Cph1. We show that signalling is achieved through ultrafast photoisomerization where localized structural change in the GAF domain is transmitted and amplified to cause larger-scale and slower conformational change in the PHY and histidine kinase domains. This hierarchy of timescales and extent of structural change orientates the histidine kinase domain to elicit the desired light-activated biological response.

Excipients differentially influence the conformational stability and pretransition dynamics of two IgG1 monoclonal antibodies

Since immunoglobulins are conformationally dynamic molecules in solution, we studied the effect of stabilizing and destabilizing excipients on the conformational stability and dynamics of two IgG1 monoclonal antibodies (mAbs; mAb-A and mAb-B) using a variety of biophysical approaches. Even though the two mAbs are of the same IgG1 subtype, the unfolding patterns, aggregation behavior, and pretransition dynamics of these two antibodies were strikingly different in response to external perturbations such as pH, temperature, and presence of excipients. Sucrose and arginine were identified as stabilizers and destabilizers, respectively, on the basis of their influence on conformational stability for both the IgG1 mAbs. The two excipients, however, had distinct effective concentrations and different effects on the conformational stability and pretransition dynamics of the two mAbs as measured by a combination of differential scanning calorimetry, high-resolution ultrasonic spectroscopy, and red-edge excitation shift fluorescence studies. Stabilizing concentrations of sucrose were found to decrease the internal motions of mAb-B, whereas arginine marginally increased its adiabatic compressibility in the pretransition region. Both sucrose and arginine did not influence the pretransition dynamics of mAb-A. The potential reasons for such differences in excipient effects between two IgG1 mAbs are discussed.

The role of conserved waters in conformational transitions of Q61H K-ras

To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the C_α atoms of G60 at switch 2 and G10 at the P-loop and the N-C_α-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition.

K-ras belongs to the Ras family of G-proteins that regulate cell proliferation and development. To execute its function, K-ras adopts different conformational states when it is active and inactive. In addition to these two states, it samples many transient intermediate conformations as it makes the transition from one state to the other. Mutations that affect the population of these states can cause cancer or developmental disorder. Using simulation approaches, here we show that a number of water molecules buried within the structure of an oncogenic K-ras protein modulate the distribution of its conformational states. Moreover, a detailed analysis based on two novel structural parameters revealed the existence of long-range water-mediated interactions that facilitate a dynamic coupling between the two lobes of the protein. These findings pave the way for a dynamics-guided strategy to inhibit abnormal Ras signaling.

Common features in the microscopic dynamics of hydration water on organic and inorganic surfaces

The microscopic dynamics of hydration water exhibits some universal features that do not depend on the nature of the hydrated surface. We show that the hydration level dependence of the dynamic transition in the mean squared atomic displacements measured by means of elastic neutron scattering is qualitatively similar for hydration water in inorganic and organic hosts. The difference is that the former are 'rigid', whereas the dynamics of the latter can be enhanced by the motions of the hydration water. The overall hydration level appears to be the main parameter governing the magnitude of the mean squared atomic displacements in the hydration water, irrespective of the details of the hydrated host.

Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water

Water-protein interactions play a direct role in protein folding. The chain collapse that accompanies protein folding involves extrusion of water from the nonpolar core. For many proteins, including apomyoglobin (apoMb), hydrophobic interactions drive an initial collapse to an intermediate state before folding to the final structure. However, the debate continues as to whether the core of the collapsed intermediate state is hydrated and, if so, what the dynamic nature of this water is. A key challenge is that protein hydration dynamics is significantly heterogeneous, yet suitable experimental techniques for measuring hydration dynamics with site-specificity are lacking. Here, we introduce Overhauser dynamic nuclear polarization at 0.35 T via site-specific nitroxide spin labels as a unique tool to probe internal and surface protein hydration dynamics with site-specific resolution in the molten globular, native, and unfolded protein states. The (1)H NMR signal enhancement of water carries information about the local dynamics of the solvent within ∼10 Å of a spin label. EPR is used synergistically to gain insights on local polarity and mobility of the spin-labeled protein. Several buried and solvent-exposed sites of apoMb are examined, each bearing a covalently bound nitroxide spin label. We find that the nonpoloar core of the apoMb molten globule is hydrated with water bearing significant translational dynamics, only 4-6-fold slower than that of bulk water. The hydration dynamics of the native state is heterogeneous, while the acid-unfolded state bears fast-diffusing hydration water. This study provides a high-resolution glimpse at the folding-dependent nature of protein hydration dynamics.

Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes

Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic α-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87% α-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35% α-helical in the dry state. However, the dry protein contained 15% β-sheets. FTIR spectroscopy revealed the β-sheets to be largely due to aggregation. β-Sheet content was reduced and α-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates.

Dynamics of biological macromolecules: not a simple slaving by hydration water

We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account.

Effects of water on the structure and low/high temperature stability of confined proteins

In this study well-characterized model proteins were confined in silica nanoporous matrices. Confinement of the proteins in silica matrices allowed us to explore the role of water hydrogen bonding on the structures of the proteins in a broad range of temperatures (-120 degrees C to 95 degrees C). At low temperatures confinement suppressed freezing of water, which remained in the liquid state. We obtained direct evidence that the changes in the hydrogen bonding of water induced changes in the structure of confined proteins. At high temperatures, a reduction of hydrogen bonding of water facilitated protein-silica interactions and the confined proteins underwent denaturation. However, the incorporation of the osmolyte, trehalose, reduced protein-silica interactions, and altered the hydrogen bonding of water. As a result, the high temperature thermal stability of the confined proteins was greatly improved.