Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory

Light Scattering and Absorption Complementarities to Neutron Scattering: In Situ FTIR and DLS Techniques at the High-Intensity and Extended Q-Range SANS Diffractometer KWS-2

Understanding soft and biological materials requires global knowledge of their microstructural features from elementary units at the nm scale up to larger complex aggregates in the micrometer range. Such a wide range of scale can be explored using the KWS-2 small-angle neutron (SANS) diffractometer. Additional information obtained by in situ complementary techniques sometimes supports the SANS analysis of systems undergoing structural modifications under external stimuli or which are stable only for short times. Observations at the local molecular level structure and conformation assists with an unambiguous interpretation of the SANS data using appropriate structural models, while monitoring of the sample condition during the SANS investigation ensures the sample stability and desired composition and chemical conditions. Thus, we equipped the KWS-2 with complementary light absorption and scattering capabilities: Fourier transform infrared (FTIR) spectroscopy can now be performed simultaneously with standard and time-resolved SANS, while in situ dynamic light scattering (DLS) became available for routine experiments, which enables the observation of either changes in the sample composition, due to sedimentation effects, or in size of morphologies, due to aggregation processes. The performance of each setup is demonstrated here using systems representative of those typically investigated on this beamline and benchmarked to studies performed offline.

Robosample: A rigid-body molecular simulation program based on robot mechanics

BACKGROUND

Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to increase configuration space sampling in molecular simulations.

METHODS

Here, we introduce Robosample, a software package that implements high-performance constrained dynamics algorithms, originally developed for robotics, and applies them to simulations of biomolecular systems. As in the gMolmodel package developed by Spiridon and Minh in 2017, Robosample uses Constrained Dynamics Hamiltonian Monte Carlo (CDHMC) as a Gibbs sampling move - a type of Monte Carlo move where a subset of coordinates is allowed to change. In addition to the previously described Cartesian and torsional dynamics moves, Robosample implements spherical and cylindrical joints that can be distributed along the molecule by the user.

RESULTS

In alanine dipeptide simulations, the free energy surface is recovered by mixing fully flexible with torsional, cylindrical, or spherical dynamics moves. Ramachandran dynamics, where only the two key torsions are mobile, accelerate the slowest transition by an order of magnitude. We also show that simulations of a complex glycan cover significantly larger regions of the configuration space when mixed with constrained dynamics.

MAJOR CONCLUSIONS

Robosample is a tool of choice for efficient conformational sampling of large biomolecules.

GENERAL SIGNIFICANCE

Robosample is intended as a reliable and user-friendly simulation package for fast biomolecular sampling that does not require extensive expertise in mechanical engineering or in the statistical mechanics of reduced coordinates.

Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions

Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has been investigated using neutron spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and completely unfolded, following two different unfolding paths: using acid or guanidinium chloride (GdmCl). While the internal dynamics of the native-like state can be understood using normal mode analysis based on high resolution structural information of myoglobin, for the unfolded and even for the molten globule states, models from polymer science are employed. The Zimm model accurately describes the slowly-relaxing, expanded GdmCl-denaturated state, ignoring the individuality of the different aminoacid side chain. The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time. Transient formation of secondary structure elements in the acid unfolded and presence of α-helices in the molten globule state lead to internal friction to a similar extent.

Protein-Nanoparticle Interactions: What Are the Protein-Corona Thickness and Organization?

Protein adsorption on a surface is generally evaluated in terms of the evolution of the proteins' structures and functions. However, when the surface is that of a nanoparticle, the protein corona formed around it possesses a particular supramolecular structure that gives a "biological identity" to the new object. Little is known about the actual shape of the protein corona. Here, the protein corona formed by the adsorption of model proteins (myoglobin and hemoglobin) on silica nanoparticles was studied. Small-angle neutron scattering and oxygenation studies were combined to assess both the structural and functional impacts of the adsorption on proteins. Large differences in the oxygenation properties could be found while no significant global shape changes were seen after adsorption. Moreover, the structural study showed that the adsorbed proteins form an organized yet discontinuous monolayer around the nanoparticles.

Relevance of Internal Friction and Structural Constraints for the Dynamics of Denatured Bovine Serum Albumin

A general property of disordered proteins is their structural expansion that results in a high molecular flexibility. The structure and dynamics of bovine serum albumin (BSA) denatured by guanidinium hydrochloride (GndCl) were investigated using small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE). SANS experiments demonstrated the relevance of intrachain interactions for structural expansion. Using NSE experiments, we observed a high internal flexibility of denatured BSA in addition to center-of-mass diffusion detected by dynamic light scattering. Internal motions measured by NSE were described using concepts based on polymer theory. The contribution of residue-solvent friction was accounted for using the Zimm model including internal friction (ZIF). Disulfide bonds forming loops of amino acids of the peptide backbone have a major impact on internal dynamics that can be interpreted with a reduced set of Zimm modes.

Homogeneous and heterogeneous dynamics in native and denatured bovine serum albumin

Quasielastic incoherent neutron spectroscopy experiments reveal that chemical denaturation significantly modifies the internal dynamics of bovine serum albumin.

Characterizing the denatured state ensemble of ubiquitin under native conditions using replica exchange molecular dynamics

The representative structures of the denatured state ensemble of ubiquitin under a native condition and heat-denatured ubiquitin simulated from a fully extended conformation.

Critical examination of the colloidal particle model of globular proteins

Recent studies of globular protein solutions have uniformly adopted a colloidal view of proteins as particles, a perspective that neglects the polymeric primary structure of these biological macromolecules, their intrinsic flexibility, and their ability to sample a large configurational space. While the colloidal perspective often serves as a useful idealization in many cases, the macromolecular identity of proteins must reveal itself under thermodynamic conditions in which the native state is no longer stable, such as denaturing solvents and high protein concentrations where macromolecules tend to have screened excluded volume, charge, and hydrodynamic interactions. Under extreme pH conditions, charge repulsion interactions within the protein chain can overcome the attractive hydrogen-bonding interactions, holding it in its native globular state. Conformational changes can therefore be expected to have great significance on the shear viscosity and other rheological properties of protein solutions. These changes are not envisioned in conventional colloidal protein models and we have initiated an investigation of the scattering and rheological properties of model proteins. We initiate this effort by considering bovine serum albumin because it is a globular protein whose solution properties have also been extensively investigated as a function of pH, temperature, ionic strength, and concentration. As we anticipated, near-ultraviolet circular dichroism measurements and intrinsic viscosity measurements clearly indicate that the bovine serum albumin tertiary structure changes as protein concentration and pH are varied. Our findings point to limited validity of the colloidal protein model and to the need for further consideration and quantification of the effects of conformational changes on protein solution viscosity, protein association, and the phase behavior. Small-angle Neutron Scattering measurements have allowed us to assess how these conformational changes influence protein size, shape, and interprotein interaction strength.

Tyrosinase degradation is prevented when EDEM1 lacks the intrinsically disordered region

EDEM1 is a mannosidase-like protein that recruits misfolded glycoproteins from the calnexin/calreticulin folding cycle to downstream endoplasmic reticulum associated degradation (ERAD) pathway. Here, we investigate the role of EDEM1 in the processing of tyrosinase, a tumour antigen overexpressed in melanoma cells. First, we analyzed and modeled EDEM1 major domains. The homology model raised on the crystal structures of human and Saccharomyces cerevisiae ER class I α1,2-mannosidases reveals that the major mannosidase domain located between aminoacids 121-598 fits with high accuracy. We have further identified an N-terminal region located between aminoacids 40-119, predicted to be intrinsically disordered (ID) and susceptible to adopt multiple conformations, hence facilitating protein-protein interactions. To investigate these two domains we have constructed an EDEM1 deletion mutant lacking the ID region and a triple mutant disrupting the glycan-binding domain and analyzed their association with tyrosinase. Tyrosinase is a glycoprotein partly degraded endogenously by ERAD and the ubiquitin proteasomal system. We found that the degradation of wild type and misfolded tyrosinase was enhanced when EDEM1 was overexpressed. Glycosylated and non-glycosylated mutants co-immunoprecipitated with EDEM1 even in the absence of its intact mannosidase-like domain, but not when the ID region was deleted. In contrast, calnexin and SEL 1L associated with the deletion mutant. Our data suggest that the ID region identified in the N-terminal end of EDEM1 is involved in the binding of glycosylated and non-glycosylated misfolded proteins. Accelerating tyrosinase degradation by EDEM1 overexpression may lead to an efficient antigen presentation and enhanced elimination of melanoma cells.

Small angle neutron scattering for the structural study of intrinsically disordered proteins in solution: a practical guide

Small angle neutron scattering (SANS) allows studying bio-macromolecular structures and interactions in solution. It is particularly well-suited to study structural properties of intrinsically disordered proteins (IDPs) over a wide range of length-scales ranging from global aspects (radii of gyration and molecular weight) down to short-distance properties (e.g., cross-sectional analysis). In this book chapter, we provide a practical guide on how to carry out SANS experiments on IDPs and discuss the complementary aspects and strengths of SANS with respect to small angle X-ray scattering (SAXS).

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering

Small-angle scattering of X-rays (SAXS) is an established method to study the overall structure and structural transitions of biological macromolecules in solution. For folded proteins, the technique provides three-dimensional low resolution structures ab initio or it can be used to drive rigid-body modeling. SAXS is also a powerful tool for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs), and is highly complementary to the high resolution methods of X-ray crystallography and NMR. Here we present the basic principles of SAXS and review the main approaches to the characterization of IDPs and flexible multidomain proteins using SAXS. Together with the standard approaches based on the analysis of overall parameters, a recently developed Ensemble Optimization Method (EOM) is now available. The latter method allows for the co-existence of multiple protein conformations in solution compatible with the scattering data. Analysis of the selected ensembles provides quantitative information about flexibility and also offers insights into structural features. Examples of the use of SAXS and combined approaches with NMR, X-ray crystallography, and computational methods to characterize completely or partially disordered proteins are presented.

Small-Angle X-Ray Scattering from RNA, Proteins, and Protein Complexes

Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Here, we review recently developed algorithms for 3-D structure modeling and applications to protein complexes. Furthermore, we discuss the emerging use of SAXS as a tool to study membrane protein-detergent complexes. SAXS is proving useful to study the folding of functional RNA molecules, and finally we discuss uses of SAXS to study ensembles of denatured proteins.

Coil dimensions of the mussel adhesive protein Mefp-1

To obtain a better understanding of factors controlling cross-linking rates of Mussel adhesive proteins, we study the conformation of the Mussel Adhesive Protein Mefp-1. The dimensions of Mefp-1 in solution are determined by dynamic light scattering. Under physiological conditions, the hydrodynamic radius RH of Mefp-1 is found to be 10.5+/-1.1 nm. Measured Mefp-1 dimensions are compared with theoretical dimensions of Mefp-1 in random coil conformations. We have strong indications that Mefp-1, under dilute and physiological conditions, has a self-avoiding random walk conformation with helix-like deca-peptide segments. With a number of segments of approximately 90, the segment length is found to be 2.7 nm.

AOT water-in-oil microemulsions as a penetration enhancer in transdermal drug delivery of 5-fluorouracil

In vitro transdermal permeation of 5-fluorouracil (antineoplastic), a hydrophilic drug encapsulated in AOT/water/isopropylmyristate water-in-oil microemulsions (MEs), were studied using a modified Keshary and Chien diffusion cell. AOT (aerosol-OT or sodium bis(2-ethylhexyl) sulfosuccinate) is an anionic surfactant, which forms 'water-in-oil' ME in non-aqueous medium. The effect of water and AOT concentrations in MEs to the transdermal permeation of 5-fluorouracil through hairless mouse skin was investigated. MEs with 5:95 weight ratio of AOT:isopropylmyristate, containing 0.9, 1.8, 2.7 and 3.6% w/w of water have showed 1.68-, 2.36-, 3.58- and 3.77-fold increases in the skin flux of 5-fluorouracil (5-FU) respectively, compared to the aqueous solution of drug. The MEs with 5:95, 9:91 and 13:87 weight ratio of AOT:isopropyl myristate at fixed water content W0=15 (W0=[H2O]/AOT]) gave 3.58-, 5.04- and 6.3-fold enhancement of drug. In addition, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy was used to examine the effect of ME on lipid alkyl chain, hydration level, and corneocyte cells of the stratum corneum (SC). Results reveal that the ME interacts with a component of the SC and perturbs its architectural structure. The extent of perturbation in the SC depends on the concentration of water and AOT in the ME. Preliminary dermal toxicity studies indicate that the AOT/water/isopropylmyristate ME be safe for the transdermal permeation of 5-FU.

Characterization of the denatured states distribution of neocarzinostatin by small-angle neutron scattering and differential scanning calorimetry

The denatured states of a small globular protein, apo-neocarzinostatin (NCS), have been characterized using several techniques. Structural properties were investigated by optical spectroscopy techniques and small-angle neutron scattering (SANS), as a function of guanidinium chloride (GdmCl) concentration. SANS experiments show that in heavy water, the protein keeps its native size at GdmCl concentrations below 2.5 M. A sharp transition occurs at about 3.6 M GdmCl, and NCS behaves like an excluded volume chain above 5 M. The same behavior is observed in deuterated buffer by fluorescence and circular dichroism measurements. For the H(2)O buffer, the transition occurs with lower concentration of denaturant, the shift being about 0.6 M. 8-Anilino-1-naphthalenesulfonate (ANS) was used as a hydrophobic fluorescent probe for studying the early stages of protein unfolding. Protein denaturation modifies the fluorescence intensity of ANS, a maximum of intensity being detected close to 2 M GdmCl in hydrogenated buffer, which shows the existence of at least one intermediate state populated at the beginning of the unfolding pathway. Differential scanning calorimetry (DSC) was used to obtain thermodynamic values for NCS denaturation. The melting curves recorded between 20 and 90 degrees C in the presence of various GdmCl concentrations (0-3 M) cannot be explained by a simple two-state model. Altogether, the data presented in this paper suggest that before unfolding the protein explores a distribution of states which is centered around compact states at denaturant concentrations below 2 M in H(2)O, and then shifts to less structured states by increasing denaturant concentrations.

Change in backbone torsion angle distribution on protein folding

Understanding protein folding requires the determination of the configurational space accessible to the protein at different stages in folding. Here, computer simulation analysis of small angle neutron scattering results is used to probe the change in the distribution of configurations on strong denaturation of a globular protein, phosphoglycerate kinase, in 4 M guanidine hydrochloride solution. To do this atomic-detail ensembles of the unfolded protein chain are modeled and their scattering profiles compared with the experiment. The local conformational statistics are found to strongly influence the experimental intensity at scattering vectors between 0.05 and 0.3 A(-1). Denaturation leads to a reduction in the protein atom-pair distance distribution function over the approximately 3-15 A region that is associated with a quantifiable shift in the backbone torsional angle (phi, psi) distribution toward the beta region of the Ramachandran plot.

Excluded volume in the configurational distribution of a strongly-denatured protein

The configurational distribution of phosphoglycerate kinase (PGK) strongly-denatured in 4 M guanidine hydrochloride solution is investigated using small-angle neutron scattering (SANS) and Monte Carlo computer simulation. It is shown that the experimental scattering profile can be represented by a random flexible chain of spheres of excess scattering density with excluded volume interactions, the best agreement being achieved when partial sphere intersection is allowed. The radius of gyration of the chain increases by a factor of 4 on denaturation, whereas the average length of segments approximately 5 residues long increases by only approximately 10%, consistent with a picture in which the large expansion on denaturation originates primarily from increased long-range flexibility of the polypeptide chain. The results provide a description of the chain statistics from which the construction of starting points for simulation studies of folding of the protein can be envisaged.

Identification of a domain on the beta-subunit of the rod cGMP-gated cation channel that mediates inhibition by calcium-calmodulin

The cGMP-gated cation channel mediating phototransduction in retinal rods has recently been shown to be inhibited by calcium-calmodulin, through direct binding of the latter to the beta-subunit of the heterotetrameric channel complex. Here, we report the characterization of this inhibition and the identification of a domain crucial for this modulation. Heterologous expression of the alpha- and beta-subunits of the human rod channel in HEK 293 cells produced a cGMP-gated current that was highly sensitive to calcium-calmodulin, with half-maximal inhibition at approximately 4 nM. In biochemical and electrophysiological experiments on deletion mutants of the beta-subunit, we have identified a region on its cytoplasmic N terminus that binds calmodulin and is necessary for the calmodulin-mediated inhibition of the channel. However, in gel shift assays and fluorescence emission experiments, peptides derived from this region indicated a low calmodulin affinity, with dissociation constants of approximately 3-10 microM. On the C terminus, a region was also found to bind calmodulin, but it was likewise of low affinity, and its deletion did not abolish the calmodulin-mediated inhibition. We suggest that although the identified region on the N terminus of the beta-subunit is crucial for the calmodulin effect, other regions are likely to be involved as well. In this respect, the rod channel appears to differ from the olfactory cyclic nucleotide-gated channel, which is also modulated by calcium-calmodulin.

Repulsive interparticle interactions in a denatured protein solution revealed by small angle neutron scattering

In order to investigate the effect of concentration in biological processes such as protein folding, small angle neutron scattering measurements were used to determine the second virial coefficient of solutions of both native and strongly denatured phosphoglycerate kinase and the radius of gyration of the protein at zero concentration. The value of the second virial coefficient is a good probe of the non-ideality of a solution. The present results show that the unfolding of the protein leads to a drastic change in the repulsive intermolecular interactions. We conclude that these interactions are due mainly to the behaviour of the denatured polypeptide chain as an excluded volume polymer.

Interdomain interactions underlying activation of cyclic nucleotide-gated channels

Cyclic nucleotide-gated (CNG) ion channels are multimeric proteins that activate in response to the binding of cyclic nucleotide to intracellular domains. Here, an intramolecular protein-protein interaction between the amino-terminal domain and the carboxyl-terminal ligand-binding domain of the rat olfactory CNG channel was shown to exert an autoexcitatory effect on channel activation. Calcium-calmodulin, which modulates CNG channel activity during odorant adaptation, blocked this interaction. A specific deletion within the amino-terminal domain disrupted the interdomain interaction in vitro and altered the gating properties and calmodulin sensitivity of expressed channels. Thus, the amino-terminal domain may promote channel opening by directly interacting with the carboxyl-terminal gating machinery; calmodulin regulates channel activity by targeting this interaction.

Insights into biomolecular function from small-angle scattering

Recent advances in neutron and X-ray sources and instrumentation, new and improved scattering techniques, and molecular biology techniques, which have permitted facile preparation of samples, have each led to new opportunities in using small-angle scattering to study the conformations and interactions of biological macromolecules in solution as a function of their properties. For example, new instrumentation on synchrotron sources has facilitated time-resolved studies that yield insights into protein folding. More powerful neutron sources, combined with molecular biology tools that isotopically label samples, have facilitated studies of biomolecular interactions, including those involving active enzymes.