Demonstration by pulsed neutron scattering that the arrangement of the Fab and Fc fragments in the overall structures of bovine IgG1 and IgG2 in solution is similar

How neutron scattering techniques benefit investigating structures and dynamics of monoclonal antibody

Over the past several decades, great progresses have been made for the pharmaceutical industry of monoclonal antibody (mAb). More and more mAb products were approved for human therapeutics. This review describes the state of art of utilizing neutron scattering to investigate mAbs, in the aspects of structures, dynamics, physicochemical stability, functionality, etc. Firstly, brief histories of mAbs and neutron scattering, as well as some basic knowledges and principles of neutron scattering were introduced. Then specific examples were demonstrated. For the structure and structural evolution investigation of in dilute and concentrated mAbs solution, in situ small angle neutron scattering (SANS) was frequently utilized. Neutron reflectometry (NR) is powerful to probe the absorption behaviors of mAbs on various surfaces and interfaces. While for dynamic investigation, quasi-elastic scattering techniques such as neutron spin echo (NSE) demonstrate the capabilities. With this review, how to utilize and take advantages of neutron scattering on investigating structures and dynamics of mAbs were demonstrated and discussed.

Structural Characterization of the Full-Length Anti-CD20 Antibody Rituximab

Rituximab, a murine–human chimera, is the first monoclonal antibody (mAb) developed as a therapeutic agent to target CD20 protein. Its Fab domain and its interaction with CD20 have been extensively studied and high-resolution atomic models obtained by X-ray diffraction or cryo-electron microscopy are available. However, the structure of the full-length antibody is still missing as the inherent protein flexibility hampers the formation of well-diffracting crystals and the reconstruction of 3D microscope images. The global structure of rituximab from its dilute solution is here elucidated by small-angle X-ray scattering (SAXS). The limited data resolution achievable by this technique has been compensated by intensive computational modelling that led to develop a new and effective procedure to characterize the average mAb conformation as well as that of the single domains. SAXS data indicated that rituximab adopts an asymmetric average conformation in solution, with a radius of gyration and a maximum linear dimension of 52 Å and 197 Å, respectively. The asymmetry is mainly due to an uneven arrangement of the two Fab units with respect to the central stem (the Fc domain) and reflects in a different conformation of the individual units. As a result, the Fab elbow angle, which is a crucial determinant for antigen recognition and binding, was found to be larger (169°) in the more distant Fab unit than that in the less distant one (143°). The whole flexibility of the antibody has been found to strongly depend on the relative inter-domain orientations, with one of the Fab arms playing a major role. The average structure and the amount of flexibility has been studied in the presence of different buffers and additives, and monitored at increasing temperature, up to the complete unfolding of the antibody. Overall, the structural characterization of rituximab can help in designing next-generation anti-CD20 antibodies and finding more efficient routes for rituximab production at industrial level.

Atomistic Modeling of Scattering Curves for Human IgG1/4 Reveals New Structure-Function Insights

Small angle x-ray and neutron scattering are techniques that give solution structures for large macromolecules. The creation of physically realistic atomistic models from known high-resolution structures to determine joint x-ray and neutron scattering best-fit structures offers a, to our knowledge, new method that significantly enhances the utility of scattering. To validate this approach, we determined scattering curves for two human antibody subclasses, immunoglobulin G (IgG) 1 and IgG4, on five different x-ray and neutron instruments to show that these were reproducible, then we modeled these by Monte Carlo simulations. The two antibodies have different hinge lengths that connect their antigen-binding Fab and effector-binding Fc regions. Starting from 231,492 and 190,437 acceptable conformations for IgG1 and IgG4, respectively, joint x-ray and neutron scattering curve fits gave low goodness-of-fit R factors for 28 IgG1 and 2748 IgG4 structures that satisfied the disulphide connectivity in their hinges. These joint best-fit structures showed that the best-fit IgG1 models had a greater separation between the centers of their Fab regions than those for IgG4, in agreement with their hinge lengths of 15 and 12 residues, respectively. The resulting asymmetric IgG1 solution structures resembled its crystal structure. Both symmetric and asymmetric solution structures were determined for IgG4. Docking simulations with our best-fit IgG4 structures showed greater steric clashes with its receptor to explain its weaker FcγRI receptor binding compared to our best-fit IgG1 structures with fewer clashes and stronger receptor binding. Compared to earlier approaches for fitting molecular antibody structures by solution scattering, we conclude that this joint fit approach based on x-ray and neutron scattering data, combined with Monte Carlo simulations, significantly improved our understanding of antibody solution structures. The atomistic nature of the output extended our understanding of known functional differences in Fc receptor binding between IgG1 and IgG4.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

The solution structure of rabbit IgG accounts for its interactions with the Fc receptor and complement C1q and its conformational stability

Solution structures for antibodies are critical to understand function and therapeutic applications. The stability of the solution structure of rabbit IgG in different buffers and temperatures was determined by analytical ultracentrifugation and X-ray and neutron scattering. Rabbit IgG showed a principally monomeric species, which is well resolved from small amounts of a dimeric species. The proportion of dimer increased with increased concentration, decreased temperature and heavy water from 8% to 25% in all buffers except for high salt (250 mM NaCl). The Guinier X-ray radius of gyration R(G) likewise increased with concentration in 137 mM NaCl buffer but was unchanged in 250 mM NaCl buffer. The Guinier neutron R(G) values increased as the temperature decreased. The X-ray and neutron distance distribution curves P(r) revealed two peaks, M1 and M2, whose positions did not change with concentration to indicate unchanged structures under all these conditions. The maximum dimension increased with concentration because of dimer formation. Constrained scattering modeling reproducibly revealed very similar asymmetric solution structures for monomeric rabbit IgG in different buffers, in which the Fab-Fc and Fab-Fab pairs were separated by maximally extended hinge structures. The dimer was best modeled by two pairs of Fab regions forming tip-to-tip contacts. The intact rabbit IgG structures explained the ability of its two ligands, the Fc receptor and complement C1q, to bind to the top of its Fc region that is fully accessible and unhindered by the Fab regions.

Real-time Recognition of Mycobacterium tuberculosis and Lipoarabinomannan using the Quartz Crystal Microbalance

A quartz crystal microbalance (QCM) immunosensor has been successfully employed to screen for both whole Mycobacteria tuberculosis (Mtb) bacilli and a Mtb surface antigen, lipoarabinomannan (LAM). One of the most abundant components of the Mtb cell surface, LAM, may be detected without the presence of the entire bacterium. Using available antibodies with proven utility in enzyme-linked immunoassays (ELISAs), a sensor was designed to measure Mtb bacilli and LAM. Equilibrium association constants (K(a)) were determined for the interaction of Mtb with immobilized α-LAM and anti-H37Rv antibodies, where avidity was seen to strengthen this interaction and provide for greater binding than might have otherwise been achieved. The binding of LAM to immobilized α-LAM had a high associate rate constant (k(a)) allowing for rapid detection. Evaluating these binding constants helped the compare the sensitivity of these immunosensors to conventional ELISAs. The use of these assays with the better antibodies may allow for immunosensor use in determining LAM as a point-of-care (POC) diagnostic for Mtb.

Masking of the Fc region in human IgG4 by constrained X-ray scattering modelling: implications for antibody function and therapy

Of the four human IgG antibody subclasses IgG1-IgG4, IgG4 is of interest in that it does not activate complement and exhibits atypical self-association, including the formation of bispecific antibodies. The solution structures of antibodies are critical to understand function and therapeutic applications. Thus IgG4 was studied by synchrotron X-ray scattering. The Guinier X-ray radius of gyration R(G) increased from 5.0 nm to 5.1 nm with an increase of concentration. The distance distribution function P(r) revealed a single peak at 0.3 mg/ml, which resolved into two peaks that shifted to smaller r values at 1.3 mg/ml, even though the maximum dimension of IgG4 was unchanged at 17 nm. This indicated a small concentration dependence of the IgG4 solution structure. By analytical ultracentrifugation, no concentration dependence in the sedimentation coefficient of 6.4 S was observed. Constrained scattering modelling resulted in solution structural determinations that showed that IgG4 has an asymmetric solution structure in which one Fab-Fc pair is closer together than the other pair, and the accessibility of one side of the Fc region is masked by the Fab regions. The averaged distances between the two Fab-Fc pairs change by 1-2 nm with the change in IgG4 concentration. The averaged conformation of the Fab regions appear able to hinder complement C1q binding to the Fc region and the self-association of IgG4 through the Fc region. The present results clarify IgG4 function and provide a starting point to investigate antibody stability.

X-ray and neutron scattering data and their constrained molecular modeling

X-ray and neutron solution scattering methods provide multiparameter structural and compositional information on proteins that complements high-resolution protein crystallography and NMR studies. We describe the procedures required to (1) obtain validated X-ray and neutron scattering data, (2) perform Guinier analyses of the scattering data to extract the radius of gyration R(G) and intensity parameters, and (3) calculate the distance distribution function P(r). Constrained modeling is important because this confirms the experimental data analysis and produces families of best-fit molecular models for comparison with crystallography and NMR structures. The modeling procedures are described in terms of (4) generating appropriate starting models, (5) randomizing these for trial-and-error scattering fits, (6) identifying the final best-fit models, and (7) applying analytical ultracentrifugation (AUC) data to validate the scattering modeling. These procedures and pitfalls in them will be illustrated using work performed in the authors' laboratory on antibodies and the complement proteins of the human immune defense system. Four different types of modeling procedures are distinguished, depending on the number and type of domains in the protein. Examples when comparisons with crystallography and NMR structures are important are described. For multidomain proteins, it is often found that scattering provides essential evidence to validate or disprove a crystal structure. If a large protein cannot be crystallized, scattering provides the only means to obtain a structure.

Semi-extended solution structure of human myeloma immunoglobulin D determined by constrained X-ray scattering

Human immunoglobulin D (IgD) occurs most abundantly as a membrane-bound antibody on the surface of mature B cells (mIgD). IgD possesses the longest hinge sequence of all the human antibody isotypes, with 64 residues connecting the Fab and Fc fragments. A novel rapid purification scheme of secreted IgD from the serum of an IgD myeloma patient using thiophilic (T-gel) and lectin affinity chromatography gave a stable, homogeneous IgD preparation. Synchrotron X-ray scattering and analytical ultracentrifugation of IgD identified the solution arrangement of its Fab and Fc fragments, and thereby its hinge structure. The Guinier X-ray radius of gyration R(G) of 6.9(+/-0.1)nm showed that IgD is more extended in solution than the immunoglobulin subclass IgA1 (R(G) of 6.1-6.2nm). Its distance distribution function P(r) showed a single peak at 4.7nm and a maximum dimension of 23nm. Velocity experiments gave a sedimentation coefficient of 6.3S, which is similar to that for IgA1 at 6.2S. The complete IgD structure was modelled using molecular dynamics to generate IgD hinge structures, to which homology models for the Fab and Fc fragments were connected. Good scattering curve fits were obtained with 18 semi-extended best fit IgD models that were filtered from 8500 trial models. These best-fit models showed that the IgD hinge does not correspond to an extended polypeptide structure. The averaged solution structure arrangement of the Fab and Fc fragments in IgD is principally T-shaped and flexible, with contribution from Y-shaped and inverted Y-shaped structures. Although the linear sequence of the IgD hinge is much longer, comparison with previous scattering modelling of IgA1 and IgA2(m)1 suggests that the hinge of IgA1 and IgD are more similar than might have been expected, Both possess flexible T-shaped solution structures, probably reflecting the presence of restraining O-linked sugars.

Nomenclature of the Proteins of Cows’ Milk—Sixth Revision

This report of the American Dairy Science Association Committee on the Nomenclature, Classification, and Methodology of Milk Proteins reviews changes in the nomenclature of milk proteins necessitated by recent advances of our knowledge of milk proteins. Identification of major caseins and whey proteins continues to be based upon their primary structures. Nomenclature of the immunoglobulins consistent with new international standards has been developed, and all bovine immunoglobulins have been characterized at the molecular level. Other significant findings related to nomenclature and protein methodology are elucidation of several new genetic variants of the major milk proteins, establishment by sequencing techniques and sequence alignment of the bovine caseins and whey proteins as the reference point for the nomenclature of all homologous milk proteins, completion of crystallographic studies for major whey proteins, and advances in the study of lactoferrin, allowing it to be added to the list of fully characterized milk proteins.

Solution Structure Determination of Monomeric Human IgA2 by X-ray and Neutron Scattering, Analytical Ultracentrifugation and Constrained Modelling: A Comparison with Monomeric Human IgA1

Immunoglobulin A (IgA), the most abundant human immunoglobulin, mediates immune protection at mucosal surfaces as well as in plasma. It exists as two subclasses IgA1 and IgA2, and IgA2 is found in at least two allotypic forms, IgA2m(1) or IgA2m(2). Compared to IgA1, IgA2 has a much shorter hinge region, which joins the two Fab and one Fc fragments. In order to assess its solution structure, monomeric recombinant IgA2m(1) was studied by X-ray and neutron scattering. Its Guinier X-ray radius of gyration R(G) is 5.18 nm and its neutron R(G) is 5.03 nm, both of which are significantly smaller than those for monomeric IgA1 at 6.1-6.2 nm. The distance distribution function P(r)for IgA2m(1) showed a broad peak with a subpeak and gave a maximum dimension of 17 nm, in contrast to the P(r) curve for IgA1, which showed two distinct peaks and a maximum dimension of 21 nm. The sedimentation coefficients of IgA1 and IgA2m(1) were 6.2S and 6.4S, respectively. These data show that the solution structure of IgA2m(1) is significantly more compact than IgA1. The complete monomeric IgA2m(1) structure was modelled using molecular dynamics to generate random IgA2 hinge structures, to which homology models for the Fab and Fc fragments were connected to generate 10,000 full models. A total of 104 compact best-fit IgA2m(1) models gave good curve fits. These best-fit models were modified by linking the two Fab light chains with a disulphide bridge that is found in IgA2m(1), and subjecting these to energy refinement to optimise this linkage. The averaged solution structure of the arrangement of the Fab and Fc fragments in IgA2m(1) was found to be predominantly T-shaped and flexible, but also included Y-shaped structures. The IgA2 models show full steric access to the two FcalphaRI-binding sites at the Calpha2-Calpha3 interdomain region in the Fc fragment. Since previous scattering modelling had shown that IgA1 also possessed a flexible T-shaped solution structure, such a T-shape may be common to both IgA1 and IgA2. The final models suggest that the combination of the more compact IgA2m(1) and the more extended IgA1 structures will enable human IgA to access a broader range of antigens than either acting alone. The hinges of both IgA subclasses appear to show reduced flexibility when compared to their equivalents in IgG, and this may be important for maintaining an extended IgA structure.

The extended multidomain solution structures of the complement protein Crry and its chimeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy

Complement receptor-related gene/protein y (Crry) is a cell membrane-bound regulator of complement activation found in mouse and rat. Crry contains only short complement/consensus repeat (SCR) domains. X-ray and neutron scattering was performed on recombinant rat Crry containing the first five SCR domains (rCrry) and mouse Crry with five SCR domains conjugated to the Fc fragment of mouse IgG1 (mCrry-Ig) in order to determine their solution structures at medium resolution. The radius of gyration R(G) of rCrry was determined to be 4.9-5.0 nm, and the R(G) of the cross-section was 1.2-1.5 nm as determined by X-ray and neutron scattering. The R(G) of mCrry-Ig was 6.6-6.7 nm, and the R(G) of the cross-section were 2.3-2.4 nm and 1.3 nm. The maximum dimension of rCrry was 18 nm and that for mCrry-Ig was 26 nm. The neutron data indicated that rCrry and mCrry-Ig have molecular mass values of 45,000 Da and 140,000 Da, respectively, in agreement with their sequences, and sedimentation equilibrium data supported these determinations. Time-derivative velocity experiments gave sedimentation coefficients of 2.4S for rCrry and 5.4S for mCrry-Ig. A medium-resolution model of rCrry was determined using homology models that were constructed for the first five SCR domains of Crry from known crystal and NMR structures, and linked by randomly generated linker peptide conformations. These trial-and-error calculations revealed a small family of extended rCrry structures that best accounted for the scattering and ultracentrifugation data. These were shorter than the most extended rCrry models as the result of minor bends in the inter-SCR orientations. The mCrry-Ig solution data were modelled starting from a fixed structure for rCrry and the crystal structure of mouse IgG1, and was based on conformational searches of the hinge peptide joining the mCrry and Fc fragments. The best-fit models showed that the two mCrry antennae in mCrry-Ig were extended from the Fc fragment. No preferred orientation of the antennae was identified, and this indicated that the accessibility of the antennae for the molecular targets C4b and C3b was not affected by the covalent link to Fc. A structural comparison between Crry and complement receptor type 1 indicated that the domain arrangement of Crry SCR 1-3 is as extended as that of the CR1 SCR 15-17 NMR structure.

Ligand-induced conformational changes in tissue transglutaminase: Monte Carlo analysis of small-angle scattering data

Small-angle neutron and x-ray scattering experiments have been performed on type 2 tissular transglutaminase to characterize the conformational changes that bring about Ca(2+) activation and guanosine triphosphate (GTP) inhibition. The native and a proteolyzed form of the enzyme, in the presence and in the absence of the two effectors, were considered. To describe the shape of transglutaminase in the different conformations, a Monte Carlo method for calculating small-angle neutron scattering profiles was developed by taking into account the computer-designed structure of the native transglutaminase, the results of the Guinier analysis, and the essential role played by the solvent-exposed peptide loop for the conformational changes of the protein after activation. Although the range of the neutron scattering data is rather limited, by using the Monte Carlo analysis, and because the structure of the native protein is available, the distribution of the protein conformations after ligand interaction was obtained. Calcium activation promotes a rotation of the C-terminal with respect to the N-terminal domain around the solvent-exposed peptide loop that connects the two regions. The psi angle between the longest axes of the two pairs of domains is found to be above 50 degrees, larger than the psi value of 35 degrees calculated for the native transglutaminase. On the other hand, the addition of GTP makes possible conformations characterized by psi angles lower than 34 degrees. These results are in good agreement with the proposed enzyme activity regulation: in the presence of GTP, the catalytic site is shielded by the more compact protein structure, while the conformational changes induced by Ca(2+) make the active site accessible to the substrate.

The Fab and Fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling

Human immunoglobulin A (IgA) is an abundant antibody that mediates immune protection at mucosal surfaces as well as in plasma. The IgA1 isotype contains two four-domain Fab fragments and a four-domain Fc fragment analogous to that in immunoglobulin G (IgG), linked by a glycosylated hinge region made up of 23 amino acid residues from each of the heavy chains. IgA1 also has two 18 residue tailpieces at the C terminus of each heavy chain in the Fc fragment. X-ray scattering using H2O buffers and neutron scattering using 100 % 2H2O buffers were performed on monomeric IgA1 and a recombinant IgA1 that lacks the tailpiece (PTerm455). The radii of gyration RG from Guinier analyses were similar at 6.11-6.20 nm for IgA1 and 5.84-6.16 nm for PTerm455, and their cross-sectional radii of gyration RXS were also similar. The similarity of the RG and RXS values suggests that the tailpiece of IgA1 is not extended outwards in solution. The IgA1 RG values are higher than those for IgG, and the distance distribution function P(r) showed two distinct peaks, whereas a single peak was observed for IgG. Both results show that the hinge of IgA1 results in an extended Fab and Fc arrangement that is different from that in IgG. Automated curve-fit searches constrained by homology models for the Fab and Fc fragments were used to model the experimental IgA1 scattering curves. A translational search to optimise the relative arrangement of the Fab and Fc fragments held in a fixed orientation resembling that in IgG was not successful in fitting the scattering data. A new molecular dynamics curve-fit search method generated IgA1 hinge structures to which the Fab and Fc fragments could be connected in any orientation. A search based on these identified a limited family of IgA1 structures that gave good curve fits to the experimental data. These contained extended hinges of length about 7 nm that positioned the Fab-to-Fab centre-to-centre separation 17 nm apart while keeping the corresponding Fab-to-Fc separation at 9 nm. The resulting extended T-shaped IgA1 structures are distinct from IgG structures previously determined by scattering and crystallography which have Fab-to-Fab and Fab-to-Fc centre-to-centre separations of 7-9 nm and 6-8 nm, respectively. It was concluded that the IgA1 hinge is structurally distinct from that in IgG, and this results in a markedly different antibody structure that may account for a unique immune role of monomeric IgA1 in plasma and mucosa.

A synthetic holliday junction is sandwiched between two tetrameric Mycobacterium leprae RuvA structures in solution: new insights from neutron scattering contrast variation and modelling

The interaction between homologous DNA molecules in recombination and DNA repair leads to the formation of crossover intermediates known as Holliday junctions. Their enzymatic processing by the RuvABC system in bacteria involves the formation of a complex between RuvA and the Holliday junction. To study the solution structure of this complex, contrast variation by neutron scattering was applied to Mycobacterium leprae RuvA (MleRuvA), a synthetic analogue of a Holliday junction with 16 base-pairs in each arm, and their stable complex. Unbound MleRuvA was octameric in solution, and formed an octameric complex with the DNA junction. The radii of gyration at infinite contrast were determined to be 3.65 nm, 2.74 nm and 4.15 nm for MleRuvA, DNA junction and their complex, respectively, showing that the complex was structurally more extended than MleRuvA. No difference was observed in the presence or absence of Mg2+. The large difference in RG values for the free and complexed protein in 65% 2H2O, where the DNA component is "invisible", showed that a substantial structural change had occurred in complexed MleRuvA. The slopes of the Stuhrmann plots for MleRuvA and the complex were 19 and 15 or less (x10(-5)), respectively, indicating that DNA passed through the centre of the complex. Automated constrained molecular modelling based on the Escherichia coli RuvA crystal structure demonstrated that the scattering curve of octameric MleRuvA in 65% and 100% 2H2O is explained by a face-to-face association of two MleRuvA tetramers stabilised by salt-bridges. The corresponding modelling of the complex in 65% 2H2O showed that the two tetramers are separated by a void space of about 1-2 nm, which can accommodate the width of B-form DNA. Minor conformational changes between unbound and complexed MleRuvA may occur. These observations show that RuvA plays a more complex role in homologous recombination than previously thought.

Possible arrangement of the five domains in human complement factor I as determined by a combination of X-ray and neutron scattering and homology modeling

Human factor I is a multidomain plasma serine protease with one factor I-membrane attack complex (FIMAC) domain, one CD5 domain, two low-density lipoprotein receptor (LDLr) domains, and one serine protease (SP) domain and is essential for the regulation of complement. The domain arrangement in factor I was determined by X-ray and neutron scattering on serum-derived human factor I (sFI) and recombinant insect cell factor I (rFI). While the radii of gyration of both were the same at 4.05 nm and both had overall lengths of 14 nm, the cross-sectional radii of gyration were different at 1.70 nm for sFI and 1.57 nm for rFI. This difference was attributed to their different means of glycosylation which is complex-type for sFI and high-mannose-type for rFI. Homology models were constructed for the FIMAC, LDLr, and SP domains of factor I using related crystal structures, and CD5 was represented as a globular protein by referencing its electron microscopy dimensions. In these models, 38 of the 40 Cys residues in factor I were predicted to form internal disulfide bridges. The two remaining Cys residues at the N terminus of the FIMAC domain and at the center of the first LDLr domain were potentially not bridged. It was postulated that, if these two Cys residues were bridged to each other, the FIMAC, CD5, and LDLr-1 domains would form a compact triangular arrangement. This hypothesis was tested by automated scattering curve fit searches based on 9600 bilobal models, setting the FIMAC, CD5, and LDLr-1 domains as one lobe and the large SP domain as the other lobe. The searches gave a single small family of similar structures with a separation of 5.9 nm between the centers of the lobes which gave similar good X-ray and neutron fits for both sFI and rFI, despite the different glycosylations of sFI and rFI. These best-fit structures for factor I showed that this domain model is plausible, and suggested that the SP and the CD5 and LDLr-1 domains may present exposed surfaces in factor I whose roles are to interact separately with its substrates C3b and C4b and with cofactor proteins.

The solution structure of human coagulation factor VIIa in its complex with tissue factor is similar to free factor VIIa: a study of a heterodimeric receptor-ligand complex by X-ray and neutron scattering and computational modeling

Factor VIIa (FVIIa) is a soluble four-domain plasma serine protease coagulation factor that forms a tight complex with the two extracellular domains of the transmembrane protein tissue factor in the initiating step of blood coagulation. To date, there is no crystal structure for free FVIIa. X-ray and neutron scattering data in solution for free FVIIa and the complex between FVIIa and soluble tissue factor (sTF) had been obtained for comparison with crystal structures of the FVIIa-sTF complex and of free factor IXa (FIXa). The solution structure of free FVIIa as derived from scattering data is consistent with the extended domain arrangement of FVIIa seen in the crystal structure of its complex with sTF, but is incompatible with the bent, less extended domain conformation seen in the FIXa crystal structure. The FVIIa scattering curve is also compatible with a subset of 317 possible extended structures derived from a constrained automated conformational search of 15 625 FVIIa domain models. Thus, the scattering data support extended domain models for FVIIa free in solution. Similar analyses showed that the solution scattering derived and crystal structures of the FVIIa-sTF complex were in good agreement. An automated constrained search for allowed structures for the complex in solution based on scattering curves showed that only a small family of compact models gave good agreement, namely those in which FVIIa and sTF interact closely over a large surface area. The general utility of this approach for structural analysis of heterodimeric complexes in solution is discussed. Analytical ultracentrifugation data and the modeling of these data were consistent with the scattering results. It is concluded that in solution FVIIa has an extended or elongated domain structure, which allows rapid interaction with sTF over a large surface area to form a high-affinity complex.

Analogy and solution scattering modelling: new structural strategies for the multidomain proteins of complement, cartilage and the immunoglobulin superfamily

Many immunologically relevant proteins possess multidomain structures. Molecular structures both at the level of the individual domain and that of the intact protein are required for a full appreciation of function and control. Two recently developed structural approaches are reviewed here. Analogy modelling methods are based on the current understanding of many protein structures, and make possible the identification of folds for superfamilies of unknown structures. An integrated multidisciplinary predictive approach has been successfully applied to the von Willebrand factor type A, proteoglycan tandem repeat and factor I/membrane attack complex domains. The available experimental and predictive evidence is assembled in order to identify a known three-dimensional structure related to the unknown one of interest. Neutron and X-ray scattering curve modelling provides information on the full multidomain structure in solution. As scattering curves can be calculated from known atomic structures, the present availability of structures for many domains in conjunction with tight constraints based on these structures and the covalent connections between them results in a small family of allowed best-fit structures for a given scattering curve. The curve-fit procedure can be automated, and whole multidomain structures can be determined to a positional precision of the order of 0.2-1 nm. Such models are informative on the steric accessibility of each domain and their functional activity, and this is illustrated for antibody, cell-surface and complement proteins.

Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm

Small-angle x-ray solution scattering (SAXS) is analyzed with a new method to retrieve convergent model structures that fit the scattering profiles. An arbitrary hexagonal packing of several hundred beads containing the problem object is defined. Instead of attempting to compute the Debye formula for all of the possible mass distributions, a genetic algorithm is employed that efficiently searches the configurational space and evolves best-fit bead models. Models from different runs of the algorithm have similar or identical structures. The modeling resolution is increased by reducing the bead radius together with the search space in successive cycles of refinement. The method has been tested with protein SAXS (0.001 < S < 0.06 A(-1)) calculated from x-ray crystal structures, adding noise to the profiles. The models obtained closely approach the volumes and radii of gyration of the known structures, and faithfully reproduce the dimensions and shape of each of them. This includes finding the active site cavity of lysozyme, the bilobed structure of gamma-crystallin, two domains connected by a stalk in betab2-crystallin, and the horseshoe shape of pancreatic ribonuclease inhibitor. The low-resolution solution structure of lysozyme has been directly modeled from its experimental SAXS profile (0.003 < S < 0.03 A(-1)). The model describes lysozyme size and shape to the resolution of the measurement. The method may be applied to other proteins, to the analysis of domain movements, to the comparison of solution and crystal structures, as well as to large macromolecular assemblies.

Methods to monitor process-induced changes in food proteins. An overview

Proteins in food systems may undergo various changes in their structural properties as a consequence of processing. Whether these changes are beneficial or detrimental in terms of the nutritional, biological or functional properties of the processed system, it is important to apply analytical methods which can monitor the course of protein structural changes, in order to elucidate the underlying mechanism behind the results of different processes. Proteins are usually found in high concentrations in foods; furthermore, these proteins frequently may either initially be part of a solid food or may become insoluble due to processing. As a result, many of the traditional biochemical methods for analysis of protein structural properties in dilute solution cannot be applied directly to study food proteins. This chapter gives an overview of some potential methods which may be used to monitor the changes in quaternary, tertiary, secondary and primary structure of proteins in food systems.

Molecular structures from low angle X-ray and neutron scattering studies

Molecular structures can be extracted from solution scattering analyses of multidomain or oligomeric proteins by a new method of constrained automated scattering curve fits. Scattering curves are calculated using a procedure tested by comparisons of crystal structures with experimental X-ray and neutron data. The domains or subunits in the protein of interest are all represented by atomic coordinates in order to provide initial constraints. From this starting model, hundreds or thousands of different possible structures are computed, from each of which a scattering curve is computed. Each model is assessed for steric overlap, radii of gyration and R-factors in order to leave a small family of good fit models that corresponds to the molecular structure of interest. This method avoids the tedium of curve fitting by hand and error limits on the ensuing models can be described. For single multidomain proteins, the key constraint is the correct stereochemical connections between the domains in all the models. Successful applications to determine structures are summarised for the Fab and Fc fragments in immunoglobulin G, the three domain pairs in the Fc subunit of immunoglobulin E and the seven, domains in carcinoembryonic antigen. For oligomeric proteins, the key constraint is provided by symmetry and successful analyses were performed for the association of the monomers of the bacterial amide sensor protein AmiC to form trimers and pentameric serum amyloid P component to form decameric structures. The successful analysis of the heterodimeric complex of tissue factor and factor VIIa required the use of constraints provided from biochemical data. The outcome of these analyses is critically appraised, in particular the biological significance of structures determined by these solution scattering curve fits.

Kinetics of Low pH Induced Aggregation of Equine IgG

The kinetics of soluble aggregate formation in equine IgG was studied in the pH 3.4-4.3 range and ionic strength between 0.02 and 0.5 M, and a diagram describing aggregation kinetics as diffusion limited, reaction limited, or transitional as a function of pH and ionic strength was constructed. Aggregation rate is limited by the degree of electrostatic repulsion between the protein molecules in the pH 4.0-4.5 range. Below pH 4.0, a greater degree of attractive force is present, most likely from protein unfolding, and electrostatic repulsion no longer determines the rate of aggregation. The aggregation rate increases with decreasing pH, and at pH 3.4 the aggregation rate is diffusion limited. The pH range separating reaction-limited and diffusion-limited kinetics decreases with increasing ionic strength, indicating charge shielding from the buffer solution influences the aggregation rate. Copyright 1997 Academic Press.

Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses

Human serum amyloid P component (SAP) is a normal plasma glycoprotein and the precursor of amyloid P component which is a universal constituent of the abnormal tissue deposits in amyloidosis. X-ray and neutron scattering data showed that pentameric or decameric ring structures for SAP in solution are readily distinguished. Further neutron data collection showed that SAP pentamers were reproducibly obtained in the presence of Ca2+ at pH 5.5 or in the presence of methyl 4,6-O-(1-carboxyethylidene)-beta-d-galactopyranoside (MObetaDG) and Ca2+ at pH 6.0 to 8.0, while SAP decamers were obtained in the presence of EDTA between pH 5.5 and 8.0. SAP pentamers have a mean X-ray RG of 3.99(+/-0.11) nm and a mean neutron RG of 3.69(+/-0.12) nm in 100% 2H2O. SAP decamers have a mean X-ray RG of 4.23(+/-0.12) nm and a mean neutron RG of 4.09(+/-0.14) nm in 100% 2H2O. The absorption coefficients of SAP pentamers and decamers differ by 10%. If we infer that the two alpha-helical A-faces are in contact with each other in the SAP decamer, the lack of structural change of the decamer with pH may be explained by the absence of His residues from the A-face of the SAP pentamer, and the change in absorption coefficients is compatible with the presence of Trp residues at this A-face. The rigid ring structure of pentameric SAP provided a test of scattering curves calculated from crystal structures. The only structural unknown is the orientation of the five chemically homogeneous oligosaccharide chains relative to the protein, but extended oligosaccharide structures were found to account for its scattering curve. X-ray scattering curves were best calculated using a hydrated structure, while neutron scattering curves were best calculated using an unhydrated structure. The outcome of these analyses was used to model the structure of decameric SAP. The evaluation of 640 structures for two SAP pentamers brought face-to-face to form SAP decamers gave better curve fits for structures in which the two A-faces were in contact with each other, in which it is likely that the two pentamers were out of alignment by a rotation of 36 degrees and the oligosaccharide chains were extended.

Oligomerization of the amide sensor protein AmiC by x-ray and neutron scattering and molecular modeling

AmiC is the negative regulator of the amidase operon which is involved in amide metabolism in the cytosol of Pseudomonas aeruginosa. Crystal structures show that AmiC contains two large domains that are very similar to the periplasmic leucine-isoleucine-valine binding protein (LivJ) of Escherichia coli. Synchrotron X-ray and neutron (in 100% 2H2O buffer) scattering data were obtained for AmiC in the presence of its substrate acetamide and its anti-inducer butyramide which binds more weakly to AmiC than acetamide. Guinier analyses to obtain radius of gyration RG and molecular weight Mr values showed that AmiC formed trimers whose formation was favored in the presence of acetamide and which exhibited concentration-dependent properties at concentrations between 0.4 and 2 mg/mL. Above 2 mg/mL, where trimers predominated, the RG data were identical within 0.05 nm for AmiC-acetamide and AmiC-butyramide with mean X-ray and neutron RG values of 3.35 and 3. 28 nm, respectively. Scattering curve fits constrained by the crystal structure of AmiC-acetamide were evaluated in order to describe a model for trimeric AmiC. A translational search of parallel alignments of three monomers to form a symmetric AmiC homotrimer gave a good X-ray curve fit. Combinations of calculated curves for monomeric, dimeric, trimeric, and tetrameric AmiC as seen in the crystal structure of AmiC gave reasonable but weaker X-ray curve fits which did not favor the existence of tetrameric AmiC. It is concluded that AmiC exhibits novel ligand-dependent oligomerization properties in solution when these are compared to other members of the periplasmic binding protein superfamily, where AmiC exists in monomeric and trimeric forms, the proportions of which depend on the presence of acetamide or butyramide.

Factor VIIa and the extracellular domains of human tissue factor form a compact complex: a study by X-ray and neutron solution scattering

The four-domain structure of human factor VIIa and the two-domain structure of tissue factor form a tight complex to initiate blood coagulation. By solution scattering, the mean X-ray and neutron radii of gyration RG (which determine macro-molecular elongation) were found to be 3.25 nm, 2.13 nm and 3.14 nm (+/- 0.13 nm) for factor VIIa, the extracellular region of tissue factor and their complex in that order. The mean cross-sectional radii of gyration RXS were 1.33 nm, 0.56 nm and 1.42 nm (+/- 0.13 nm) in that order. The mean lengths were 10.3 nm, 7.7 nm and 10.2 nm in that order. The data show that, in solution, the free proteins have extended domain structures, and the complex is formed by a compact side-by-side alignment of the two proteins along their long axes. The high binding affinity of tissue factor for factor VIIa may thus be accounted for by the occurrence of many intermolecular contacts in the complex.