Quaternary structure heterogeneity of oligomeric proteins: a SAXS and SANS study of the dissociation products of Octopus vulgaris hemocyanin

A nucleotide-dependent oligomerization of the Escherichia coli replication initiator DnaA requires residue His136 for remodeling of the chromosomal origin

Escherichia coli replication initiator protein DnaA binds ATP with high affinity but the amount of ATP required to initiate replication greatly exceeds the amount required for binding. Previously, we showed that ATP-DnaA, not ADP-DnaA, undergoes a conformational change at the higher nucleotide concentration, which allows DnaA oligomerization at the replication origin but the association state remains unclear. Here, we used Small Angle X-ray Scattering (SAXS) to investigate oligomerization of DnaA in solution. Whereas ADP-DnaA was predominantly monomeric, AMP–PNP–DnaA (a non-hydrolysable ATP-analog bound-DnaA) was oligomeric, primarily dimeric. Functional studies using DnaA mutants revealed that DnaA(H136Q) is defective in initiating replication in vivo. The mutant retains high-affinity ATP binding, but was defective in producing replication-competent initiation complexes. Docking of ATP on a structure of E. coli DnaA, modeled upon the crystallographic structure of Aquifex aeolicus DnaA, predicts a hydrogen bond between ATP and imidazole ring of His136, which is disrupted when Gln is present at position 136. SAXS performed on AMP–PNP–DnaA (H136Q) indicates that the protein has lost its ability to form oligomers. These results show the importance of high ATP in DnaA oligomerization and its dependence on the His136 residue.

Ion Mobility-Mass Spectrometry Reveals That α-Hemolysin from Staphylococcus aureus Simultaneously Forms Hexameric and Heptameric Complexes in Detergent Micelle Solutions

Many soluble and membrane proteins form symmetrical homooligomeric complexes. However, determining the oligomeric state of protein complexes can be difficult. Alpha-hemolysin (αHL) from Staphylococcus aureus is a symmetrical homooligomeric protein toxin that forms transmembrane β-barrel pores in host cell membranes. The stable pore structure of αHL has also been exploited in vitro as a nanopore tool. Early structural experiments suggested αHL forms a hexameric pore, while more recent X-ray crystal structure and solution studies have identified a heptameric pore structure. Here, using native ion mobility-mass spectrometry (IM-MS) we find that αHL simultaneously forms hexameric and heptameric oligomers in both tetraethylene glycol monooctyl ether (C₈E₄) and tetradecylphosphocholine (FOS-14) detergent solutions. We also analyze intact detergent micelle-embedded αHL porelike complexes by native IM-MS without the need to fully strip the detergent micelle, which can cause significant gas-phase unfolding. The highly congested native mass spectra are deconvolved using Fourier- and Gábor-transform (FT and GT) methods to determine charge states and detergent stoichiometry distributions. The intact αHL micelle complexes are found to contain oligomeric state-proportional numbers of detergent molecules. This evidence, combined with IM data and results from vacuum molecular dynamics simulations, is consistent with both the hexamer and the heptamer forming porelike complexes. The ability of αHL to form both oligomeric states simultaneously has implications for its use as a nanopore tool and its pore formation mechanism in vivo. This study also demonstrates more generally the power of FT and GT to deconvolve the charge state and stoichiometry distributions of polydisperse ions.

Cryo-EM reveals the asymmetric assembly of squid hemocyanin

The oxygen transporter of molluscs, hemocyanin, consists of long pearl-necklace-like subunits of several globular domains. The subunits assemble in a complex manner to form cylindrical decamers. Typically, the first six domains of each subunit assemble together to form the cylinder wall, while the C-terminal domains form a collar that fills or caps the cylinder. During evolution, various molluscs have been able to fine-tune their oxygen binding by deleting or adding C-terminal domains and adjusting their inner-collar architecture. However, squids have duplicated one of the wall domains of their subunits instead. Here, using cryo-EM and an optimized refinement protocol implemented in SPHIRE, this work tackled the symmetry-mismatched structure of squid hemocyanin, revealing the precise effect of this duplication on its quaternary structure and providing a potential model for its structural evolution.

Structure-based modelling of hemocyanin allergenicity in squid and its response to high hydrostatic pressure

The secondary, tertiary, and quaternary structures of squid hemocyanin (Hc) were characterised, and the relationship between Hc structure and allergenicity responses to high hydrostatic pressure (HHP) was modelled. The Hc allergenicity varied with its protein structure. Electrophoresis analysis revealed that HHP treatment significantly decreased the band intensity of Hc when increasing pressure from 200 and 400 MPa to 600 MPa. The protein structure analysis of squid Hc showed that while HHP treatment decreased the α-helix content, free sulfhydryl content, and R_g, it increased the random coil content, surface hydrophobicity index (Ho), Guinier aggregation number (〈N_agg〉_G) and average aggregation number (〈N_agg〉_Q). The α-helix and random coil contents of the 600 MPa treated samples were 23.67% and 37.54%, respectively, compared to 32.37% and 32.02% in the control, respectively. HHP treatment decreased the IgE and IgG-binding capacities, indicating a significant decrease in the allergenicity (P< 0.05) of squid Hc. This study provided meaningful information of applying HHP to reduce allergenicity, and explained the responses of Hc protein structure to HHP for lowering the allergenicity of squid.

Entrapment and characterization of functional allosteric conformers of hemocyanin in sol–gel matrices

Entrapment of hemocyanin in sol–gel stabilizes conformations scarcely populated in solution, allowing for their structural and functional analysis.

Quaternary structures of GroEL and naïve-Hsp60 chaperonins in solution: a combined SAXS-MD study

Analysis with QUAFIT software combined with SAXS-MD data, allows resolution of GroEL and naïve-Hsp60 oligomeric structures in solution.

Structure of mega-hemocyanin reveals protein origami in snails

Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional 550 kDa subunits. Together, they form a large, completely filled cylinder. The structural basis for this highly complex protein packing is not known so far. Here, we report the electron cryomicroscopy (cryo-EM) structure of mega-hemocyanin complexes from two different snail species. The structures reveal that mega-hemocyanin is composed of flexible building blocks that differ in their conformation, but not in their primary structure. Like a protein origami, these flexible blocks are optimally packed, implementing different local symmetries and pseudosymmetries. A comparison between the two structures suggests a surprisingly simple evolutionary mechanism leading to these large oxygen transporters.

GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro-molecules in solution

Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.

Using Small-Angle Scattering Techniques to Understand Mechanical Properties of Biopolymer-Based Biomaterials

The design and engineering of innovative biopolymer-based biomaterials for a variety of biomedical applications should be based on the understanding of the relationship between their nanoscale structure and mechanical properties. Down the road, such understanding could be fundamental to tune the properties of engineered tissues, extracellular matrices for cell delivery and proliferation/differentiation, etc. In this tutorial review, we attempt to show in what way biomaterial structural data can help to understand the bulk material properties. We begin with some background on common types of biopolymers used in biomaterials research, discuss some typical mechanical testing techniques and then review how others in the field of biomaterials have utilized small-angle scattering for material characterization. Detailed examples are then used to show the full range of possible characterization techniques available for biopolymer-based biomaterials. Future developments in the area of material characterization by small-angle scattering will undoubtedly facilitate the use of structural data to control the kinetics of assembly and final properties of prospective biomaterials.

Evolution of molluscan hemocyanin structures

Hemocyanin transports oxygen in the hemolymph of many molluscs and arthropods and is therefore a central physiological factor in these animals. Molluscan hemocyanin molecules are oligomers composed of many protein subunits that in turn encompass subsets of distinct functional units. The structure and evolution of molluscan hemocyanin have been studied for decades, but it required the recent progress in DNA sequencing, X-ray crystallography and 3D electron microscopy to produce a detailed view of their structure and evolution. The basic quaternary structure is a cylindrical decamer 35nm in diameter, consisting of wall and collar (typically at one end of the cylinder). Depending on the animal species, decamers, didecamers and multidecamers occur in the hemolymph. Whereas the wall architecture of the decamer seems to be invariant, four different types of collar have been identified in different molluscan taxa. Correspondingly, there exist four subunit types that differ in their collar functional units and range from 350 to 550kDa. Thus, molluscan hemocyanin subunits are among the largest polypeptides in nature. In this report, recent 3D reconstructions are used to explain and visualize the different functional units, subunits and quaternary structures of molluscan hemocyanins. Moreover, on the basis of DNA analyses and structural considerations, their possible evolution is traced. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.