Higher-order Assemblies Research Articles

Molecular arrangement of cellulose bio-nanofibers in formation of higherorder assemblies

Molecular arrangement of cellulose bio-nanofibers in formation of higherorder assemblies

Hierarchical assembly of intrinsically disordered short peptides

The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.

Disulfide bond in SUN2 regulates dynamic remodeling of LINC complexes at the nuclear envelope.

The LINC complex tethers the cell nucleus to the cytoskeleton to regulate mechanical forces during cell migration, differentiation, and various diseases. The function of LINC complexes relies on the interaction between highly conserved SUN and KASH proteins that form higher-order assemblies capable of load bearing. These structural details have emerged from in vitro assembled LINC complexes; however, the principles of in vivo assembly remain obscure. Here, we report a conformation-specific SUN2 antibody as a tool to visualize LINC complex dynamics in situ. Using imaging, biochemical, and cellular methods, we find that conserved cysteines in SUN2 undergo KASH-dependent inter- and intra-molecular disulfide bond rearrangements. Disruption of the SUN2 terminal disulfide bond compromises SUN2 localization, turnover, LINC complex assembly in addition to cytoskeletal organization and cell migration. Moreover, using pharmacological and genetic perturbations, we identify components of the ER lumen as SUN2 cysteines redox state regulators. Overall, we provide evidence for SUN2 disulfide bond rearrangement as a physiologically relevant structural modification that regulates LINC complex functions.

Small GTPase Cdc42, WASP, and scaffold proteins for higher-order assembly of the F-BAR domain protein.

The higher-order assembly of Bin-amphiphysin-Rvs (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, into lattice on the membrane is essential for the formation of subcellular structures. However, the regulation of their ordered assembly has not been elucidated. Here, we show that the higher ordered assembly of growth-arrested specific 7 (GAS7), an F-BAR domain protein, is regulated by the multivalent scaffold proteins of Wiskott-Aldrich syndrome protein (WASP)/neural WASP, that commonly binds to the BAR domain superfamily proteins, together with WISH, Nck, the activated small guanosine triphosphatase Cdc42, and a membrane-anchored phagocytic receptor. The assembly kinetics by fluorescence resonance energy transfer monitoring indicated that the GAS7 assembly on liposomes started within seconds and was further increased by the presence of these proteins. The regulated GAS7 assembly was abolished by Wiskott-Aldrich syndrome mutations both in vitro and in cellular phagocytosis. Therefore, Cdc42 and the scaffold proteins that commonly bind to the BAR domain superfamily proteins promoted GAS7 assembly.

Photo-Excited Toluidine Blue Disaggregates the Repeat Tau and Modulates End-Binding Protein EB1, Cytoskeletal Structure in Neuronal Cells

Alzheimer's disease is a progressive neurological disorder characterized by the intracellular accumulation of Tau protein aggregates. In the present work, we studied the effect of Toluidine Blue and photo-excited Toluidine Blue on the aggregation of repeat Tau using in vitro assays. The in vitro experiments were carried out on recombinant repeat Tau which was purified by cation exchange chromatography. The ThS fluorescence analysis was used to study the aggregation kinetics of Tau. CD spectroscopy and electron microscopy were used to study the secondary structure and morphology of Tau respectively. The actin cytoskeleton modulation was studied in Neuro2a cells with help of immunofluorescent microscopy. Results showed that Toluidine Blue efficiently inhibited the formation of higher-order aggregates, which was evidenced by Thioflavin S fluorescence assay, SDS-PAGE, and TEM. Immunofluorescence studies on the cytoskeleton of Neuro2a cells showed that Toluidine Blue and photo-excited Toluidine Blue treatment at a non-toxic concentration of 0.5 µM stimulated the formation of actin-rich lamellipodia and filopodia structures. Tubulin networks were also differentially modulated after the treatment of Toluidine Blue and photo-excited Toluidine Blue. End-binding protein 1 (EB1) levels were observed to increase after Toluidine Blue and photo-excited Toluidine Blue treatment indicating accelerated microtubule polymerization. The overall study suggested that Toluidine Blue inhibited the aggregation of soluble Tau and photo-excited Toluidine Blue disaggregated the pre-formed Tau filaments. In our study, TB and PE-TB were observed to be potent against Tau aggregation. We observed a distinctive modulation of actin, tubulin networks, and EB1 levels after TB and PE-TB treatment, which suggested that TB and PE-TB have potency against cytoskeleton deformities.

A prolyl oligopeptidase inhibitor reduces tau pathology in cellular models and in mice with tauopathy.

Tauopathies are neurodegenerative diseases that are characterized by accumulation of hyperphosphorylated tau protein, higher-order aggregates, and tau filaments. Protein phosphatase 2A (PP2A) is a major tau dephosphorylating phosphatase, and a decrease in its activity has been demonstrated in tauopathies, including Alzheimer's disease. Prolyl oligopeptidase is a serine protease that is associated with neurodegeneration, and its inhibition normalizes PP2A activity without toxicity under pathological conditions. Here, we assessed whether prolyl oligopeptidase inhibition could protect against tau-mediated toxicity in cellular models in vitro and in the PS19 transgenic mouse model of tauopathy carrying the human tau-P301S mutation. We show that inhibition of prolyl oligopeptidase with the inhibitor KYP-2047 reduced tau aggregation in tau-transfected HEK-293 cells and N2A cells as well as in human iPSC-derived neurons carrying either the P301L or tau-A152T mutation. Treatment with KYP-2047 resulted in increased PP2A activity and activation of autophagic flux in HEK-293 cells and N2A cells and in patient-derived iNeurons, as indicated by changes in autophagosome and autophagy receptor markers; this contributed to clearance of insoluble tau. Furthermore, treatment of PS19 transgenic mice for 1 month with KYP-2047 reduced tau burden in the brain and cerebrospinal fluid and slowed cognitive decline according to several behavioral tests. In addition, a reduction in an oxidative stress marker was seen in mouse brains after KYP-2047 treatment. This study suggests that inhibition of prolyl oligopeptidase could help to ameliorate tau-dependent neurodegeneration.

Hourglass-Shaped Nanocages with Concaved Structures Based on Selective Self-Complementary Coordination Ligands and Tunable Hierarchical Self-Assembly.

Three-dimensional (3D) structures constructed via coordination-driven self-assemblies have recently garnered increasing attention due to the challenges in structural design and potential applications. In particular, developing new strategy for the convenient and precise self-assemblies of 3D supramolecular structures is of utmost interest. Introducing the concept of self-coordination ligands, herein the design and synthesis of two meta-modified terpyridyl ligands with selective self-complementary coordination moiety are reported and their capability to assemble into two hourglass-shaped nanocages SA and SB is demonstrated. Within these 3D structures, the meta-modified terpyridyl unit preferably coordinates with itself to serve as concave part. By changing the arm length of the ligands, hexamer (SA) and tetramer (SB) are obtained respectively. In-depth studies on the assembly mechanism of SA and SB indicate that the dimers could be formed first via self-complementary coordination and play crucial roles in controlling the final structures. Moreover, both SA and SB can go through hierarchical self-assemblies in solution as well as on solid-liquid interface, which are characterized by transmission electron microscope (TEM) and scanning tunneling microscopy (STM). It is further demonstrated that various higher-order assembly structures can be achieved by tuning the environmental conditions.

Graph context-attention network via low and high order aggregation

Graph attention networks (GATs) have been shown effectively for representation learning. However, existing GATs only employ the first-order attention mechanism and thus fail to fully exploit and learn node’s contextual feature representations. To address this issue, we propose a novel Graph Context-Attention Network (GCAN) via low and high order aggregation for representation learning. The proposed model fully exploits both low-order and high-order information of nodes for representation learning by employing high-order attention mechanism and adversary regularization constraints. The main benefit of the proposed method is that it can effectively capture the discriminative feature differences among node representations while enhancing the diversity and richness of node features. Thus it can alleviate the issue of over-smoothing in the network learning. We perform extensive experiments on nine datasets and the experimental results demonstrate the effectiveness and better performance of our approach.

Dynamic and Reversible Decoration of DNA-Based Scaffolds.

An approach to achieving dynamic and reversible decoration of DNA-based scaffolds is demonstrated here. To do this, rationally engineered DNA tiles containing enzyme-responsive strands covalently conjugated to different molecular labels are employed. These strands are designed to be recognized and degraded by specific enzymes (i.e., Ribonuclease H, RNase H, or Uracil DNA Glycosylase, UDG) inducing their spontaneous de-hybridization from the assembled tile and replacement by a new strand conjugated to a different label. Multiple enzyme-responsive strands that specifically respond to different enzymes allow for dynamic, orthogonal, and reversible decoration of the DNA structures. As a proof-of-principle of the strategy, the possibility to orthogonally control the distribution of different labels (i.e., fluorophores and small molecules) on the same scaffold without crosstalk is demonstrated. By doing so, DNA scaffolds that display different antibody recognition patterns are obtained. The approach offers the possibility to control the decoration of higher-order supramolecular assemblies (including origami) with several functional moieties to achieve functional biomaterials with improved adaptability, precision, and sensing capabilities.

Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils.

Coiled coils (CCs) are key building blocks of biogenic materials and determine their mechanical response to large deformations. Of particular interest is the observation that CC-based materials display a force-induced transition from α-helices to mechanically stronger β-sheets (αβT). Steered molecular dynamics simulations predict that this αβT requires a minimum, pulling speed-dependent CC length. Here, de novo designed CCs with a length between four to seven heptads are utilized to probe if the transition found in natural CCs can be mimicked with synthetic sequences. Using single-molecule force spectroscopy and molecular dynamics simulations, these CCs are mechanically loaded in shear geometry and their rupture forces and structural responses to the applied load are determined. Simulations at the highest pulling speed (0.01nm ns-1 ) show the appearance of β-sheet structures for the five- and six-heptad CCs and a concomitant increase in mechanical strength. The αβT is less probable at a lower pulling speed of 0.001nm ns-1 and is not observed in force spectroscopy experiments. For CCs loaded in shear geometry, the formation of β-sheets competes with interchain sliding. β-sheet formation is only possible in higher-order CC assemblies or in tensile-loading geometries where chain sliding and dissociation are prohibited.

Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis

During muscle cell differentiation, the alternatively spliced, acidic β-domain potentiates transcription of Myocyte-specific Enhancer Factor 2 (Mef2D). Sequence analysis by the FuzDrop method indicates that the β-domain can serve as an interaction element for Mef2D higher-order assembly. In accord, we observed Mef2D mobile nuclear condensates in C2C12 cells, similar to those formed through liquid-liquid phase separation. In addition, we found Mef2D solid-like aggregates in the cytosol, the presence of which correlated with higher transcriptional activity. In parallel, we observed a progress in the early phase of myotube development, and higher MyoD and desmin expression. In accord with our predictions, the formation of aggregates was promoted by rigid β-domain variants, as well as by a disordered β-domain variant, capable of switching between liquid-like and solid-like higher-order states. Along these lines, NMR and molecular dynamics simulations corroborated that the β-domain can sample both ordered and disordered interactions leading to compact and extended conformations. These results suggest that β-domain fine-tunes Mef2D higher-order assembly to the cellular context, which provides a platform for myogenic regulatory factors and the transcriptional apparatus during the developmental process.

Molecular origin of the two-step mechanism of gellan aggregation

Among hydrocolloids, gellan is one of the most studied polysaccharides due to its ability to form mechanically stable gels. Despite its long-standing use, the gellan aggregation mechanism is still not understood because of the lack of atomistic information. Here, we fill this gap by developing a new gellan force field. Our simulations offer the first microscopic overview of gellan aggregation, detecting the coil to single-helix transition at dilute conditions and the formation of higher-order aggregates at high concentration through a two-step process: first, the formation of double helices and then their assembly into superstructures. For both steps, we also assess the role of monovalent and divalent cations, complementing simulations with rheology and atomic force microscopy experiments and highlighting the leading role of divalent cations. These results pave the way for future use of gellan-based systems in a variety of applications, from food science to art restoration.

Optical and Structural Properties of Composites Based on Poly(urethane) and TiO2 Nanowires.

This article's objective is the synthesis of new composites based on thermoplastic polyurethane (TPU) and TiO2 nanowires (NWs) as free-standing films, highlighting their structural and optical properties. The free-standing TPU-TiO2 NW films were prepared by a wet chemical method accompanied by a thermal treatment at 100 °C for 1 h, followed by air-drying for 2 h. X-ray diffraction (XRD) studies indicated that the starting commercial TiO2 NW sample contains TiO2 tetragonal anatase (A), cubic Ti0.91O (C), and orthorhombic Ti2O3 (OR), as well as monoclinic H2Ti3O7 (M). In the presence of TPU, an increase in the ratio between the intensities of the diffraction peaks at 43.4° and 48° belonging to the C and A phases of titanium dioxide, respectively, is reported. The increase in the intensity of the peak at 43.4° is explained to be a consequence of the interaction of TiO2 NWs with PTU, which occurs when the formation of suboxides takes place. The variation in the ratio of the absorbance of the IR bands peaked at 765-771 cm-1 and 3304-3315 cm-1 from 4.68 to 4.21 and 3.83 for TPU and the TPU-TiO2 NW composites, respectively, with TiO2 NW concentration equal to 2 wt.% and 17 wt.%, indicated a decrease in the higher-order aggregates of TPU with a simultaneous increase in the hydrogen bonds established between the amide groups of TPU and the oxygen atoms of TiO2 NWs. The decrease in the ratio of the intensity of the Raman lines peaked at 658 cm-1 and 635 cm-1, which were assigned to the vibrational modes Eg in TiO2 A and Eg in H2Ti3O7 (ITiO2-A/IH2Ti3O7), respectively, from 3.45 in TiO2 NWs to 0.94-0.96 in the TPU-TiO2 NW composites, which indicates that the adsorption of TPU onto TiO2 NWs involves an exchange reaction of TPU in the presence of TiO2 NWs, followed by the formation of new hydrogen bonds between the -NH- of the amide group and the oxygen atoms of TixO2x-mn, Ti2O3, and Ti0.91O. Photoluminescence (PL) studies highlighted a gradual decrease in the intensity of the TPU emission band, which is situated in the spectral range 380-650 nm, in the presence of TiO2 NW. After increasing the TiO2 NW concentration in the TPU-TiO2 NW composite mass from 0 wt.% to 2 wt.% and 17 wt.%, respectively, a change in the binding angle of the TPU onto the TiO2 NW surface from 12.6° to 32° and 45.9°, respectively, took place.

An N-terminal peptide of Tar DNA binding Protein 43 lacking nuclear localization signal translocates to the nucleus of GC-1 spermatogonial cells

Objectives: TAR DNA-binding protein of 43 kDa (TDP-43) is an RNA/DNA binding protein expressed in the brain and the testis. Mutations in TDP-43 lead to mislocalization and cytoplasmic aggregation of this protein causing neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43 has also been implicated in maintaining spermatogenesis. While homodimerization of TDP-43 is critical for its physiological functions, higher-order aggregation of this protein impairs its functions. This study was aimed to map the critical amino acids of the N-terminus of this protein in mediating its homodimerization. Materials and Methods: We generated deletion constructs of Tdp-43 containing NRRM1 domain alone (TDP-43∆3-183) and N-terminal peptide of TDP-43 which lacks the nuclear localization signal (NLS) (TDP-43∆1-50) with fluorescent reporters having non-overlapping emission properties. These constructs were co-transfected into a mouse spermatogonial cell line to examine their dimerization and nuclear translocation capabilities in vitro. Results: We found that TDP-43∆3-183 alone was not capable of homodimerization. On the other hand, TDP-43∆1-50 when co-transfected into GC1-spg cells along with full length TDP-43 translocated to the nucleus oligomerized with the latter and translocated to the nucleus, indicating the importance of amino acids 1-50 of TDP-43 in dimerization. Conclusion: The N-terminal segment of TDP-43 spanning amino acids 1-50 is responsible for dimerization, while that spanning amino acids 51-183 directs it to the nucleus.The physiological and pathological implications of this finding need to be examined.

Molecular superglue-mediated higher-order assembly of TRAIL variants with superior apoptosis induction and antitumor activity

Prompting higher-order death receptor (DR) clustering by increasing the valency of DR agonist is efficient to induce apoptosis of tumor cells. As an attractive DR agonist with superior biosafety, the trimeric tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) exerts limited antitumor effect in patients, which is predominantly attributed to its low DR clustering ability and short serum half-life. Previous antibody scaffolds-based engineering strategies to increase the valency and/or prolong the serum half-life of TRAIL improve apoptosis induction, however, often produce large proteins with poor tumor penetration. Covalent protein ligation mediated by small molecular superglues such as SpyTag/SpyCatcher might be a novel strategy to assemble higher-order TRAIL variants. Upon fusion to TRAIL promotor, SpyTag/SpyCatcher molecular superglue preferentially ligated two trimeric TRAIL to produce a hexameric TRAIL variant, HexaTR, exhibiting a significantly increased apoptosis induction. In addition, an albumin-binding HexaTR, ABD-HexaTR, with a prolonged serum half-life by binding to endogenous albumin was also produced using the same strategy. Compared to the trimeric TRAIL, the hexameric HexaTR and ABD-HexaTR showed 20–50 times greater in vivo antitumor effect, resulting in eradication of several types of large (150–300 mm3) tumor xenografts. Combination with bortezomib carried by liposome further improved the antitumor effects of the hexavalent HexaTR and ABD-HexaTR in refractory cancer. Our results indicate that the superglue-mediated higher-order assembly is promising to improve the DR clustering and proapoptotic signaling of TRAIL, showing great advantages in constructing the next generation of DR agonists for cancer therapy.

Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization.

The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.

Investigating the interaction of TDP-43 with RNA using structural mass spectrometry.

Deposits of TDP-43, a disordered RNA-binding protein, in the brain is hallmark of amyotrophic lateral sclerosis (ALS). Binding of TDP-43 to RNA protects from aggregation. However, the structure(s) and conformational dynamics of monomeric TDP-43, its higher order assemblies, and the TDP-43-RNA complex remain elusive, despite their importance in understanding disease progression. Here we have used a combination of biophysical analyses and powerful mass spectrometry (MS) techniques to interrogate the conformational dynamics of monomeric full-length TDP-43 and its assemblies with RNA. Our results from HDX-MS show that, in the presence of RNA we observe allosteric protection from exchange in areas associated with amyloid formation suggesting a possible structural rearrangement that protects RNA bound TDP-43 from aggregation. We also identify allosteric changes within the short alpha helix motif located in the CTD upon RNA binding. These allosterically altered regions are known to influence the ability of TDP-43 to self-assemble and can fine-tune its RNA binding repertoire. Taken together, these data reveal new insights into the structure and dynamics of TDP-43, alongside the intra-protein and protein-RNA interactions which likely play a key role in fine tuning TDP-43 self-assembly into both condensates and amyloid fibrils. Understanding the molecular mechanism of these processes is key to elucidating the role of TDP-43 in the pathology of ALS and FTLD and may lead to new therapeutics to treat these diseases.

Force transmission and SUN-KASH higher-order assembly in the LINC complex models.

The linker of the nucleoskeleton and cytoskeleton (LINC) complex comprises of SUN (Sad-1 and UNC-84) and KASH (Klarsicht, ANC-1, SYNE homology) domain proteins, which connect the inner and outer nuclear membrane, thereby mediating the transfer of physical forces between the cytoskeleton and the nucleoskeleton. While impaired SUN and KASH proteins are associated with structural and functional cell defects, the precise mechanism of force transduction and the assembly of these proteins remain unknown. Recent studies suggested a higher order assembly of SUN and KASH instead of a more widely accepted linear trimer model for the LINC complex. In the present study, we use molecular dynamics simulations to investigate the mechanism of force transfer across the two proposed models of LINC complex assembly, namely the 3:3 linear trimer model and the 6:6 higher-order model. Employing steered molecular dynamics simulations with forces at different rates and directions on various structures, we examine the structural stability of the two models under various biologically relevant conditions. Our results suggest that both models can withstand and transfer significant levels of force while retaining their structural integrity. However, some of the structures were more stable under specific forces compared to other structures. Slower pulling rates resulted in higher mean square fluctuations of the proteins compared to the fast pulling. Interestingly, the higher-order assembly tends to provide an additional range of motion flexibility and might be more suitable for describing the interaction between SUN and KASH under compressive and shear forces. These findings offer insights into how the SUN and KASH proteins maintain the structural integrity of the nuclear membrane.

Membrane protein structural symmetry and assembly patterns.

The evolution of membrane proteins depends on the physicochemical constraints imposed by the lipid bilayer, and by extension, their folding mechanisms. Repetition of well-folded motifs following these rules is frequently observed within protein sequences and has allowed efficient creation of larger macromolecules capable of more complex functions. Such repeated elements within individual protein chains can result in structural symmetry, as does association of subunits into higher-order assemblies. Nevertheless, much remains to be learned about interplay between folding, assembly, symmetry, and evolution. Structural data obtained by crystallography or electron cryo-microscopy provides an evolutionary snapshot with which to examine these questions in greater detail. At the time of writing, almost 8000 membrane protein structures have been collated into our structure and symmetry database, EncoMPASS. We present a systematic analysis of these data and discuss the implications for folding, function, and evolution.

Understanding the effects of higher-order assembly on the structure of the sulfite reductase.

The redox state of sulfur determines its bioavailbility and its reduction to sulfide is required for assimilation of sulfur into amino acids and cofactors.The NADPH-dependent assimilatory sulfite reductase (SiR) is a metabolic enzyme that performs the six-electron reduction of sulfite to sulfide. Escherichia coli SiR is composed of eight flavoprotein (SiRFP, ⍺) and four hemoprotein (SiRHP, β) subunits that associate in α8:β4 holoenzyme. This dodecameric assembly is unique because SiRs from other sulfur reducing organisms are dimers of reductase and oxidase subunits. Both SiR subunits are modular. SiRFP is a fusion between flavodoxin domain and a ferredoxin-NADP+ reductase domain that assembles through its 52 N-terminal amino acids into an octamer. SiRHP is a monomeric metalloenzyme that houses the active site. Despite almost 30 years of effort across many laboratories, structures of SiR complexes have remained recalcitrant to X-ray crystallography and cryo-EM because of its structural heterogeneity aising from intrinsically disordered regions throughout the complex, including the flexible linker joining SiRFP's flavin binding domain. Thus we do not know how the domains assemble, which leaves a gap in understanding about how these domains coordinate to perform electron transfer. Here, we use neutron contrast variation (NCV) and small angle neutron scattering (SANS) to observe the relative subunit positioning within the SiR complex. To better understand the electron transfer mechanism, we have generated conformationally restricted variant of SiRFP that either locks its flavin binding domains in an open conformation by shortening the linker between domains, or in closed conformation by engineering disulfide bonds. SANS and NCV study reveal SiR's asymmetric complex, and the resulting maps supports a redundant, cis/trans mechanism of electron transfer between the reductase subunits as well as between the tightly or transiently bound reductase and oxidase domains.