Conserved and repetitive motifs in an intrinsically disordered protein drive ⍺-carboxysome assembly
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Biochemistry & Molecular Biology↗
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Explainable machine learning reveals that local structural motifs encode the thermodynamic state across the CuZr metallic glass-forming range
Metallic glasses derive their properties from the statistics of local atomic motifs rather than from long-range order, yet a quantitative, chemistry-specific link between motif populations and the underlying glassy state has remained elusive. In this work we combine large-scale molecular dynamics, Voronoi tessellation, deep neural networks, and SHapley Additive exPlanations (SHAP) to identify which local structural motifs define the glassy state of Cu—Zr metallic glasses. A dataset of 17,180 atomistic configurations spanning ten compositions (Cu 20 Zr 80 –Cu 80 Zr 20 ) and four quench rates (10 9 –10 12 K/s) is used to train a feed-forward neural network that regresses temperature across the 50–2000 K liquid–supercooled–glass range, achieving a mean absolute error of 19.89 K and R 2 = 0.9974, confirming that the local structural state is faithfully encoded in motif-level structure. SHAP analysis then reveals that a tightly coupled near-icosahedral family of motifs (coordination numbers (CN) 11–13, including the full icosahedron 001200 and its single-atom-perturbation sibling 10930) collectively encodes the thermodynamic state of the system across the full glass-forming range. The CN = 11–13 ordered members carry negative SHAP values at high populations, tracking the most deeply-quenched configurations, while 10930 shows the reversed signature consistent with its role as a soft-spot host whose population shrinks as the icosahedral network deepens. The analysis demonstrates that explainable machine learning can isolate the minimal motif vocabulary defining the glassy state and recovers the near-icosahedral building blocks previously identified by data-driven analyses of Cu—Zr. The approach provides a general, chemistry-specific route for characterizing the structural state of disordered materials.
36 MATERIALS SCIENCE↗
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif
Abstract The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
Science & Technology - Other Topics↗
Venturing into Unexplored Phase Space: Synthesis, Structure, and Properties of MgCo 3 B 2 Featuring a Rumpled Kagomé Network
MgCo 3 B 2 , a novel ternary boride in a previously unexplored phase space, was synthesized using the hydride route. In situ powder X-ray diffraction and DFT calculations aided in the discovery of this compound, whose structure was then determined by single-crystal X-ray diffraction. Like the closely related CeCo 3 B 2 , MgCo 3 B 2 crystallizes in centrosymmetric space group P6/mmm (a = 4.883(2) Å, c = 2.926(2) Å at 210 K, Z = 1). Unlike CeCo 3 B 2 , however, it adopts a disordered structure that features a rumpled Kagomé network of Co atoms, and Mg atoms fill the channels of a Co–B framework. Although the structural disorder leads to motifs that are similar to those observed in MgNi 3 B 2 and other related ternary borides, no evidence of an ordered superstructure was found by single-crystal X-ray diffraction or high-resolution powder X-ray diffraction. In the case of CeCo 3 B 2 , boron atoms occupy the center of regular Co 6 trigonal prisms; in MgCo 3 B 2 , boron atoms are shifted from the center of the prism to form B–B dimers with roughly the same length as those found in MgNi 3 B 2 . Magnetic susceptibility data exhibit an unusual temperature dependence that cannot be convincingly modeled by the modified Curie–Weiss equation, consistent with DFT calculations predicting a nonmagnetic ground state. Intrinsic susceptibility at 300 K is 1.42 × 10 –3 emu/mol Oe, which is comparable to that of paramagnetic YCo 3 B 2 and CeCo 3 B 2 with a similar structure and composition. Here, this study showcases the efficacy of combining several methodologies to discover new solids in unexplored phase spaces. This approach includes in situ PXRD data to monitor reactions of precursors upon heating, a diffusion-enhanced synthesis method, and DFT assessment of compound stability.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis
In plants, the pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, in this study, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance. We discovered that Arabidopsis AtDGCR14L is required for maintaining plant salt stress tolerance and the constitutively spliced and active isoforms of important stress- and/or abscisic acid (ABA)-responsive genes. We also identified the interaction between AtDGCR14L and splicing factor U1-70k, which needs a highly conserved three amino acid (TWG) motif in DGCR14. Different from wild-type AtDGCR14L, the overexpression of TWG-substituted AtDGCR14L mutant did not change salt stress tolerance or pre-mRNA splicing of stress/ABA-responsive genes. Additionally, SWITCH3A (SWI3A) is a core subunit of the SWI/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes. We found that SWI3A, whose splicing depends on AtDGCR14L, actively enhances salt stress tolerance. These results revealed that AtDGCR14L may play an essential role in crosstalk between plant salt-stress response and pre-mRNA splicing mechanisms. We also unveiled the potential role of SWI3A in controlling salt stress tolerance. The TWG motif in the intrinsically disordered region of AtDGCR14L is highly conserved and crucial for DGCR14 functions.
59 BASIC BIOLOGICAL SCIENCES↗
Complex Dynamics in Argyrodite Solid-State Ion Conductors
Argyrodites are a compositionally diverse family of materials that exhibit remarkable ion transport properties. While the average crystal structures of argyrodites have been extensively studied, ion transport in these materials is governed by a confluence of dynamic processes spanning the cation, anion, and polyanionic sublattices. This Perspective synthesizes recent advances in understanding the role of dynamics in structural behavior and ion transport properties. We examine the compositional and structural motifs that govern order−disorder transitions within the argyrodite family and further explore how ion hopping is facilitated by lattice dynamics, from long-range phonons to local rotational dynamics of polyanionic species. Through the lens of dynamics spanning multiple time and length scales, we establish guiding principles that govern transport phenomena and highlight avenues of future study for the argyrodite family of ion conductors.
36 MATERIALS SCIENCE↗
Suppression of Disorder in Benzamide and Thiobenzamide Crystals by Fluorine Substitution
Disorder is a common feature of molecular crystals that complicates determination of structures and can potentially affect electric and mechanical properties. Suppression of disorder is observed in otherwise severely disordered benzamide and thiobenzamide crystals by substituting hydrogen with fluorine in the ortho-position of the phenyl ring. Fluorine occupancies of 20–30% are sufficient to suppress disorder without changing the packing motif. Crystal structure prediction calculations reveal a much denser lattice energy landscape for benzamide compared to 2-fluorobenzamide, suggesting that fluorine substitution makes disorder less likely.
36 MATERIALS SCIENCE↗
Amorphization mechanism of SrIrO 3 electrocatalyst: How oxygen redox initiates ionic diffusion and structural reorganization
The use of renewable electricity to prepare materials and fuels from abundant molecules offers a tantalizing opportunity to address concerns over energy and materials sustainability. The oxygen evolution reaction (OER) is integral to nearly all material and fuel electrosyntheses. However, very little is known about the structural evolution of the OER electrocatalyst, especially the amorphous layer that forms from the crystalline structure. Here, we investigate the interfacial transformation of the SrIrO 3 OER electrocatalyst. The SrIrO 3 amorphization is initiated by the lattice oxygen redox, a step that allows Sr 2+ to diffuse and O 2− to reorganize the SrIrO 3 structure. This activation turns SrIrO 3 into a highly disordered Ir octahedral network with Ir square-planar motif. The final Sr y IrO x exhibits a greater degree of disorder than IrO x made from other processing methods. Our results demonstrate that the structural reorganization facilitated by coupled ionic diffusions is essential to the disordered structure of the SrIrO 3 electrocatalyst.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin
Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.
Biochemistry & Molecular Biology↗
B56$δ$ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations
Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.
59 BASIC BIOLOGICAL SCIENCES↗
Uncovering metallic glasses hidden vacancy-like motifs using machine learning
Vacancies are a ubiquitous type of defect in crystalline materials that can affect their properties and behavior, including atomic diffusivity, deformation processes, thermal conductivity, and electrical conductivity. While well-defined in crystals, it is challenging to identify such topological footprints in the amorphous structure of metallic glasses (MGs). Here, we uncover an unforeseen vacancy-like structural motif named Q7, which refers to an atomic Voronoi polyhedron with seven quadrangular faces, by investigating MG local atomic configurations with the help of machine learning. The Q7 motif exhibits characteristics similar to crystalline vacancies and plays a significant role in short-range structural disorder in MGs. The atoms at the center of the Q7 motif display larger local entropy, atomic volume, and local tension. Additionally, its concentration follows an Arrhenius-like relationship with temperature, accurately indicating the glass transition temperature, and is strongly correlated with the yield and failure of MGs during mechanical deformation. The discovery of the Q7 motif provides new insights into understanding the intricate relationship between local disorder and structural relaxation in MGs, offering a remarkable ability to predict their thermal and mechanical behavior. This potentially paves the way for enhancements in the design and manufacturing processes of MGs and other amorphous materials.
36 MATERIALS SCIENCE↗
Direct observation of magnetic ordering induced via systematic lattice disorder in artificial rhombus spin ices
It is critical to understand the effect of lattice geometry on the order parameter of a condensed matter system, as it controls phase transitions in such systems. Artificial spin ices (ASIs) are two-dimensional lattices of Ising-like nanomagnets that provide an opportunity to explore such phenomena by lithographically controlling the lattice geometry to observe its influence on magnetic ordering and frustration effects. Here we report a systematic approach to studying the effects of disorder in rhombus ASIs generated from combinations of five vertex motifs. We investigate four geometries characterized by a geometric order parameter, with symmetries ranging from periodic to quasiperiodic to random. Lorentz transmission electron microscopy data indicates magnetic domain behavior depends on chains of strongly-coupled islands in the periodic and sixfold-twinned lattices, while the behavior of the disordered lattice is dominated by vertex motifs with large configurational degeneracy. Utilizing micromagnetic simulations, a quantitative analysis of the lattice energetics showed that the experimental rotationally-demagnetized state of the disordered ASI was closer in energy to the idealized ground state compared to other periodic and twinned ASIs. Finally, our work provides a unique pathway for using degeneracy, magnetic frustration, and order to control the magnetization behavior of designer disordered systems.
36 MATERIALS SCIENCE↗
Short-Range Order Tunes Optical Properties in Long-Range Disordered ZnSnN2-ZnO Alloy
Local site ordering offers a new paradigm for property control in functional materials. However, systems that exhibit a propensity for local order and global disorder are often challenging to characterize, and demonstrations of ordering-induced property tuning are few and far between. Here, we demonstrate that short-range ordering tunes the optical absorption edge in the long-range disordered alloy system (ZnSnN2)1-x(ZnO)2x at x = 0.25. We use combinatorial cosputtering to synthesize a set of thin-film samples spanning this alloy space. X-ray diffraction demonstrates lattice contraction as a function of alloy composition, confirming that a mixed-anion and -cation alloy has been synthesized. Using N and O K-edge X-ray absorption near-edge structure in conjunction with simulations of cation-disordered supercell structures, we find that samples exhibit octet-rule-breaking motifs around both anions. Upon annealing at an alloy composition of x = 0.25, X-ray absorption analysis suggests that local motif structure shifts toward octet-rule-conserving while long-range disorder is maintained. Spectroscopic ellipsometry reveals that local ordering increases the absorption edge energy at constant composition. Additionally, alloy-induced optical absorption edge tuning is demonstrated. This work paves the way toward property tuning with short-range ordering in (ZnSnN2)1-x(ZnO)2x and beyond.
36 MATERIALS SCIENCE↗
Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition
Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme–PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.
59 BASIC BIOLOGICAL SCIENCES↗
Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation
The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent Cα model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.
59 BASIC BIOLOGICAL SCIENCES↗
Robustness of Optical Response for Self-Assembled Plasmonic Metamaterials with Morphological Disorder and Surface Roughness
Bottom-up fabrication of metallized biotemplated nanostructures to form specific plasmonic nanoresonators holds promise as a means of achieving large-scale optical metamaterials. However, in contrast to top-down methods, the stochastic growth of self-assembled nanoresonators is prone to significant disorder and surface roughness, which naturally raise an important question about the robustness of their resonant properties in terms of structural imperfections. An aggregated-random-sphere model is developed to mimic the nucleated growth of metallized DNA origami assembly, leading to meta-atoms with realistic, experimentally observed morphological disorder and surface roughness. Using the well-known split-ring-resonator (SRR) motif as an example, the resonant properties of meta-atoms under different levels of roughness are investigated and a strong tolerance of optical response against morphological disorder is revealed. It is found that in SRRs, even with dramatic roughness introduced, the expected resonances are still observed, despite broadening line shapes compared to ideal smooth structure. Only for extreme disorder, which causes drastic segmentation of SRRs, does the resonant response disappear. Finally, the demonstrations are very encouraging for the prospects of bottom-up fabrication toward versatile functional metamaterials and metadevices.
36 MATERIALS SCIENCE↗
Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation
Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO 2 -concentrating mechanism by facilitating high CO 2 concentrations near the carboxylase Rubisco. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the α-carboxysome, there is little molecular insight into protein–protein interactions that drive the assembly process. In this work, studies on the α-carboxysome from Halothiobacillus neapolitanus demonstrate that Rubisco interacts with the N terminus of CsoS2, a multivalent, intrinsically disordered protein. X-ray structural analysis of the CsoS2 interaction motif bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate that this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate that CsoS2 acts as an interaction hub to condense Rubisco and enable efficient α-carboxysome formation.
59 BASIC BIOLOGICAL SCIENCES↗
Unexpected crystalline homogeneity from the disordered bond network in La(Cr 0.2 Mn 0.2 Fe 0.2 Co 0.2 Ni 0.2 )O 3 films
Designing and understanding functional electronic and magnetic properties in perovskite oxides requires controlling and tuning the underlying crystal lattice. In this work, we report the structure, including oxygen and cation positions, of a single-crystal, entropy stabilized perovskite oxide film of La(Cr 0.2 Mn 0.2 Fe 0.2 Co 0.2 Ni 0.2 )O 3 grown on SrTiO3 (001). The parent materials range from orthorhombic (LaCrO 3 , LaMnO 3 , and LaFeO 3 ) to rhombohedral (LaCoO 3 and LaNiO 3 ), and first principles calculations indicate that these structural motifs are nearly degenerate in energy and should be highly distorted site to site. Despite this extraordinary local configurational disorder on the B-site sublattice, we find a structure with unexpected macroscopic crystalline homogeneity with a clear orthorhombic unit cell, whose orientation is demonstrated to be controlled by the strain and crystal structure of the substrate for films grown on (La 0.3 Sr 0.7 )(Al 0.65 Ta 0.35 )O 3 and NdGaO 3 (110). Furthermore, quantification of the atom positions within the unit cell reveals that the orthorhombic distortions are small, close to LaCrO 3, which may be driven by a combination of disorder averaging and the average ionic radii. This is a step toward understanding the rules for designing crystal motifs and tuning functional properties through controlled configurational complexity.
36 MATERIALS SCIENCE↗