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108 records · Page 6

Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies

Human monoclonal antibodies (mAbs) against the central repeat and junction domain of Plasmodium falciparum circumsporozoite protein (PfCSP) have been studied extensively to guide malaria vaccine design compared to antibodies against the PfCSP C terminus. Here, we describe the molecular characteristics and protective potential of 73 germline and mutated human mAbs against the highly immunogenic PfCSP C-terminal domain. Two mAbs recognized linear epitopes in the C-terminal linker with sequence similarity to repeat and junction motifs, whereas all others targeted conformational epitopes in the α-thrombospondin repeat (α-TSR) domain. Specificity for the polymorphic Th2R/Th3R but not the conserved RII+/CS.T3 region in the α-TSR was associated with IGHV3-21/IGVL3-21 or IGLV3-1 gene usage. Although the C terminus specific mAbs showed signs of more efficient affinity maturation and class-switching compared to anti-repeat mAbs, live sporozoite binding and inhibitory activity was limited to a single C-linker reactive mAb with cross-reactivity to the central repeat and junction. The data provide novel insights in the human anti-C-linker and anti-α-TSR antibody response that support exclusion of the PfCSP C terminus from malaria vaccine designs.

60 APPLIED LIFE SCIENCES↗

Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Gαi1

Abstract Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Gα) and serves as an essential Gα chaperone. Mechanisms by which Ric-8A catalyzes these activities, which are stimulated by Casein Kinase II phosphorylation, are unknown. We report the structure of the nanobody-stabilized complex of nucleotide-free Gα bound to phosphorylated Ric-8A at near atomic resolution by cryo-electron microscopy and X-ray crystallography. The mechanism of Ric-8A GEF activity differs considerably from that employed by G protein-coupled receptors at the plasma membrane. Ric-8A engages a specific conformation of Gα at multiple interfaces to form a complex that is stabilized by phosphorylation within a Ric-8A segment that connects two Gα binding sites. The C-terminus of Gα is ejected from its beta sheet core, thereby dismantling the GDP binding site. Ric-8A binds to the exposed Gα beta sheet and switch II to stabilize the nucleotide-free state of Gα.

59 BASIC BIOLOGICAL SCIENCES↗

Towards an “$\mathrm{AdS}_1$/$\mathrm{CFT}_0$” correspondence from the $\mathrm{D}$(-1)/$\mathrm{D}$7 system?

We argue that a type IIB Euclidean supergravity solution of the form $\mathbb{R}$ x S 1 x $\mathbb{T}$ 8 with imaginary self-dual F 1 flux through $\mathbb{R}$ x S 1 belongs to the chain of AdS d x S d x $\mathbb{T}$ 10-2d vacua with (imaginary) self-dual Fd flux, where d ≤ 5. Such vacua come from the near-horizon of D(d - 2)/D(8 - d) branes and are supersymmetric for odd values of d. For d = 1 we speculate that the hallmark of conformal symmetry for the matrix model dual is a vanishing free energy. The matrix dual was recently constructed by [1] by adding matrix interactions coming from strings stretching between the D(-1) and D7 branes to the IKKT matrix model. We find that the corresponding supergravity solution indeed has vanishing on-shell action. Specific F 5 fluxes need to be switched on as a consequence of (a T-dual version of) the Hanany-Witten effect.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

97 MATHEMATICS AND COMPUTING↗

Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser

NendoU from SARS-CoV-2 is responsible for the virus’s ability to evade the innate immune system by cleaving the polyuridine leader sequence of antisense viral RNA. Here we report the room-temperature structure of NendoU, solved by serial femtosecond crystallography at an X-ray free-electron laser to 2.6 Å resolution. The room-temperature structure provides insight into the flexibility, dynamics, and other intrinsic properties of NendoU, with indications that the enzyme functions as an allosteric switch. Functional studies examining cleavage specificity in solution and in crystals support the uridine-purine cleavage preference, and we demonstrate that enzyme activity is fully maintained in crystal form. Optimizing the purification of NendoU and identifying suitable crystallization conditions set the benchmark for future time-resolved serial femtosecond crystallography studies. This could advance the design of antivirals with higher efficacy in treating coronaviral infections, since drugs that block allosteric conformational changes are less prone to drug resistance.

59 BASIC BIOLOGICAL SCIENCES↗

LHCSR1 Functions as a Dimmer Switch for Light Harvesting

In oxygenic photosynthesis, high light leads to a set of photoprotective processes, known as nonphotochemical quenching, that are required for fitness. In moss and algae, the pigment−protein complex, light-harvesting stress-related (LHCSR), is crucial for photoprotection. Acidification of the thylakoid lumen under high light triggers the activation of LHCSR and the conversion of the xanthophyll violaxanthin into zeaxanthin, which is found within LHCSR. These interrelated molecular components combine to turn on a safety valve that dissipates excess energy as heat. Previous studies of detergent-solubilized LHCSR1 found that pH and zeaxanthin regulate distinct quenching sites via the protein conformation. However, protein function in the native membrane environment can be significantly different. In this work, we applied single-molecule fluorescence spectroscopy to LHCSR1 in membrane nanodiscs. The membrane environment enhanced total quenching, regardless of pH or zeaxanthin-binding. pH-dependent quenching was still observed whereas zeaxanthin-dependent quenching was suppressed. Conformational changes also increased in the membrane, establishing that the local environment can change the nature of the equilibrium between light harvesting and photoprotection.

Hoffmann, Madeline P. [Massachusetts Inst. of Tech↗

Ferroelectricity in Atomic Layer Deposited Wurtzite Zinc Magnesium Oxide Zn 1– x Mg x O

Conformal deposition of wurtzite ferroelectrics, which is needed for their use in scaled nonvolatile memories, is challenging using current physical vapor deposition techniques. To overcome the conformality barrier, this work demonstrates ferroelectricity in wurtzite Zn 1− x Mg x O thin films prepared by plasma-enhanced atomic layer deposition, which is a non-line-of-sight deposition method. Films ranging in composition from x = 0.00 to x = 0.58 are predominantly wurtzite phase and exhibit a (0001)-texture. Increasing the magnesium content decreases the c/a ratio, increases the optical bandgap energy, increases the piezoelectric response, and enables polarization reversal. Clear polarization switching is demonstrated in 50 nm thick Zn 1− x Mg x O films by piezoresponse force microscopy in compositions containing x = 0.46 and x = 0.58.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sn-InAs Nanowire Shadow-Defined Josephson Junctions

Hybrid superconductor–semiconductor platforms are foundational to advancing quantum information technologies, motivating the integration of materials with clean interfaces, robust superconductivity, and scalable architectures. Here, in this work, we report the synthesis and analysis of inclined InAs nanowires, conformally coated with β-Sn shells. These nanowires extend in opposite in-plane directions, forming a self-aligned, criss-cross network. This enables the deterministic formation of nanowire-shadow Josephson junctions through angle-controlled, low-temperature Sn deposition. Structural characterization shows uniform polycrystalline β-Sn shells forming a sharp, diffusion-free interface with InAs. Low-temperature transport measurements reveal a hard induced superconducting gap ≈ 600 μeV, switching currents up to ≈ 500 nA, and parallel magnetic field resilience beyond 1T. These results establish β-Sn/InAs nanowire networks as a promising platform for superconducting qubits, low-noise microwave devices, and the exploration of exotic superconducting phases including triplet pairing and topological superconductivity.

B-Sn↗

Origins of Electrostriction in Poly(vinylidene fluoride)-Based Ferroelectric Polymers

Although electrostriction is ubiquitous for dielectric polymers, giant electrostriction has not been observed until relaxor ferroelectric (RFE) poly(vinylidene fluoride) (PVDF)-based polymers are achieved. However, the exact origin for giant electrostriction in these polymers has not been fully understood. By studying the electrostriction in the uniaxially stretched films of a ferroelectric poly(VDF-co-trifluoroethylene) [P(VDF-TrFE)] random copolymer and an RFE poly(VDF-co-TrFE-co-chlorotrifluoroethylene) [P(VDF-TrFE-CTFE)] random terpolymer in this work, we confirmed that ferroelectric switching with large hysteresis, such as in the case of P(VDF-TrFE), was not genuine electrostriction. By decreasing large ferroelectric domains to the nanometer scale (i.e., 2–3 nm), such as in the case of the P(VDF-TrFE-CTFE) terpolymer, electrostriction with low hysteresis could be achieved. Here, two origins of the large electrostriction in these polymers were identified. The first was the mechano-electrostriction due to the poling field-induced conformation transformation of oriented polymer chains. The second was the electric repulsion of electrically aligned nanodomains. These effects could occur in both crystals and the oriented amorphous fraction, which links between the nanocrystals and the isotropic amorphous fraction. When the poling field was relatively low (e.g., <40 MV/m), the mechano-electrostriction was the major contribution and the electric repulsion effect was a minor contribution to electrostriction. Meanwhile, a strong temperature dependence of the low-field electrostriction coefficient was observed. Finally, we found an empirical inverse relationship between the electrostriction coefficient and the product of Young’s modulus and dielectric constant. The knowledge obtained from this study provides an insightful understanding of the electrostriction mechanism in PVDF-based electroactive polymers, which will find potential applications in sensors and actuators for wearable electronics and soft robotics.

36 MATERIALS SCIENCE↗

Controlling protein adsorption modes electrostatically

Protein adsorption on surfaces is ubiquitous in biology and in biotechnology. There are various forces required for controlling protein adsorption. Here, we introduce an explicit ion coarse-grained molecular dynamics simulation approach for studying the effects of electrostatics on protein adsorption, and 2D protein assembly on charged surfaces. Our model accounts for the spatial distribution of protein charges. We use catalase as our model protein. We find that the preferential adsorption mode of proteins at low protein concentration on a charged surface is “standing up”. When the protein concentration in a solution increases to reach a critical density on the surface, the adsorption mode switches from “standing up” to a mixed state “flat on” and “standing up”, which increases the lateral correlations among the adsorbed proteins. As such, the changes in the adsorption mode arise from the protein adsorption that cancel the surface charge and the protein–protein repulsion. This correlated surface structure melts as the salt concentration increases because the charged surface is cancelled by the salt ions and the proteins de-adsorb. For the case of strongly charged surfaces the “standing up” conformation remains more favorable even at high protein adsorption at low salt concentrations since in that conformation the surface charge is cancelled more effectively, generating an even more laterally correlated structure. We elucidate the effects of parameters such as surface charge density, salt concentration, and protein charges on the different adsorption modes and the structure and organization of proteins on the charged surfaces. Finally, this study provides a guide for controlling protein assembly on surfaces.

59 BASIC BIOLOGICAL SCIENCES↗

Mobile barrier mechanisms for Na + -coupled symport in an MFS sugar transporter

While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na + -bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.

59 BASIC BIOLOGICAL SCIENCES↗

Megavolt bremsstrahlung measurements from linear induction accelerators demonstrate possible use as a FLASH radiotherapy source to reduce acute toxicity

Abstract Recent studies indicate better efficacy and healthy tissue sparing with high dose-rate FLASH radiotherapy (FLASH-RT) cancer treatment. This technique delivers a prompt high radiation dose rather than fractional doses over time. While some suggest thresholds of > 40 Gy s −1 with a maximal effect at > 100 Gy s −1 , accumulated evidence shows that instantaneous dose-rate and irradiation time are critical. Mechanisms are still debated, but toxicity is minimized while inducing apoptosis in malignant tissue. Delivery technologies to date show that a capability gap exists with clinic scale, broad area, deep penetrating, high dose rate systems. Based on these trends, if FLASH-RT is adopted, it may become a dominant approach except in the least technologically advanced countries. The linear induction accelerator (LIA) developed for high instantaneous and high average dose-rate, species independent charged particle acceleration, has yet to be considered for this application. We review the status of LIA technology, explore the physics of bremsstrahlung-converter-target interactions and our work on stabilizing the electron beam. While the gradient of the LIA is low, we present our preliminary work to improve the gradient by an order of magnitude, presenting a point design for a multibeam FLASH-RT system using a single accelerator for application to conformal FLASH-RT.

42 ENGINEERING↗

Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR

Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Discovery of BBO-8520, a First-In-Class Direct and Covalent Dual Inhibitor of GTP-Bound (ON) and GDP-Bound (OFF) KRASG12C

Abstract Approved inhibitors of KRASG12C prevent oncogenic activation by sequestering the inactive, GDP-bound (OFF) form rather than directly binding and inhibiting the active, GTP-bound (ON) form. This approach provides no direct target coverage of the active protein. Expectedly, adaptive resistance to KRASG12C (OFF)-only inhibitors is observed in association with increased expression and activity of KRASG12C(ON). To provide optimal KRASG12C target coverage, we have developed BBO-8520, a first-in-class, direct dual inhibitor of KRASG12C(ON) and (OFF) forms. BBO-8520 binds in the Switch-II/Helix3 pocket, covalently modifies the target cysteine, and disables effector binding to KRASG12C(ON). BBO-8520 exhibits potent signaling inhibition in growth factor–activated states, in which current (OFF)-only inhibitors demonstrate little measurable activity. In vivo, BBO-8520 demonstrates rapid target engagement and inhibition of signaling, resulting in durable tumor regression in multiple models, including those resistant to KRASG12C(OFF)-only inhibitors. BBO-8520 is in phase 1 clinical trials in patients with KRASG12C non–small cell lung cancer. Significance: BBO-8520 is a first-in-class direct, small molecule covalent dual inhibitor that engages KRASG12C in the active (ON) and inactive (OFF) conformations. BBO-8520 represents a novel mechanism of action that allows for optimal target coverage and delays the emergence of adaptive resistance seen with (OFF)-only inhibitors in the clinic. See related commentary by Zhou and Westover, p. 455

Oncology↗

N -Arylimide Molecular Balances: A Comprehensive Platform for Studying Aromatic Interactions in Solution

Noncovalent interactions of aromatic surfaces play a key role in many biological processes and in determining the properties and utility of synthetic materials, sensors, and catalysts. However, the study of aromatic interactions has been challenging because these interactions are usually very weak and their trends are modulated by many factors such as structural, electronic, steric, and solvent effects. Recently, N-arylimide molecular balances have emerged as highly versatile and effective platforms for studying aromatic interactions in solution. These molecular balances can accurately measure weak noncovalent interactions in solution via their influence on the folded–unfolded conformational equilibrium. The structure (i.e., size, shape, π-conjugation, and substitution) and nature (i.e., element, charge, and polarity) of the π-surfaces and interacting groups can be readily varied, enabling the study of a wide range of aromatic interactions. These include aromatic stacking, heterocyclic aromatic stacking, and alkyl–π, chalcogen–π, silver–π, halogen–π, substituent–π, and solvent–π interactions. The ability to measure a diverse array of aromatic interactions within a single model system provides a unique perspective and insights as the interaction energies, stability trends, and solvent effects for different types of interactions can be directly compared. Some broad conclusions that have emerged from this comprehensive analysis include: (1) The strongest aromatic interactions involve groups with positive charges such as pyridinium and metal ions which interact with the electrostatically negative π-face of the aromatic surface via cation–π or metal–π interactions. Attractive electrostatic interactions can also form between aromatic surfaces and groups with partial positive charges. (2) Electrostatic interactions involving aromatic surfaces can be switched from repulsive to attractive using electron-withdrawing substituents or heterocycles. These electrostatic trends appear to span many types of aromatic interactions involving a polar group interacting with a π-surface such as halogen–π, chalcogen–π, and carbonyl–π. (3) Nonpolar groups form weak but measurable stabilizing interactions with aromatic surfaces in organic solvents due to favorable dispersion and/or solvophobic effects. Furthermore, a good predictor of the interaction strength is provided by the change in solvent-accessible surface area. (4) Solvent effects modulate the aromatic interactions in the forms of solvophobic effects and competitive solvation, which can be modeled using solvent cohesion density and specific solvent–solute interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Freeform thermoelectrics in single-step manufacturing: additive manufacturing of bismuth-telluride thermoelectrics

The project succeeded in producing crack-free Bismuth Telluride thermoelectric parts with density exceeding 98% through laser powder bed fusion (LPBF) additive manufacturing (AM). This greatly exceeded the highest previously reported density of 88% and is the highest among all semiconducting materials processed by LPBF. The additively manufactured material shows comparable Seebeck coefficient as conventional form and can be made into complex geometries with reduced material loss. On the other hand, measured properties are dramatically sensitive to the AM process parameters used, such that with identical composition, the Seebeck coefficient can be controllably tuned from +120 µV/K to -207 µV/K, which means the material switches between an n-type to a p-type semiconductor depending on processing. These changes are accompanied by significant differences in the as-processed microstructure due to rapid solidification. A machine learning protocol was developed and greatly reduced the experimental burden of the project, reducing the typical process optimization period of 2 years to 6 months. The project was fully successful in the objective of producing defect-free, complex geometry of bismuth-telluride parts through LPBF, but only partially successful in achieving performance goals. First, cost reduction of manufacturing, as measured by material waste, was successfully reduced by up to 70% compared to conventional manufacturing methods. This exceeded the proposed 30% reduction in materials waste needed to reach the 20% cost reduction goal of the project. On the other hand, the device performance, as measured by Seebeck coefficient, failed to reach the 40% improvement in efficiency. Rather, we observe comparable Seebeck coefficient between AM samples and conventionally processed counterparts. The device-level efficiency improvement does exceed 40% for complex geometry samples due to shape-induced increase in temperature gradients, but this was not the originally proposed metric. The machine learning approach developed in this project greatly accelerated the process optimization and can be adopted for fast development of AM processing parameters for other brittle and otherwise difficult-to-print materials. For the public, we deliver an efficient and widely adoptable process for incorporating waste-heat harvesting thermoelectric devices in both industrial and commercial heat exchangers. The geometric flexibility allows the capturing device to conform to the shape of the heat source to improve the system-level conversion efficiency. The technique can be deployed on any commercial LBPF systems with zero modifications, thus poses minimal adoption barrier for any manufacturer that already employed AM technology. Beyond bismuth-telluride, the machine-learning guided optimization protocol can be used in the future to reduce both the time and cost of process development for AM of other energy conversion and harvesting materials.

36 MATERIALS SCIENCE↗

Tubulin Double Helix: Lateral and Longitudinal Curvature Changes of Tubulin Protofilament

By virtue of their native structures, tubulin dimers are protein building blocks that are naturally pre-programmed to assemble into cytoskeletal polymers known as microtubules (MTs). Here we demonstrate polycation-directed (i.e. electrostatically tunable) assembly of tubulins through tubulin protofilament conformational changes in the longitudinal and lateral directions, creating novel tubulin double helices and various tubular architectures. Synchrotron small angle X-ray scattering and transmission electron microscopy reveal a remarkable range of nanoscale assembly structures: single- and double-layered double-helix tubulin tubules. The phase transitions from MTs into the new assemblies are dependent on the size and concentration of polycations. Two characteristic scales that determine the number of observed phases are the size of polycation compared to the size of tubulin (≈4 nm) and MT diameter (≈25 nm). This work suggests the feasibility of “programmable breakdown” of protein nanotubes, tearing MTs into double-stranded tubulins and building up previously undiscovered nanostructures, by using polycations with scissor- and glue-like properties. Importantly, we define a new role of tubulins as two-dimensionally shape-controllable building blocks for novel supramolecular architectures. Furthermore, these findings provide insight into the design of protein-based functional materials, for example, as metallization templates for nanoscale electronic devices, kinesin motor-driving molecular screws, and anticancer drug delivery vehicles.

2D shape‐control↗