Helical Motif Research Articles

Conserved helical motifs in the IKZF1 disordered region mediate NuRD interaction and transcriptional repression

The transcription factor IKZF1 is essential for B cell development, and recurrently mutated in human B-ALL. IKZF1 has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of IKZF1-associated coregulators and their contribution to IKZF1-mediated gene regulation are not well understood. To address this, we performed an unbiased identification of IKZF1-interacting proteins in pre-B cells and found that IKZF1 interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to IKZF1 induction. Transcriptional repression preceded transcriptional activation by several hours, manifesting as a decrease in the fraction of transcriptional bursts at the single molecule level. Repression was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. We identified highly conserved helical motifs within the intrinsically disordered region in IKZF1 that mediate its association with the NuRD corepressor complex through critical “KRK” residues that bind the NuRD subunit RBBP4, a mechanism shared with the TFs FOG1, BCL11A, and SALL4. Functional characterization reveals this region is necessary for to the efficient silencing of target genes and antiproliferative functions of IKZF1 in B-ALL.

Stapled Peptides as Inhibitors of mRNA Deadenylation

Therapeutic intervention targeting mRNA typically aims at reducing the levels of disease‐causing sequences. Achieving the opposite effect of blocking the destruction of beneficial mRNA remains underexplored. The degradation of mRNA starts with the removal of poly(A) tails reducing their stability and translational activity which is mainly regulated by the CCR4‐NOT complex. The subunit NOT9 binds various RNA binding proteins which recruit mRNA in a sequence‐specific manner to the CCR4‐NOT complex to promote their deadenylation. These RNA binding proteins interact with NOT9 through a helical NOT9 binding motif which we used as a starting point for development of the hydrocarbon stapled peptide NIP‐2. The peptide (KD = 60.4 nM) was able to inhibit RNA‐binding (IC50 = 333 nM) as well as the deadenylation activity of the CCR4‐NOT complex in vitro while being cell‐permeable (EC50 = 2.44 μM). A co‐crystal structure of NIP‐2 bound to NOT9 allowed further optimization of the peptide through point mutation leading to NIP‐2‐H27A‐N3(KD = 122 nM) with high cell permeability (cell‐permeability EC50 = 0.34 μM). The optimized peptide was able to inhibit deadenylation of target mRNAs when used in HeLa cells at a concentration of 100 μM demonstrating the feasibility of increasing mRNA stability.

Stapled Peptides as Inhibitors of mRNA Deadenylation.

Therapeutic intervention targeting mRNA typically aims at reducing the levels of disease-causing sequences. Achieving the opposite effect of blocking the destruction of beneficial mRNA remains underexplored. The degradation of mRNA starts with the removal of poly(A) tails reducing their stability and translational activity which is mainly regulated by the CCR4-NOT complex. The subunit NOT9 binds various RNA binding proteins which recruit mRNA in a sequence-specific manner to the CCR4-NOT complex to promote their deadenylation. These RNA binding proteins interact with NOT9 through a helical NOT9 binding motif which we used as a starting point for development of the hydrocarbon stapled peptide NIP-2. The peptide (KD = 60.4 nM) was able to inhibit RNA-binding (IC50 = 333 nM) as well as the deadenylation activity of the CCR4-NOT complex in vitro while being cell-permeable (EC50 = 2.44 μM). A co-crystal structure of NIP-2 bound to NOT9 allowed further optimization of the peptide through point mutation leading to NIP-2-H27A-N3(KD = 122 nM) with high cell permeability (cell-permeability EC50 = 0.34 μM). The optimized peptide was able to inhibit deadenylation of target mRNAs when used in HeLa cells at a concentration of 100 μM demonstrating the feasibility of increasing mRNA stability.

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations.

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. We present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.

Non-coding RNAs play a major role in diverse processes in living cells with their sequence and spatial structure serving as the principal determinants of their function. Superposition of RNA 3D structures is the most accurate method for comparative analysis of RNA molecules and for inferring structure-based sequence alignments. Topology-independent superposition is particularly relevant, as evidenced by structurally similar RNAs with sequence permutations such as tRNA and Y RNA. To date, state-of-the-art methods for RNA 3D structure superposition rely on intricate heuristics, and the potential for topology-independent superposition has not been exhausted. Recently, we introduced the ARTEM method for unrestrained pairwise superposition of RNA 3D modules and now we developed it further to solve the global RNA 3D structure alignment problem. Our new tool ARTEMIS significantly outperforms state-of-the-art tools in both sequentially-ordered and topology-independent RNA 3D structure superposition. Using ARTEMIS we discovered a helical packing motif to be preserved within different backbone topology contexts across various non-coding RNAs, including multiple ribozymes and riboswitches. We anticipate that ARTEMIS will be essential for elucidating the landscape of RNA 3D folds and motifs featuring sequence permutations that thus far remained unexplored due to limitations in previous computational approaches.

Probing conformational dynamics of EGFR mutants via SEIRA spectroscopy: potential implications for tyrosine kinase inhibitor design.

Missense mutations in EGFR's catalytic domain alter its function, promoting cancer. SEIRA spectroscopy, supported by MD simulations, reveals structural differences in the compactness and hydration of helical motifs between active and inactive EGFR conformations models. These findings provide novel insights into the biophysical mechanisms driving EGFR activation and drug resistance, offering a robust method for studying emerging EGFR mutations and their structural impacts on TKIs' efficacy.

Crystal structures and properties of derivatives of the alkaloid matrine: salts and hydrate forms.

We report the crystal structures of three matrine derivatives, namely, the salts (1R,2R,9S,17S)-6-oxo-7,13-diazatetracyclo[7.7.1.02,7.013,17]heptadecan-13-ium (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate (matrine caffeinate) sesquihydrate, C15H25N2O+·C9H7O4-·1.5H2O (Matrine-CA), and the 2-hydroxybenzoate (salicylate) monohydrate, C15H25N2O+·C7H5O3-·H2O (Matrine-SA), as well as the 1.75-hydrate form, (1R,2R,9S,17S)-7,13-diazatetracyclo[7.7.1.02,7.013,17]heptadecan-6-one 1.75-hydrate, C15H24N2O·1.75H2O (Matrine-H). Each derivative exhibited a consistent molecular conformation for the matrine core, which is notably distinct from that of the anhydrous form. Notably, both salts crystallized in the orthorhombic space group P212121, with an asymmetric unit featuring one cation and one anion. Within the two salt structures, intermolecular proton transfer between matrine and the acid is observed, culminating in the formation of a matrine cation protonated at the tertiary amine N site. The Matrine-CA crystal packing is manifested as a three-dimensional (3D) network arising from one-dimensional (1D) supramolecular helical chains, stabilized by N-H...O and O-H...O hydrogen bonds. In the case of Matrine-SA, the matrine cation is interconnected via hydrogen bonds with salicylate anions and water molecules, also forming a 1D helical motif. The structure of the hydrate form, Matrine-H, is reported again with the disordered solvent molecules accurately located. To further elucidate the structural attributes, Hirshfeld surface analysis and fingerprint plots are employed, offering a nuanced perspective on the intermolecular contacts and interactions within these crystalline forms.

Design of Dendritic Foldamers as Catalysts for Organic Synthesis

Background:: Multistranded foldamers mimic biopolymer architecture, through the assembly and folding of intrinsically flexible polymeric chains attached to polyol core have been synthesised here. The synthesised dendritic motifs possess helical cavities with properly arranged active sites. As these cavities are large enough to accommodate guest molecules, their application as synthetic foldamer catalyst were investigated in Knoevenagel and Mannich reactions. Methods:: It is presumed to be the potentiality of dendritic foldamers to form reverse micelle in the interior of helical motif containing many reactive sites. Results:: Inside the dendritic foldamer, the substrates are adequately concentrated, work together in cooperation for ligand-binding, and stabilize the transition state as in enzymes that helps to accelerate the reaction rate many times greater than in bulk solution. Conclusion:: An unrivalled reaction rate and high yield of products were obtained within a short time in both Knoevenagel and Mannich reactions by using dendritic foldamers as catalysts.

Multiple-stimuli fluorescent responsive metallo-organic helicated cage arising from monomer and excimer emission

Effectively regulating monomer and excimer emission in a singular supramolecular luminous platform is challenging due to high difficulty of precise control over its aggregation and dispersion behavior when subjected to external stimuli. Here, we show a metallo-cage (MTH) featuring a triple helical motif that displays a unique dual emission. It arises from both intramolecular monomer and intermolecular excimer, respectively. The distorted molecular conformation and the staggered stacking mode of MTH excimer are verified through single crystal X-ray diffraction analysis. These structural features facilitate the switch between monomer and excimer emission, which are induced by changes in concentration and temperature. Significantly, adjusting the equilibrium between these two states in MTH enables the production of vibrant white light emission in both solution and solid state. Moreover, when combined with a PMMA (polymethyl methacrylate) substrate, the resulting thin films can serve as straightforward fluorescence thermometer and thermally activated information encryption materials.

Molecular Bases and Specificity behind the Activation of the Immune System OAS/RNAse L Pathway by Viral RNA.

The first line of defense against invading pathogens usually relies on innate immune systems. In this context, the recognition of exogenous RNA structures is primordial to fight, notably, against RNA viruses. One of the most efficient immune response pathways is based on the sensing of RNA double helical motifs by the oligoadenylate synthase (OAS) proteins, which in turn triggers the activity of RNase L and, thus, cleaves cellular and viral RNA. In this contribution, by using long-range molecular dynamics simulations, complemented with enhanced sampling techniques, we elucidate the structural features leading to the activation of OAS by interaction with a model double-strand RNA oligomer mimicking a viral RNA. We characterize the allosteric regulation induced by the nucleic acid leading to the population of the active form of the protein. Furthermore, we also identify the free energy profile connected to the active vs. inactive conformational transitions in the presence and absence of RNA. Finally, the role of two RNA mutations, identified as able to downregulate OAS activation, in shaping the protein/nucleic acid interface and the conformational landscape of OAS is also analyzed.

Poly(l-proline)-Stabilized Polypeptide Nanostructures via Ring-Opening Polymerization-Induced Self-Assembly (ROPISA).

Poly(proline) II helical motifs located at the protein-water interface stabilize the three-dimensional structures of natural proteins. Reported here is the first example of synthetic biomimetic poly(proline)-stabilized polypeptide nanostructures obtained by a straightforward ring-opening polymerization-induced self-assembly (ROPISA) process through consecutive N-carboxyanhydride (NCA) polymerization. It was found that the use of multifunctional 8-arm initiators is critical for the formation of nanoparticles. Worm-like micelles as well as spherical morphologies were obtained as confirmed by dynamic light scattering (DLS), transmission electron microscopy (TEM), and small angle X-ray scattering (SAXS). The loading of the nanostructures with dyes is demonstrated. This fast and open-vessel procedure gives access to amino acids-based nanomaterials with potential for applications in nanomedicine.

A Double Twisted Nanographene with a Contorted Pyrene Core

AbstractThe mature synthetic methodologies enable us to rationally design and produce chiral nanographenes (NGs), most of which consist of multiple helical motifs. However, inherent chirality originating from twisted geometry has just emerged to be employed in chiral NGs. Herein, we report a red‐emissive chiral NG constituted of orthogonally arranged two‐fold twisted π‐skeletons at a contorted pyrene core which contributes to optical transitions of S0→S1 and vice versa. The thus‐obtained NG exhibited a robustness on its redox properties through 2e− uptake/release. The chemical oxidation generated stable radical cation whose absorption covers near‐infrared I and II regions. Overall, the contorted pyrene core governs electronic nature of the chiral NG. The twist operation on NGs would be, therefore, a design strategy to alter conventional chirality induction on NGs.

A Double Twisted Nanographene with a Contorted Pyrene Core.

The mature synthetic methodologies enable us to rationally design and produce chiral nanographenes (NGs), most of which consist of multiple helical motifs. However, inherent chirality originating from twisted geometry has just emerged to be employed in chiral NGs. Herein, we report a red-emissive chiral NG constituted of orthogonally arranged two-fold twisted π-skeletons at a contorted pyrene core which contributes to optical transitions of S0→S1 and vice versa. The thus-obtained NG exhibited a robustness on its redox properties through 2e- uptake/release. The chemical oxidation generated stable radical cation whose absorption covers near-infrared I and II regions. Overall, the contorted pyrene core governs electronic nature of the chiral NG. The twist operation on NGs would be, therefore, a design strategy to alter conventional chirality induction on NGs.

FAM122A ensures cell cycle interphase progression and checkpoint control by inhibiting B55α/PP2A through helical motifs

The Ser/Thr protein phosphatase 2 A (PP2A) regulates the dephosphorylation of many phosphoproteins. Substrate recognition are mediated by B regulatory subunits. Here, we report the identification of a substrate conserved motif [RK]-V-x-x-[VI]-R in FAM122A, an inhibitor of B55α/PP2A. This motif is necessary for FAM122A binding to B55α, and computational structure prediction suggests the motif, which is helical, blocks substrate docking to the same site. In this model, FAM122A also spatially constrains substrate access by occluding the catalytic subunit. Consistently, FAM122A functions as a competitive inhibitor as it prevents substrate binding and dephosphorylation of CDK substrates by B55α/PP2A in cell lysates. FAM122A deficiency in human cell lines reduces the proliferation rate, cell cycle progression, and hinders G1/S and intra-S phase cell cycle checkpoints. FAM122A-KO in HEK293 cells attenuates CHK1 and CHK2 activation in response to replication stress. Overall, these data strongly suggest that FAM122A is a short helical motif (SHeM)-dependent, substrate-competitive inhibitor of B55α/PP2A that suppresses multiple functions of B55α in the DNA damage response and in timely progression through the cell cycle interphase.

Designing Coiled Coils for Heterochiral Complexation to Enhance Binding and Enzymatic Stability.

Coiled coils, commonly found in native proteins, are helical motifs important for mediating intermolecular interactions. While coiled coils are attractive for use in new therapies and biomaterials, the lack of enzymatic stability of naturally occurring l-peptides may limit their implementation in biological environments. d-peptides are of interest for biomedical applications as they are resistant to enzymatic degradation and recent reports indicate that stereochemistry-driven interactions, achieved by blending d- and l-peptides, yield access to a greater range of binding affinities and a resistance to enzymatic degradation compared to l-peptides alone. To our knowledge, this effect has not been studied in coiled coils. Here, we investigate the effects of blending heterochiral E/K coiled coils, which are a set of coiled coils widely used in biomaterials. We found that we needed to redesign the coiled coils from a repeating pattern of seven amino acids (heptad) to a repeating pattern of 11 amino acids (hendecad) to make them more amenable to heterochiral complex formation. The redesigned hendecad coiled coils form both homochiral and heterochiral complexes, where the heterochiral complexes have stronger heats of binding between the constituent peptides and are more enzymatically stable than the analogous homochiral complexes. Our results highlight the ability to design peptides to make them amenable to heterochiral complexation, so as to achieve desirable properties like increased enzymatic stability and stronger binding. Looking forward, understanding how to engineer peptides to utilize stereochemistry as a materials design tool will be important to the development of next-generation therapeutics and biomaterials.

Critical size and internal force analysis of tendril-inspired spontaneous Helicalization mechanism

Tendrils initially exhibit straight morphologies before gradually transforming into helical conformations during longitudinal growth. Tendril-inspired helical structures possess advantageous physical properties and functions including versatile morphologies, adaptability, enhanced strength, and scalability. With advancements in nanoscience and nanotechnology, helical architectures across various length scales have been discovered or artificially synthesized. However, the fundamental mechanisms underlying the formation and evolution of helical structures remain elusive. This lack of mechanistic insight has impeded the controlled design and fabrication of helical structures, especially three-dimensional functional devices with integrated helical motifs. Here a mechanical model is systematically proposed for the spontaneous formation of the helical structures, based on the hypothesis of decoupled curling and warping phases. Applying nonlinear elasticity theory, a detailed analysis of the energetics and thermodynamics is presented, accounting for the large deformation that may emerge during planar curling. Additionally, differential relations between internal forces and associated displacements induced by bending and twisting of a slender curved beam under out-of-plane loading are derived, obtaining solutions via Laplace and inverse transforms. The theoretical solutions closely match ex- perimental evidence from shape memory polymers. Furthermore, the theoretical model is utilized to guide the fabrication of the smart helical antenna proposed in our previous work, and discuss the influence of configuration changes on the electromagnetic properties. Elucidating these fundamental mechanisms will facilitate the development of next-generation technologies exploiting helical architectures for diverse applications including flexible electronics, optics, and soft robotics.

Enantiomeric ni-cluster organic frameworks containing helixes constructed from alanine derivatives

Chiral metal-organic frameworks (CMOFs) [Ni((L)-ccba)(1,3,5-tmib)(H2O)0.5]n (HU17-L ) and [Ni((D)-ccba)(1,3,5-tmib)(H2O)0.5]n (HU17-D ) were prepared from alanine derivatives (L)-H2ccba and (D)-H2ccba in the presence of auxiliary N-donor linker 1,3,5-tmib (H2ccba = 4-((1-carboxyethyl)-carbamoyl)benzoic acid, 1,3,5-tmib = 1,3,5-tris(2-methyl-1H-imidazol-1-yl)benzene). HU17-L and HU17-D are three-dimensional (3D) enantiomers based on dinuclear [Ni2(CO2)2(H2O)]2+ clusters. Helical motifs are their outstanding structural features. In HU17-L and HU17-D , (L)-ccba2- and (D)-ccba2- anions constructed left-handed (L)-ccba-Ni chain and right-handed (D)-ccba-Ni chain through chiral transfer, respectively. Moreover, achiral 1,3,5-tmib linkers were bridged together by Ni(II) centers to obtain left-handed 1,3,5-tmib-Ni chain in HU17-L and right-handed 1,3,5-tmib-Ni chain in HU17-D via asymmetric induction, respectively. Topological analysis revealed that these frameworks are 8-connected fcu nets with point symbol (424.64). Magnetic tests indicate that antiferromagnetic interactions exist in these complexes.

Adapting to the Abyss: Passive Ventilation in the Deep-Sea Glass Sponge Euplectella aspergillum.

We analyze the flow physics inside the body cavity and downstream the deep-sea glass sponge Euplectella aspergillum. We provide evidence that the helical skeletal motifs of the sponge give rise to a rich fluid dynamic field, allowing the organism to scavenge flow from the bottom of the sea and promoting a spontaneous, organized vertical flow within its body cavity toward the osculum. Our analysis points at a functional adaptation of the organism, which can passively divert flow through the osculum in unfavorable, low ambient currents, with no need for active pumping, with potential repercussions in functional ecology, as well as the design of chemical reactors, air-treatment units, and civil and aeronaval structures.

A strained N-capping motif in α-helices of βαβ-units

A novel helical N-capping motif has been considered. It occurs in the βα-arches of right-handed βαβ-units and contains an N-cap residue in a sterically strained conformation. Moreover, this amino acid position contains almost no glycines, that could relieve strain. It was shown that the N-cap adopts this conformation as a result of the unusual convergence between the second and third amino acid positions of the α-helix (counting from the N-cap) and the second position of the preceding β-strand. This is achieved by the presence of glycines in the specified positions (i.e. positions i – 2, i + 2 and i + 3, if N-cap is i). The N-cap conformation is stabilized by a hydrogen bond between the backbone amide group in the second position of the α-helix and the carbonyl group in the first position of the β-strand. The occurrence of similar N-capping motifs in different types of βαβ-units was compared and their structural differences caused by the influence of the environment were described. Study results may be useful for protein design and ab initio prediction of the 3D protein structure.

Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists

Although stapled α-helical peptides can address challenging targets, their advancement is impeded by poor understandings for making them cell permeable while avoiding off-target toxicities. By synthesizing >350 molecules, we present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects. Key insights include a clear correlation between lipophilicity and permeability, removal of positive charge to avoid off-target toxicities, judicious anionic residue placement to enhance solubility/behavior, optimization of C-terminal length/helicity to enhance potency, and optimization of staple type/number to avoid polypharmacology. Workflow application gives peptides with >292x improved cell proliferation potencies and no off-target cell proliferation effects ( > 3800x on-target index). Application of these ‘design rules’ to a distinct Mdm2(X) peptide series improves ( > 150x) cellular potencies and removes off-target toxicities. The outlined workflow should facilitate therapeutic impacts, especially for those targets such as Mdm2(X) that have hydrophobic interfaces and are targetable with a helical motif.