Dynamic Helix Research Articles

Conformational analysis of a new peptide derived from feline immunodeficiency virus gp36 in SDS micelles: An NMR-MD based investigation.

Feline immunodeficiency virus (FIV) shares structural similarities with human immunodeficiency virus (HIV): the surface glycoprotein gp36 corresponds to the HIV gp41, which drives virus-host cell interactions and is targeted by the peptide entry inhibitor enfuvirtide. Following a similar drug design strategy for the development of an anti-FIV therapy, the present study investigates 627-646gp36 NHR, a peptide sequence derived from a region of gp36 that was previously found to interfere with the antiviral activity of the peptide C8, which instead derives from the gp36 MPER. CD, NMR, and MD simulations were employed to probe the conformational characteristics of 627-646gp36 NHR in the membrane-mimicking environment of SDS micelles. Our data show that 627-646gp36 NHR is characterized by three dynamic helix structures. MD simulations involving 627-646gp36 NHR, C8, and a larger protein, including the CHR and MPER regions, suggest that the interaction of C8 with the MPER region, the origin of the antiviral activity of C8, is disfavored in the presence of 627-646gp36 NHR in the simulation. This evidence can be useful for interpreting the molecular mechanism that leads to interference with the activity of C8, providing information on the folding/unfolding mechanism of the viral glycoprotein to design new strategies to inhibit viral entry.

Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin.

Human calcitonin (hCT) regulates calcium-phosphorus metabolism, but its amyloid aggregation disrupts physiological activity, increases thyroid carcinoma risk, and hampers its clinical use for bone-related diseases like osteoporosis and Paget's disease. Improving hCT with targeted modifications to mitigate amyloid formation while maintaining its function holds promise as a strategy. Understanding how each residue in hCT's amyloidogenic core affects its structure and aggregation dynamics is crucial for designing effective analogues. Mutants F16L-hCT and F19L-hCT, where Phe residues in the core are replaced with Leu as in nonamyloidogenic salmon calcitonin, showed different aggregation kinetics. However, the molecular effects of these substitutions in hCT are still unclear. Here, we systematically investigated the folding and self-assembly conformational dynamics of hCT, F16L-hCT, and F19L-hCT through multiple long-time scale independent atomistic discrete molecular dynamics (DMD) simulations. Our results indicated that the hCT monomer primarily assumed unstructured conformations with dynamic helices around residues 4-12 and 14-21. During self-assembly, the amyloidogenic core of hCT14-21 converted from dynamic helices to β-sheets. However, substituting F16L did not induce significant conformational changes, as F16L-hCT exhibited characteristics similar to those of wild-type hCT in both monomeric and oligomeric states. In contrast, F19L-hCT exhibited substantially more helices and fewer β-sheets than did hCT, irrespective of their monomers or oligomers. The substitution of F19L significantly enhanced the stability of the helical conformation for hCT14-21, thereby suppressing the helix-to-β-sheet conformational conversion. Overall, our findings elucidate the molecular mechanisms underlying hCT aggregation and the effects of F16L and F19L substitutions on the conformational dynamics of hCT, highlighting the critical role of F19 as an important target in the design of amyloid-resistant hCT analogs for future clinical applications.

Lethal Giant Disc is a target of Cdk1 and regulates ESCRT-III localization during germline stem cell abscission.

Abscission is the final step of cytokinesis that allows the physical separation of sister cells through the scission of the cellular membrane. This deformation is driven by ESCRT-III proteins, which can bind membranes and form dynamic helices. A crucial step in abscission is the recruitment of ESCRT-III proteins at the right time and place. Alix is one of the best characterized proteins that recruits ESCRT-III proteins from yeast to mammals. However, recent studies in vivo have revealed that pathways acting independently or redundantly with Alix are also required at abscission sites in different cellular contexts. Here, we show that Lgd acts redundantly with Alix to properly localize ESCRT-III to the abscission site in germline stem cells (GSCs) during Drosophila oogenesis. We further demonstrate that Lgd is phosphorylated at multiple sites by the CycB/Cdk1 kinase. We found that these phosphorylation events potentiate the activity of Shrub, a Drosophila ESCRT-III, during abscission of GSCs. Our study reveals that redundancy between Lgd and Alix, and coordination with the cell cycle kinase Cdk1, confers robust and timely abscission of Drosophila germline stem cells.

Deciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin.

The abnormal aggregation of human calcitonin (hCT) hormone peptides impairs their physiological function, leading to harmful immune responses and cytotoxicity, which limits their clinical utility. Interestingly, a representative hCT analog incorporating Y12L and N17H substitutions (DM-hCT) has shown reduced aggregation tendencies while maintaining bioactivity. But the molecular mechanism of Y12L and N17H substitutions on the conformational dynamics of hCT remains unclear. Here, we systematically investigated the folding and self-assembly dynamics of hCT and DM-hCT using atomistic discrete molecular dynamics (DMD) simulations. Our findings revealed that hCT monomers predominantly adopted unstructured conformations with dynamic helices. Oligomerization of hCT resulted in the formation of β-sheet-rich aggregates and β-barrel intermediates. The Y12L and N17H substitutions enhanced helical conformations and suppressed β-sheet formation in both monomers and oligomers. These substitutions stabilized the dynamic helices and disrupted aromatic interactions responsible for β-sheet formation at residue 12. Notably, DM-hCT assemblies still exhibited β-sheets in phenylalanine-rich and C-terminal hydrophobic regions, suggesting that future optimizations should focus on these areas. Our simulations provide insights into the molecular mechanisms underlying hCT aggregation and the amyloid-resistant effects of Y12L and N17H substitutions. These findings have valuable implications for the development of clinical hCT analogs.

Mammalian trans-editing factor ProX is able to deacylate tRNAThr mischarged with alanine

The precise coupling of tRNAs with their cognate amino acids, known as tRNA aminoacylation, is a stringently regulated process that governs translation fidelity. To ensure fidelity, organisms deploy multiple layers of editing mechanisms to correct mischarged tRNAs. Prior investigations have unveiled the propensity of eukaryotic AlaRS to erroneously attach alanine onto tRNACys and tRNAThr featuring the G4:U69 base pair. In light of this, and given ProXp-ala's capacity in deacylating Ala-tRNAPro, we embarked on exploring whether this trans-editing factor could extend its corrective function to encompass these mischarged tRNAs. Our in vitro deacylation assays demonstrate that murine ProXp-ala (mProXp-ala) is able to efficiently hydrolyze Ala-tRNAThr, while Ala-tRNACys remains unaffected. Subsequently, we determined the first structure of eukaryotic ProXp-ala, revealing a dynamic helix α2 involved in substrate binding. By integrating molecular dynamics simulations and biochemical assays, we pinpointed the pivotal interactions between mProXp-ala and Ala-tRNA, wherein the basic regions of mProXp-ala as well as the C3-G70 plays essential role in recognition. These observations collectively provide a cogent rationale for mProXp-ala's deacylation proficiency against Ala-tRNAThr. Our findings offer valuable insights into the translation quality control within higher eukaryotic organisms, where the fidelity of translation is safeguarded by the multi-functionality of extensively documented proteins.

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR.

α-Synuclein (αS) is a presynaptic protein that binds to cell membranes and is linked to Parkinson’s disease (PD). Binding of αS to membranes is a likely first step in the molecular pathophysiology of PD. The αS molecule can adopt multiple conformations, being largely disordered in water, adopting a β-sheet conformation when present in amyloid fibrils, and forming a dynamic multiplicity of α-helical conformations when bound to lipid bilayers and related membrane-mimetic surfaces. Multiscale molecular dynamics simulations in conjunction with nuclear magnetic resonance (NMR) and cross-linking mass spectrometry (XLMS) measurements are used to explore the interactions of αS with an anionic lipid bilayer. The simulations and NMR measurements together reveal a break in the helical structure of the central non-amyloid-β component (NAC) region of αS in the vicinity of residues 65–70, which may facilitate subsequent oligomer formation. Coarse-grained simulations of αS starting from the structure of αS when bound to a detergent micelle reveal the overall pattern of protein contacts to anionic lipid bilayers, while subsequent all-atom simulations provide details of conformational changes upon membrane binding. In particular, simulations and NMR data for liposome-bound αS indicate incipient β-strand formation in the NAC region, which is supported by intramolecular contacts seen via XLMS and simulations. Markov state models based on the all-atom simulations suggest a mechanism of conformational change of membrane-bound αS via a dynamic helix break in the region of residue 65 in the NAC region. The emergent dynamic model of membrane-interacting αS advances our understanding of the mechanism of PD, potentially aiding the design of novel therapeutic approaches.

Glycomacrocycle-Based Azobenzene Derivatives as Chiral Dopants for Photoresponsive Cholesteric Liquid Crystals.

We demonstrate photoresponsive cholesteric liquid crystals (CLCs) doped with glycomacrocyclic azobenzene derivatives, which exhibit large conformational changes, providing dynamic control of helical superstructures in response to a light stimulus. An unprecedented shortening of the helical pitch length and the empowerment of helical twisting power up to 500% are observed upon trans (E) to cis (Z) photoisomerization. Light-driven dynamic helix twisting and untwisting behavior affords the first example of glycomacrocyclic azobenzene-based CLCs, which can drive the mechanical movement of micro-objects. Two modes of rotation-two-directional or one-directional rotational motion (crankshaft mode)-are realized. In particular, the latter mode based on the reversible cholesteric texture transition between homogeneous stripes and focal conics leads to the accumulation of the rotation angles achieving the amplified mechanical movements.

Helicity of a polyacetylene directed by molecular recognition of biscalixarene and fullerene.

Chiral biscalixarenes and a C60-appended polyphenylacetylene have been synthesized. The chiral biscalixarene encapsulated the C60 unit of the phenylpolyacetylene, which induced the preferred helicity of the polyacetylene.

Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer

The C-terminus of α-tubulin undergoes a detyrosination/tyrosination cycle and dysregulation of this cycle is associated with cancer and other diseases. The molecular mechanisms of tubulin tyrosination are well studied, however it has remained unknown how tyrosine is cleaved from the tubulin tail. Here, we report the crystal structure of the long-sought detyrosination enzyme, the VASH2/SVBP heterodimer at 2.2 Å resolution and the structure of the tail/VASH2/SVBP complex at 2.5 Å resolution. VASH2 possesses a non-canonical Cys-His-Ser catalytic architecture for tyrosine cleavage. The dynamics of the α1- and α2- helices of VASH2 are related to the insolubility of VASH2. SVBP plays a chaperone-like role by extensively interacting with VASH2 and stabilizing these dynamic helices. A positively charged groove around the catalytic pocket and the α1- and α2- helices of VASH2 targets the tubulin tail for detyrosination. We provide insights into the mechanisms underlying the cycle of tubulin tyrosine cleavage and religation.

Conformational Changes in the Cytoplasmic Region of KIR3DL1 upon Interaction with SHP-2

KIR3DL1 is an inhibitory killer cell immunoglobulin-like receptor (KIR) that negatively regulates natural killer cell cytotoxicity. The KIR3DL1 cytoplasmic region (3DL1-cyto) is disordered and can be dissected into three segments: (I) H340-V351; (II) M352-D371; and (III) P372-P423. NMR studies indicate that segment II can dynamically adopt a loop-like conformation, and segments I and III can form dynamic helices that may mediate binding to membranes, particularly in the region around the N-terminal (N) immunoreceptor tyrosine-based inhibitory motif (ITIM), consistent with its role in signaling. Furthermore, individual SH2 domains of SHP-2 strongly engage with the unphosphorylated N-ITIM of 3DL1-cyto, while binding of the tandem SHP-2 SH2 domains to the bis-phosphorylated ITIMs results in more extensive conformational changes in segments I and III. The findings enhance our understanding of KIR function and how ITIMs in a target receptor operate in concert to engage the tandem SH2 domains of SHP-2.

Enhancing Aromatic Foldamer Helix Dynamics to Probe Interactions with Protein Surfaces

Dynamic helices that undergo exchange between P and M conformations can be used as sensors when their interactions with chiral substances results in a helix handedness bias. For instance, chiral induction in short helically folded aromatic oligoamides based on 8‐amino‐2‐quinoline carboxylic acid (Q) has been used to detect interactions with proteins and nucleic acids. However, the stability of these helices in water increases rapidly with oligomer length to the extent that helix dynamics become too slow for sensing applications. We have developed an approach to enhance the helix dynamics of these oligomers through the introduction of more flexible 6‐aminomethyl‐2‐pyridinecarboxylic acid units (P) while preserving helix integrity. A series of P/Q hybrid oligoamides were synthesized and their rate of helix handedness inversion was evaluated by monitoring induced circular dichroism so as to define the requirements to bring kinetics in a practical range for sequences as long as fourteen units. Proof of principle was then brought by confining such sequences at the surface of carbonic anhydrase and showing that protein‐mediated helix handedness induction occurs.

Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators

Transcriptional coactivators are a molecular recognition marvel because a single domain within these proteins, the activator binding domain or ABD, interacts with multiple compositionally diverse transcriptional activators. Also remarkable is the structural diversity among ABDs, which range from conformationally dynamic helical motifs to those with a stable core such as a β-barrel. A significant objective is to define conserved properties of ABDs that allow them to interact with disparate activator sequences. The ABD of the coactivator Med25 (activator interaction domain or AcID) is unique in that it contains secondary structural elements that are on both ends of the spectrum: helices and loops that display significant conformational mobility and a seven-stranded β-barrel core that is structurally rigid. Using biophysical approaches, we build a mechanistic model of how AcID forms binary and ternary complexes with three distinct activators; despite its static core, Med25 forms short-lived, conformationally mobile, and structurally distinct complexes with each of the cognate partners. Further, ternary complex formation is facilitated by allosteric communication between binding surfaces on opposing faces of the β-barrel. The model emerging suggests that the conformational shifts and cooperative binding is mediated by a flexible substructure comprised of two dynamic helices and flanking loops, indicating a conserved mechanistic model of activator engagement across ABDs. Targeting a region of this substructure with a small-molecule covalent cochaperone modulates ternary complex formation. Our data support a general strategy for the identification of allosteric small-molecule modulators of ABDs, which are key targets for mechanistic studies as well as therapeutic applications.

Different Origins of Strain-Induced Chirality Inversion of Co2+-Triggered Supramolecular Peptide Polymers

We report a distinctly different dynamic helix inversion pathway of self-assembled terpyridine-based ligands composed of different numbers of peptide moieties with Co2+ and its amplification of strain-induced chirality from an achiral terpyridine moiety. The helical chirality of the metal centers, coordinated by terpyridine ligands, is controlled by strain-induced chirality with complex ligand-to-Co2+ ratios. We also show that the distinct helical inversion mechanism is significantly dependent on the number of peptides attached to ligands. The helical inversion pathway of the self-assembled ligand (R-1 and S-1) complexes composed of one alanine analogue (R- or S-2-amino-1-propyl moiety) and one long saturated alkyl chain relies on two steps of chirality with different complex geometries, first from strain-induced chirality originating from an octahedral structure to octahedral structure with different helical direction and then on to helical chirality in a square-pyramidal structure. In contrast, the heli...

Assigning Function to the D and E Helices of HCN CNBD

HCN (hyperpolarization-activated cyclic-nucleotide sensitive cation nonselective) channels are activated by voltage and modulated by the direct binding of cAMP to their cytoplasmic C-terminal region named CNBD (cyclic nucleotide binding domain) (Zagotta et al., 2003). HCN channels are further regulated by TRIP8b, a brain-specific auxiliary subunit which controls channel trafficking and gating. In particular, TRIP8b interacts with the HCN channel CNBD and antagonizes the facilitatory effect of cAMP on channel opening (Hu et al., 2013 ). Recently, the cryo-EM structure of human HCN1 was solved in both the cAMP-free and cAMP-bound states (Lee and Mackinnon, 2017). A comparison of the two structures shows that, in the full-length protein, cAMP binding induces all the same changes previously highlighted in the isolated CNBD fragment using NMR (Saponaro et al., 2014), plus the unexpected folding of two additional helices at the C-terminus of the CNBD. These helices were not included in any of the previous experiments conducted using the isolated C-linker/CNBD fragment. To understand whether these two dynamic helices play a role in regulating both cAMP and TRIP8b binding, we have compared, using an in vitro binding assay, two CNBD constructs with or without the newly discovered helices. Surprisingly, their presence increases the affinity for cAMP without affecting TRIP8b binding. This result assigns to the new C-terminal helices of the HCN channel CNBD a specific role in controlling cyclic nucleotide affinity.

Conformational Changes in the Cytoplasmic Region of KIR3DL1 Upon Interaction with SHP-2

KIR3DL1 is an inhibitory killer cell Ig-like receptor (KIR) that negatively regulates natural killer (NK) cell cytotoxicity. The KIR3DL1 cytoplasmic region (3DL1-cyto) is disordered and can be dissected into three segments: (I) H340-V351; (II) M352-D371; and (III) P372-P423. NMR studies indicate that segment II adopts a transient loop-like conformation, and segments I and III can form dynamic helices that mediate binding to membranes, particularly surrounding the N-terminal (N) immunoreceptor tyrosine-based inhibitory motif (ITIM) in segment III, consistent with its role in signaling. Furthermore, individual SH2 domains of SHP-2 strongly engage with the unphosphorylated N-ITIM of 3DL1-cyto, while binding of the tandem SHP-2 SH2 domains to the bis-phosphorylated ITIMs results in more extensive conformational changes in segments I and III. The findings enhance our understanding of KIR function and how ITIMs in a target receptor operate in concert to engage the tandem SH2 domains of SHP-2.

Quenching protein dynamics interferes with HIV capsid maturation

Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of the C-terminal region of CA and the peptide SP1 (CA–SP1), which represents an intermediate during maturation of the HIV-1 virus. By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA–SP1 tubes assembled in vitro, which represent the features of an intermediate assembly state during maturation, the SP1 peptide exists in a dynamic helix–coil equilibrium, and that the addition of the maturation inhibitors Bevirimat and DFH-055 causes stabilization of a helical form of SP1. Moreover, the maturation-arresting SP1 mutation T8I also induces helical structure in SP1 and further global dynamical and conformational changes in CA. Overall, our results show that dynamics of CA and SP1 are critical for orderly HIV-1 maturation and that small molecules can inhibit maturation by perturbing molecular motions.

Conformational and chemical selection by a trans-acting editing domain

Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNAPro, the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNAPro and mischarged Ala-tRNAAla is unclear. Deacylation assays using substrate analogs reveal that size discrimination is only one component of selectivity. We used NMR spectroscopy and sequence conservation to guide extensive site-directed mutagenesis of Caulobacter crescentus ProXp-ala, along with binding and deacylation assays to map specificity determinants. Chemical shift perturbations induced by an uncharged tRNAPro acceptor stem mimic, microhelixPro, or a nonhydrolyzable mischarged Ala-microhelixPro substrate analog identified residues important for binding and deacylation. Backbone 15N NMR relaxation experiments revealed dynamics for a helix flanking the substrate binding site in free ProXp-ala, likely reflecting sampling of open and closed conformations. Dynamics persist on binding to the uncharged microhelix, but are attenuated when the stably mischarged analog is bound. Computational docking and molecular dynamics simulations provide structural context for these findings and predict a role for the substrate primary α-amine group in substrate recognition. Overall, our results illuminate strategies used by a trans-editing domain to ensure acceptance of only mischarged Ala-tRNAPro, including conformational selection by a dynamic helix, size-based exclusion, and optimal positioning of substrate chemical groups.

Architecture of Chiral Poly(phenylacetylene)s: From Compressed/Highly Dynamic to Stretched/Quasi-Static Helices.

The remarkable consequences in elongation, dynamic character, response to external stimuli (e.g., solvent effects, metal cations), and aggregation observed in helical poly(phenylacetylene)s (PPAs) when either the type of linkage with the pendant groups (i.e., anilide, benzamide) or the aromatic substitution pattern (i.e., ortho, meta, para) of the parent phenylacetylene monomer undergo modification are analyzed in depth. Two series of PPAs substituted at the phenyl ring in ortho, meta, and para with either (S)-α-methoxy-α-phenylacetic acid (MPA) or (S)-phenylglycine methyl ester (PGME) linked through anilide or benzamide bonds were prepared (i.e., o-, m-, p-poly-1 and poly-2 series) and characterized both in solution and in the solid state (CD, UV-vis, Raman, NMR, DSC, TGA, X-ray, AFM, SEM). Para-substituted polymers (p-poly-1 and p-poly-2) present the most compressed and dynamic helices, which respond easily to external stimuli. Meta-substituted PPAs (m-poly-1 and m-poly-2) exist as a mixture in equilibrium of two different helices (compressed and stretched), both less dynamic than the para counterparts and with a weak response to external stimuli. Moreover, in the solid state, m-poly-1 and m-poly-2 show separate fields for the compressed and for the stretched helices. For its part, the ortho-substituted PPA (o-poly-1) presents a highly stretched, almost planar and practically rigid helical structure, inert to external stimuli and prone to aggregate. These structural changes (elongation/dynamic behavior) are rationalized on the basis of the increasing difficulties imposed by the meta- and ortho-substitution on the accommodation of the pendants within the helical structure.

Province/Ministry-Coordinated Industry-University-Institute Cooperation and University Development: Based on the Experiences of Guangdong Province

The industry S&T missioners, industry-university-institute innovation alliances, industry-university-institute regional model bases, and other provincial-level industry-university-institute cooperation mechanisms that Guangdong Province has formed through its practical efforts play an important role in training a large batch of practical talent in universities, forging the teacher corps combining theoretical and practical skills, perfecting the teacher evaluation system, raising standards for discipline building, enhancing the ability of universities to serve society, improving school administration, and other areas. Practice has proven that the beneficial interaction of the dynamic triple helix formed by universities, industry, and governments can promote innovation in administrative mechanisms and talent training models at universities.

The PNT domain fromDrosophilapointed-P2 contains a dynamic N-terminal helix preceded by a disordered phosphoacceptor sequence

Pointed-P2, the Drosophila ortholog of human ETS1 and ETS2, is a transcription factor involved in Ras/MAP kinase-regulated gene expression. In addition to a DNA-binding ETS domain, Pointed-P2 contains a PNT (or SAM) domain that serves as a docking module to enhance phosphorylation of an adjacent phosphoacceptor threonine by the ERK2 MAP kinase Rolled. Using NMR chemical shift, ¹⁵N relaxation, and amide hydrogen exchange measurements, we demonstrate that the Pointed-P2 PNT domain contains a dynamic N-terminal helix H0 appended to a core conserved five-helix bundle diagnostic of the SAM domain fold. Neither the secondary structure nor dynamics of the PNT domain is perturbed significantly upon in vitro ERK2 phosphorylation of three threonine residues in a disordered sequence immediately preceding this domain. These data thus confirm that the Drosophila Pointed-P2 PNT domain and phosphoacceptors are highly similar to those of the well-characterized human ETS1 transcription factor. NMR-monitored titrations also revealed that the phosphoacceptors and helix H0, as well as region of the core helical bundle identified previously by mutational analyses as a kinase docking site, are selectively perturbed upon ERK2 binding by Pointed-P2. Based on a homology model derived from the ETS1 PNT domain, helix H0 is predicted to partially occlude the docking interface. Therefore, this dynamic helix must be displaced to allow both docking of the kinase, as well as binding of Mae, a Drosophila protein that negatively regulates Pointed-P2 by competing with the kinase for its docking site.