Promoting Ruddlesden-Popper Perovskite Formation by Tailoring Spacer Intramolecular Interaction for Efficient and Stable Solar Cells

Low-dimensional Ruddlesden-Popper phase (LDRP) perovskites are widely studied in the field of photovoltaics due to their tunable energy-band properties, enhanced photostability, and improved environmental stability compared to the 3D perovskites. However, the insulating spacers with weak intramolecular interaction used in LDRP materials limit the out-of-plane charge transport, leading to poor device performance of LDRP perovskite solar cells (PSCs). Here, a functional ligand, 3-guanidinopropanoic acid (GPA), which is capable of forming strong intramolecular hydrogen bonds through the carboxylic acid group, is employed as an organic spacer for LDRP PSCs. Owing to the strong interaction between GPA molecules, high-quality LDRP (GPA)2 (MA)n-1 Pbn I3n+1 film with promoted formation of n = 5 phase, improved crystallinity, preferential vertical growth orientations, reduced trap-state density, and prolonged carrier lifetime is achieved using GPAI as the dimensionality regulator compared to butylamine hydroiodide (BAI). As a result, GPA-based LDRP PSC exhibits a champion power conversion efficiency of 18.16% that is much superior to the BA-based LDRP PSC (15.43%). Importantly, the optimized GPA-based LDRP PSCs without encapsulation show enhanced illumination, thermal, storage, and humidity stability compared to BA-based ones. This work provides new insights into producing high n value LDRP films and their efficient and stable PSCs.

Computational analysis of regulatory regions in human protein kinases

Eukaryotic proteins often feature modular domain structures comprising globular domains that are connected by linker regions and intrinsically disordered regions that may contain important functional motifs. The intramolecular interactions of globular domains and nonglobular regions can play critical roles in different aspects of protein function. However, studying these interactions and their regulatory roles can be challenging due to the flexibility of nonglobular regions, the long insertions separating interacting modules, and the transient nature of some interactions. Obtaining the experimental structures of multiple domains and functional regions is more difficult than determining the structures of individual globular domains. High-quality structural models generated by AlphaFold offer a unique opportunity to study intramolecular interactions in eukaryotic proteins. In this study, we systematically explored intramolecular interactions between human protein kinase domains (KDs) and potential regulatory regions, including globular domains, N- and C-terminal tails, long insertions, and distal nonglobular regions. Our analysis identified intramolecular interactions between human KDs and 35 different types of globular domains, exhibiting a variety of interaction modes that could contribute to orthosteric or allosteric regulation of kinase activity. We also identified prevalent interactions between human KDs and their flanking regions (N- and C-terminal tails). These interactions exhibit group-specific characteristics and can vary within each specific kinase group. Although long-range interactions between KDs and nonglobular regions are relatively rare, structural details of these interactions offer new insights into the regulation mechanisms of several kinases, such as HASPIN, MAPK7, MAPK15, and SIK1B.

Orthologous genes Pm12 and Pm21 from two wild relatives of wheat show evolutionary conservation but divergent powdery mildew resistance

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating disease that threatens wheat production worldwide. Pm12, which originated from Aegilops speltoides, a wild relative of wheat, confers strong resistance to powdery mildew and therefore has potential use in wheat breeding. Using susceptible mutants induced by gamma irradiation, we physically mapped and isolated Pm12 and showed it to be orthologous to Pm21 from Dasypyrum villosum, also a wild relative of wheat. The resistance function of Pm12 was validated via ethyl methanesulfonate mutagenesis, virus-induced gene silencing, and stable genetic transformation. Evolutionary analysis indicates that the Pm12/Pm21 loci in wheat species are relatively conserved but dynamic. Here, we demonstrated that the two orthologous genes, Pm12 and Pm21, possess differential resistance against the same set of Bgt isolates. Overexpression of the coiled-coil domains of both PM12 and PM21 induces cell death in Nicotiana benthamiana leaves. However, their full-length forms display different cell death-inducing activities caused by their distinct intramolecular interactions. Cloning of Pm12 will facilitate its application in wheat breeding programs. This study also gives new insight into two orthologous resistance genes, Pm12 and Pm21, which show different race specificities and intramolecular interaction patterns.

A potential long-range RNA-RNA interaction in the HIV-1 RNA

It is well-established that viral and cellular mRNAs alike harbour functional long-range intra-molecular RNA-RNA interactions. Despite the biological importance of such interactions, their identification and characterization remain challenging. Here we present a computational method for the identification of certain kinds of long-range intra-molecular RNA-RNA interactions involving the loop nucleotides of a hairpin loop. Using the computational method, we analysed 4272 HIV-1 genomic mRNAs. A potential long-range intra-molecular RNA-RNA interaction within the HIV-1 genomic RNA was identified. The long-range interaction is mediated by a kissing loop structure between two stem-loops of the previously reported SHAPE-based secondary structure of the entire HIV-1 genome. Structural modelling studies were carried out to show that the kissing loop structure not only is sterically feasible, but also contains a conserved RNA structural motif often found in compact RNA pseudoknots. The computational method should be generally applicable to the identification of potential long-range intra-molecular RNA-RNA interactions in any viral or cellular mRNA sequence.Communicated by Ramaswamy H. Sarma.

Pyrrolizidine alkaloids from Jacobaea vulgaris Gaertn and theoretical studies on intramolecular interactions

Two undescribed pyrrolizidine alkaloids, 13-dehydrosenkirkine (1) and chloromethylretrorsine (2), along with three known analogues, onetine (3), retrorsine (4), and usaramine N-oxide (5), were isolated from Jacobaea vulgaris Gaertn. The structures of the undescribed compounds were elucidated by extensive spectrometric and spectroscopic techniques, including HRESIMS, NMR, calculated 13C-NMR DP4+ analysis and comparison with experimental and calculated ECD spectra. The undescribed compounds were evaluated for their antitumour activity against HT29, HeLa, and HepG2 cells. In addition, the intramolecular interactions and quadrupolar couplings were revealed by investigating the geometrical and electronic properties of three typical otonecine-type PAs in DFT theory.

The disordered MAX N-terminus modulates DNA binding of the transcription factor MYC:MAX

The intrinsically disordered protein MYC belongs to the family of basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors (TFs). In complex with its cognate binding partner MAX, MYC preferentially binds to E-Box promotor sequences where it controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. Intramolecular regulation of MYC:MAX has not yet been investigated in detail. In this work, we use Nuclear Magnetic Resonance (NMR) spectroscopy to identify and map interactions between the disordered MAX N-terminus and the MYC:MAX DNA binding domain (DBD). We find that this binding event is mainly driven by electrostatic interactions and that it is competitive with DNA binding. Using Nuclear Magnetic resonance (NMR) spectroscopy and Surface Plasmon Resonance (SPR), we demonstrate that the MAX N-terminus serves to accelerate DNA binding kinetics of MYC:MAX and MAX:MAX dimers, while it simultaneously provides specificity for E-Box DNA. We also establish that these effects are further enhanced by Casein Kinase 2-mediated phosphorylation of two serine residues in the MAX N-terminus. Our work provides new insights how bHLH-LZ TFs are regulated by intramolecular interactions between disordered regions and the folded DNA binding domain.

An H2 O2 Molecule Stabilized inside Open-Cage C60 Derivatives by a Hydroxy Stopper

An H₂ O₂ molecule was isolated inside hydroxylated open-cage fullerene derivatives by mixing an H₂ O₂ solution with a precursor molecule followed by reduction of one of carbonyl groups on its orifice. Depending on the reduction site, two structural isomers for H₂ O₂ @open-fullerenes were obtained. A high encapsulation ratio of 81 % was attained at low temperature. The structures of the peroxosolvate complexes thus obtained were studied by ¹ H NMR spectroscopy, X-ray analysis, and DFT calculations, showing strong hydrogen bonding between the encapsulated H₂ O₂ and the hydroxy group located at the center of the orifice. This OH group was found to act as a kinetic stopper, and the formation of the hydrogen bonding caused thermodynamic stabilization of the H₂ O₂ molecule, both of which prevent its escape from the cage. One of the peroxosolvates was isolated by HPLC, affording H₂ O₂ @open-fullerene with 100 % encapsulation ratio, likely due to the intramolecular hydrogen-bonding interaction.

The CH···HC interaction in biphenyl is a delocalized, molecular-wide and entirely non-classical interaction: Results from FALDI analysis

In this study we aim to determine the origin of the electron density describing a CH···HC interaction in planar and twisted conformers of biphenyl. In order to achieve this, the fragment, atomic, localized, delocalized, intra- and inter-atomic (FALDI) decomposition scheme was utilized to decompose the density in the inter-nuclear region between the ortho-hydrogens in both conformers. Importantly, the structural integrity, hence also topological properties, were fully preserved as no 'artificial' partitioning of molecules was implemented. FALDI-based qualitative and quantitative analysis revealed that the majority of electron density arises from two, non-classical and non-local effects: strong overlap of ortho CH σ-bonds, and long-range electron delocalization between the phenyl rings and ortho carbons and hydrogens. These effects resulted in a delocalized electron channel, that is, a density bridge or a bond path in a QTAIM terminology, linking the H-atoms in the planar conformer. The same effects and phenomena are present in both conformers of biphenyl. We show that the CH···HC interaction is a molecular-wide event due to large and long-range electron delocalization, and caution against approaches that investigate CH···HC interactions without fully taking into account the remainder of the molecule.

Conserved Residues in the C-Terminal Domain Affect the Structure and Function of CYP38 in Arabidopsis

Arabidopsis cyclophilin38 (CYP38) is a thylakoid lumen protein critial for PSII assembly and maintenance, and its C-terminal region serves as the target binding domain. We hypothesized that four conserved residues (R290, F294, Q372, and F374) in the C-terminal domain are critical for the structure and function of CYP38. In yeast two-hybrid and protein pull-down assays, CYP38s with single-sited mutations (R290A, F294A, Q372A, or F374A) did not interact with the CP47 E-loop as the wild-type CYP38. In contrast, CYP38 with the R290A/F294A/Q372A/F374A quadruple mutation could bind the CP47 E-loop. Gene transformation analysis showed that the quadruple mutation prevented CYP38 to efficiently complement the mutant phenotype of cyp38. The C-terminal domain half protein with the quadruple mutation, like the wild-type one, could interact with the N-terminal domain or the CP47 E-loop in vitro. The cyp38 plants expressing CYP38 with the quadruple mutation showed a similar BN-PAGE profile as cyp38, but distinct from the wild type. The CYP38 protein with the quadruple mutation associated with the thylakoid membrane less efficiently than the wild-type CYP38. We concluded that these four conserved residues are indispensable as changes of all these residues together resulted in a subtle conformational change of CYP38 and reduced its intramolecular N-C interaction and the ability to associate with the thylakoid membrane, thus impairing its function in chloroplast.

Structure Controlling Factors of Oxido-Bridged Dinuclear Iron(III) Complexes

Oxido bridges commonly form between iron(III) ions, but their bond angles and symmetry vary with the circumstances. A large number of oxido-bridged dinuclear iron(III) complexes have been structurally characterized. Some of them belong to the C₂ point group, possessing bent Fe–O–Fe bonds, while some others belong to the C_i symmetry, possessing the linear Fe–O–Fe bonds. The question in this study is what determines the structures and symmetry of oxido-bridged dinuclear iron(III) complexes. In order to gain further insights, three oxido-bridged dinuclear iron(III) complexes were newly prepared with 2,2′-bipyridine (bpy) and 1,10-phenanthroline (phen) ligands: [Fe₂OCl₂(bpy)₄][PF₆]₂ (1), [Fe₂O(NO₃)₂(bpy)₄][PF₆]₂·0.6MeCN·0.2(2-PrOH) (2), and [Fe₂OCl₂(phen)₄][PF₆]₂·MeCN·0.5H₂O (3). The crystal structures of 1, 2, and 3 were determined by the single-crystal X-ray diffraction method, and all of them were found to have the bent Fe–O–Fe bonds. Judging from the crystal structure, some intramolecular interligand hydrogen bonds were found to play an important role in fixing the structures. Additional density functional theory (DFT) calculations were conducted, also for a related oxido-bridged dinuclear iron(III) complex with a linear Fe–O–Fe bond. We conclude that the Fe–O–Fe bridge tends to bend like a water molecule, but is often stretched by interligand steric repulsion, and that the structures are mainly controlled by the intramolecular interligand interactions.

A phosphorylation-dependent switch in the disordered p53 transactivation domain regulates DNA binding

The tumor-suppressor p53 is a critical regulator of the cellular response to DNA damage and is tightly regulated by posttranslational modifications. Thr55 in the AD2 interaction motif of the N-terminal transactivation domain functions as a phosphorylation-dependent regulatory switch that modulates p53 activity. Thr55 is constitutively phosphorylated, becomes dephosphorylated upon DNA damage, and is subsequently rephosphorylated to facilitate dissociation of p53 from promoters and inactivate p53-mediated transcription. Using NMR and fluorescence spectroscopy, we show that Thr55 phosphorylation inhibits DNA-binding by enhancing competitive interactions between the disordered AD2 motif and the structured DNA-binding domain (DBD). Nonphosphorylated p53 exhibits positive cooperativity in binding DNA as a tetramer. Upon phosphorylation of Thr55, cooperativity is abolished and p53 binds initially to cognate DNA sites as a dimer. As the concentration of phosphorylated p53 is further increased, a second dimer binds and causes p53 to dissociate from the DNA, resulting in a bell-shaped binding curve. This autoinhibition is driven by favorable interactions between the DNA-binding surface of the DBD and the multiple phosphorylated AD2 motifs within the tetramer. These interactions are augmented by additional phosphorylation of Ser46 and are fine-tuned by the proline-rich domain (PRD). Removal of the PRD strengthens the AD2-DBD interaction and leads to autoinhibition of DNA binding even in the absence of Thr55 phosphorylation. This study reveals the molecular mechanism by which the phosphorylation status of Thr55 modulates DNA binding and controls both activation and termination of p53-mediated transcriptional programs at different stages of the cellular DNA damage response.

A Critical Overview of Current Theoretical Methods of Estimating the Energy of Intramolecular Interactions

This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system.

Boosting the Quantum Efficiency of Ultralong Organic Phosphorescence up to 52 % via Intramolecular Halogen Bonding

Ultralong organic phosphorescence (UOP) has attracted increasing attention due to its potential applications in optoelectronics, bioelectronics, and security protection. However, achieving UOP with high quantum efficiency (QE) over 20 % is still full of challenges due to intersystem crossing (ISC) and fast non-radiative transitions in organic molecules. Here, we present a novel strategy to enhance the QE of UOP materials by modulating intramolecular halogen bonding via structural isomerism. The QE of CzS2Br reaches up to 52.10 %, which is the highest afterglow efficiency reported so far. The crucial reason for the extraordinary QE is intramolecular halogen bonding, which can not only effectively enhance ISC by promoting spin-orbit coupling, but also greatly confine motions of excited molecules to restrict non-radiative pathways. This work provides a reasonable strategy to develop highly efficient UOP materials for practical applications.

Pm21 CC domain activity modulated by intramolecular interactions is implicated in cell death and disease resistance

Nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs) provide resistance against several plant pathogens. We previously cloned the wheat powdery mildew resistance gene Pm21, which encodes a coiled-coil (CC) NLR that confers broad-spectrum resistance against Blumeria graminis f. sp. tritici. Here, we report comprehensive biochemical and functional analyses of Pm21 CC domain in Nicotiana benthamiana. Transient overexpression assay suggested that only the extended CC (eCC, amino acid residues 1-159) domain has cell-death-inducing activity, whereas the CC-containing truncations, including CC-NB and CC-NB-LRR, do not induce cell-death responses. Coimmunoprecipitation (Co-IP) assay showed that the eCC domain self-associates and interacts with the NB and LRR domains in planta. These results imply that the activity of the eCC domain is inhibited by the intramolecular interactions of different domains in the absence of pathogens. We found that the LRR domain plays a crucial role in D491V-mediated full-length (FL) Pm21 autoactivation. Some mutations in the CC domain leading to the loss of Pm21 resistance to powdery mildew impaired the CC activity of cell-death induction. Two mutations (R73Q and E80K) interfered with D491V-mediated Pm21 autoactivation without affecting the cell-death-inducing activity of the eCC domain. Notably, some susceptible mutants harbouring mutations in the CC domain still exhibited cell-death-inducing activity. Taken together, these results implicate the CC domain of Pm21 in cell-death signalling and disease-resistance signalling, which are potentially independent of each other.

The heme-regulatory motifs of heme oxygenase-2 contribute to the transfer of heme to the catalytic site for degradation

Heme-regulatory motifs (HRMs) are present in many proteins that are involved in diverse biological functions. The C-terminal tail region of human heme oxygenase-2 (HO2) contains two HRMs whose cysteine residues form a disulfide bond; when reduced, these cysteines are available to bind Fe3+-heme. Heme binding to the HRMs occurs independently of the HO2 catalytic active site in the core of the protein, where heme binds with high affinity and is degraded to biliverdin. Here, we describe the reversible, protein-mediated transfer of heme between the HRMs and the HO2 core. Using hydrogen-deuterium exchange (HDX)-MS to monitor the dynamics of HO2 with and without Fe3+-heme bound to the HRMs and to the core, we detected conformational changes in the catalytic core only in one state of the catalytic cycle-when Fe3+-heme is bound to the HRMs and the core is in the apo state. These conformational changes were consistent with transfer of heme between binding sites. Indeed, we observed that HRM-bound Fe3+-heme is transferred to the apo-core either upon independent expression of the core and of a construct spanning the HRM-containing tail or after a single turnover of heme at the core. Moreover, we observed transfer of heme from the core to the HRMs and equilibration of heme between the core and HRMs. We therefore propose an Fe3+-heme transfer model in which HRM-bound heme is readily transferred to the catalytic site for degradation to facilitate turnover but can also equilibrate between the sites to maintain heme homeostasis.

Structural insights into the intramolecular interactions of centromere protein CENP-I

In mitosis, the accurate segregation of sister chromosomes relies on kinetochore, a multiple subunits complex assembled on centromere of each sister chromosome. As a core component of inner kinetochore, CENP-I plays important functions to mediate kinetochore assembly and supports the faithful chromosome segregation. The structures of the N-terminus and C-terminus of CENP-I homologs in complex with CENP-H/K have been reported, respectively. Unfortunately, the intramolecular interactions of CENP-I are poorly understood, and how CENP-I interacts with CENP-M remains unknown. Here, we verified a unique helix α11, which forms the intramolecular interactions with N-terminal HEAT repeats in fungal CENP-I. Deletion of the helix α11 exposed the hydrophobic surface and resulted in the in vitro protein aggregation of N-terminal HEAT repeats of fungal CENP-I. The corresponding helix and its intramolecular interaction are highly conserved in human CENP-I. Deletion of the corresponding helix in human CENP-I dramatically reduced the functional activity to interact with CENP-H and CENP-M. Mutations of the conserved residues on the helix in human CENP-I significantly weakened the binding to CENP-M, but not CENP-H, in HeLa cells. Therefore, our findings for the first time unveiled a conserved helix of CENP-I, which is important for the intramolecular interaction and function, and would be helpful for understanding the structure basis of how CENP-I mediates the kinetochore assembly during cell cycle and mitosis.

Roles of YIGL sequence of Ebola virus VP40 on genome replication and particle production

Ebola virus (EBOV) VP40 is a major driving force of nascent virion production and a negative regulator of genome replication/transcription. Here, we showed that the YIGL sequence at the C-terminus of EBOV VP40 is important for virus-like particle (VLP) production and the regulation of genome replication/transcription. Accordingly, a mutation in the YIGL sequence caused defects in VLP production and genome replication/transcription. The residues I293 and L295 in the YIGL sequence were particularly critical for VLP production. Furthermore, an in silico analysis indicated that the amino acids surrounding the YIGL sequence contribute to intramolecular interactions within VP40. Among those surrounding residues, F209 was shown to be critical for VLP production. These results suggested that the VP40 YIGL sequence regulates two different viral replication steps, VLP production and genome replication/transcription, and the nearby residue F209 influences VLP production.

Direct Binding between Pre-S1 and TRP-like Domains in TRPP Channels Mediates Gating and Functional Regulation by PIP2

Transient receptor potential (TRP) channels are regulated by diverse stimuli comprising thermal, chemical, and mechanical modalities. They are also commonly regulated by phosphatidylinositol-4,5-bisphosphate (PIP2), with underlying mechanisms largely unknown. We here revealed an intramolecular interaction of the TRPP3 N and C termini (N-C) that is functionally essential. The interaction was mediated by aromatic Trp81 in pre-S1 domain and cationic Lys568 in TRP-like domain. Structure-function analyses revealed similar N-C interaction in TRPP2 as well as TRPM8/-V1/-C4 via highly conserved tryptophan and lysine/arginine residues. PIP2 bound to cationic residues in TRPP3, including K568, thereby disrupting the N-C interaction and negatively regulating TRPP3. PIP2 had similar negative effects on TRPP2. Interestingly, we found that PIP2 facilitates the N-C interaction in TRPM8/-V1, resulting in channel potentiation. The intramolecular N-C interaction might represent a shared mechanism underlying the gating and PIP2 regulation of TRP channels.

Zheng et al. show that an aromatic Trp residue in pre-S1 and a cationic Lys residue in the TRP-like domain of TRP polycystin channels mediate N-C binding, which underlies TRPPs gating and PIP2 regulation. The conservation of these residues suggests that this may be a shared mechanism of TRP channel gating.

Mutagenesis of the dengue virus NS4A protein reveals a novel cytosolic N-terminal domain responsible for virus-induced cytopathic effects and intramolecular interactions within the N-terminus of NS4A

The NS4A protein of dengue virus (DENV) has a cytosolic N terminus and four transmembrane domains. NS4A participates in RNA replication and the host antiviral response. However, the roles of amino acid residues within the N-terminus of NS4A during the life cycle of DENV are not clear. Here we explore the function of DENV NS4A by introducing a series of alanine substitutions into the N-terminus of NS4A in the context of a DENV infectious clone or subgenomic replicon. Nine of 17 NS4A mutants displayed a lethal phenotype due to the impairment of RNA replication. M2 and M14 displayed a more than 10 000-fold reduction in viral yields and moderate defects in viral replication by a replicon assay. Sequencing analyses of pseudorevertant viruses derived from M2 and M14 viruses revealed one consensus reversion mutation, A21V, within NS4A. The A21V mutation apparently rescued viral RNA replication in the M2 and M14 mutants although not to wild-type (WT) levels but resulted in 100- and 1000-fold lower titres than that of the WT, respectively. M2 Rev1 (M2+A21V) and M14 Rev1 (M14+A21V) mutants displayed phenotypes of smaller plaque size and WT-like assembly/secretion by a transpackaging assay. A defect in the virus-induced cytopathic effect (CPE) was observed in HEK-293 cells infected with either M2 Rev1 or M14 Rev1 mutant virus by MitoCapture staining, cell proliferation and lactate dehydrogenase release assays. In conclusion, the results revealed the essential roles of the N-terminal NS4A in both RNA replication and virus-induced CPE. Intramolecular interactions in the N-terminus of NS4A were implicated.

Isatin-1,8-Naphthalimide Hydrazones: A Study of Their Sensor and ON/OFF Functionality

Five novel hydrazones derived from substituted isatins were synthesized as potential anion sensors. Using UV-VIS, FTIR, NMR and fluorescence spectroscopy, these compounds’ tautomeric equilibrium and Z-E photoisomerization were studied in DMF and CHCl₃, depending on the hydrazone concentrations, the presence of basic anions and light stimulation. Anion recognition aspects (PF₆⁻, HSO₄⁻, Br⁻, Cl⁻, NO₃⁻, F⁻ and CH₃COO⁻) and these receptors’ detection limits were also studied. We also tested the light-stimulated ON-OFF functionality of these compounds in the presence or absence of these anions.

Hypervalent organoselenium compounds stabilized by intramolecular coordination: synthesis and crystal structures

Two novel hypervalent selenium(IV) compounds stabilized by intramolecular interactions, namely 6-phenyl-6,7-dihydro-5H-2,3-dioxa-2aλ⁴-selenacyclopenta[hi]indene, C₁₄H₁₂O₂Se, 14, and 5-phenyl-5,6-dihydro-4H-benzo[c][1,2]oxaselenole-7-carbaldehyde, C₁₄H₁₂OSe₂, 15, have been synthesized by the reaction of 2-chloro-1-formyl-3-(hydroxymethylene)cyclohexene with in-situ-generated disodium diselenide (Na₂Se₂). The title compounds were characterized by FT-IR spectroscopy, ESI-MS, and single-crystal X-ray diffraction studies. For 14, there is whole-molecule disorder, with occupancies of 0.605 (10) and 0.395 (10), a double bond between C and Se, and the five-membered selenopentalene rings are coplanar. The packing is stabilized by π-π stacking interactions involving one of the five-membered Se/C/C/C/O rings [centroid-centroid (Cg...Cg) distance = 3.6472 (18) Å and slippage = 1.361 Å], as well as C-H...π interactions involving a C-H group and the phenyl ring. In addition, there are bifurcated C-H...Se,O interactions which link the molecules into ribbons in the c direction. For 15, the C-Se bond lengths are longer than those of 14. The two five-membered rings are coplanar. There are no π-π or C-H...π interactions; however, molecules are linked by C-H...O interactions into centrosymmetric dimers, with graph-set notation R₂²(16).

FALDI-based criterion for and the origin of an electron density bridge with an associated (3,-1) critical point on Bader's molecular graph

The total electron density (ED) along the λ₂ -eigenvector is decomposed into contributions which either facilitate or hinder the presence of an electron density bridge (DB, often called an atomic interaction line or a bond path). Our FALDI-based approach explains a DB presence as a result of a dominating rate of change of facilitating factors relative to the rate of change of hindering factors; a novel and universal criterion for a DB presence is, thus, proposed. Importantly, facilitating factors show, in absolute terms, a concentration of ED in the internuclear region as commonly observed for most chemical bonds, whereas hindering factors show a depletion of ED in the internuclear region. We test our approach on four intramolecular interactions, namely (i) an attractive classical H-bond, (ii) a repulsive O⋅⋅⋅O interaction, (iii) an attractive Cl⋅⋅⋅Cl interaction, and (iv) an attractive CH⋅⋅⋅HC interaction. (Dis)appearance of a DB is (i) shown to be due to a "small" change in molecular environment and (ii) qualitatively and quantitatively linked with specific atoms and atom-pairs. The protocol described is equally applicable (a) to any internuclear region, (b) regardless of what kind of interaction (attractive/repulsive) atoms are involved in, (c) at any level of theory used to compute the molecular structure and corresponding wavefunction, and (d) equilibrium or nonequilibrium structures. Finally, we argue for a paradigm shift in the description of chemical interactions, from the ED perspective, in favor of a multicenter rather than diatomic approach in interpreting ED distributions in internuclear regions. © 2018 Wiley Periodicals, Inc.

Functional Relevance of Missense Mutations Affecting the N-Terminal Part of Shank3 Found in Autistic Patients

Genetic defects in SHANK genes are associated with autism. Deletions and truncating mutations suggest haploinsufficiency for Shank3 as a major cause of disease which may be analyzed in appropriate Shank deficient mouse models. Here we will focus on the functional analysis of missense mutations found in SHANK genes. The relevance of most of these mutations for Shank function, and their role in autism pathogenesis is unclear. This is partly due to the fact that mutations spare the most well studied functional domains of Shank3, such as the PDZ and SAM domains, or the short proline-rich motifs which are required for interactions with postsynaptic partners Homer, Cortactin, dynamin, IRSp53 and Abi-1. One set of mutations affects the N-terminal part, including the highly conserved SPN domain and ankyrin repeats. Functional analysis from several groups has indicated that these mutations (e.g., R12C; L68P; R300C, and Q321R) interfere with the critical role of Shank3 for synapse formation. More recently the structural analysis of the SPN-ARR module has begun to shed light on the molecular consequences of mutations in the SPN of Shank3. The SPN was identified as a Ras association domain, with high affinities for GTP-bound, active forms of Ras and Rap. The two autism related mutations in this part of the protein, R12C and L68P, both abolish Ras binding. Further work is directed at identifying the consequences of Ras binding to Shank proteins at postsynaptic sites.

A PH-like domain of the Rab12 guanine nucleotide exchange factor DENND3 binds actin and is required for autophagy

Rab GTPases are key regulators of membrane trafficking, and many are activated by guanine nucleotide exchange factors bearing a differentially expressed in normal and neoplastic cells (DENN) domain. By activating the small GTPase Rab12, DENN domain-containing protein 3 (DENND3) functions in autophagy. Here, we identified a structural domain (which we name PHenn) containing a pleckstrin homology subdomain that binds actin and is required for DENND3 function in autophagy. We found that a hydrophobic patch on an extended β-turn of the PHenn domain mediates an intramolecular interaction with the DENN domain of DENND3. We also show that DENND3 binds actin through a surface of positively charged residues on the PHenn domain. Substitutions that blocked either DENN or actin binding compromised the role of DENND3 in autophagy. These results provide new mechanistic insight into the structural determinants regulating DENND3 in autophagy and lay the foundation for future investigations of the DENN protein family.

IgG cooperativity - Is there allostery? Implications for antibody functions and therapeutic antibody development

A central dogma in immunology is that an antibody's in vivo functionality is mediated by 2 independent events: antigen binding by the variable (V) region, followed by effector activation by the constant (C) region. However, this view has recently been challenged by reports suggesting allostery exists between the 2 regions, triggered by conformational changes or configurational differences. The possibility of allosteric signals propagating through the IgG domains complicates our understanding of the antibody structure-function relationship, and challenges the current subclass selection process in therapeutic antibody design. Here we review the types of cooperativity in IgG molecules by examining evidence for and against allosteric cooperativity in both Fab and Fc domains and the characteristics of associative cooperativity in effector system activation. We investigate the origin and the mechanism of allostery with an emphasis on the C-region-mediated effects on both V and C region interactions, and discuss its implications in biological functions. While available research does not support the existence of antigen-induced conformational allosteric cooperativity in IgGs, there is substantial evidence for configurational allostery due to glycosylation and sequence variations.

Autophosphorylation of calcium/calmodulin-dependent protein kinase (CCaMK) at S343 or S344 generates an intramolecular interaction blocking the CaM-binding

The Ca²⁺ and Ca²⁺/calmodulin-dependent protein kinase (CCaMK) is an important effector protein of Ca²⁺/calmodulin-mediated signaling, and in legumes, it is a critical regulator of plant-rhizobia and mycorrhizal symbioses. CCaMK contains a kinase domain, a calmodulin-binding/autoinhibitory domain and a visinin-like domain. Previous studies revealed the presence of 2 phosphorylation sites, S343 and S344, in the calmodulin-binding domain. Mutations at these sites affected the kinase activity and downstream rhizobium and mycorrhizal symbioses, which highlighted the importance of these residues in regulating protein activity. This addendum further clarifies the regulation of CCaMK by identifying an intramolecular interaction between residue(s) in the kinase domain and phosphorylation sites S343 and S344. This interaction turns off the substrate phosphorylation capacity of CCaMK.

A Study of Intramolecular Hydrogen Bonding in Levoglucosan Derivatives

Organofluorine is a weak hydrogen-bond (HB) acceptor. Bernet et al. have demonstrated its capability to perturb OH···O intramolecular hydrogen bonds (IMHBs), using conformationally rigid carbohydrate scaffolds including levoglucosan derivatives. These investigations are supplemented here by experimental and theoretical studies involving six new levoglucosan derivatives, and complement the findings of Bernet et al. However, it is shown that conformational analysis is instrumental in interpreting the experimental data, due to the occurrence of non-intramolecular hydrogen-bonded populations which, although minor, cannot be neglected and appears surprisingly significant. The DFT conformational analysis, together with the computation of NMR parameters (coupling constants and chemical shifts) and wavefunction analyses (AIM, NBO), provides a full picture. Thus, for all compounds, the most stabilized structures show the OH groups in a conformation allowing IMHB with O5 and O6, when possible. Furthermore, the combined approach points out the occurrence of various IMHBs and the effect of the chemical modulations on their features. Thus, two-center or three-center IMHB interactions are observed in these compounds, depending on the presence or absence of additional HB acceptors, such as methoxy or fluorine.

Checkpoint-Independent Regulation of Origin Firing by Mrc1 through Interaction with Hsk1 Kinase

Mrc1 is a conserved checkpoint mediator protein that transduces the replication stress signal to the downstream effector kinase. The loss of mrc1 checkpoint activity results in the aberrant activation of late/dormant origins in the presence of hydroxyurea. Mrc1 was also suggested to regulate orders of early origin firing in a checkpoint-independent manner, but its mechanism was unknown. Here we identify HBS (Hsk1 bypass segment) on Mrc1. An ΔHBS mutant does not activate late/dormant origin firing in the presence of hydroxyurea but causes the precocious and enhanced activation of weak early-firing origins during normal S-phase progression and bypasses the requirement for Hsk1 for growth. This may be caused by the disruption of intramolecular binding between HBS and NTHBS (N-terminal target of HBS). Hsk1 binds to Mrc1 through HBS and phosphorylates a segment adjacent to NTHBS, disrupting the intramolecular interaction. We propose that Mrc1 exerts a "brake" on initiation (through intramolecular interactions) and that this brake can be released (upon the loss of intramolecular interactions) by either the Hsk1-mediated phosphorylation of Mrc1 or the deletion of HBS (or a phosphomimic mutation of putative Hsk1 target serine/threonine), which can bypass the function of Hsk1 for growth. The brake mechanism may explain the checkpoint-independent regulation of early origin firing in fission yeast.

Regulation of DENND3, the exchange factor for the small GTPase Rab12 through an intramolecular interaction

The Rab family of small GTPases functions in multiple aspects of cellular membrane trafficking. Proteins bearing a differentially expressed in normal and neoplastic cells (DENN) domain have emerged as the largest family of Rab-activating guanine nucleotide exchange factors (GEFs). Rab12 functions in the initiation of starvation-induced autophagy, and our previous work revealed that its activator, DENN domain-containing protein 3 (DENND3), is phosphorylated and activated upon starvation. However, how the GEF activity of DENND3 toward Rab12 is regulated at the molecular level is still not understood. Here, we combine size-exclusion chromatography, Förster resonance energy transfer, pulldown, and in vitro GEF assays to demonstrate that regulation of GEF activity is achieved through an intramolecular interaction that is controlled by a key residue in DENND3, tyrosine 940. Our study sheds light on the regulation of Rab12 activation and lays the groundwork for characterizing the regulation of other DENN domain-containing proteins.

Unraveling the Deleterious Effects of Cancer-Driven STK11 Mutants Through Conformational Sampling Approach

Tumor suppressor gene, STK11, encodes for serine-threonine kinase, which has a critical role in regulating cell growth and apoptosis. Mutations of the same lead to the inactivation of STK11, which eventually causes different types of cancer. In this study, we focused on identifying those driver mutations through analyzing structural variations of mutants, viz., D194N, E199K, L160P, and Y49D. Native and the mutants were analyzed to determine their geometrical deviations such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, potential energy, and solvent-accessible surface area using conformational sampling technique. Additionally, the global minimized structure of native and mutants was further analyzed to compute their intramolecular interactions and distribution of secondary structure. Subsequently, simulated thermal denaturation and docking studies were performed to determine their structural variations, which in turn alter the formation of active complex that comprises STK11, STRAD, and MO25. The deleterious effect of the mutants would result in a comparative loss of enzyme function due to variations in their binding energy pertaining to spatial conformation and flexibility. Hence, the structural variations in binding energy exhibited by the mutants, viz., D194N, E199K, L160P, and Y49D, to that of the native, consequently lead to pathogenesis.

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis

Two very different quantum mechanically based energy decomposition analyses (EDA) schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS) based on the Amsterdam Density Functional (ADF) package and the other is natural EDA (NEDA) based in the General Atomic and Molecular Electronic Structure System (GAMESS) package. It reveals that in addition to the model (theory and basis set), the fragmentation channels more significantly affect the interaction energy terms (ΔE) between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel—the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative) polarization (POL) and charge transfer (CL) energies prefers the eclipsed ferrocene. The repulsive (positive) deformation (DEF) energy, which is dominated by the cyclopentadienyle (Cp) rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO) analysis indicates that all NBO energies, total Lewis (no Fe) and lone pair (LP) deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP) of the Fe atom and the acceptor antibond (BD*) NBOs of all C–C and C–H bonds in the ligand, LP(Fe)-BD*(C–C & C–H), which strongly stabilizes the eclipsed (D_5h) conformation by −457.6 kcal·mol⁻¹.

Peptide folding driven by Van der Waals interactions

Contrary to the widespread view that hydrogen bonding and its entropy effect play a dominant role in protein folding, folding into helical and hairpin-like structures is observed in molecular dynamics (MD) simulations without hydrogen bonding in the peptide-solvent system. In the widely used point charge model, hydrogen bonding is calculated as part of the interaction between atomic partial charges. It is removed from these simulations by setting atomic charges of the peptide and water to zero. Because of the structural difference between the peptide and water, van der Waals (VDW) interactions favor peptide intramolecular interactions and are a major contributing factor to the structural compactness. These compact structures are amino acid sequence dependent and closely resemble standard secondary structures, as a consequence of VDW interactions and covalent bonding constraints. Hydrogen bonding is a short range interaction and it locks the approximate structure into the specific secondary structure when it is included in the simulation. In contrast to standard molecular simulations where the total energy is dominated by charge-charge interactions, these simulation results will give us a new view of the folding mechanism.

Why human disease-associated residues appear as the wild-type in other species: genome-scale structural evidence for the compensation hypothesis

Many human-disease associated amino acid residues (DARs) appear as the wild-type in other species. This phenomenon is commonly explained by the presence of compensatory residues in these other species that alleviate the deleterious effects of the DARs. The general validity of this hypothesis, however, is unclear, because few compensatory residues have been identified. Here we test the compensation hypothesis by assembling and analyzing 1,077 DARs located in 177 proteins of known crystal structures. Because destabilizing protein structures is a primary reason why DARs are deleterious, we focus on protein stability in this analysis. We discover that, in species where a DAR represents the wild-type, the destabilizing effect of the DAR is generally lessened by the observed amino acid substitutions in the spatial proximity of the DAR. This and other findings provide genome-scale evidence for the compensation hypothesis and have important implications for understanding epistasis in protein evolution and for using animal models of human diseases.

Anion-π interactions influence pK(a) values

Five 8-(4-R-phenyl)-1-naphthol derivatives were prepared by PdCl(2)-catalysed electrophilic aromatic substitution. The pK(a)' values for these 1,8-disubstituted arene naphthols have been measured in acetonitrile/water (R = NO(2), 8.42; R = Cl, 8.52; R = H, 8.56; R = Me 8.68; and R = OMe, 8.71) and indicate a correlation with the electronic nature of the arene substituent, as determined through LFER analysis. Contributions to the relative pK(a)' values have been interpreted, using M06-2X DFT calculations, as consisting of two components: A small contribution from initial OH-π bonding in the starting materials and a larger contribution from anion-π interactions in the products. Such effects have implications for a range of other systems.

Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon

The yeast long terminal repeat (LTR) retrotransposon Ty1, like retroviruses, encodes a terminally redundant RNA, which is packaged into virus-like particles (VLPs) and is converted to a DNA copy by the process of reverse transcription. Mutations predicted to interfere with the priming events during reverse transcription and hence inhibit replication are known to dramatically decrease transposition of Ty1. However, additional cis-acting sequences responsible for Ty1 replication and RNA dimerization and packaging have remained elusive. Here we describe a modular mini-Ty1 element encoding the minimal sequence that can be retrotransposed by the Ty1 proteins, supplied in trans by a helper construct. Using a mutagenic screening strategy, we recovered transposition-deficient modular mini-Ty1-HIS3 elements with mutations in sequences required in cis for Ty1 replication and integration. Two distinct clusters of mutations mapped near the 5'-end of the Ty1 RNA. The clusters define a GAGGAGA sequence at the extreme 5'-end of the Ty1 transcript and a complementary downstream UCUCCUC sequence, 264 nt into the RNA. Disruption of the reverse complementarity of these two sequences decreased transposition and restoration of complementarity rescued transposition to wild-type levels. Ty1 cDNA was reduced in cells expressing RNAs with mutations in either of these short sequences, despite nearly normal levels of Ty1 RNA and VLPs. Our results suggest that the intramolecular interaction between the 5'-GAGGAGA and UCUCCUC sequences stabilizes an RNA structure required for efficient initiation of reverse transcription.