Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Weak interactions in furan dimers.

ABSTRACT: Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C-H?O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.

SUBMITTER: Majerz I

PROVIDER: S-EPMC6267657 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Weak interactions in furan dimers.

Majerz Irena I

Journal of computer-aided molecular design 20180914 11

Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C-H⋯O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings. ...[more]

PMID: 30218198

Similar Datasets

Furan warheads for covalent trapping of weak protein-protein interactions: specific cross-linking of thymosin β4 to actin

Project description:We describe furan as a triggerable ‘warhead’ for site-specific cross-linking using the actin and thymosin β4 (Tβ4)-complex as model of a weak and dynamic protein-protein interaction with known 3D structure and with application potential in disease contexts. The presented in vitro validation of covalently acting ‘furan-armed’ Tβ4-variants provides initial proof to further exploit furan-technology for covalent drug design.

2021-05-13 | PXD025066 | Pride

Weak Interactions and Instability Cascades.

Project description:Food web theory states that a weak interactor which is positioned in the food web such that it tends to deflect, or mute, energy away from a potentially oscillating consumer-resource interaction often enhances community persistence and stability. Here we examine how adding other weak interactions (predation/harvesting) on the stabilizing weak interactor alters the stability of food web using a set of well-established food web models/modules. We show that such "weak on weak" interaction chains drive an indirect dynamic cascade that can rapidly ignite a distant consumer-resource oscillator. Nonetheless, we also show that the "weak on weak" interactions are still more stable than the food web without them, and so weak interactions still generally act to stabilize food webs. Rather, these results are best interpreted to say that the degree of the stabilizing effect of a given important weak interaction can be severely compromised by other weak interactions (including weak harvesting).

| S-EPMC4518242 | biostudies-literature

Weak Molecular Interactions in Clathrin-Mediated Endocytosis.

Project description:Clathrin-mediated endocytosis is a process by which specific molecules are internalized from the cell periphery for delivery to early endosomes. The key stages in this step-wise process, from the starting point of cargo recognition, to the later stage of assembly of the clathrin coat, are dependent on weak interactions between a large network of proteins. This review discusses the structural and functional data that have improved our knowledge and understanding of the main weak molecular interactions implicated in clathrin-mediated endocytosis, with a particular focus on the two key proteins: AP2 and clathrin.

| S-EPMC5694535 | biostudies-literature

Weak interactions in higher-order chromatin organization.

Project description:The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.

| S-EPMC7229822 | biostudies-literature

Dispersion Interactions and the Stability of Amine Dimers.

Project description:Weak, intermolecular interactions in amine dimers were studied by using the combination of a dispersionless density functional and a function that describes the dispersion contribution to the interaction energy. The validity of this method was shown by comparison of structural and energetic properties with data obtained with a conventional density functional and the coupled cluster method. The stability of amine dimers was shown to depend on the size, the shape, and the relative orientation of the alkyl substituents, and it was shown that the stabilization energy for large substituents is dominated by dispersion interactions. In contrast to traditional chemical explanations that attribute stability and condensed matter properties solely to hydrogen bonding and, thus, to the properties of the atoms forming the hydrogen bridge, we show that without dispersion interactions not even the stability and structure of the ammonia dimer can be correctly described. The stability of amine dimers depends crucially on the interaction between the non-polar alkyl groups, which is dominated by dispersion interactions. This interaction is also responsible for the energetic part of the free energy interaction used to describe hydrophobic interactions in liquid alkanes. The entropic part has its origin in the high degeneracy of the interaction energy for complexes of alkane molecules, which exist in a great variety of conformers, having their origin in internal rotations of the alkane chains.

| S-EPMC5542769 | biostudies-literature

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers.

Project description:Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers. For validation we used mutagenesis, electron microscopy and biochemical assays under non-denaturing conditions. We show that partial disruption of a predicted interface through charge reversal mutation of apposed residues reduces oligomerization while introduction of cysteines at these positions enhanced dimerization likely through the formation of an intermolecular disulfide bond. Free energy calculations indicated that K-Ras dimerization involves direct but weak protein-protein interactions in solution, consistent with the notion that dimerization is facilitated by membrane binding. Taken together, our atomically detailed analyses provide unique mechanistic insights into K-Ras dimer formation and membrane organization as well as the conformational fluctuations and equilibrium thermodynamics underlying these processes.

| S-EPMC5220301 | biostudies-literature

Weak interactions, omnivory and emergent food-web properties.

Project description:Empirical studies have shown that, in real ecosystems, species-interaction strengths are generally skewed in their distribution towards weak interactions. Some theoretical work also suggests that weak interactions, especially in omnivorous links, are important for the local stability of a community at equilibrium. However, the majority of theoretical studies use uniform distributions of interaction strengths to generate artificial communities for study. We investigate the effects of the underlying interaction-strength distribution upon the return time, permanence and feasibility of simple Lotka-Volterra equilibrium communities. We show that a skew towards weak interactions promotes local and global stability only when omnivory is present. It is found that skewed interaction strengths are an emergent property of stable omnivorous communities, and that this skew towards weak interactions creates a dynamic constraint maintaining omnivory. Omnivory is more likely to occur when omnivorous interactions are skewed towards weak interactions. However, a skew towards weak interactions increases the return time to equilibrium, delays the recovery of ecosystems and hence decreases the stability of a community. When no skew is imposed, the set of stable omnivorous communities shows an emergent distribution of skewed interaction strengths. Our results apply to both local and global concepts of stability and are robust to the definition of a feasible community. These results are discussed in the light of empirical data and other theoretical studies, in conjunction with their broader implications for community assembly.

| S-EPMC1691599 | biostudies-literature

Multivalent weak interactions enhance selectivity of interparticle binding.

Project description:Targeted drug delivery critically depends on the binding selectivity of cargo-transporting colloidal particles. Extensive theoretical work has shown that two factors are necessary to achieve high selectivity for a threshold receptor density: multivalency and weak interactions. Here, we study a model system of DNA-coated particles with multivalent and weak interactions that mimics ligand-receptor interactions between particles and cells. Using an optomagnetic cluster experiment, particle aggregation rates are measured as a function of ligand and receptor densities. The measured aggregation rates show that the binding becomes more selective for shorter DNA ligand-receptor pairs, proving that multivalent weak interactions lead to enhanced selectivity in interparticle binding. Simulations confirm the experimental findings and show the role of ligand-receptor dissociation in the selectivity of the weak multivalent binding.

| S-EPMC7502730 | biostudies-literature

Evolution of weak cooperative interactions for biological specificity.

Project description:A hallmark of biological systems is that particular functions and outcomes are realized in specific contexts, such as when particular signals are received. One mechanism for mediating specificity is described by Fisher's "lock and key" metaphor, exemplified by enzymes that bind selectively to a particular substrate via specific finely tuned interactions. Another mechanism, more prevalent in multicellular organisms, relies on multivalent weak cooperative interactions. Its importance has recently been illustrated by the recognition that liquid-liquid phase transitions underlie the formation of membraneless condensates that perform specific cellular functions. Based on computer simulations of an evolutionary model, we report that the latter mechanism likely became evolutionarily prominent when a large number of tasks had to be performed specifically for organisms to function properly. We find that the emergence of weak cooperative interactions for mediating specificity results in organisms that can evolve to accomplish new tasks with fewer, and likely less lethal, mutations. We argue that this makes the system more capable of undergoing evolutionary changes robustly, and thus this mechanism has been repeatedly positively selected in increasingly complex organisms. Specificity mediated by weak cooperative interactions results in some useful cross-reactivity for related tasks, but at the same time increases susceptibility to misregulation that might lead to pathologies.

| S-EPMC6255166 | biostudies-literature

Weak interactions but potent effect: tunable mechanoluminescence by adjusting intermolecular C-H···? interactions.

Project description:A new mechanoluminescent material (4-(diphenylamino)phenyl)(4-(diphenylphosphanyl)phenyl)methanone (CDpP), which displays tunable mechanoluminescent emission colors, has been designed and successfully synthesized. CDpP shows two distinct mechanoluminescent colors (blue and green) in different crystalline states. Single-crystal analyses and femtosecond transient emission studies reveal that the striking tunable mechanoluminescence properties of CDpP mainly originate from the different C-H···? interactions in the crystal structures. CDpP crystals with more C-H···? interactions show blue mechanoluminescence (ML), and the emission is attributed to the locally excited (LE)-state because the twisting process for the excited state is restricted by C-H···? interactions. Conversely, CDpP crystals with fewer C-H···? interactions display green ML, in which the red-shifted emission band originates from the twisted intramolecular charge transfer (TICT) excited state because the diphenylamine moiety is relatively free to rotate. The manipulation of weak intermolecular interactions in the crystalline state is a useful and reliable strategy for the tuning of the ML emission wavelengths.

| S-EPMC6050600 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data