Phenyl Ring: A Steric Hindrance or a Source of Different Hydrogen Bonding Patterns in Self-Organizing Systems?
Ontology highlight
ABSTRACT:
SUBMITTER: Nowok A
PROVIDER: S-EPMC8034769 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:During eukaryotic transcription, RNA-polymerase activity generates torsional stress in DNA, having a negative impact on the elongation process. Using our previous studies of chromatin fiber structure and conformational transitions, we suggest that this torsional stress can be alleviated, thanks to a tradeoff between the fiber twist and nucleosome conformational transitions into an activated state named "reversome". Our model enlightens the origin of polymerase pauses, and leads to the counterintuitive conclusion that chromatin-organized compaction might facilitate polymerase progression. Indeed, in a compact and well-structured chromatin loop, steric hindrance between nucleosomes enforces sequential transitions, thus ensuring that the polymerase always meets a permissive nucleosomal state.
| S-EPMC2830436 | biostudies-literature
Project description:1H-15N HMBC spectra of norditerpenoid alkaloids and their synthetic azabicyclic analogues were obtained to investigate the impacts of the through-space effect of steric compression, protonation, and formation of intramolecular hydrogen bonding on the 15N NMR spectroscopy of these natural products and their piperidine-containing analogues. A rare 15N NMR effect of steric compression is demonstrated in half-cage A/E-rings of norditerpenoid alkaloid free bases and their synthetic azabicyclic analogues, in which the distribution of the lone pair of electrons of the tertiary amine N-atom is sterically restricted by bridged cycloalkanes, e.g., cyclopentane, cyclohexane, and cycloheptane rings. This results in significant changes in the 15N chemical shift, typically by at least ?10 ppm. The lone pair of electrons of the N-atom in the piperidine ring are sterically compressed whether the bridged cyclohexane ring adopts a chair or boat conformation. The 15N chemical shifts of 1?-OMe norditerpenoid alkaloid free bases significantly increase (??N ? 15.6 ppm) on alkaloid protonation and thence the formation of an intramolecular hydrogen bond between N +-H and 1?-OMe. The intramolecular hydrogen bonds between the N-atom and 1?-OH of 1?-OH norditerpenoid alkaloid free bases, karacoline, condelphine, and neoline stabilize their A-rings, adopting an unusual twisted-boat conformation, and they also significantly increase ?N of the tertiary amine N-atom.
| S-EPMC7301575 | biostudies-literature
Project description:Cell migration through the extracellular matrix is governed by the interplay between cell-generated propulsion forces, adhesion forces, and resisting forces arising from the steric hindrance of the matrix. Steric hindrance in turn depends on matrix porosity, matrix deformability, cell size, and cell deformability. In this study, we investigate how cells respond to changes in steric hindrance that arise from altered cell mechanical properties. Specifically, we measure traction forces, cell morphology, and invasiveness of MDA-MB 231 breast cancer cells in three-dimensional collagen gels. To modulate cell mechanical properties, we either decrease nuclear deformability by twofold overexpression of the nuclear protein lamin A or we introduce into the cells stiff polystyrene beads with a diameter larger than the average matrix pore size. Despite this increase of steric hindrance, we find that cell invasion is only marginally inhibited, as measured by the fraction of motile cells and the mean invasion depth. To compensate for increased steric hindrance, cells employ two alternative strategies. Cells with higher nuclear stiffness increase their force polarity, whereas cells with large beads increase their net contractility. Under both conditions, the collagen matrix surrounding the cells stiffens dramatically and carries increased strain energy, suggesting that increased force polarity and increased net contractility are functionally equivalent strategies for overcoming an increased steric hindrance.
| S-EPMC6451061 | biostudies-literature
Project description:BackgroundIn computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of structural evolution and it guides our efforts to predict protein structures from their amino acid sequences. Most methods for structural alignment of protein structures optimize the distances between aligned and superimposed residue pairs, i.e., the distances traveled by the aligned and superimposed residues during linear interpolation. Considering such a linear interpolation, these methods do not differentiate if there is room for the interpolation, if it causes steric clashes, or more severely, if it changes the topology of the compared protein backbone curves.ResultsTo distinguish such cases, we analyze the linear interpolation between two aligned and superimposed backbones. We quantify the amount of steric clashes and find all self-intersections in a linear backbone interpolation. To determine if the self-intersections alter the protein's backbone curve significantly or not, we present a path-finding algorithm that checks if there exists a self-avoiding path in a neighborhood of the linear interpolation. A new path is constructed by altering the linear interpolation using a novel interpretation of Reidemeister moves from knot theory working on three-dimensional curves rather than on knot diagrams. Either the algorithm finds a self-avoiding path or it returns a smallest set of essential self-intersections. Each of these indicates a significant difference between the folds of the aligned protein structures. As expected, we find at least one essential self-intersection separating most unknotted structures from a knotted structure, and we find even larger motions in proteins connected by obstruction free linear interpolations. We also find examples of homologous proteins that are differently threaded, and we find many distinct folds connected by longer but simple deformations. TM-align is one of the most restrictive alignment programs. With standard parameters, it only aligns residues superimposed within 5 Ångström distance. We find 42165 topological obstructions between aligned parts in 142068 TM-alignments. Thus, this restrictive alignment procedure still allows topological dissimilarity of the aligned parts.ConclusionsBased on the data we conclude that our program ProteinAlignmentObstruction provides significant additional information to alignment scores based solely on distances between aligned and superimposed residue pairs.
| S-EPMC7913338 | biostudies-literature
Project description:A series of symmetrical and unsymmetrical alkyl tren based tris-thiourea anion transporters were synthesised and their anion binding and transport properties studied. Overall, increasing the steric bulk of the substituents resulted in improved chloride binding and transport abilities. Including a macrocycle in the scaffold enhanced the selectivity of chloride transport in the presence of fatty acids, by reducing the undesired H⁺ flux facilitated by fatty acid flip-flop. This study demonstrates the benefit of including enforced steric hindrance and encapsulation in the design of more selective anion receptors.
| S-EPMC6480120 | biostudies-literature
Project description:IN THE ASYMMETRIC UNIT OF THE TITLE SALT [SYSTEMATIC NAME: 2,4-diamino-5-(4-chloro-phen-yl)-6-ethyl-pyrimidin-1-ium pyri-dine-3-sulfonate], C(12)H(14)N(4)Cl(+)·C(5)H(4)NSO(3) (-), there are two independent pyrimethaminium cations and two 3-pyridine sulfonate anions. Each sulfonate group inter-acts with the corresponding protonated pyrimidine ring through two N-H?O hydrogen bonds, forming a cyclic hydrogen-bonded bimolecular R(2) (2)(8) motif. Even though the primary mode of association is the same, the next higher level of supra-molecular architectures are different due to different hydrogen-bonded networks. In one of the independent molecules in the asymmetric unit, the pyrimethamine cation is paired centrosymmetrically through N-H?N hydrogen bonds, generating an R(2) (2)(8) ring motif. In the other molecule, the pyrimethamine cation does not form any base pairs; instead it forms hydrogen bonds with the 3-pyridine sulfonate anion. The structure is further stabilized by C-H?O, C-H?N and ?-? stacking [centroid-centroid distance = 3.9465?(13)?Å] inter-actions.
| S-EPMC3007288 | biostudies-other
Project description:As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.
| S-EPMC4547818 | biostudies-literature
Project description:In O-ethyl N-benzoylthiocarbamate, C(10)H(11)NO(2)S, the molecules are linked into sheets by a combination of two-centre N-H...O and C-H...S hydrogen bonds and a three-centre C-H...(O,S) hydrogen bond. A combination of two-centre N-H...O and C-H...O hydrogen bonds links the molecules of O-ethyl N-(4-methylbenzoyl)thiocarbamate, C(11)H(13)NO(2)S, into chains of rings, which are linked into sheets by an aromatic pi-pi stacking interaction. In O,S-diethyl N-(4-methylbenzoyl)imidothiocarbonate, C(13)H(17)NO(2)S, pairs of molecules are linked into centrosymmetric dimers by pairs of symmetry-related C-H...pi(arene) hydrogen bonds, while the molecules of O,S-diethyl N-(4-chlorobenzoyl)imidothiocarbonate, C(12)H(14)ClNO(2)S, are linked by a single C-H...O hydrogen bond into simple chains, pairs of which are linked by an aromatic pi-pi stacking interaction to form a ladder-type structure.
| S-EPMC2855573 | biostudies-literature
Project description:In DNA, bases pair in a molecular interaction that is both highly predictable and exquisitely specific. Therefore researchers have generally believed that the insertion of the matching nucleotide opposite a template base by DNA polymerases (pols) required Watson-Crick (W-C) hydrogen bond formation. However pioneering work by Kool and co-workers using hydrophobic base analogs such as the thymine (T) isostere 2,4-difluorotoluene (F) showed that shape rather than H-bonding served as the primary source of specificity in DNA replication by certain pols. This steric hypothesis for DNA replication has gained popularity, perhaps discouraging further experimental studies to address potential limitations of this new idea. The idea that shape trumps H-bonding in terms of pol selectivity largely hinges on the belief that fluorine is a poor H-bond acceptor. However, the shape complementarity model was embraced in the absence of any detailed structural data for match (F:A) and mismatch pairs (F:G, F:C, F:T) in DNA duplexes or at active sites of pols. Although the F and T nucleosides are roughly isosteric, it is unclear whether F:A and T:A pairs exhibit similar geometries. If the F:A pair is devoid of H-bonding, it will be notably wider than a T:A pair. Because shape and size and H-bonding are intimately related, it may not be possible to separate these two properties. Thus the geometries of an isolated F:A pair in water may differ considerably from an F:A pair embedded in a stretch of duplex DNA, at the tight active site of an A-family replicative pol, or within the spacious active site of a Y-family translesion pol. The shape complementarity model may have more significance for pol accuracy than efficiency: this model appears to be most relevant for replicative pols that use specific residues to probe the identity of the nascent base pair from the minor groove side. However, researchers have not fully considered the importance of such interactions that include H-bonds compared with W-C H-bonds in terms of pol fidelity and the shape complementarity model. This Account revisits the steric hypothesis for DNA replication in light of recent structural data and discusses the role of fluorine as an H-bond acceptor. Over the last 5 years, crystal structures have emerged for nucleic acid duplexes with F paired opposite to natural bases or located at the active sites of DNA pols. These data permit a more nuanced understanding of the role of shape in DNA replication and the capacity of fluorine to form H-bonds. These studies and additional research involving RNA or other fluorine-containing nucleoside analogs within duplexes indicate that fluorine engages in H-bonding in many cases. Although T and F are isosteric at the nucleoside level, replacement of a natural base by F in pairs often changes their shapes and sizes, and dF in DNA behaves differently from rF in RNA. Similarly, the pairing geometries observed for F and T opposite dATP, dGTP, dTTP, or dCTP and their H-bonding patterns at the active site of a replicative pol differ considerably.
| S-EPMC3419310 | biostudies-literature
Project description:We present two iridium complexes 1H + and 2H + that contain cationic ligands to extend the knowledge of charge-assisted hydrogen bonding (CAHB), which counts among the strongest non-covalent bonding interactions. Upon protonation, both complexes were converted into new hydrogen-bonding arrays with various selectivity for respective H-bonding partners. This study compares the association strengths of four hydrogen-bonding co-systems, emphasizing the roles of CAHB in supramolecular systems. We determined that the cationic charge in these systems contributed up to 2.7 kJ mol-1 in the H-bonding complexation processes.
| S-EPMC8421767 | biostudies-literature