Showing papers on "Dihedral angle published in 2023"

Selecting Features for Markov Modeling: A Case Study on HP35.

Abstract: Markov state models represent a popular means to interpret molecular dynamics trajectories in terms of memoryless transitions between metastable conformational states. To provide a mechanistic understanding of the considered biomolecular process, these states should reflect structurally distinct conformations and ensure a time scale separation between fast intrastate and slow interstate dynamics. Adopting the folding of villin headpiece (HP35) as a well-established model problem, here we discuss the selection of suitable input coordinates or "features", such as backbone dihedral angles and interresidue distances. We show that dihedral angles account accurately for the structure of the native energy basin of HP35, while the unfolded region of the free energy landscape and the folding process are best described by tertiary contacts of the protein. To construct a contact-based model, we consider various ways to define and select contact distances and introduce a low-pass filtering of the feature trajectory as well as a correlation-based characterization of states. Relying on input data that faithfully account for the mechanistic origin of the studied process, the states of the resulting Markov model are clearly discriminated by the features, describe consistently the hierarchical structure of the free energy landscape, and─as a consequence─correctly reproduce the slow time scales of the process.

Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins

Abstract: Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α‐synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.

Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations

Abstract: The manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers connecting the units, which can be obtained, for example, using carbon ion-beam irradiation. In this work, we investigate, via molecular dynamics simulations, the mechanical properties of twisted nanotube bundles in which the linkers are composed of interstitial single carbon atoms. We find a significant interplay between the twist and the percentage of linkers. Finally, we evaluate the suitability of two different force fields for the description of these systems: the dihedral-angle-corrected registry-dependent potential, which we couple for non-bonded interaction with either the AIREBO potential or the screened potential ReboScr2. We show that both of these potentials show some shortcomings in the investigation of the mechanical properties of bundles with carbon linkers.

Quandle coloring quivers of (p,3)-torus links

Abstract: Recently, Cho and Nelson introduced a quiver structure, quandle coloring quiver, which is new enhancement of the quandle counting invariant. A few years later, Basi and Caprau studied the quandle coloring quivers of (p,2)-torus links. In this paper, we studied the quandle coloring quivers of (p,3)-torus links using dihedral quandles.

Torsion angles to map and visualize the conformational space of a protein

Abstract: Present understanding of protein structure dynamics trails behind that of static structures. A torsionangle based approach, called representation of protein entities (RoPE), derives an interpretable conformational space which correlates with data collection temperature, resolution and reaction coordinate. For more complex systems, atomic coordinates fail to separate functional conformational states, which are still preserved by torsion angle-derived space. This indicates that torsion angles are often a more sensitive and biologically relevant descriptor for protein conformational dynamics than atomic coordinates.

Anomalous deep-red luminescence of perylene black analogues with strong π-π interactions

Abstract: Perylene bisimide (PBI) dyes are known as red, maroon and black pigments, whose colors depend on the close π-π stacking arrangement. However, contrary to the luminescent monomers, deep-red and black PBI pigments are commonly non- or only weakly fluorescent due to (multiple) quenching pathways. Here, we introduce N-alkoxybenzyl substituted PBIs that contain close π stacking arrangement (exhibiting dπ-π ≈ 3.5 Å, and longitudinal and transversal displacements of 3.1 Å and 1.3 Å); however, they afford deep-red emitters with solid-state fluorescence quantum yields (ΦF) of up to 60%. Systematic photophysical and computational studies in solution and in the solid state reveal a sensitive interconversion of the PBI-centred locally excited state and a charge transfer state, which depends on the dihedral angle (θ) between the benzyl and alkoxy groups. This effectively controls the emission process, and enables high ΦF by circumventing the common quenching pathways commonly observed for perylene black analogues.

Amplification of Dissymmetry Factors by Dihedral Angle Engineering in Donor–Acceptor Type Circularly Polarized Luminescence Materials

Abstract: By employing aza[7]helicene as the chiral donor and triazine as the acceptor, we have developed a new type of circularly polarized luminescence materials. The influence of the dihedral angle between...

Systematic construction of progressively larger capsules from a fivefold linking pyrrole-based subcomponent

Abstract: Biological encapsulants, such as viral capsids and ferritin protein cages, use many identical subunits to tile the surface of a polyhedron. Inspired by these natural systems, synthetic chemists have prepared artificial nanocages with well-defined shapes and cavities. Rational control over the self-assembly of discrete, nanometre-scale, hollow coordination cages composed of simple components remains challenging as a result of the entropic costs associated with binding many subunits together, difficulties in the error-correction processes associated with assembly and increasing surface energy as their size grows. Here we demonstrate the construction of nanocages of increasing size derived from a single pentatopic pyrrole-based subcomponent. Reasoned shifts in the preferred coordination number of the metal ions used, along with the denticity and steric hindrance of the ligands, enabled the generation of progressively larger cages. These structural changes of the cages are reminiscent of the differences in the folding of proteins caused by minor variations in their amino acid sequences; understanding how they affect capsule structure and thus cavity size may help to elucidate the construction principles for larger and functional capsules, capable of binding and carrying large biomolecules as cargoes. Controlling the self-assembly of large coordination cages is challenging owing to entropic costs and difficulties in error correction. Now an array of large cages prepared by the rational design of alterations that allow for the tuning of the dihedral angle between pentagonal subunits is reported.

Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding.

Abstract: Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α- and β-subunits that catalyzes the last two steps of L-tryptophan (L-Trp) biosynthesis. The first stage of the reaction at the β-subunit is called β-reaction stage I, which converts the β-ligand from an internal aldimine [E(Ain)] to an α-aminoacrylate [E(A-A)] intermediate. The activity is known to increase 3-10-fold upon the binding of 3-indole-D-glycerol-3'-phosphate (IGP) at the α-subunit. The effect of α-ligand binding on β-reaction stage I at the distal β-active site is not well understood despite the abundant structural information available for TRPS. Here, we investigate the β-reaction stage I by carrying out minimum-energy pathway searches based on a hybrid quantum mechanics/molecular mechanics (QM/MM) model. The free-energy differences along the pathway are also examined using QM/MM umbrella sampling simulations with QM calculations at the B3LYP-D3/aug-cc-pVDZ level of theory. Our simulations suggest that the sidechain orientation of βD305 near the β-ligand likely plays an essential role in the allosteric regulation: a hydrogen bond is formed between βD305 and the β-ligand in the absence of the α-ligand, prohibiting a smooth rotation of the hydroxyl group in the quinonoid intermediate, whereas the dihedral angle rotates smoothly after the hydrogen bond is switched from βD305-β-ligand to βD305-βR141. This switch could occur upon the IGP-binding at the α-subunit, as evidenced by the existing TRPS crystal structures.

Tetranuclear Copper(I) and Silver(I) Pyrazolate Adducts with 1,1′-Dimethyl-2,2’-bibenzimidazole: Influence of Structure on Photophysics

Abstract: A reaction of a cyclic trinuclear copper(I) or silver(I) pyrazolate complex ([MPz]3, M = Cu, Ag) with 1,1′-dimethyl-2,2’-bibenzimidazole (L) leads to the formation of tetranuclear adducts decorated by one or two molecules of a diimine ligand, depending on the amount of the ligand added (0.75 or 1.5 equivalents). The coordination of two L molecules stabilizes the formation of a practically idealized tetrahedral four-metal core in the case of a copper-containing complex and a distorted tetrahedron in the case of a Ag analog. In contrast, complexes containing one molecule of diimine possess two types of metals, two- and three-coordinated, forming the significantly distorted central M4 cores. The diimine ligands are twisted in these complexes with dihedral angles of ca. 50–60°. A TD-DFT analysis demonstrated the preference of a triplet state for the twisted 1,1′-dimethyl-2,2’-bibenzimidazole and a singlet state for the planar geometry. All obtained complexes demonstrated, in a solution, the blue fluorescence of the ligand-centered (LC) nature typical for free diimine. In contrast, a temperature decrease to 77 K stabilized the structure close to that observed in the solid state and activated the triplet states, leading to green phosphorescence at ca. 500 nm. The silver-containing complex Ag4Pz4L exhibited dual emission from both the singlet and triplet states, even at room temperature.

Selecting Features for Markov Modeling: A Case Study on HP35

Abstract: Markov state models represent a popular means to interpret molecular dynamics trajectories in terms of memoryless transitions between metastable conformational states. To provide a mechanistic understanding of the considered biomolecular process, these states should reflect structurally distinct conformations and ensure a timescale separation between fast intrastate and slow interstate dynamics. Adopting the folding of villin headpiece (HP35) as a well-established model problem, here we discuss the selection of suitable input coordinates or `features', such as backbone dihedral angles and interresidue distances. We show that dihedral angles account accurately for the structure of the native energy basin of HP35, while the unfolded region of the free energy landscape and the folding process are best described by tertiary contacts of the protein. To construct a contact-based model, we consider various ways to define and select contact distances, and introduce a low-pass filtering of the feature trajectory as well as a correlation-based characterization of states. Relying on input data that faithfully account for the mechanistic origin of the studied process, the states of the resulting Markov model are clearly discriminated by the features, describe consistently the hierarchical structure of the free energy landscape, and$\unicode{0x2014}$as a consequence$\unicode{0x2014}$correctly reproduce the slow timescales of the process.

Red-Shifting the Excitation Energy of Carbonic Acid Clusters Via Nonminimum Structures.

Abstract: Nonminimum carbonic acid clusters provide excitation energies and oscillator strengths in line with observed ice-phase UV absorptions better than traditional optimized minima. This equation-of-motion coupled cluster quantum chemical analysis on carbonic acid monomers and dimers shows that shifts to the dihedral angle for the internal heavy atoms in the monomer produce UV electronic excitations close to 200 nm with oscillator strengths that would produce observable features. This τ(OCOO) dihedral is actually a relatively floppy motion unlike what is often expected for sp2 carbons and can be distorted by 30° away from equilibrium for an energy cost of only 11 kcal/mol. As this dihedral decreases beyond 30°, the excitation energies decrease further. The oscillator strengths do, as well, but only to a point. Hence, the lower-energy distortions of τ(OCOO) are sufficient to produce structures that exhibit excitation energies and oscillator strengths that would red-shift observed spectra of carbonic acid ices away from the highest UV absorption feature at 139 nm. Such data imply that colder temperatures (20 K) in the experimental treatment of carbonic acid ices are freezing these structures out after annealing, whereas the warmer temperature experiments (80 K) are not.

Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA

Abstract: Proteins are linear polymers built from a repertoire of 20 different amino acids, which are considered building blocks of proteins. The diversity and versatility of these 20 building blocks with regard to their conformations are key to adopting three-dimensional structures that facilitate proteins to undergo important mechanistic biological processes in living systems. The present investigation reports a conformational search of 20 different amino acids, building blocks of proteins, using three different force fields, CHARMM, AMBER, and OPLS-AA, implemented in the gradient gravitational search algorithm. The search technique (ConfGGS) includes the contribution from both bonded and nonbonded terms using Cartesian coordinates. The efficiency of such conformational searches has also been compared with other optimization algorithms: DE/Best, DE/Rand, and PSO algorithms with respect to computational time and accuracy based on the minimum number of iteration steps and computed lowest mean absolute error (MAE) and mean standard deviation (MSD) values for dihedral angles of respective near-optimal structures. Moreover, the ConfGGS technique has also been extended to an ordered protein fragment (PQITL) extracted from HIV-1 protease (PDB ID: 1YTH), an intrinsically disordered protein fragment, i.e., an amyloid-forming segment (AVVTGVTAV), from the NAC domain of Parkinson's disease protein α-synuclein, residues 69-77 (PDB ID: 4RIK), the experimental NMR atomic-resolution structure of α-synuclein fibrils (PDB ID: 2N0A), and a disulfide bond-containing protein fragment sequence (PCYGWPVCY), residues 59-67 (PDB ID: 6Y4F) toward structure prediction as a close homologue compared with experimental accuracy, using the CHARMM force field. The MolProbity validation results for the protein fragment (PQITL) obtained by ConfGGS/CHARMM are in better agreement with the native protein fragment structure of HIV-1 protease (PDB ID: 1YTH). Furthermore, the computed results have also been compared with the coordinates obtained from the AlphaFold network.

ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes

Abstract: Abstract ASC-G4 is an algorithm for the calculation of the advanced structural characteristics of G-quadruplexes (G4). It allows the unambiguous determination of the intramolecular G4 topology, based on the oriented strand numbering. It also resolves the ambiguity in the determination of the guanine glycosidic configuration. With this algorithm, we showed that the use of the C3’ or C5’ atoms to calculate the groove width in G4 is more appropriate than the P atoms and that the groove width does not always reflect the space available within the groove. For the latter, the minimum groove width is more appropriate. The application of ASC-G4 to 207 G4 structures guided the choices made for the calculations. A website based on ASC-G4 (http://tiny.cc/ASC-G4) was created, where the user uploads his G4 structure and gets its topology, the types of its loops and their lengths, the presence of snapbacks and bulges, the distribution of guanines in the tetrads and strands, the glycosidic configuration of these guanines, their rise, the groove widths, the minimum groove widths, the tilt and twist angles, the backbone dihedral angles, etc. It also provides a large number of atom-atom and atom-plane distances that are relevant to evaluating the quality of the structure.

SPSiPs, A New Class of Biphosphine Ligands Based on SPSiOL with a Large Dihedral Angle

Abstract: Here, we demonstrate the development and the synthetic applications of a novel class of diphosphine ligands (SPSiP) based on chiral spirosilabiindane diol (SPSiOL). Starting from SPSiOL, the biphosphine ligands could be readily prepared in three steps with high efficiency. This novel class of biphosphine ligands features rigid configuration, a large dihedral angle, a large P–M–P angle, and a long P–P distance, which might possess unique catalytic reactivities. The potentials of SPSiPs in asymmetric catalysis have also been preliminary disclosed by Rh-catalyzed asymmetric hydrogenation, Rh-catalyzed tandem hydrosilylation, and Pd-catalyzed asymmetric allylic alkylation.

Linking the Interatomic Exchange-Correlation Energy to Experimental J-Coupling Constants

Abstract: The main aim of the current work is to find an experimental connection to the interatomic exchange-correlation energy as defined by the energy decomposition method Interacting Quantum Atoms (IQA). A suitable candidate as (essentially) experimental quantity is the nuclear magnetic resonance (NMR) J-coupling constant denoted 3J(H,H′), which a number of previous studies showed to correlate well with QTAIM’s delocalization index (DI), which is essentially a bond order. Inspired by Karplus equations, here, we investigate correlations between 3J(H,H′) and a relevant dihedral angle in six simple initial compounds of the shape H3C-YHn (Y = C, N, O, Si, P, and S), N-methylacetamide (as prototype of the peptide bond), and five peptide-capped amino acids (Gly, Ala, Val, Ile, and Leu) because of the protein direction of the force field FFLUX. In conclusion, except for methanol, the inter-hydrogen exchange-correlation energy Vxc(H,H′) makes the best contact with experiment, through 3J(H,H′), when multiplied with the internuclear distance RHH′.

Real Characters in Nilpotent Blocks

Abstract: Abstract We prove that the number of irreducible real characters in a nilpotent block of a finite group is locally determined. We further conjecture that the Frobenius–Schur indicators of those characters can be computed for $$p=2$$ p = 2 in terms of the extended defect group. We derive this from a more general conjecture on the Frobenius–Schur indicator of projective indecomposable characters of 2-blocks with one simple module. This extends results of Murray on 2-blocks with cyclic and dihedral defect groups.

Precise Control of the Molecular Arrangement of Organic Semiconductors for High Charge Carrier Mobility.

Abstract: Organic semiconductors are well-known to exhibit high charge carrier mobility based on their spread of the π-orbital. In particular, the π-orbital overlap between neighboring molecules significantly affects their charge carrier mobility. This study elucidated the direct effect of subtle differences in the π-orbital overlap on charge carrier mobility, by precisely controlling only molecular arrangements without any chemical modifications. We synthesized disulfonic acid composed of a [1]benzothieno[3,2-b][1]benzothiophene (BTBT) moiety, and prepared organic salts with four butylamine isomers. Regardless of the type of butylamine combined, electronic states of the constituent BTBT derivative were identical, and all BTBT arrangements were edge-to-face herringbone-type. However, depending on the difference of steric hindrance, center-to-center distances and dihedral angles between neighboring BTBT moieties slightly varied. Despite a similar arrangement, the photoconductivity of four organic salts differed by a factor of approximately two. Additionally, theoretical charge carrier mobilities from their crystal structures exhibited a strong correlation with their photoconductivity.