Conformational Dependence Research Articles

Conformational Heterogeneity in Large Macrocyclic Thiophenes.

For conjugated macrocycles, conformational disorder plays a key role in determining whether the unique form of excitons that are fully delocalized over the cyclic framework (cyclic excitons) is formed by photoexcitation. We have investigated the ring size dependence of conformations and photophysical properties of macrocyclic thiophenes of varying ring sizes (C-5NTNV) by using single-molecule fluorescence spectroscopy. We measured modulation depth, M, values and fluorescence intensities. As the ring size increases, the correlation plots of the two parameters show bimodal distributions, revealing that larger macrocycles exhibit extremely congested linear structures. The size dependence of structural changes in macrocyclic thiophenes have been clearly confirmed by molecular dynamics simulation. The number of torsional defects from simulated structures, in conjunction with survival times from fluorescence intensity trajectories and photon coincidence measurements, demonstrated the existence of multiple acyclic chromophores in the larger macrocycles from the ground state due to complete deformation of circular structures.

Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs.

In many cases, native states of proteins may be predicted with sufficient accuracy by molecular dynamics simulations (MDSs) with modern force fields. Enhanced sampling methods based on MDS are applied for exploring the phase space of a protein sequence and to overcome barriers on rough conformational energy landscapes. The minimum free energy state is obtained with sampling algorithms providing sufficient convergence and accuracy. A reliable but computationally very expensive method is replica exchange molecular dynamics, with many modifications to this approach presented in the past. Recently, we demonstrated how our temperature intervals with global exchange of replicas hybrid (TIGER2h) solvent sampling algorithm made a good compromise between efficiency and accuracy. There, all states are sampled under full explicit solvent conditions with a freely chosen number of replicas, whereas an implicit solvent is used during the swap decisions. This hybrid method yielded a much better approximation to the agreement with calculations in an explicit solvent than fully implicit solvent simulations. Here, we present an extension of TIGER2h and add a few layers of explicit water molecules around the peptide for the energy calculations, whereas the dynamics in fully explicit water is maintained. We claim that these water layers better reproduce steric effects, the polarization of the solvent, and the resulting reaction field energy than typical implicit solvent models. By investigating the protein-solvent interactions across comprehensive thermodynamic state ensembles, we found a strong conformational dependence of this reaction field energy. All simulations were performed with nanoscale molecular dynamics on two peptides, the α-helical peptide (AAQAA)3 and the β-hairpin peptide HP7. A production-ready TIGER2hs implementation is supplied, approaching the accuracy of full explicit solvent sampling at a fraction of computational resources.

Biradical rotamer states tune electron J coupling and MAS dynamic nuclear polarization enhancement

Cross Effect (CE) Dynamic Nuclear Polarization (DNP) relies on the dipolar (D) and exchange (J) coupling interaction between two electron spins. Until recently only the electron spin D coupling was explicitly included in quantifying the DNP mechanism. Recent literature discusses the potential role of J coupling in DNP, but does not provide an account of the distribution and source of electron spin J coupling of commonly used biradicals in DNP. In this study, we quantified the distribution of electron spin J coupling in AMUPol and TOTAPol biradicals using a combination of continuous wave (CW) X-band electron paramagnetic resonance (EPR) lineshape analysis in a series of solvents and at variable temperatures in solution – a state to be vitrified for DNP. We found that both radicals show a temperature dependent distribution of J couplings, and the source of this distribution to be conformational dynamics. To qualify this conformational dependence of J coupling in both molecules we carry out Broken Symmetry DFT calculations which show that the biradical rotamer distribution can account for a large distribution of J couplings, with the magnitude of J coupling directly depending on the relative orientation of the electron spin pair. We demonstrate that the electron spin J couplings in both AMUPol and TOTAPol span a much wider distribution than suggested in the literature. We affirm the importance of electron spin J coupling for DNP with density matrix simulations of DNP in Liouville space and under magic angle spinning, showcasing that a rotamer with high J coupling and optimum relative g-tensor orientation can significantly boost the DNP performance compared to random orientations of the electron spin pair. We conclude that moderate electron spin J coupling above a threshold value can facilitate DNP enhancements.

Conformation dependence of tyrosine binding on the surface of graphene: Bent prefers over parallel orientation

Binding of tyrosine (Tyr) with two finite size graphene sheets of 62 and 186 carbon atoms was investigated using M06-2X/6-31G(d) level. Thorough conformational analysis was done for tyrosine to select few conformers to explore their complexation by considering different orientations on the surface of graphene. The binding energy values are not significantly changed while moving from small to large graphene. Tyrosine exhibits strong π-π interactions that support recent experiments on binding of aromatic amino acids on the surface of graphene and modified graphene. The binding energies of 9.4–9.9 kcal/mol were obtained for different conformers of tyrosine binding with graphene via parallel orientation (having π-π and C(β)-H…π interactions). Owing to multiple interactions including C-H…π, N-H/O-H…π and π-π, the bent prefers over parallel orientation (by 1 kcal/mol) for the high energy conformer of Tyr adsorption on graphene. The binding energies in the aqueous medium are slightly lower than those obtained in the gas phase. HOMO-LUMO energy gaps calculated at the TPSSh/6-31G(d) level suggest that adsorption of tyrosine conformers with different orientations on the surface of graphene does not affect the band gap value of graphene (1.43 and 0.08 eV correspondingly for small and large graphene). Intermolecular orbital interactions support the π-π interactions in bent and parallel orientations of tyrosine with graphene.

Conformation Dependence of Diphenylalanine Self-Assembly Structures and Dynamics: Insights from Hybrid-Resolution Simulations.

The molecular design of peptide-assembled nanostructures relies on extensive knowledge pertaining to the relationship between conformational features of peptide constituents and their behavior regarding self-assembly, and characterizing the conformational details of peptides during their self-assembly is experimentally challenging. Here, we demonstrate that a hybrid-resolution modeling method can be employed to investigate the role that conformation plays during the assembly of terminally capped diphenylalanines (FF) through microsecond simulations of hundreds or thousands of peptides. Our simulations discovered tubular or vesicular nanostructures that were consistent with experimental observation while reproducing critical self-assembly concentration and secondary structure contents in the assemblies that were measured in our experiments. The atomic details provided by our method allowed us to uncover diverse FF conformations and conformation dependence of assembled nanostructures. We found that the assembled morphologies and the molecular packing of FFs in the observed assemblies are linked closely with side-chain angle and peptide bond orientation, respectively. Of various conformations accessible to soluble FFs, only a select few are compatible with the assembled morphologies in water. A conformation resembling a FF crystal, in particular, became predominant due to its ability to permit highly ordered and energetically favorable FF packing in aqueous assemblies. Strikingly, several conformations incompatible with the assemblies arose transiently as intermediates, facilitating key steps of the assembly process. The molecular rationale behind the role of these intermediate conformations were further explained. Collectively, the structural details reported here advance the understanding of the FF self-assembly mechanism, and our method shows promise for studying peptide-assembled nanostructures and their rational design.

Combined experimental and theoretical study of long-range H-F interactions in α-fluoro amides.

A combined experimental and computational approach provided insight into the nature and conformational dependence of long-range 4JHF couplings in α-fluoro amides. The dependence of 4JHF on substituents and the solvent was investigated. H-F coupling constants determined by NMR spectroscopy are in agreement with DFT calculations. NBO analysis revealed that a favourable nF→σNH* interaction correlates with the magnitude of 4JHF.

Solvent Quality Controls Macromolecular Structural Dynamics of a Dendrimeric Hydrogenase Model.

We report a spectroscopic investigation of the ultrafast dynamics of the second-generation poly(aryl ether) dendritic hydrogenase model using two-dimensional infrared (2D-IR) spectroscopy to probe the metal carbonyl vibrations of the dendrimer and a reference small molecule, [Fe(μ-S)(CO)3]2. We find that the structural dynamics of the dendrimer are reflected in a slow phase of the spectral diffusion, which is absent from [Fe(μ-S)(CO)3]2, and we relate the slow phase to the quality of the solvent for poly(aryl ether) dendrimers. We observe a solvent-dependent modulation of the initial phase of vibrational relaxation of the carbonyl groups, which we attribute to an inhibition of solvent assistance in the intramolecular vibrational redistribution process for the dendrimer. There is also a clear solvent dependence of the vibrational frequencies of both the dendrimer and [Fe(μ-S)(CO)3]2. Our data represent the first 2D-IR study of a dendritic complex and provide insight into the solvent dependence of molecular conformation in solution and the ultrafast dynamics of moderately sized, conformationally mobile compounds.

Large Variations in the Single-Molecule Conductance of Cyclic and Bicyclic Silanes.

Linear silanes are efficient molecular wires due to strong σ-conjugation in the transoid conformation; however, the structure-function relationship for the conformational dependence of the single-molecule conductance of silanes remains untested. Here we report the syntheses, electrical measurements, and theoretical characterization of four series of functionalized cyclic and bicyclic silanes including a cyclotetrasilane, a cyclopentasilane, a bicyclo[2.2.1]heptasilane, and a bicyclo[2.2.2]octasilane, which are all extended by linear silicon linkers of varying length. We find an unusual variation of the single-molecule conductance among the four series at each linker length. We determine the relative conductance of the (bi)cyclic silicon structures by using the common length dependence of the four series rather than comparing the conductance at a single length. In contrast with the cyclic π-conjugated molecules, the conductance of σ-conjugated (bi)cyclic silanes is dominated by a single path through the molecule and is controlled by the dihedral angles along this path. This strong sensitivity to molecular conformation dictates the single-molecule conductance of σ-conjugated silanes and allows for systematic control of the conductance through molecular design.

Understanding the Effect of Conformation on Hole Delocalization in Poly(dimethylsilane).

Density functional theory calculations confirm that the simple explanation of the origin of the striking conformational dependence of σ-electron localization/delocalization in polysilanes offered by the extremely simple Ladder C model is correct.

Molecular weight dependence of chain conformation of strong polyelectrolytes.

Using sodium polystyrene sulfonate (NaPSS) and quarternized poly 4-vinylpyridine (QP4VP) as model systems, the chain conformation of polyelectrolytes under finite salt concentrations is investigated at a single molecular level. By fluorescence correlation spectroscopy (FCS), the hydrodynamic radius (R h) of the samples with the molecular weight ranging more than one order of magnitude was measured. The variations of R h as a function of molecular weight reveal the molecular weight dependence: under moderate salt concentrations (such as 10-4 and 0.1M), the shorter chains of both NaPSS and QP4VP take the rod-like conformation, while the longer chains take the coiled conformation (random coil or swelled random coil conformation, respectively). At high enough salt levels, both the charged chains take the coiled conformations. Photon counting histogram (PCH) measurements of the local pH value at the vicinity of the NaPSS chain expose the higher extent of counterion adsorption for longer chains as well as higher salt concentrations, telling that the charge regularization process is the major governing factor.

Molecular Actuators in Action: Electron-Transfer-Induced Conformation Transformation in Cofacially Arrayed Polyfluorenes.

There is much current interest in the design of molecular actuators, which undergo reversible, controlled motion in response to an external stimulus (light, heat, oxidation, etc.). Here we describe the design and synthesis of a series of cofacially arrayed polyfluorenes (MeF nH m) with varied end-capping groups, which undergo redox-controlled electromechanical actuation. Such cofacially arrayed polyfluorenes are a model molecular scaffold to investigate fundamental processes of charge and energy transfer across a π-stacked assembly, and we show with the aid of NMR and optical spectroscopies, X-ray crystallography and DFT calculations that in the neutral state the conformation of MeF nH1 and MeF nH2 is open rather than cofacial, with a conformational dependence that is highly influenced by the local environment. Upon (electro)chemical oxidation, these systems undergo a reversible transformation into a closed fully π-stacked conformation, driven by charge-resonance stabilization of the cationic charge. These findings are expected to aid the design of novel wire-like cofacially arrayed systems capable of undergo redox-controlled actuation.

The Effect of Lipidation on the Self-Assembly of the Gut-Derived Peptide Hormone PYY3-36.

Lipidation is a powerful strategy to improve the stability in vivo of peptide drugs. Attachment of a lipid chain to a hydrophilic peptide leads to amphiphilicity and the potential for surfactant-like self-assembly. Here, the self-assembly and conformation of three lipidated derivatives of the gastrointestinal peptide hormone PYY3-36 is examined using a comprehensive range of spectroscopic, scattering, and electron microscopy methods and compared to those of the parent PYY3-36 peptide. The peptides are lipidated at Ser(11), Arg(17), or Arg(23) in the peptide; the former is within the β-turn domain (based on the published solution NMR structure), and the latter two are both within the α-helical domain. We show that it is possible to access a remarkable diversity of nanostructures ranging from micelles to nanotapes and fibrillar hydrogels by control of assembly conditions (concentration, pH, and temperature). All of the lipopeptides self-assemble above a critical aggregation concentration (cac), determined through pyrene fluorescence probe measurements, and they all have predominantly α-helical secondary structure at their native pH. The pH and temperature dependence of the α-helical conformation were probed via circular dichroism spectroscopy experiments. Lipidation was found to provide enhanced stability against changes in temperature and pH. The self-assembled structures were investigated using small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM). Distinct differences in nanostructure were observed for lipidated and unlipidated peptides, also depending on the position of lipidation. Remarkably, micelles containing lipopeptides with α-helical peptide conformation were observed. Gelation was observed at higher concentrations in certain pH intervals for the lipidated peptides, but not for unlipidated PYY3-36. Thus, lipidation, in addition to enhancing stability against pH and temperature variation, also provides a route to prepare PYY peptide hydrogels. These findings provide important insights into the control of PYY3-36 conformation and aggregation by lipidation, relevant to the development of future therapeutics based on this peptide hormone, for example, in treatments for obesity.

Mapping Bridge Conformational Effects on Electronic Coupling in Mo2-Mo2 Mixed-Valence Systems.

The large bridging ligand 9,10-anthracenedicarboxylate and its thiolated derivatives have been employed to assemble two dimolybdenum complex units and develop three Mo2 dimers, [Mo2(DAniF)3]2(μ-9,10-O2CC14H8CO2), [Mo2(DAniF)3]2(μ-9,10-OSCC14H8COS), and [Mo2(DAniF)3]2(μ-9,10-S2CC14H8CS2) (DAniF = N, N'-di( p-anisyl)formamidinate), for the study of conformation dependence of the electronic coupling between the two Mo2 centers. These compounds feature a large deviation of the central anthracene ring from the plane defined by the Mo-Mo bond vectors, with the torsion angles (ϕ = 50-76°) increasing as the chelating atoms of the bridging ligand vary from O to S. Consequently, the corresponding mixed-valence complexes do not exhibit characteristic intervalence charge transfer absorptions in the near-IR spectra, in contrast to the phenylene and naphthalene analogues, from which these systems are assigned to the Class I in Robin-Day's scheme. Together with the phenylene and naphthalene series, the nine total mixed-valence complexes in three series complete a transition from the electronically uncoupled Class I to the strongly coupled Class II-III borderline via moderately coupled Class II and permit a systematic mapping of the bridge conformation effects on electronic coupling. Density functional theory calculations show that the HOMO-LUMO energy gap, corresponding to the metal (δ) to ligand (π*) transition energy, and the magnitude of HOMO-HOMO-1 splitting in energy are linearly related to cos2 ϕ. Therefore, our experimental and theoretical results concur to indicate that the coupling strength decreases in the order of the bridging units: phenylene > naphthalene > anthracene, which verifies the through-bond superexchange mechanism for electronic coupling and electron transfer.

The influence of flexibility on the spectroscopic properties for organic molecules in solution: A theoretical study applied to A3R polypeptide

Here we reported the impact of flexibility of solvent effects on the optical absorption, nuclear magnetic resonance (NMR) and electrical properties of A3R, a tetrapeptide compound derived from peptide bonds in the α-helix form of 3-alanines and one arginine, in aqueous environment. The in-water A3R configurations were generated by S-MM/QM and MD procedures and also using the PCM model. We have used the ASEC approach with 100 uncorrelated settings obtained from Monte Carlo simulation to achieve the convergence of the dipole moment for each in-water geometry in all steps between MC and QM calculations. The converged values of μ for A3R-MD geometries present increments between 69 and 392% in comparison with the gas phase value. Our results for optical absorption demonstrate the possibility of absorption in large range, with strong dependence of the geometric conformation of the A3R molecule. Our findings corroborate both the importance of the solute polarization and the geometric flexibility in the analyzed properties. Spectroscopic results obtained experimentally for the σ(13C) indicates that our A3R-MD geometry calculations are consistent with the adopted model.

Evaluating the Effects of Geometry and Charge Flux in Force Field Modeling

We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the R-(CH2) n-R structure (R = Cl, F, OH, SH, COOH, CONH2, and NH2 and n = 4-6). Atomic charges were obtained by fitting to results from density functional theory calculations using the HLY procedure, and their geometry dependence is decomposed into contributions from changes in bond lengths, bond angles, and torsional angles. The torsional degrees of freedom are the main contribution to the conformational dependence of atomic charges and molecular dipole moments, but indirect effects due to changes in bond distances and angles account for ∼15% of the variations. While the magnitude of charge flux and geometry effects have been found to be independent of the number of internal degrees of freedom, the nature of the R- group has a moderate influence. The indirect effects are comparable for all of the R-groups and are approximately one-half the magnitude of the corresponding effects in peptide models. However, the magnitudes are different, yet the relative importance of geometry and charge flux effects are completely similar to those of the peptide models, which suggests that modeling the charge flux effects for changes in bond lengths, bond angles, and torsional angles should be considered for developing improved force fields.

Aggregation of Insulin on Langmuir Monolayers

The polypeptide hormone, insulin, is known to aggregate into a hexamer in the presence of zinc ions. The Langmuir monolayer technique can be used to examine the transition between active monomeric insulin molecules and the hexameric form which is more difficult for the body to use. Distinctive isotherm characteristics for both monomeric insulin and hexameric insulin were observed. Zinc (II) chloride is added to the model membrane system to create hexamers of insulin. Conditions of the system are altered to learn about the dependence of insulin's molecular conformation on factors such as pH and concentration. Chelating agents, such as (ethylenediaminetetraacetic acid) EDTA and citrate are added to effectively remove the zinc ion from the solution and observe the behavior of the insulin molecules. With the addition of EDTA to the monolayer of zinc exposed insulin, monomeric isotherm characteristics were noted, indicating the removal of zinc from the insulin hexamer and the creation of monomeric insulin. These molecular conformational changes affect the function of the insulin molecule in the human body.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Experimental validation of calculated atomic charges in ionic liquids.

A combination of X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy has been used to provide an experimental measure of nitrogen atomic charges in nine ionic liquids (ILs). These experimental results are used to validate charges calculated with three computational methods: charges from electrostatic potentials using a grid-based method (ChelpG), natural bond orbital population analysis, and the atoms in molecules approach. By combining these results with those from a previous study on sulfur, we find that ChelpG charges provide the best description of the charge distribution in ILs. However, we find that ChelpG charges can lead to significant conformational dependence and therefore advise that small differences in ChelpG charges (<0.3 e) should be interpreted with care. We use these validated charges to provide physical insight into nitrogen atomic charges for the ILs probed.

Dihydrogen contacts observed by through-space indirect NMR coupling.

"Through-space" indirect spin-spin couplings between hydrogen atoms formally separated by up to 18 covalent bonds have been detected by NMR experiments in model helical molecules. It is demonstrated that this coupling can provide crucial structural information on the molecular conformation in solution. The coupling pathways have been visualised and analysed by computational methods. The conformational dependence of the coupling is explained in terms of orbital interactions.

Distinct Signaling Patterns of Allosteric Antagonism at the P2Y1 Receptor

Traditionally, G protein-coupled receptor antagonists are classified as competitive or noncompetitive and surmountable or insurmountable based on functional antagonism. P2Y1 receptor (P2Y1R) structures showed two antagonists binding to two spatially distinct sites: nucleotide MRS2500 (orthosteric, contacting the helical bundle) and urea BPTU (allosteric, on the external receptor surface). However, the nature of their P2Y1R antagonism has not been characterized. Here we characterized BPTU antagonism at various signaling pathways activated by structurally diverse agonists. BPTU rightward shifted the concentration-response curves of both 2-methylthioadenosine 5'-diphosphate trisodium salt and MRS2365 (5'-diphosphates) in some signaling events, such as extracellular signal-regulated kinase 1/2 and label free, in a parallel manner without affecting the maximum agonist effect (Emax) but antagonized insurmountably (suppressed agonist Emax) in signaling events such as guanosine 5'-3-O-(thio)triphosphate binding and β-arrestin2 recruitment. However, with dinucleotide Ap4A as an agonist, BPTU suppressed the Emax insurmountably in all signaling pathways. By comparison, MRS2500 behaved as surmountable antagonist rightward-shifting concentration-response curves of all three agonists in a parallel manner for all signaling pathways measured. Thus, we demonstrated a previously undocumented phenomenon that P2Y1R antagonism patterns could vary in different signaling pathways, which could be related to conformational selection, signaling amplification, and probe dependence. This phenomenon may apply generally to other receptors considering that antagonism by a specific ligand is often not compared at multiple signaling pathways. Thus, antagonism can be surmountable or insurmountable depending on the signaling pathways measured and the agonists used, which should be of broad relevance to drug discovery and disease treatment.

Theoretical Investigation of C-H Vibrational Spectroscopy. 1. Modeling of Methyl and Methylene Groups of Ethanol with Different Conformers.

A flexible and polarizable molecular model of ethanol is developed to extend our investigation of thermodynamic, structural, and vibrational properties of the liquid and interface. A molecular dynamics (MD) simulation with the present model confirmed that this model well reproduces a number of properties of liquid ethanol, including density, heat of vaporization, surface tension, molecular dipole moment, and trans/gauche ratio. In particular, the present model can describe vibrational IR, Raman, and sum frequency generation (SFG) spectra of ethanol and partially deuterated analogues with reliable accuracy. The improved accuracy is largely attributed to proper modeling of the conformational dependence and the intramolecular couplings including Fermi resonance in C-H vibrations. Precise dependence of torsional motions is found to be critical in representing vibrational spectra of the C-H bending. This model allows for further vibrational analysis of complicated alkyl groups widely observed in various organic molecules with MD simulation.