Jiyoung Heo

Predicted structure of agonist-bound glucagon-like peptide 1 receptor, a class B G protein-coupled receptor

The glucagon-like peptide 1 receptor (GLP1R) is a G protein-coupled receptor (GPCR) involved in insulin synthesis and regulation; therefore, it is an important drug target for treatment of diabetes. However, GLP1R is a member of the class B1 family of GPCRs for which there are no experimental structures. To provide a structural basis for drug design and to probe class B GPCR activation, we predicted the transmembrane (TM) bundle structure of GLP1R bound to the peptide Exendin-4 (Exe4; a GLP1R agonist on the market for treating diabetes) using the MembStruk method for scanning TM bundle conformations. We used protein–protein docking methods to combine the TM bundle with the X-ray crystal structure of the 143-aa N terminus coupled to the Exe4 peptide. This complex was subjected to 28 ns of full-solvent, full-lipid molecular dynamics. We find 14 strong polar interactions of Exe4 with GLP1R, of which 8 interactions are in the TM bundle (2 interactions confirmed by mutation studies) and 6 interactions involve the N terminus (3 interactions found in the crystal structure). We also find 10 important hydrophobic interactions, of which 4 interactions are in the TM bundle (2 interactions confirmed by mutation studies) and 6 interactions are in the N terminus (6 interactions present in the crystal structure). Thus, our predicted structure agrees with available mutagenesis studies. We suggest a number of mutation experiments to further validate our predicted structure. The structure should be useful for guiding drug design and can provide a structural basis for understanding ligand binding and receptor activation of GLP1R and other class B1 GPCRs.

Ultraviolet–Ultraviolet Hole Burning Spectroscopy in a Quadrupole Ion Trap: Dibenzo[18]crown‐6 Complexes with Alkali Metal Cations

Conformation selective: A new technique of ultraviolet-ultraviolet hole burning spectroscopy that can be applied to ions stored in a quadrupole ion trap (QIT) is developed and used to obtain the conformation-selective electronic spectra of dibenzo[18]crown-6 complexes with alkali metal cations (M(+), see picture; F(+) = fragment).

Ultraviolet Photodepletion Spectroscopy of Dibenzo-18-Crown-6-Ether Complexes with Alkaline Earth Metal Divalent Cations

Ultraviolet photodepletion spectra of dibenzo-18-crown-6-ether complexes with alkaline earth metal divalent cations (A(2+)-DB18C6, A = Ba, Sr, Ca, and Mg) were obtained in the gas phase using electrospray ionization quadrupole ion-trap reflectron time-of-flight mass spectrometry. Each spectrum exhibits the lowest energy absorption band in the wavenumber region of 35 400-37 800 cm(-1), which is tentatively assigned as the origin of the S(0)-S(1) transition of A(2+)-DB18C6. This origin band shows a red shift as the size of the metal dication increases from Mg(2+) to Ba(2+). The binding energies of the metal dications to DB18C6 at the S(0) state were calculated at the lowest energy structures optimized by the density functional theory and employed with the experimental energies of the origin bands to estimate the binding energies at the S(1) state. We suggest that the red shifts of the origin bands arise from the decrease in the binding energies of the metal dications at the S(1) state by nearly constant ratios with respect to the binding energies at the S(0) state, which decrease with increasing size of the metal dication. This unique relationship of the binding energies between the S(0) and S(1) states gives rise to a linear correlation between the relative shift of the origin band of A(2+)-DB18C6 and the binding energy of the metal dication at the S(0) state. The size effects of the metal cations on the properties of metal-DB18C6 complex ions are also manifested in the linear plot of the relative shift of the origin band as a function of the size to charge ratio of the metal cations, where the shifts of the origin bands for all DB18C6 complexes with alkali and alkaline earth metal cations are fit to the same line.

Prediction of the 3D structure of FMRF-amide neuropeptides bound to the mouse MrgC11 GPCR and experimental validation.

We report the 3D structure predicted for the mouse MrgC11 (mMrgC11) receptor by using the MembStruk computational protocol, and the predicted binding site for the F‐M‐R‐F‐NH2 neuropeptide together with four singly chirally modified ligands. We predicted that the R‐F‐NH2 part of the tetrapeptide sticks down into the protein between the transmembrane (TM) domains 3, 4, 5, and 6. The Phe (F‐NH2) interacted favorably with Tyr110 (TM3), while the Arg makes salt bridges to Asp161 (TM4) and Asp179 (TM5). We predicted that the Met extends from the binding site, but the terminal Phe residue sticks back into an aromatic/hydrophobic site flanked by Tyr237, Leu238, Leu240, and Tyr256 (TM6), and Trp162 (TM4). We carried out subsequent mutagenesis experiments followed by intracellular calcium‐release assays that demonstrated the dramatic decrease in activity for the Tyr110Ala, Asp161Ala, and Asp179Ala substitutions, which was predicted by our model. These experiments provide strong evidence that our predicted G protein‐coupled receptor (GPCR) structure is sufficiently accurate to identify binding sites for selective ligands. Similar studies were made with the mMrgA1 receptor, which did not bind the R‐F‐NH2 dipeptide; we explain this to be due to the increased hydrophobic character of the binding pocket in mMrgA1.

Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors.

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions. (1) We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5-HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist- and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region.

Binding selectivity of dibenzo-18-crown-6 for alkali metal cations in aqueous solution: A density functional theory study using a continuum solvation model

BackgroundDibenzo-18-crown-6 (DB18C6) exhibits the binding selectivity for alkali metal cations in solution phase. In this study, we investigate the main forces that determine the binding selectivity of DB18C6 for the metal cations in aqueous solution using the density functional theory (DFT) and the conductor-like polarizable continuum model (CPCM).ResultsThe bond dissociation free energies (BDFE) of DB18C6 complexes with alkali metal cations (M+-DB18C6, M = Li, Na, K, Rb, and Cs) in aqueous solution are calculated at the B3LYP/6-311++G(d,p)//B3LYP/6-31 + G(d) level using the CPCM. It is found that the theoretical BDFE is the largest for K+-DB18C6 and decreases as the size of the metal cation gets larger or smaller than that of K+, which agrees well with previous experimental results.ConclusionThe solvation energy of M+-DB18C6 in aqueous solution plays a key role in determining the binding selectivity of DB18C6. In particular, the non-electrostatic dispersion interaction between the solute and solvent, which depends strongly on the complex structure, is largely responsible for the different solvation energies of M+-DB18C6. This study shows that the implicit solvation model like the CPCM works reasonably well in predicting the binding selectivity of DB18C6 in aqueous solution.

Conformation-Specific Circular Dichroism Spectroscopy of Cold, Isolated Chiral Molecules†

The CD spectroscopy of a chiral compound in solution yields an average CD value derived from all of the conformations of a chiral molecule. By contrast, CD spectroscopy of cold chiral molecules in the gas phase distinguishes specific conformers of a chiral molecule, but the weak CD effect has limited the practical application of this technique. Reported herein is the first resonant two-photon ionization CD spectra of ephedrines in a supersonic jet using circularly polarized laser pulses, which were generated by synchronizing the oscillation of the photoelastic modulator with the laser firing. The spectra exhibited well-resolved CD bands which were specific for the conformations and vibrational modes of each enantiomer. The CD signs and magnitudes of the jet-cooled chiral molecules were very sensitive to their conformations and thus offered crucial information for determining the three-dimensional structures of chiral species, as conducted in combination with quantum chemical calculations.

The predicted binding site and dynamics of peptide inhibitors to the Methuselah GPCR from Drosophila melanogaster

Peptide inhibitors of Methuselah (Mth), a G protein-coupled receptor (GPCR), were reported that can extend the life span of Drosophila melanogaster. Mth is a class B GPCR, which is characterized by a large, N-terminal ectodomain that is often involved with ligand recognition. The crystal structure of the Mth ectodomain, which binds to the peptide inhibitors with high affinity, was previously determined. Here we report the predicted structures for RWR motif peptides in complex with the Mth ectodomain. We studied representatives of both Pro-class and Arg-class RWR motif peptides and identified ectodomain residues Asp139, Phe130, Asp127, and Asp78 as critical in ligand binding. To validate these structures, we predicted the effects of various ligand mutations on the structure and binding to Mth. The binding of five mutant peptides to Mth was characterized experimentally by surface plasmon resonance, revealing measured affinities that are consistent with predictions. The electron density map calculated from our MD structure compares well with the experimental map of a previously determined peptide/Mth crystal structure and could be useful in refining the current low-resolution data. The elucidation of the ligand binding site may be useful in analyzing likely binding sites in other class B GPCRs.

Femtosecond Decay Dynamics of Intact Adenine and Thymine Base Pairs in a Supersonic Jet

We investigated the decay dynamics of the DNA base pairs adenine-adenine (A(2)), adenine-thymine (AT), and thymine-thymine (T(2)) produced in a supersonic jet by femtosecond (fs) time-resolved photoionization spectroscopy. The base pair was excited by a fs pump pulse at 267 nm and the population change of its excited state was monitored by non-resonant three-photon ionization using a fs probe pulse at 800 nm after a certain time delay. All of the transients recorded in the mass channel of the parent ion exhibited a tri-exponential decay, with time constants ranging from 100 fs to longer than 100 ps. Most of these time constants coincide well with the previous values deduced indirectly from the transients of protonated adenine (AH(+)) and thymine (TH(+)), which were assumed to be produced by fragmentation of the base-pair ions. Notably, for the transient of T(2), we observed a new decay component with a time constant of 2.3 ps, which was absent in the transient of TH(+). We suggest that the new decay component arises from the decay of stacked T(2) dimers that are mostly ionized to T(2)(+), whereas the decay signal recorded in the mass channel of TH(+) is merely from the relaxation of hydrogen-bonded T(2) dimers. From the amplitude of the new decay component, the population of the stacked T(2) dimers relative to the hydrogen-bonded dimers was estimated to be ∼2 % in the supersonic jet, which is about fifteen times higher than the theoretical value.

On the structure of Si(100) surface: Importance of higher order correlations for buckled dimer

We revisit a dangling theoretical question of whether the surface reconstruction of the Si(100) surface would energetically favor the symmetric or buckled dimers on the intrinsic potential energy surfaces at 0 K. This seemingly simple question is still unanswered definitively since all existing density functional based calculations predict the dimers to be buckled, while most wavefunction based correlated treatments prefer the symmetric configurations. Here, we use the doubly hybrid density functional (DHDF) geometry optimizations, in particular, XYGJ-OS, complete active space self-consistent field theory, multi-reference perturbation theory, multi-reference configuration interaction (MRCI), MRCI with the Davidson correction (MRCI + Q), multi-reference average quadratic CC (MRAQCC), and multi-reference average coupled pair functional (MRACPF) methods to address this question. The symmetric dimers are still shown to be lower in energy than the buckled dimers when using the CASPT2 method on the DHDF optimized geometries, consistent with the previous results using B3LYP geometries [Y. Jung, Y. Shao, M. S. Gordon, D. J. Doren, and M. Head-Gordon, J. Chem. Phys. 119, 10917 (2003)]. Interestingly, however, the MRCI + Q, MRAQCC, and MRACPF results (which give a more refined description of electron correlation effects) suggest that the buckled dimer is marginally more stable than its symmetric counterpart. The present study underlines the significance of having an accurate description of the electron-electron correlation as well as proper multi-reference wave functions when exploring the extremely delicate potential energy surfaces of the reconstructed Si(100) surface.