Polarizable Hydrogen Bonds Research Articles

Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from Molecular Dynamics

The dynamics of HIV-1 protease (HIV-pr), a drug target for HIV infection, has been studied extensively by both computational and experimental methods. The flap dynamics of HIV-pr is considered to be more important for better ligand binding and enzymatic actions. Moreover, it has been demonstrated that the drug-induced mutations can change the flap dynamics of HIV-pr affecting the binding affinity of the ligands. Therefore, detailed understanding of flap dynamics is essential for designing better inhibitors. Previous computational investigations observed significant variation in the flap opening in nanosecond time scale indicating that the dynamics is highly sensitive to the simulation protocols. To understand the sensitivity of the flap dynamics on the force field and simulation protocol, molecular dynamics simulations of HIV-pr have been performed with two different AMBER force fields, ff99 and ff02. Two different trajectories (20 ns each) were obtained using the ff99 and ff02 force field. The results showed polarizable force field (ff02) make the flap tighter than the nonpolarizable force field (ff99). Some polar interactions and hydrogen bonds involving flap residues were found to be stronger with ff02 force field. The formation of interchain hydrophobic cluster (between flap tip of one chain and active site wall of another chain) was found to be dominant in the semi-open structures obtained from the simulations irrespective of the force field. It is proposed that an inhibitor, which will promote this interchain hydrophobic clustering, may make the flaps more rigid, and presumably the effect of mutation would be small on ligand binding.

Direct folding simulation of a long helix in explicit water

A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.

Cooperation of Hydrogen-Bond and Charge-Transfer Interactions in Molecular Complexes in the Solid State

Abstract Our recent studies for the development of conducting charge-transfer complexes with well-defined assembled structures based on the cooperation of hydrogen-bond and charge-transfer interactions are described. We have designed and synthesized hydrogen-bonded charge-transfer complexes based on (1) tetrathiafulvalene derivatives having nucleobases, aminobenzo and imidazole moieties, and (2) tetracyanoquinodimethane radical anion salts with hydrogen-bond-functionalized phenalenyl and protonated oligo(imidazole) cations. The directional and site-selective hydrogen-bonds formed various supramolecular network structures, constructing segregated columns as the conduction path. Furthermore, the high polarity of hydrogen-bonds caused strong donor–acceptor or cation–anion electrostatic interactions modulating the ionicity of component molecules and the electronic structure of conduction columns. Such electronic modulation effects in addition to controlling the molecular arrangement realized the first purely organic molecular metal based on a hydrogen-bonded charge-transfer complex in the p-chloranil complex of an imidazole-functionalized tetrathiafulvalene derivative. The proton-donating/accepting ability of the hydrogen-bonding sites afforded the simultaneous proton- and charge-transfer complexes, demonstrating an important prompt for the realization of cooperative proton–electron-transfer systems.

An Unprecedented Self-Assembled Porous Framework Constructed by Intermolecular S…S Contacts

Department of Chemistry, Soongsil University, Seoul 156-743, KoreaReceived April 30, 2012, Accepted May 8, 2012Key Words : ET, Ferrocene, Self-assembly, Porous fra mework, Intermolecular S···S contact In contrast to the polar hydrogen bond donor-acceptorpairs, thiol-containing moieties are not regarded as goodhydrogen bond tectons due to their insufficient polarity.

The mechanism of proton conduction in phosphoric acid

Neat liquid phosphoric acid (H(3)PO(4)) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.

Effect of interprotein polarization on protein–protein binding energy

Molecular dynamics simulation in explicit water for the binding of the benchmark barnase-barstar complex was carried out to investigate the effect polarization of interprotein hydrogen bonds on its binding free energy. Our study is based on the AMBER force field but with polarized atomic charges derived from fragment quantum mechanical calculation for the protein complex. The quantum-derived atomic charges include the effect of polarization of interprotein hydrogen bonds, which was absent in the standard force fields that were used in previous theoretical calculations of barnase-barstar binding energy. This study shows that this polarization effect impacts both the static (electronic) and dynamic interprotein electrostatic interactions and significantly lowers the free energy of the barnase-barstar complex.

Effects of hydrogen bond and solvent polarity on the C=O stretching of bis(2-thienyl)ketone in solution

The optimized structural parameters, the absorption and the resonance Raman spectra have been investigated for the bis(2-thienyl)ketone in gas phase, in cyclohexane, methanol, and acetonitrile solvents by means of time dependent density functional theory calculations, the solvent electronic polarization effect on the solvation shift is examined and in well accordance with the calculation. The effect of increasing the polarity of the solvent is well represented by the polarizable continuum model, both for the absorption spectra and resonance Raman intensities. The Raman spectra of the C=O stretching mode, which is sensitive to the intermolecular interaction for bis(2-thienyl)ketone dissolved in solvents, were systematically studied. It was found that the hydrogen bond effect plays an important role in reducing the carbonyl stretching wavenumbers. The results of Raman shifts were interpreted through the dilution effect, solvation effects, and hydrogen bond-forming effects. Furthermore, the excitation profiles of several important Raman bands of bis(2-thienyl)ketone molecule in different solvents have been critically analyzed. The solvent effects on structural and symmetry properties of the molecule in S2 electronic state as well as the short-time photo relaxation dynamics have been discussed.

Conformational Flexibility and Cation–Anion Interactions in 1-Butyl-2,3-dimethylimidazolium Salts

The butyl group in 1-butyl-2,3-dimethylimidazolium (BMMI) salts, a common group of low-melting solids, was found to exhibit different conformations in the solid state. Crystal structures of pure BMMI azide, thiocyanate, propynoate, hexachlorocerate(IV), chlorocyanocuprate(I), nonachlorodititanate(IV), and mixed azide/chloride and cyanide/chloride salts were determined by single crystal X-ray diffraction, and their butyl chain conformations were examined. The twist angle of the C(α)–C(β) bond out of the plane of the imidazole ring ranges from 57° to 90°, whereas the torsion angle along the C(α)–C(β) bond determines the overall conformation: 63° to 97° (gauche) and 170° to 179° (trans). The preferred conformations of the butyl group are trans–trans and gauche–trans, but trans–gauche and gauche–gauche were also observed. More than one conformer was present in disordered structures. Numerous polar hydrogen bonds between cations and anions were identified. Five structures exhibit stacking of the aromatic imida...

Folding of a Helix Is Critically Stabilized by Polarization of Backbone Hydrogen Bonds: Study in Explicit Water

Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure.

Privileged Scaffolds or Promiscuous Binders: A Comparative Study on Rhodanines and Related Heterocycles in Medicinal Chemistry

Rhodanines and related five-membered heterocycles with multiple heteroatoms have recently gained a reputation of being unselective compounds that appear as "frequent hitters" in screening campaigns and therefore have little value in drug discovery. However, this judgment appears to be based mostly on anecdotal evidence. Having identified various rhodanines and related compounds in screening campaigns, we decided to perform a systematic study on their promiscuity. An amount of 163 rhodanines, hydantoins, thiohydantoins, and thiazolidinediones were synthesized and tested against several targets. The compounds were also characterized with respect to aggregation and electrophilic reactivity, and the binding modes of rhodanines and related compounds in published X-ray cocrystal structures were analyzed. The results indicate that the exocyclic, double bonded sulfur atom in rhodanines and thiohydantoins, in addition to other structural features, offers a particularly high density of interaction sites for polar interactions and hydrogen bonds. This causes a promiscuous behavior at concentrations in the "screening range" but should not be regarded as a general knockout criterion that excludes such screening hits from further development. It is suggested that special criteria for target affinity and selectivity are applied to these classes of compounds and that their exceptional and potentially valuable biomolecular binding properties are consequently exploited in a useful way.

Topological sub-structural molecular design approach: Radical scavenging activity

In the last decades phenolic compounds have gained enormous interest because of their beneficial health effects such as anti-inflammatory, anticancer, or antiviral activities. The pharmacological effects of phenolic compounds are mainly due to their antioxidant activity and their inhibition of certain enzymes. This antoxidant activity is related to the structure and has been extensively reported throught SAR or QSAR models. These studies confirmed that the number and position of hydroxyl groups, the related glycosylation and other substitutions in the phenolic ring largely determined radical scavenging activity. Most of these models are based on certain families of chemicals (flavonoids, cinnamic acids, etc…) and the model by itself is not useful for other substances of a different family. In this study we developed a QSAR model for a heterogeneous group of substances with TOPS-MODE descriptors for an interpretation of the antioxidant activity of these compounds in the form of bond contributions. The model developed, able to describe more than 90% of the variance in the experimental activity, also has a good predictive ability and stability. The information extracted from the QSAR model revealed that the major driving forces for radical scavenging activity are hydrogen bond donation and polarity. With this work we have managed to unify the different families of antioxidants in a single model with sufficient capacity to make predictions of radical scavenging activity for unknown substances.

Experimental and Computational Active Site Mapping as a Starting Point to Fragment‐Based Lead Discovery

Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D-xylose isomerase, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge-based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small-molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment-based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.

Structures and Interaction Analyses of Integrin αMβ2 Cytoplasmic Tails

Integrins are heterodimeric (α and β subunits) signal transducer proteins involved in cell adhesions and migrations. The cytosolic tails of integrins are essential for transmitting bidirectional signaling and also implicated in maintaining the resting states of the receptors. In addition, cytosolic tails of integrins often undergo post-translation modifications like phosphorylation. However, the consequences of phosphorylation on the structures and interactions are not clear. The leukocyte-specific integrin αMβ2 is essential for myeloid cell adhesion, phagocytosis, and degranulation. In this work, we determined solution structures of the myristoylated cytosolic tail of αM and a Ser phosphorylated variant in dodecylphosphocholine micelles by NMR spectroscopy. Furthermore, the interactions between non-phosphorylated and phosphorylated αM tails with β2 tail were investigated by NMR and fluorescence resonance energy transfer (FRET). The three-dimensional structures of the 24-residue cytosolic tail of αM or phosphorylated αM are characterized by an N-terminal amphipathic helix and a loop at the C terminus. The residues at the loop are involved in packing interactions with the hydrophobic face of the helix. 15N-1H heteronuclear single quantum coherence experiments identified residues of αM and β2 tails that may be involved in the formation of a tail-tail heterocomplex. We further examined interactions between myristoylated β2 tail in dodecylphosphocholine micelles with dansylated αM tail peptides by FRET. These studies revealed enhanced interactions between αM or phosphorylated αM tails with β2 tail with Kd values ∼5.2±0.6 and ∼4.4±0.7 μm, respectively. Docked structures of tail-tail complexes delineated that the αM/β2 interface at the cytosolic region could be sustained by a network of polar interactions, ionic interactions, and/or hydrogen bonds.

Fourier transform infrared spectroscopic investigation of humic substance samples of different origin and typology supported by chemometric tools

In this paper 198 FTIR spectra of humic substance (HS) extracted from lake, marine sediments, soils and by Antarctic seawater were examined by Principal Component Analysis (PCA), Independent Component Analysis (ICA) and Two-dimensional Mapping (2DMAP) to identify the compositional and structural characteristics which characterise the typologies of samples examined and which are hardly detectable by means of an ordinary visual examination of FTIR spectra. PCA was able to characterise the HS fraction with the highest amount of polymerised molecules consisting of humic acids (HA) essentially. 2DMAP allowed a direct qualitative comparison among different typologies of HS samples. At last, ICA application showed that HS samples are characterised by structures where the humification process is supported by polymerisation reactions and in addition by formation of supramolecular compounds arising from polar (hydrogen bond) and non-polar (Van der Walls) interactions among the several biomolecules present.

Effect of polarization on the stability of a helix dimer

Molecular dynamics (MD) simulations have been carried out to study helix–helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein–protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix–helix interaction and helix bundle structures.

ChemInform Abstract: Complex Formation and Proton Transfer in the Polarizable Hydrogen Bonds of Two N,N′-Dioxides + Substituted Phenol Systems as a Function of the pKa of the Phenols. An FTIR Study

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

X-ray powder diffraction, solid-state NMR and dispersion-corrected DFT calculations to investigate the solid state structure of 2-ammonio-5-chloro-4-methylbenzenesulfonate

The title compound, also called CLT acid, is an industrial intermediate in the synthesis of laked red azo pigments for newspaper printing. Solid-state NMR and IR experiments revealed the compound to exist as the zwitter- ionic tautomer in the solid state. The crystal structure was solved from X-ray powder dif- fraction data by means of real-space methods using the program DASH 3.1. Subsequently the structure was refined by the Rietveld method with TOPAS 4.1. The zwitterionic tautomer gave better confidence values than the non-zwit- terionic tautomer. Finally the structure was confirmed by dispersion-corrected density-functional calculations. The compound crystallises in the monoclinic space group Ia, Z ¼ 4 with a ¼ 5.49809(7) � b ¼ 32.8051(5) � c ¼ 4.92423(7) �, b ¼ 93.5011(7) � and V ¼ 886.50(2) � 3 . The molecules form a herringbone pattern with a double layer structure consisting of alternating polar and non-po- lar layers. Within the polar layers hydrogen bonds and ionic interactions are dominant, whereas the fragments in the non-polar layers are connected by van der Waals inter- actions.

Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds

We report direct folding of a 17-residue helix protein (pdb:2I9M) by standard molecular dynamics simulation (single trajectory) at room temperature with implicit solvent. Starting from a fully extended structure, 2I9M successfully folds into the native conformation within 16 ns using adaptive hydrogen bond-specific charges to take into account the electrostatic polarization effect. Cluster analysis shows that conformations in the native state cluster have the highest population (78.4%) among all sampled conformations. Folding snapshots and the secondary structure analysis demonstrate that the folding of 2I9M begins at terminals and progresses toward the center. A plot of the free energy landscape indicates that there is no significant free energy barrier during folding, which explains the observed fast folding speed. For comparison, exactly the same molecular dynamics simulation but carried out under existing AMBER charges failed to fold 2I9M into native-like structures. The current study demonstrates that electrostatic polarization of intraprotein hydrogen bonding, which stabilizes the helix, is critical to the successful folding of 2I9m.

VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents.

Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.

An amantadine-sensitive chimeric BM2 ion channel of influenza B virus has implications for the mechanism of drug inhibition

Influenza A virus M2 (A/M2) and the influenza B virus BM2 are both small integral membrane proteins that form proton-selective ion channels. Influenza A virus A/M2 channel is the target of the antiviral drug amantadine (and its methyl derivative rimantadine), whereas BM2 channel activity is not affected by the drug. The atomic structure of the pore-transmembrane (TM) domain peptide has been determined by x-ray crystallography [Stouffer et al. (2008) Nature 451:596-599] and of a larger M2 peptide by NMR methods [Schnell and Chou (2008) Nature 451:591-595]. The crystallographic data show electron density (at 3.5 A resolution) in the channel pore, consistent with amantadine blocking the pore of the channel. In contrast, the NMR data show 4 rimantadine molecules bound on the outside of the helices toward the cytoplasmic side of the membrane. Drug binding includes interactions with residues 40-45 and a polar hydrogen bond between rimantadine and aspartic acid residue 44 (D44). These 2 distinct drug-binding sites led to 2 incompatible drug inhibition mechanisms. We have generated chimeric channels between amantadine-sensitive A/M2 and amantadine-insensitive BM2 designed to define the drug-binding site. Two chimeras containing 5 residues of the A/M2 ectodomain and residues 24-36 of the A/M2 TM domain show 85% amantadine/rimantadine sensitivity and specific activity comparable to that of WT BM2. These functional data suggest that the amantadine/rimantadine binding site identified on the outside of the 4 helices is not the primary site associated with the pharmacologic inhibition of the A/M2 ion channel.