When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins

Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction.

Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.

Protection of tissue physicochemical properties using polyfunctional crosslinkers

Understanding complex biological systems requires the system-wide characterization of both molecular and cellular features. Existing methods for spatial mapping of biomolecules in intact tissues suffer from information loss caused by degradation and tissue damage. We report a tissue transformation strategy named stabilization under harsh conditions via intramolecular epoxide linkages to prevent degradation (SHIELD), which uses a flexible polyepoxide to form controlled intra- and intermolecular cross-link with biomolecules. SHIELD preserves protein fluorescence and antigenicity, transcripts and tissue architecture under a wide range of harsh conditions. We applied SHIELD to interrogate system-level wiring, synaptic architecture, and molecular features of virally labeled neurons and their targets in mouse at single-cell resolution. We also demonstrated rapid three-dimensional phenotyping of core needle biopsies and human brain cells. SHIELD enables rapid, multiscale, integrated molecular phenotyping of both animal and clinical tissues.

Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways

The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential cleavage pathways and resulting fragments that are formed during depolymerization of lignin oligomers containing two to six monomers. We have developed a chemical discovery technique to identify the chemically relevant putative fragments in eight known polymeric linkage types of lignin. Obtaining these structures is a crucial precursor to the development of any further kinetic modeling. We have developed this approach by adapting steered molecular dynamics calculations under constant force and varying the points of applied force in the molecule to diversify the screening approach. Key observations include relationships between abundance and breaking frequency, the relative diversity of potential pathways for a given linkage, and the observation that readily cleaved bonds can destabilize adjacent bonds, causing subsequent automatic cleavage.

hCLCA1 DNA vaccine suppresses cell hyperplasia and mucin expression of goblet cells in vitro

BACKGROUND

Excessive airway mucus secretion is a remarkable trait of asthma. Mucus overproduction mainly resulted from an increase in goblet cell numbers, which causes considerable damage to health. However, effective therapeutic treatments are still lacking for mucus hypersecretion. Human calcium-activated chloride channel 1 (hCLCA1) has been identified to be predominantly responsible for mucus hypersecretion.

OBJECTIVES

In this study, we investigated the effects of an hCLCA1 DNA vaccine on the control of mucus production and goblet cell proliferation using an in vitro model goblet cell line (NCI-H292).

METHODS

The effect of the hCLCA1 DNA vaccine on cell viability and proliferative activity of NCI-H292/hCLCA1 was analyzed by electron microscopy, MTT assay, and flow cytometry. Expression of mucins and MUC5AC, a major member of the mucin gene family in airway goblet cells, was assessed under hCLCA1 DNA vaccine challenges by periodic acid-Schiff staining, quantitative real-time PCR and Western blot, respectively, and the expression profile of granulocyte-macrophage colony-stimulating factor (GM-CSF), a critical cytokine in airway inflammation, was also examined by real-time PCR and immunocytochemistry.

RESULTS

Results showed that hCLCA1 overexpression caused high cell proliferation and mucin expression, whereas the hCLCA1 DNA vaccine could effectively reverse these abnormal effects. In addition, GM-CSF expression was highly induced by hCLCA1 overexpression and efficiently suppressed by hCLCA1 DNA vaccine.

CONCLUSIONS

These results illustrate that the hCLCA1 DNA vaccine effectively inhibits cell hyperplasia and mucin gene expression of goblet cells, suggesting that the hCLCA1 DNA vaccine has potential value in the treatment of human asthma.

Water 16-mers and hexamers: assessment of the three-body and electrostatically embedded many-body approximations of the correlation energy or the nonlocal energy as ways to include cooperative effects

This work presents a new fragment method, the electrostatically embedded many-body expansion of the nonlocal energy (EE-MB-NE), and shows that it, along with the previously proposed electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), produces accurate results for large systems at the level of CCSD(T) coupled cluster theory. We primarily study water 16-mers, but we also test the EE-MB-CE method on water hexamers. We analyze the distributions of two-body and three-body terms to show why the many-body expansion of the electrostatically embedded correlation energy converges faster than the many-body expansion of the entire electrostatically embedded interaction potential. The average magnitude of the dimer contributions to the pairwise additive (PA) term of the correlation energy (which neglects cooperative effects) is only one-half of that of the average dimer contribution to the PA term of the expansion of the total energy; this explains why the mean unsigned error (MUE) of the EE-PA-CE approximation is only one-half of that of the EE-PA approximation. Similarly, the average magnitude of the trimer contributions to the three-body (3B) term of the EE-3B-CE approximation is only one-fourth of that of the EE-3B approximation, and the MUE of the EE-3B-CE approximation is one-fourth that of the EE-3B approximation. Finally, we test the efficacy of two- and three-body density functional corrections. One such density functional correction method, the new EE-PA-NE method, with the OLYP or the OHLYP density functional (where the OHLYP functional is the OptX exchange functional combined with the LYP correlation functional multiplied by 0.5), has the best performance-to-price ratio of any method whose computational cost scales as the third power of the number of monomers and is competitive in accuracy in the tests presented here with even the electrostatically embedded three-body approximation.

Safety and immunogenicity of a DNA vaccine encoding human calcium-activated chloride channel 1 (hCLCA1) in asthmatic mice

BACKGROUND

Calcium-activated chloride channels (CLCAs) have been found to be preferentially expressed on the secretory epithelium. They may play a pivotal role in mucous overproduction by bronchial goblet cells in asthma. It has been reported that the inhibition of CLCAs with niflumic acid could relieve the symptoms of asthma. However, niflumic acid has serious adverse effects. DNA vaccination is considered to be a promising strategy to treat allergic diseases such as asthma and dust mite allergy.

METHODS

We constructed a vaccine encoding human CLCA1 (hCLCA1) and evaluated its effects on promoting antibodies against hCLCA1 and the related preventive function in a mouse model of asthma.

RESULTS

Our results reveal that the induced hCLCA1 antibodies can be detected in the first 2 weeks after immunization with hCLCA1 plasmids (hCLCA1-p) by intramuscular injection and augmented gradually in the following several weeks. The autoantibodies against hCLCA1 induced by the DNA vaccine bound to three segments of the mouse CLCA3 (mCLCA3) protein, including the amino terminal (PepN), the carboxyl terminal (PepC) and the middle of the protein (PepM). In our study, mice immunized with hCLCA1-p developed fewer pathological changes compared with other control groups, including a remarkable reduction in the air pressure-time index of the trachea, the number of eosinophils and mast cells in the bronchoalveolar lavage fluid and the mRNA level of MUC5AC in goblet cells.

CONCLUSION

Taken together, our results suggest that a DNA vaccine encoding the CLCA protein may have potential as a useful pharmacotherapy for asthma in the future.

Assessing the Accuracy of Density Functional and Semiempirical Wave Function Methods for Water Nanoparticles: Comparing Binding and Relative Energies of (H2O)16 and (H2O)17 to CCSD(T) Results

The binding energies and relative conformational energies of five configurations of the water 16-mer are computed using 61 levels of density functional (DF) theory, 12 methods combining DF theory with molecular mechanics damped dispersion (DF-MM), seven semiempirical-wave function (SWF) methods, and five methods combining SWF theory with molecular mechanics damped dispersion (SWF-MM). The accuracies of the computed energies are assessed by comparing them to recent high-level ab initio results; this assessment is more relevant to bulk water than previous tests on small clusters because a 16-mer is large enough to have water molecules that participate in more than three hydrogen bonds. We find that for water 16-mer binding energies the best DF, DF-MM, SWF, and SWF-MM methods (and their mean unsigned errors in kcal/mol) are respectively M06-2X (1.6), ωB97X-D (2.3), SCC-DFTB-γ(h) (35.2), and PM3-D (3.2). We also mention the good performance of CAM-B3LYP (1.8), M05-2X (1.9), and TPSSLYP (3.0). In contrast, for relative energies of various water nanoparticle 16-mer structures, the best methods (and mean unsigned errors in kcal/mol), in the same order of classes of methods, are SOGGA11-X (0.3), ωB97X-D (0.2), PM6 (0.4), and PMOv1 (0.6). We also mention the good performance of LC-ωPBE-D3 (0.3) and ωB97X (0.4). When both relative and binding energies are taken into consideration, the best methods overall (out of the 85 tested) are M05-2X without molecular mechanics and ωB97X-D when molecular mechanics corrections are included; with considerably higher average errors and considerably lower cost, the best SWF or SWF-MM method is PMOv1. We use six of the best methods for binding energies of the water 16-mers to calculate the binding energies of water hexamers and water 17-mers to test whether these methods are also reliable for binding energy calculations on other types of water clusters.

Biological treatment of ammonia gas at high loading

The exhaust gas from compost processing plants contains a large amount of ammonia. To treat ammonia gas at high loads, bench-scale experiments were carried out. First, nitrifying bacteria were enriched from soil and immobilized on porous ceramics. The ceramics were packed in an acrylic cylinder (diameter, 100 mm; packed height, 190 mm) and ammonia gas was introduced to the top of the cylinder. The concentration and flow rate of ammonia gas were gradually increased and finally 85 ppm was introduced at a space velocity of 800 h(-1) (empty bed residence time (EBRT), 4.5 sec). The ammonia load was 1.0 kg N/m3 day(-1). The exhaust contained 1.5-2 ppm of ammonia. Then the packed ceramics were transferred to another acrylic cylinder (diameter, 50 mm; packed height, 800 mm). A high concentration of ammonia gas (1,000 ppm) was introduced at a space velocity of 96 h(-1) (ammonia loading, 1.44 kg N/m3 day(-1); EBRT, 37.5 sec). The exhaust contained 2 ppm of ammonia (removal rate, 99.8%). The packed bed was washed with water intermittently or continuously, and the wastewater from the cylinder contained a large amount of ammonium and nitrate ions of at a 1:1 ratio. Stoichiometric analysis showed that half of the introduced ammonia was oxidized to nitrate, and the rest was converted to ammonium ion. Thus, ammonia gas was effectively treated at a high load by biofiltration with nitrifying bacteria.

[A study of the effects of L-arginine in pathogenesis of hypoxic pulmonary hypertension]

AIM

To investigate the role of nitric oxide (NO), nitric oxide synthase (NOS) and endothelin-1 (ET-1) in the pathogenesis of hypoxic pulmonary hypertension and inhibiting effects of L-Arginine.

METHODS

30 rats were divided into 3 groups, normal control group (group NC); Hypoxic group (group HP): exposed to 10% O2 8 h/day, 3 weeks; Hypoxic + L-arginine (group LT): fed L-arginine 200 mg/kg before hypoxia. After exposed to hypoxia 21 days, hemodynamics were measured. Lung speciments were examined by light and electronic microscopes and morphometric analysis. NO, ET-1 levels in lung tissue were measured, the cNOS quantitative in the pulmonary endothelium were examined.

RESULTS

In HP group, the mean pulmonary arterial pressure (m PAP), pulmonary vascular resistance (PVR) the percentage of completely muscular coattype medial muscle layer of pulmonary artery in intra-acine and ET-1 level of HP group increased (P < 0.01), but NO and cNOS level decreased (P < 0.01). Examined by electron micrograph, endothelium cells appeared swollen, broken and pealed of, basal lamina parted. The changes above in LT group reversed partly. But the changes above were still several than that of group NC (P < 0.05).

CONCLUSION

The structure remodel of pulmonary arteries and endothelium lesion in hypoxia cause m PAP, PVP arising, that are correlated with the levels of ET-1 increasing and NO, cNOS decreasing. For L-arginine can partly supply NO, it may partly reverse the changes of HPH.