A Multifunctional Additive Based on the Cation-Anion Synergistic Effect for Highly Stable Zinc Metal Anodes.

The Zn dendrite and hydrogen evolution reaction have been a "stubborn illness" for the life span of zinc anodes, which significantly hinders the development of aqueous zinc batteries (AZBs). Herein, considering the ingenious molecular structure, a multifunctional additive based on the synergistic regulation of cations and anions at the interface is designed to promote a dendrite-free and stable Zn anode. Theoretical calculations and characterization results verified that the electrostatic shield effect of the cation, the solvation sheath structure, and the bilayer structural solid electrolyte film (SEI) jointly account for the uniform Zn deposition and side reaction suppression. Ultimately, a remarkably high average Coulombic efficiency (CE) of 99.4% is achieved in the Zn||Cu cell for 300 cycles, and a steady charge/discharge cycling over 3000 and 300 h at 1.0 mA cm-2/1.0 mAh cm-2 and 10 mA cm-2/10 mAh cm-2 is obtained in the Zn||Zn cell. Furthermore, the assembled full battery demonstrates a prolonged cycle life of 2000 cycles.

Effects of laser needle-knife therapy on vertebroarterial morphology and protein expression of PI-3K, AKT and VEGF in the carotid artery in a rabbit model of cervical spondylotic arteriopathy.

PURPOSE: To explore how the use of a laser needle-knife affects vertebroarterial morphology and protein expression of PI-3K, AKT and VEGF in the carotid artery of a rabbit model of cervical spondylotic arteriopathy (CSA), and to determine its primary treatment mechanism. METHODS: The CSA rabbit model consisted of 30 rabbits with CSA that were randomly divided into a model group (n = 10), an acupuncture group (n = 10) and a laser needle-knife group (n = 10) plus a further 10 wild type rabbits placed into a normal group. Rabbits in the acupuncture group were treated by needling the Fengchi (GB 20) and Jiaji (EX-B2) acupoints, while those in the laser needle-knife group were treated with a laser needle-knife on the Jiaji (EX-B2) near the spinous process of the fifth cervical vertebra, the rabbit in both groups immobilized during treatment. Rabbits in the other two groups received no treatment, but were immobilized for a similar duration. The morphology of the right vertebral artery and the distribution of pore size before and after treatment were compared using BET and SEM, and the protein expression of PI-3K, AKT and VEGF in the carotid artery of the four groups measured using Western blot analysis. RESULTS: The pore diameter and specific surface area of the right vertebral artery increased after treatment, as did the number of micropores. Compared with the normal group, the protein expression of PI-3K, AKT and VEGF in the carotid artery of the model group was significantly lower (P < 0.05), while that of the laser needle-knife group was significantly higher (P < 0.05 and P < 0.01). In addition, rabbits from the acupuncture and laser needle-knife groups demonstrated significantly higher levels of protein expression of PI-3K and VEGF in the carotid artery compared with the model group (P < 0.05 and P < 0.01). CONCLUSIONS: By promoting micrangium hyperplasia within the vertebral artery of rabbits with CSA, treatment with a laser needle-knife modified the protein expression of PI-3K, AKT and VEGF, suggesting that laser needle-knife therapy possibly treats CSA though these signaling pathways.

An efficient perturbation method to predict the functionally key sites of glutamine binding protein.

Glutamine-Binding Protein (GlnBP) of Escherichia coli, an important member of the periplasmic binding protein family, is responsible for the first step in the active transport of glutamine across the cytoplasmic membrane. In this work, the functionally key regulation sites of GlnBP were identified by utilizing a perturbation method proposed by our group, in which the residues whose perturbations markedly change the binding free energy between GlnBP and glutamine are considered to be functionally key residues. The results show that besides the substrate binding sites, some other residues distant from the binding pocket, including the ones in the hinge regions between the two domains, the front- and back- door channels and the exposed region, are important for the function of glutamine binding and transport. The predicted results are well consistent with the theoretical and experimental data, which indicates that our method is an effective approach to identify the key residues important for both ligand binding and long-range allosteric signal transmission. This work can provide some insights into the function performance of GlnBP and the physical mechanism of its allosteric regulation.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling.

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future.

Design, synthesis and activity evaluation of novel peptide fusion inhibitors targeting HIV-1 gp41.

Human immunodeficiency virus type 1 (HIV-1), the pathogen of acquired immunodeficiency syndrome (AIDS), causes about 2 million people to death every year. Fusion inhibitors targeted the envelope protein (gp41) represent a novel and alternative approach for anti-AIDS therapy, which terminates the HIV-1 life cycle at an early stage. Using CP621-652 as a template, a series of peptides were designed, synthesized and evaluated in vitro assays. An interesting phenomenon was found that the substitution of hydrophobic residues at solvent accessible sites could increase the anti-HIV activity when the C-terminal sequence was extended with an enough numbers of amino acids. After the active peptides was synthesized and evaluated, peptide 8 showed the best anti-HIV-1 IIIB whole cell activity (MAGI IC50=53.02 nM). Further study indicated that peptide 8 bound with the gp41 NHR helix, and then blocked the conformation of 6-helix, thus inhibited virus-cell membrane fusion. The results would be helpful for the design of peptide fusion inhibitors against HIV-1 infection.

Molecular dynamics studies of the inhibitor C34 binding to the wild-type and mutant HIV-1 gp41: inhibitory and drug resistant mechanism.

Mutations on NHR (N-terminal heptad repeat) associated with resistance to fusion inhibitor were observed. In addition, mutations on CHR (C-terminal heptad repeat) accompanied NHR mutations of gp41 are noted in many cases, like N43D/S138A double mutation. In this work, we explored the drug resistant mechanism of N43D mutation and the role of S138A second mutation in drug resistance. The binding modes of the wild type gp41 and the two mutants, N43D and N43D/S138A, with the HIV-1 fusion inhibitor C34, a 34-residue peptide mimicking CHR of gp41, were carried out by using molecular dynamics simulations. Based on the MD simulations, N43D mutation affects not only the stability of C34 binding, but also the binding energy of the inhibitor C34. Because N43D mutation may also affect the stable conformation of 6-HB, we introduced S138A second mutation into CHR of gp41 and determined the impact of this mutation. Through the comparative analysis of MD results of the N43D mutant and the N43D/S138A mutant, we found that CHR with S138A mutation shown more favorable affinity to NHR. Compelling differences in structures have been observed for these two mutants, particularly in the binding modes and in the hydrophobic interactions of the CHR (C34) located near the hydrophobic groove of the NHR. Because the conformational stability of 6-HB is important to HIV-1 infection, we suggested a hypothetical mechanism for the drug resistance: N43D single mutation not only impact the binding of inhibitor, but also affect the affinity between NHR and CHR of gp41, thus may reduce the rate of membrane fusion; compensatory mutation S138A would induce greater hydrophobic interactions between NHR and CHR, and render the CHR more compatible to NHR than inhibitors.

Cation-pi interactions at non-redundant protein--RNA interfaces.

Cation-pi interactions have proved to be important in proteins and protein-ligand complexes. Here, cation-pi interactions are analyzed for 282 non-redundant protein-RNA interfaces. The statistical results show that this kind of interactions exists in 65% of the interfaces. The four RNA bases are ranked as Gua>Ade>Ura>Cyt according to their propensity to participate in cation-pi interactions. The corresponding ranking for the involved amino acid residues is: Arg>Lys>Asn>Gln. The same trends are obtained based on the empirical energy calculation. The Arg-Gua pairs have the greatest stability and are also most frequently observed. The number of cation-pi pairs involving unpaired bases is 2.5 times as many as those involving paired bases. Hence, cation-pi interactions show sequence and structural specificities. For the bicyclic bases, Gua and Ade, their 5-atom rings participate in cation-pi interactions somewhat more than the 6-atom rings, with percentages of 54 and 46%, respectively, which is due to the higher cation-pi participation proportion (63%) of 5-atom rings in the paired bases. These results give a general view of cation-pi interactions at protein-RNA interfaces and are helpful in understanding the specific recognition between protein and RNA.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.

Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation.

The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel ß-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.

[Effect of pre-electroacupuncture at "Zusanli" (ST 36) on DA and 5-HT contents and their ratio in hypothalamus and striatum in exercise rats].

OBJECTIVE: To observe anti-fatigue effect and mechanisms of pre-electroacupuncture (EA) at "Zusanli" (ST 36) in rats undergoing acute treadmill running. METHODS: Fifty male SD rats were randomly divided into three groups: a quiet group (group Q, n = 10), a model group (group M, n = 20) and an EA preconditioning group (group EAP, n = 20). After adaptation for undergoing treadmill running, all the rats in group M and group EAP were trained on acute treadmill running. Besides, EA with continuous waves, 2 Hz in frequency and 2 mA in intensity was applied at bilateral "Zusanli" (ST 36) for 30 min, which was applied once daily for continuous 6 days before treadmill running for the rats in Group EAP. Plasma lactate contents were measured immediately and 3 hours after treadmill running, respectively. Changes of dopamine (DA) and serotonin (5-HT) contents obtained immediately and 3 hours after treadmill running, respectively, in hypothalamus and striatum, were detected and compared, and DA/5-HT ratios were calculated. RESULTS: Compared with group Q, the levels of blood lactate and hypothalamic 5-HT tented to increase in rats of group M, and the contents of hypothalamic DA increased significantly (P < 0.01), while the contents of striatal DA and 5-HT in group M decreased significantly (both P < 0.01) at 3 h after treadmill running. Immediately after treadmill running, the contents of DA and 5-HT increased significantly in hypothalamus (both P < 0.01), but decreased significantly in striatum (both P < 0.01) in group EAP, compared with those in group M. Moreover, EA pretreatment markedly decreased the levels of blood lactate (P < 0.05) and hypothalamic 5-HT (P < 0.01), and obviously elevated the ratio of DA/5-HT in the hypothalamus (P < 0.01) at 3 h after treadmill running. CONCLUSION: Preventive EA at "Zusanli" (ST 36) can accelerate recovery from fatigue, which may be related to its reducing accumulation of blood lactate, elevating DA/ 5-HT ratio in the hypothalamus of the rats undergoing treadmill running.

A holistic molecular docking approach for predicting protein-protein complex structure.

A holistic protein-protein molecular docking approach, HoDock, was established, composed of such steps as binding site prediction, initial complex structure sampling, refined complex structure sampling, structure clustering, scoring and final structure selection. This article explains the detailed steps and applications for CAPRI Target 39. The CAPRI result showed that three predicted binding site residues, A191HIS, B512ARG and B531ARG, were correct, and there were five submitted structures with a high fraction of correct receptor-ligand interface residues, indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring.

Protein-protein docking has made much progress in recent years, but challenges still exist. Here we present the application of our docking approach HoDock in CAPRI. In this approach, a binding site prediction is implemented to reduce docking sampling space and filter out unreasonable docked structures, and a network-based enhanced combinatorial scoring function HPNCscore is used to evaluate the decoys. The experimental information was combined with the predicted binding site to pick out the most likely key binding site residues. We applied the HoDock method in the recent rounds of the CAPRI experiments, and got good results as predictors on targets 39, 40, and 41. We also got good results as scorers on targets 35, 37, 40, and 41. This indicates that our docking approach can contribute to the progress of protein-protein docking methods and to the understanding of the mechanism of protein-protein interactions.

Synthesis of polyhydroxylated aromatics having amidation of piperazine nitrogen as HIV-1 integrase inhibitor.

(E)-N-[3-(4-cinnamoylpiperazin-1-yl)propyl]-3,4-dihydroxybenzamide and (E)-N-[3-(4-cinnamoylpiperazin-1-yl)propyl]-3,4,5-trihydroxybenzamide were designed and synthesized as potential HIV-1 integrase inhibitors and evaluated their inhibition to the strand transfer process of HIV-1 integrase. The result indicates that 3,4,5-trihydroxylated aromatic derivatives exhibit good inhibition to HIV-1 integrase, however, corresponding 3,4-dihydroxylated aromatic derivatives appear little inhibition of HIV-1 integrase.

Development of a high-throughput assay for the HIV-1 integrase disintegration reaction.

Both HIV-1 integrase (IN) and the central catalytic domain of IN (IN-CCD) catalyze the disintegration reaction in vitro. In this study, IN and IN-CCD proteins were expressed and purified, and a high-throughput format enzyme-linked immunosorbent assay (ELISA) was developed for the disintegration reaction. IN exhibited a marked preference for Mn(2+) over Mg(2+) as the divalent cation cofactor in disintegration. Baicalein, a known IN inhibitor, was found to be an IN-CCD inhibitor. The assay is sensitive and specific for the study of disintegration reaction as well as for the in vitro identification of antiviral drugs targeting IN, especially targeting IN-CCD.

Molecular dynamics simulation of the transmembrane subunit of BtuCD in the lipid bilayer.

Based on the crystal structure of the vitamin B(12) transporter protein of Escherichia coli (BtuCD) a system consisting of the BtuCD transmembrane domain (BtuC) and the palmitoyloleoyl phosphatidylcholine (POPC) lipid bilayer was constructed in silica, and a more-than-57-nanosecond molecular dynamics (MD) simulation was performed on it to reveal the intrinsic functional motions of BtuC. The results showed that a stable protein-lipid bilayer was obtained and the POPC lipid bilayer was able to adjust its thickness to match the embedded BtuC which underwent relatively complicated motions. These results may help to understand the mechanism of transmembrane substrate transport at the atomic level.

Design, synthesis and anti-HIV integrase evaluation of N-(5-chloro-8-hydroxy-2-styrylquinolin-7-yl)benzenesulfonamide derivatives.

Styrylquinoline derivatives are demonstrated to be HIV-1 integrase inhibitors. On the basis of our previous CoMFA analysis of a series of styrylquinoline derivatives, N-[(2-substituted-styryl)-5-chloro-8-hydroxyquinolin-7-yl]-benzenesulfonamide derivatives were designed and synthesized,and their possible HIV IN inhibitory activity was evaluated.

Uncovering the properties of energy-weighted conformation space networks with a hydrophobic-hydrophilic model.

The conformation spaces generated by short hydrophobic-hydrophilic (HP) lattice chains are mapped to conformation space networks (CSNs). The vertices (nodes) of the network are the conformations and the links are the transitions between them. It has been found that these networks have "small-world" properties without considering the interaction energy of the monomers in the chain, i. e. the hydrophobic or hydrophilic amino acids inside the chain. When the weight based on the interaction energy of the monomers in the chain is added to the CSNs, it is found that the weighted networks show the "scale-free" characteristic. In addition, it reveals that there is a connection between the scale-free property of the weighted CSN and the folding dynamics of the chain by investigating the relationship between the scale-free structure of the weighted CSN and the noted parameter Z score. Moreover, the modular (community) structure of weighted CSNs is also studied. These results are helpful to understand the topological properties of the CSN and the underlying free-energy landscapes.

Evolving model of amino acid networks.

The three-dimensional structure of a protein can be treated as a complex network composed of amino acids, and the network properties can help us to understand the relationship between structure and function. Since the amino acid network of a protein is formed in the process of protein folding, it is difficult for general network models to explain its evolving mechanism. Based on the perspective of protein folding, we propose an evolving model for amino acid networks. In our model, the evolution starts from the amino acid sequence of a native protein and it is guided by two generic assumptions: i.e., the neighbor preferential rule and the energy preferential rule. We find that the neighbor preferential rule predominates the general network properties and the energy preferential rule predominates the specific biological structure characteristics. Applied to native proteins, our model mimics the features of amino acid networks well.

[Effects of transcutaneous electric acupoint stimulation on plasma SOD and MDA in rats with sports fatigue].

OBJECTIVE: To observe the effect of transcutaneous electric acupoint stimulation (TEAS) on plasma superoxide dismutase (SOD) and malondialdehyde (MDA) in rats with sports fatigue so as to explore its mechanisms in resisting exercise-induced fatigue. METHODS: Twenty-seven male adult SD rats were randomly divided into control group (n 9), model group (n=9) and TEAS group (n=9). Sports fatigue model was established by using treadmill method, i.e. forcing the rat to run 10 min at a speed of 10 m/min, 15 m/min, 20 m/min, 24 m/min and 28 m/min, once daily for 6 days. TEAS (continuous waves, 2 Hz, 5 mA) was applied to unilateral "Zusanli" (ST 36) for 30 min, once per day for 7 days. The exhausted exercise time from starting running to exhaustion was recorded on the 7th day and the lactate levels, SOD activity and MDA contents in plasma were measured by lactate oxidase method, xanthine oxidase method and thiobarbituric acid method respectively. RESULTS: The duration of exhausted exercise in model group and TEAS group were (56.00 +/- 12.27) min and (70.88 +/- 13.74) min respectively, displaying significant increase in exercise tolerance after TEAS (P<0.05). The lactate level and MDA content in model group were markedly higher than those in control group (P<0.05); while compared with model group, lactate and MDA contents in TEAS group were significantly lower (P<0.05), and plasma SOD activity in TEAS group was significantly higher (P<0.01). No significant differences were found in plasma lactate content between control and TEAS groups and in SOD activity between model group and control group (P>0.05). SOD/MDA of model group was significantly lower than those of control group and TEAS group (P<0.05, 0.01). CONCLUSION: TEAS at "Zusanli"(ST 36) can effectively postpone exercise-induced fatigue by reducing accumulation of blood lactate, improving anti-oxidative ability and relieving lipid peroxidation in the rat.