Low-frequency normal modes in horse liver alcohol dehydrogenase and motions of residues involved in the enzymatic reaction

Normal mode analysis using the elastic network model has provided characteristics and directions of the low-frequency large domain motions of horse liver alcohol dehydrogenase. Three normal modes (mode 1, mode 7, and mode 8) were identified as representative domain motions that may promote the onset of Near Attack Conformers or facilitate the product to be released. The pattern of the atomic displacement for some key residues (such as Val292 and Val203) revealed in this study is in line with experimental structural and kinetic studies and theoretical simulations.     

Interpreting the structural mechanism of action for MT7 and human muscarinic acetylcholine receptor 1 complex by modeling protein-protein interaction

MT7 is a selective human muscarinic acetylcholine receptor 1 (hM1) allosteric binder with subnanomolar affinity. Understanding the binding mode of hM1-MT7 will give insights to discover small molecular ligand for hM1. MT7 is a peptide, and hM1 is a G-protein-coupled membrane receptor. Therefore, we have employed homology modeling, protein-protein docking, explicit membrane molecular dynamics (MD) simulations, and molecular mechanic/Poisson-Boltzmann surface area energy decomposition analysis approaches to reveal the hM1-MT7 binding mode. The binding mode is consistent with the experimental data. We have discovered that the binding mode consists of three interaction regions in five residue interaction clusters. By analyzing the cluster representative structures, the cluster residues form an interaction network, which shows a multiple-point-to-site binding mode. Hydrogen binding statistical analysis reveals that E170 (hM1) and R34 (MT7) are both locked in electrostatic cages with counter charges, respectively. This is confirmed by the dynamic distances calculation between these residues, and biological mutant experiments.     

Interpreting the structural mechanism of action for MT7 and human muscarinic acetylcholine receptor 1 complex by modeling protein–protein interaction

MT7 is a selective human muscarinic acetylcholine receptor 1 (hM1) allosteric binder with subnanomolar affinity. Understanding the binding mode of hM1–MT7 will give insights to discover small molecular ligand for hM1. MT7 is a peptide, and hM1 is a G-protein-coupled membrane receptor. Therefore, we have employed homology modeling, protein–protein docking, explicit membrane molecular dynamics (MD) simulations, and molecular mechanic/Poisson-Boltzmann surface area energy decomposition analysis approaches to reveal the hM1–MT7 binding mode. The binding mode is consistent with the experimental data. We have discovered that the binding mode consists of three interaction regions in five residue interaction clusters. By analyzing the cluster representative structures, the cluster residues form an interaction network, which shows a multiple-point-to-site binding mode. Hydrogen binding statistical analysis reveals that E170 (hM1) and R34 (MT7) are both locked in electrostatic cages with counter charges, respectively. This is confirmed by the dynamic distances calculation between these residues, and biological mutant experiments.     

Multifunctional chiral aminophosphines for enantiodivergent catalysis in a palladium-catalyzed allylic alkylation reaction

Trifunctional MAP-based chiral phosphines were tested as new ligands in a Pd-catalyzed asymmetric allylic alkylation, demonstrating fast and enantiodivergent catalysis. The palladium complexes of representative ligands by X-ray analysis revealed a novel mode of P,N-coordination of the ligand to the palladium center, which may contribute to switching the sense of the asymmetric induction via combined steric and tunable H-bonding interactions between the metal complex and the substrates.     

Flexibility of alpha-helices: results of a statistical analysis of database protein structures

Alpha-helices stand out as common and relatively invariant secondary structural elements of proteins. However, alpha-helices are not rigid bodies and their deformations can be significant in protein function (e.g. coiled coils). To quantify the flexibility of alpha-helices we have performed a structural principal-component analysis of helices of different lengths from a representative set of protein folds in the Protein Data Bank. We find three dominant modes of flexibility: two degenerate bend modes and one twist mode. The data are consistent with independent Gaussian distributions for each mode. The mode eigenvalues, which measure flexibility, follow simple scaling forms as a function of helix length. The dominant bend and twist modes and their harmonics are reproduced by a simple spring model, which incorporates hydrogen-bonding and excluded volume. As an application, we examine the amount of bend and twist in helices making up all coiled-coil proteins in SCOP. Incorporation of alpha-helix flexibility into structure refinement and design is discussed.     

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations

We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C _α , C, N, and C _β are considered. Combinations of some of these atoms are also tested. The force constants between the representative atoms are extracted from the Hessian matrix of the energy function and served as the force constants between the corresponding residues. The residue mean-square-fluctuations and their correlations with the experimental B-factors are calculated for a large set of proteins. The results are compared with all-atom normal mode analysis and the residue-level Gaussian Network Model. The coarse-grained methods perform more efficiently than all-atom normal mode analysis, while their B-factor correlations are also higher. Their B-factor correlations are comparable with those estimated by the Gaussian Network Model and in many cases better. The extracted force constants are surveyed for different pairs of residues with different numbers of separation residues in sequence. The statistical averages are used to build a refined Gaussian Network Model, which is able to predict residue-level structural fluctuations significantly better than the conventional Gaussian Network Model in many test cases.     

Analysis of the stress effects of endocrine disrupting chemicals (EDcs) on Escherichia coli

In this study, three of the representative EDCs, 17beta-estradiol, bisphenol A, and styrene, were employed to find their mode of toxic actions in E. coli. To accomplish this, four different stress response genes, recA, katG, fabA, and grpE genes, were used as a representative for DNA, oxidative, membrane, or protein damage, respectively. The expression levels of these four genes were quantified using a real-time RT-PCR after challenge with three different EDCs individually. Bisphenol A and styrene caused high-level expression of recA and katG genes, respectively, whereas 17beta-estradiol made no significant changes in expression of any of those genes. These results lead to the classification of the mode of toxic actions of EDCs on E. coli.     

Covalent complexes of proteasome model with peptide aldehyde inhibitors MG132 and MG101: docking and molecular dynamics study

20S proteasome plays a critical role in the regulation of several important cellular processes and has drawn extensive interest in the field of anti-tumor research. Peptide aldehydes can inhibit the 20S proteasome activity by covalently binding to the active site of the β subunits. In this work, covalent docking in conjunction with molecular dynamics (MD) simulation was used to explore the binding mode of MG132. Two conformations with the lowest docking energy were selected as the representative binding modes. One of the conformations was confirmed as a more reasonable binding mode by molecular dynamics simulations. The binding mode analysis revealed that a space demanding aromatic group with a short linker at the P4 site of the peptide aldehyde inhibitor would form favorable hydrophobic contacts with the neighboring subunit. A bulky substituent at the P2 position would also increase the binding stability by reducing water accessibility of the covalent bond. This study contributed to our understanding of the mechanism and structure-activity relationship of the peptide aldehyde inhibitors and may provide useful information for rational drug design.     

Prediction of the binding mode between BMS-378806 and HIV-1 gp120 by docking and molecular dynamics simulation

BMS-378806 is a newly discovered small molecule that effectively blocks the binding of CD4 with gp120. The binding mode of this kind of inhibitor remains unknown. In this paper, AutoDock 3.0 in conjunction with molecular dynamics simulation, accommodating the receptor's flexibility, was used to explore the binding mode between BMS-378806 and gp120. Two structures, Mode I and Mode II, with the lowest docking energy were selected as different representative binding modes. The analysis of the results from the molecular dynamics simulation indicated that the binding of BMS-348806 in Mode II is more stable. The average structure of Mode II was analyzed and compared with the experimental data. The conclusion was that BMS-378806 inserts the azaindole ring deeply into the PHE43 cavity and makes contact with a number of residues in the cavity, on the cavity and near the cavity. This study benefits the understanding of the mechanism of this kind of inhibitor and may provide useful information for rational drug design.     

宏基因组学分析揭示深古菌Bathyarchaeota B242的代谢特征

【背景】海洋沉积物中蕴含着丰富的微生物资源,估算约2.9×1029个细胞,与海水中的微生物总量相当。但是由于缺少可培养物,大部分的微生物缺乏生理特征、代谢方式以及生态功能的相关研究。深古菌(Bathyarchaeota)是一类典型的未培养微生物,在全球海洋沉积物中普遍存在,并且具有很高的丰度。【目的】对深古菌代谢潜能及其在海洋沉积物中发挥的生态功能进行更加深入的研究。【方法】应用宏基因组学的技术手段,对采集自瓜伊马斯盆地的深海热液沉积物样本进行了分析,获得了一个接近完整的深古菌基因组Bathyarchaeota B242。【结果】对Bathyarchaeota B242基因组的分析发现,其具有以降解蛋白质和多种碳水化合物为主的异养代谢途径,同时还具有通过还原型乙酰辅酶A途径实现的自养途径。【结论】同时具有自养和异养代谢途径对Bathyarchaeota B242适应低物质能量供给环境下的生存起到重要作用。     

The development of 2-benzimidazole substituted pyrimidine based inhibitors of lymphocyte specific kinase (Lck)

This communication details the synthesis, biological activity, and binding mode of a novel class of 2-benzimidazole substituted pyrimidines. The most potent analogs disclosed showed low nanomolar activity for the inhibition of Lck kinase and a representative analog was co-crystallized with Hck (a structurally related member of the Src family kinases).     

Structure-based design and protein X-ray analysis of a protein kinase inhibitor.

A 5-aryl-1H-pyrazole molecular scaffold was designed to ligate the ATP binding site of cyclin dependent kinase 2 (CDK2) on the basis of crystallographic information. A search of the compound collection of Novartis using this scaffold as substructure query led to the identification of PKF049-365 as a representative of a new class of inhibitors of the cell cycle kinases CDK1/2. The three-dimensional structure of CDK2 in complex with PKF049-365 was subsequently determined by protein crystallography and refined to 1.53 A resolution. The X-ray analysis confirmed the binding mode expected from the design hypothesis. In addition, it revealed an alternative binding orientation involving a second tautomeric form of the inhibitor that was not envisaged during the design stage.     

生态产品价值实现模式应用场景及其运行机制——基于典型案例文本数据的实证分析

因地制宜选择实现模式是建立健全生态产品价值实现机制、践行"两山理论"的重要举措。利用自然资源部和生态环境部推介的生态产品价值实现典型案例文本词频数据,采用随机森林分析方法,从自然资本、生态服务和参与主体三个角度,实证总结了不同价值实现模式的应用场景及其运行机制。研究表明:生态产业化经营模式主要是用于农地自然资本,通过市场手段激励农户等经营主体参与,提升农地供给生态产品的功能。生态资源指标及产权交易模式主要是用于林地自然资本,通过生态权益交易,协调公共和私人部门之间的利益,以保护森林的调节服务功能。生态补偿模式主要是用于水域自然资本,通过建立受益者和保护者之间的补偿机制,提升水域的调节和供给服务功能。生态修复及价值提升模式主要是用于废弃工矿用地自然资本,通过政府部门和市场主体联合开展修复整治,提升废弃工矿用地的文化服务和供给功能。研究结果为因地制宜建立生态产品价值实现推进机制提供政策参考。     

Biodelivery of a fullerene derivative

Most current nanotoxicology research is focused on examining the influence of nanomaterials at the tissue and cellular levels. To explore these interactions on the molecular level, new carboxyfullerenes interact with transport proteins at the molecular level. The carboxyfullerenes exhibited an unusual mode of binding outside the calyx of beta-lactoglobulin (a typical representative of lipocalin family of barrier liquid proteins). The complexes were studied by various techniques, including mass spectrometry, UV/vis and circular dichroism spectroscopy, chromatographic methods, gel electrophoresis, and dynamic light scattering. The fullerene ligands were transferred from beta-lactoglobulin to human serum albumin (a representative of a blood transport protein), thus providing a model of how fullerene-based nanomaterials interact with biomolecules and are transported in biological systems.     

Benzimidazole inhibitors of the protein kinase CHK2: Clarification of the binding mode by flexible side chain docking and protein–ligand crystallography

Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature.     

Monosaccharide inhibitors targeting carbohydrate esterase family 4 de-N-acetylases

The Carbohydrate Esterase family 4 contains virulence factors which modify peptidoglycan and biofilm-related exopolysaccharides. Despite the importance of this family of enzymes, a potent mechanism-based inhibition strategy has yet to emerge. Based on the postulated tridentate binding mode of the tetrahedral de-N-acetylation intermediate, GlcNAc derivatives bearing metal chelating groups at the 2 and 3 positions were synthesized. These scaffolds include 2-C phosphonate, 2-C sulfonamide, 2-thionoacetamide warheads as well as derivatives bearing thiol, amine and azide substitutions at the 3-position. The inhibitors were assayed against a representative peptidoglycan deacetylase, Pgda from Streptococcus pneumonia, and a representative biofilm-related exopolysaccharide deacetylase, PgaB from Escherichia coli. Of the inhibitors evaluated, the 3-thio derivatives showed weak to moderate inhibition of Pgda. The strongest inhibitor was benzyl 2,3-dideoxy-2-thionoacetamide-3-thio-β-d-glucoside, whose inhibitory potency showed an unexpected dependence on metal concentration and was found to have a partial mixed inhibition mode (K_i?=?2.9?±?0.6?μM).     

Synthesis and structural analysis of palladium biscarbene complexes derived from bisimidazolium ligand precursors

The palladation of potentially chelating bisimidazolium ligand precursors with palladium acetate gives bridging bimetallic, chelating monometallic, and homoleptic tetracarbene complexes. The coordination mode of the biscarbene ligand has been identified by spectroscopic analysis and crystallographic characterization of representative complexes, including the first example of a biscarbene A-frame structure. Substantial concentrations of free acetate favor the formation of tetracarbene over biscarbene palladium complexes, while in the absence of a base, the concentration of reactants influences the selectivity for bridging bimetallic versus chelating monometallic species. Preliminary kinetic and mechanistic studies indicate that chelating biscarbene palladium acetate complexes are intermediates in the formation of the homoleptic tetracarbene complexes. Probably due to the high trans effect of the biscarbene ligand, such complexes are more efficient palladating agents for bisimidazolium salts than palladium acetate.     

Pyrrolo[2,3-b]quinoxalines as inhibitors of firefly luciferase: Their Cu-mediated synthesis and evaluation as false positives in a reporter gene assay

2-Substituted pyrrolo[2,3-b]quinoxalines having free NH were prepared directly from 3-alkynyl-2-chloroquinoxalines in a single pot by using readily available and inexpensive methane sulfonamide (or p-toluene sulfonamide) as an ammonia surrogate. The reaction proceeded in the presence of Cu(OAc)₂ affording the desired product in moderate yield. The crystal structure analysis of a representative compound and its supramolecular interactions are presented. Some of the compounds synthesized exhibited inhibitory activities against luciferase that was supported by the predictive binding mode of these compounds with luciferase enzyme through molecular docking studies. The key observations disclosed here can alert users of luciferase reporter gene assays for possible false positive results due to the direct inhibition of luciferase.     

Halothiophene benzimidazoles as P1 surrogates of inhibitors of blood coagulation factor Xa

Neutral weak halothiophene benzimidazole inhibitors of the serine protease factor Xa were identified via screening of a compound library. The X-ray crystal structure of representative 3a bound to human fXa confirmed the S1 binding mode. Starting from 3a a series of halothiophene benzimidazoles was synthesized and investigated for their factor Xa inhibitory activity. This led to potent and selective achiral inhibitors against fXa such as compounds 9k and 9w.     

Australian aborigines represent the first branch from Eurasian antecedents: odontometric evidence

Most genetic data suggest that Australian aborigines and Southeast Asians associate, but their relative evolutionary relationship has remained obscure. Historically, the study of tooth crown variables has been important in establishing phylogenetic relationships. Through the quantification of whole tooth structure (GDP), including root, pulp, and enamel, a likely Eurasian phylogeny emerged from a canonical discriminant analysis of the microevolution among the populations. The analysis suggested that in modern human evolutionary history, Australian aborigines are the best representative extant population (first branch) from an unknown antecedent Eurasian founder population. The next branch from the Asian-based antecedent population was Caucasoids. Within the resident antecedent East Asian population, Southeast Asians then evolved, followed by a branch that lead to antecedent east Central Asians. Mongolians and all Native Americans independently evolved from this antecedent east Central Asian population. The relatively short morphogenetic separation between two areas that have been isolated for great periods of time, i.e., Australian aborigines and Native Americans, suggests that their association is not due to gene flow.