Aromatic interactions at atom-to-atom contact and just beyond: a case study of protein interactions of NAD⁺/NADP⁺

We probed aromatic-protein interactions based on specificity of enrichment of protein residues across a contact-based cutoff. Thus, 155 protein-NAD⁺/NADP⁺ complexes were analyzed for enrichments within 10 Å of centroids of aromatic groups of the ligand when the residues were contacted and not contacted with the aromatic ligand. Specifically, neutral-adenine and cationic-nicotinamide groups of the oxidized coenzymes evoked interest to know whether the contrast of charge or the shared aromaticity will manifest in the enrichments across the cutoff. We found that when in contact, the enrichments are highly specific for nicotinamide and adenine-aromatic structures, and thus possibly complex in the basis, but when not in contact, they are generic for charge and aromaticity of the structures, and thus possibly specific in the basis. The order of enrichments over the contacted residues is Tyr > Cys > Thr > His > Asn > Ser > Met > Ile > Phe against nicotinamide-π⁺ structure and Asp > Ile > Thr > His > Arg > Tyr > Gly > Val against adenine-π structure, while the order over the non-contacted residues is Trp > Gly > His > Asn > Cys > Met > Tyr > Ser > Thr > Phe against nicotinamide-π⁺ structure and Asn > Thr > Ser > Gly > Cys > His > Val against adenine-π structure. Neutral Trp, His, Tyr, and Phe, but not cationic Arg, are thus the non-contacted residues enriched specifically against nicotinamide-π⁺ structure, while Asn, Gly, Thr, Ser, and Cys are the non-contacted residues enriched generically against both the nicotinamide-π⁺ and adenine-π aromatic structures. By analyzing the enriched groups in their geometric specificities, we found that, the enrichments against nicotinamide cation manifest the specificity expected of cation-π interaction and against nicotinamide- and adenine-aromatic groups manifest the specificity expected of dipole-π interaction. The cutoff-based method is proven valuable in probing protein-ligand interactions in the physics involved.     

Halogenated Benzenes Bound within a Non-polar Cavity in T4 Lysozyme Provide Examples of I?S and I?Se Halogen-bonding

We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume ∼ 150 Å³ that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystallography and related techniques to analyze the binding of halogen-incorporated benzenes typified by C₆F₅X, where X = H, F, Cl, Br or I, and C₆H₅X, where X = H or I was also studied. Because of the increased electron density of fluorine relative to hydrogen, the geometry of binding of the fluoro compounds can often be determined more precisely than their hydrogen-containing analogs. All of the ligands bind in essentially the same plane but the center of the phenyl ring can translate by up to 1.2 Å. In no case does the ligand rotate freely within the cavity. The walls of the cavity consist predominantly of hydrocarbon atoms, and in several cases it appears that van der Waals interactions define the geometry of binding. In comparing the smallest with the largest ligand, the cavity volume increases from 181 Å³ to 245 Å³. This shows that the protein is flexible and adapts to the size and shape of the ligand. There is a remarkably close contact of 3.0 Å between the iodine atom on C₆F₅I and the sulfur or selenium atom of Met or SeMet102. This interaction is 1.0 Å less than the sum of the van der Waals radii and is a clear example of a so-called halogen bond. Notwithstanding this close approach, the increase in binding energy for the halogen bond relative to a van der Waals contact is estimated to be only about 0.5-0.7 kcal/mol.     

农林复合系统种间关系研究进展

种间相互作用在很大程度上决定了农林复合系统的生产力和可持续性,理解种间相互作用是经营和管理农林复合系统的关键。地上部分相互作用主要包括复合系统组分对光的竞争与互利、小气候的改变对系统生产力的影响;地下部分相互作用主要包括复合系统组分对水分和养分资源的竞争与互利、固氮树种对系统生产力的影响以及化感作用。今后需加强不同立地条件下的不同农林复合系统种间关系的比较、农林复合系统组分的空间分布格局、化感作用以及农林复合系统种间关系模型等研究。     

计算方法在蛋白质相互作用研究中的应用

计算方法在蛋白质相互作用研究的各个阶段扮演了一个重要的角色。对此,作者将从以下几个方面对计算方法在蛋白质相互作用及相互作用网络研究中的应用做一个概述：蛋白质相互作用数据库及其发展;数据挖掘方法在蛋白质相互作用数据收集和整合中的应用;高通量方法实验结果的验证;根据蛋白质相互作用网络预测和推断未知蛋白质的功能;蛋白质相互作用的预测。     

Interaction between nickel and iron in the rat

The interaction between nickel and iron was confirmed in rat metabolism. In a fully-crossed, two-way, three by four, factorially designed experiment, female weanling rats were fed a basal diet supplemented with iron at 0, 25, 50, and 100 μg/g and with nickel at 0, 5, and 50 μg/g. The basal diet contained about 10 ng of nickel and 2.3 μg of iron/g. After nine weeks, dietary iron affected growth, hematocrit, hemoglobin, plasma cholesterol, and in liver affected total lipids, phospholipids, and the contents of copper, iron, manganese, and zinc. By manipulating the iron content of the diet, effects of dietary nickel were shown in rats that were not from dams fed a nickel-deprived diet. Nickel affected growth, hematocrit, hemoglobin, plasma alkaline phosphatase activity, plasma total lipids, and in liver affected total lipids, and the contents of copper, manganese, and nickel. The interaction between nickel and iron affected hematocrit, hemoglobin, plasma alkaline phosphatase activity, and plasma phospholipids, and in liver affected size, content of copper, and perhaps of manganese and nickel. In severely iron-deficient rats, the high level of dietary nickel partially alleviated the drastic depression of hematocrit and hemoglobin, and the elevation of copper in liver. Simultaneously, high dietary nickel did not increase the iron level in liver and was detrimental to growth and appearance of severely iron-deficient rats. In nickel-deprived rats fed the borderline iron-deficient diet (25 μg/g) hematocrit and hemoglobin also were depressed. However, 5 μg Ni/g of diet were just as effective as 50 μg Ni/g of diet in preventing those signs of nickel deprivation. The findings in the present study suggested that nickel and iron interact with each other at more than one locus.     

The role of hydrophobic interactions in ankyrin-spectrin complex formation

Spectrin and ankyrin are the key components of the erythrocyte cytoskeleton. The recently published crystal structure of the spectrin-ankyrin complex has indicated that their binding involves complementary charge interactions as well as hydrophobic interactions. However, only the former is supported by biochemical evidence. We now show that nonpolar interactions are important for high affinity complex formation, excluding the possibility that the binding is exclusively mediated by association of distinctly charged surfaces. Along these lines we report that substitution of a single hydrophobic residue, F917S in ankyrin, disrupts the structure of the binding site and leads to complete loss of spectrin affinity. Finally, we present data showing that minimal ankyrin binding site in spectrin is formed by helix 14C together with the loop between helices 15 B/C.     

The dynamics of predation risk assessment: responses of anuran larvae to chemical cues of predators

1. While the antipredator behaviour of prey has been well studied, little is known about the rules governing the predation risk assessment of prey. In this study, I measured the activity levels of predator-naive green frog (Rana clamitans) tadpoles during and after exposures to the chemical cue of predatory larval dragonflies (Anax spp.). I then used the lengths of the time lags from the end of the cue exposures until the tadpoles returned to a control level of activity as an index of the perceived risk of the tadpoles. 2. While tadpoles always responded upon exposure to the Anax chemical cue by strongly reducing their activity level, their perceived risk increased asymptotically over time during the initial period of the cue exposure. Tadpoles of all size classes perceived increasing risk in proportion to chemical cue concentration, but the length of time that tadpoles responded during cue exposure and the length of their post-exposure time lags decreased with increasing body mass. 3. The results suggest that the perceived risk of green frog tadpoles varies over time and does not correspond directly to their behavioural response (i.e. activity level). However, their perceived risk does appear to vary in accordance with the predation risk associated with the Anax chemical cue and the reliability of the information from the cue, and therefore may be predictable.     

Detecting temporal protein complexes from dynamic protein-protein interaction networks

Background

Proteins dynamically interact with each other to perform their biological functions. The dynamic operations of protein interaction networks (PPI) are also reflected in the dynamic formations of protein complexes. Existing protein complex detection algorithms usually overlook the inherent temporal nature of protein interactions within PPI networks. Systematically analyzing the temporal protein complexes can not only improve the accuracy of protein complex detection, but also strengthen our biological knowledge on the dynamic protein assembly processes for cellular organization.

Results

In this study, we propose a novel computational method to predict temporal protein complexes. Particularly, we first construct a series of dynamic PPI networks by joint analysis of time-course gene expression data and protein interaction data. Then a Time Smooth Overlapping Complex Detection model (TS-OCD) has been proposed to detect temporal protein complexes from these dynamic PPI networks. TS-OCD can naturally capture the smoothness of networks between consecutive time points and detect overlapping protein complexes at each time point. Finally, a nonnegative matrix factorization based algorithm is introduced to merge those very similar temporal complexes across different time points.

Conclusions

Extensive experimental results demonstrate the proposed method is very effective in detecting temporal protein complexes than the state-of-the-art complex detection techniques.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-335) contains supplementary material, which is available to authorized users.     

基于蛋白质组芯片的结核分枝杆菌系统生物学研究进展

近些年全球结核病疫情愈发严重,耐药性结核病使其雪上加霜。一个重要原因是结核病新药的匮乏以及结核分枝杆菌相关基础研究的不足。因此迫切需要开发新的技术以促进结核病系统生物学基础研究,并在此基础上研究新机制,发现新靶标,开发新药物。结核分枝杆菌功能蛋白质组芯片的出现旨在促进结核病相关研究工作。考虑到结核分枝杆菌高毒力、复制周期长和需要在生物安全三级实验室中开展研究等特点和难点,该工具为结核病相关研究人员提供了一个强有力的武器。目前这一技术手段的应用已经使我们对结核分枝杆菌-宿主相互作用、小分子-蛋白结合以及抗生素耐药性机制等关键生物过程有了更深入的了解。为了更好地帮助同行了解这一有效的工具,本文综述了结核分枝杆菌功能蛋白组芯片的几种主要应用,期望同行专家能更好地将其应用于结核病相关的基础研究中。     

Recent advances in RNA-protein interaction studies

Conclusions The RNA binding sites for several small proteins have been characterised. These sites include double helical regions with hairpins, bulged bases and internal loops. As seen in Flock House virus structure, some proteins may recognise phosphate backbone of the canonical A-form helix not in a sequence-specific manner. If sequence-specific base contacts are to be made, then the A-helic major groove must be widened. This can be accomplished by introducing bulges, internal loops and hairpin loops into double helical regions. In these cases proteins may recognise both distorted backbone conformations and read out base sequences in a widened major groove. Crystallographic studies on complexes of aminoacyl-tRNA synthetase and tRNA showed that even RNAs with stable tertiary fold undergo substantial structural changes upon binding to the synthetases. The structural variability of RNA as well as the ability of RNA to distort upon protein binding may be crucial in RNA-protein interactions.     

蛋白质相互作用数据库及其应用

对蛋白质相互作用及其网络的了解不仅有助于深入理解生命活动的本质和疾病发生的机制,而且可以为药物研发提供靶点.目前,通过高通量筛选、计算方法预测和文献挖掘等方法,获得了大批量的蛋白质相互作用数据,并由此构建了很多内容丰富并日益更新的蛋白质相互作用数据库.本文首先简要阐述了大规模蛋白质相互作用数据产生的3种方法,然后重点介绍了几个人类相关的蛋白质相互作用公共数据库,包括HPRD、BIND、 IntAct、MINT、 DIP 和MIPS,并概述了蛋白质相互作用数据库的整合情况以及这些数据库在蛋白质相互作用网络构建上的应用.     

Identification of electrostatic interaction sites between the regulatory and catalytic subunits of cyclic AMP-dependent protein kinase

Two classes of molecules inhibit the catalytic subunit (C) of the cyclic AMP-dependent protein kinase (cAPK), the heat-stable protein kinase inhibitors (PKIs) and the regulatory (R) subunits. Basic sites on C, previously identified as important for R/C interaction in yeast TPKI and corresponding to Lys213, Lys217, and Lys189 in murine Cα, were replaced with either Ala or Thr and characterized for their kinetic properties and ability to interact with RI and PKI. rC(K213A) and rC(K217A) were both defective in forming holoenzyme with RI but were inhibited readily with PKI. This contrasts with rC(R133A), which is defective in binding PKI but not RI (Wen & Taylor, 1994). Thus, the C-subunit employs two distinct electrostatic surfaces to achieve high-affinity binding with these two types of inhibitory molecules even though all inhibitors share a common consensus site that occupies the active site cleft. Unlike TPK1, mutation of Lys189 had no effect. The mutant C subunits that were defective in binding RI, rC(K213A) and rC(K217A), were then paired with three RI mutants, rRI(D140A), rRI(E143A), and rRI(D258A), shown previously to be defective in recognition of C. Although the mutations at Asp140 and Asp258 in RI were additive with respect to the C mutations, rC(K213A) and rRI(E143A) were compensatory, thus identifying a specific electrostatic interaction site between RI and C. The results are discussed in terms of the RI and C crystal structures and the sequence homology between the yeast and mammalian enzymes.     

Oviposition behavior ofDrosophila subobscura and its parasitoidAsobara tabida in the laboratory

At 18°C, adultAsobara tabida emerge 21 days after oviposition within the host;Drosophila subobscura emerges 18 days after oviposition. The relatively short pre-oviposition period of adultA. tabida (4 days), compared to that ofD. subobscura (4–8 days) results in the generation times of both host and parasitoid being approximately similar. A yeast source is necessary forD. subobscura females to mature their eggs; female flies will not oviposit on patches without a yeast source. While surface roughness is an important characteristic for maximumD. subobscura oviposition,A. tabida oviposition, and consequent levels of parasitism, is enhanced by coating patches with askin of active yeast. When presented with a multi-patch environment, experienced and inexperienced female wasps showed no significant difference in their level of attack.     

Predator avoidance behavior in the pea aphid: costs,frequency, and population consequences

Induced prey defenses can be costly. These costs have the potential to reduce prey survival or reproduction and, therefore, prey population growth. I estimated the potential for predators to suppress populations of pea aphids (Acyrthosiphon pisum) in alfalfa fields through the induction of pea aphid predator avoidance behavior. I quantified (1) the period of non-feeding activity that follows a disturbance event, (2) the effect of frequent disturbance on aphid reproduction, and (3) the frequency at which aphids are disturbed by predators. In combination, these three values predict that the disturbances induced by predators can substantially reduce aphid population growth. This result stems from the high frequency of predator-induced disturbance, and the observation that even brief disturbances reduce aphid reproduction. The potential for predators to suppress prey populations through induction of prey defenses may be strongest in systems where (1) predators frequently induce prey defensive responses, and (2) prey defenses incur acute survival or reproductive costs. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Analysis and prediction of drug–drug interaction by minimum redundancy maximum relevance and incremental feature selection

Drug–drug interaction (DDI) defines a situation in which one drug affects the activity of another when both are administered together. DDI is a common cause of adverse drug reactions and sometimes also leads to improved therapeutic effects. Therefore, it is of great interest to discover novel DDIs according to their molecular properties and mechanisms in a robust and rigorous way. This paper attempts to predict effective DDIs using the following properties: (1) chemical interaction between drugs; (2) protein interactions between the targets of drugs; and (3) target enrichment of KEGG pathways. The data consisted of 7323 pairs of DDIs collected from the DrugBank and 36,615 pairs of drugs constructed by randomly combining two drugs. Each drug pair was represented by 465 features derived from the aforementioned three categories of properties. The random forest algorithm was adopted to train the prediction model. Some feature selection techniques, including minimum redundancy maximum relevance and incremental feature selection, were used to extract key features as the optimal input for the prediction model. The extracted key features may help to gain insights into the mechanisms of DDIs and provide some guidelines for the relevant clinical medication developments, and the prediction model can give new clues for identification of novel DDIs.     

Analyzing protein–protein interactions in the post-interactomic era. Are we ready for the endgame?

Mapping protein–protein interactions in genome-wide scales revealed thousands of novel binding partners in each of the explored model organisms. Organizing these hits in comprehensive ways is becoming increasingly important for systems biology approaches to understand complex cellular processes and diseases. However, proteome wide interaction techniques and their resulting global networks are not revealing the topologies of networks that are truly operating in the cell. In this short review I will discuss which prerequisites have to be fulfilled and which experimental methods might be practicable to translate primary protein interaction data into network presentations that help in understanding cellular processes.     

蛋白质－DNA相互作用与真核基因转录

结合最近几年对真核转录调节因子和ＤＮＡ的结构与机能研究,概述了蛋白质－蛋白质及蛋白质－ＤＮＡ相互作用方式以及介导相互作用的分子结构基础,论述了转录因子之间,转录因子与ＤＮＡ之间相互作用过程中的同与拮抗作用,发生机制及其在真核基因转录调节中的遍性和重要意义。     

Predicting enhancer-promoter interaction from genomic sequence with deep neural networks

Background: In the human genome, distal enhancers are involved in regulating target genes through proximal promoters by forming enhancer-promoter interactions. Although recently developed high-throughput experimental approaches have allowed us to recognize potential enhancer-promoter interactions genome-wide, it is still largely unclear to what extent the sequence-level information encoded in our genome help guide such interactions. Methods: Here we report a new computational method (named “SPEID”) using deep learning models to predict enhancer-promoter interactions based on sequence-based features only, when the locations of putative enhancers and promoters in a particular cell type are given. Results: Our results across six different cell types demonstrate that SPEID is effective in predicting enhancer-promoter interactions as compared to state-of-the-art methods that only use information from a single cell type. As a proof-of-principle, we also applied SPEID to identify somatic non-coding mutations in melanoma samples that may have reduced enhancer-promoter interactions in tumor genomes. Conclusions: This work demonstrates that deep learning models can help reveal that sequence-based features alone are sufficient to reliably predict enhancer-promoter interactions genome-wide.