Linkers in the structural biology of protein–protein interactions

Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly‐rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly‐rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein–protein complex. Gly‐rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand‐binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X‐ray crystallography, nuclear magnetic resonance and cryo‐electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein–protein complexes, and to obtain protein dimers.     

Swissknife - 'lazy parsing' of SWISS-PROT entries.

SUMMARY: We present Swissknife, a set of Perl modules which provides a fast and reliable object-oriented interface to parsing and modifying files in SWISS-PROT format. AVAILABILITY: The Swissknife modules are available at ftp://ftp.ebi.ac. uk/pub/software/swissprot/. CONTACT: hhe@ebi.ac.uk     

The ModFOLD server for the quality assessment of protein structural models

The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment. AVAILABILITY: http://www.biocentre.rdg.ac.uk/bioinformatics/ModFOLD/.     

Metal–ion interactions and the structural organization of Sepia eumelanin

The structural organization of melanin granules isolated from ink sacs of Sepia officinalis was examined as a function of metal ion content by scanning electron microscopy and atomic force microscopy. Exposing Sepia melanin granules to ethelenediaminetetraacetic acid (EDTA) solution or to metal salt solutions changed the metal content in the melanin, but did not alter granular morphology. Thus ionic forces between the organic components and metal ions in melanin are not required to sustain the natural morphology once the granule is assembled. However, when aqueous suspensions of Sepia melanin granules of varying metal content are ultra‐sonicated, EDTA‐washed and Fe‐saturated melanin samples lose material to the solution more readily than the corresponding Ca(II) and Mg(II)‐loaded samples. The solubilized components are found to be 5,6‐dihydroxyindole‐2‐carboxylic acid (DHICA)‐rich constituents. Associated with different metal ions, Na(I), Ca(II) and Mg(II) or Fe(III), these DHICA‐rich entities form distinct two‐dimensional aggregation structures when dried on the flat surface of mica. The data suggest multiply‐charged ions play an important role in assisting or templating the assembly of the metal‐free organic components to form the three‐dimensional substructure distributed along the protein scaffold within the granule.     

Evaluation of the structural quality of modeled proteins by using globularity criteria

Background  

The knowledge of the three-dimensional structure of globular proteins is fundamental for a detailed investigation of their functional properties. Experimental methods are too slow for structure investigation on a large scale, while computational prediction methods offer alternatives that are continuously being improved. The international Comparative Assessment of Structure Prediction (CASP), an "a posteriori" evaluation of the quality of theoretical models when the experimental structure becomes available, demonstrates that predictions can be successful as well as unsuccessful, and this suggests the necessity for evaluations able to discard "a priori" the wrong models.     

Sol–sol structural transition of aqueous agarose systems

A structural transition is reported to occur in aqueous sols of agarose, an electrically uncharged biostructural polysaccharide. The transition has no measurable effect on size dispersity on the shape of the solute polysaccharide as observed by precision photon correlation spectroscopy. It originates a low-angle pattern of scattered light similar to that which monitors phase separations in polymer blends. Thus, it must be due to some extent to spatially modulated polymer clustering, typical of spinodal decomposition. In the interval of temperatures studied, it precedes very distinctly in time the thermoreversible sol–gel transition, which is known to be promoted at higher concentrations. It also anticipates to an appreciable extent the spatial density modulation observed in the gel. Although reported here for the first time, a spinodal decomposition of the sol that precedes and possibly triggers the processes leading to gelation does not come unexpectedly in terms of site-bond correlated-percolation theory. In general, this occurrence raises the question as to whether the spontaneous onset of regions of higher and lower polymer concentration (spinodal separation) may be regarded as a novel path for biomolecular interactions and the self-assembly of order in biomolecular systems.     

Trade-associated pathways of alien forest insect entries in Canada

Long-distance introductions of new invasive species have often been driven by socioeconomic factors, such that traditional “biological” invasion models may not be capable of estimating spread fully and reliably. In this study we present a new methodology to characterize and predict pathways of human-assisted entries of alien forest insects. We have developed a stochastic quantitative model of how these species may be moved with commodity flow through a network of international marine ports and major transportation corridors in Canada. The study makes use of a Canadian roadside survey database and data on Canadian marine imports, complemented with geo-referenced information on ports of entry, populated places and empirical observations of historical spread rates for invasive pests. The model is formulated as a probabilistic pathway matrix, and allows for quantitative characterization of likelihoods and vectors of new pest introductions from already or likely-to-be infested locations. We applied the pathway model to estimate the rates of human-assisted entry of alien forest insect species across Canada as well as cross-border transport to locations in the US. Results suggest a relatively low nationwide entry rate for Canada when compared to the US (0.338 new forest insect species per year vs. 1.89). Among Canadian urban areas, Greater Toronto and Greater Vancouver appear to have the highest alien forest insect entry potential, exhibiting species entry rates that are comparable with estimated rates at mid-size US urban metropolises.     

Many Genbank entries for complete microbial genomes violate the Genbank standard

A survey of Genbank entries for complete microbial genomes reveals that the majority do not conform to the Genbank standard. Typical deviations from the Genbank standard include records with information in incorrect fields, addition of extraneous and confusing information within a field, and omission of useful fields. This situation results from two principal causes: genome centres do not submit Genbank records in the proper form and the Genbank, EMBL and DDBJ staffs do not enforce the database standards that they have defined.     

Stabilizing cumulative incidence estimation of pregnancy outcome with delayed entries

A pregnancy may end up with (at least) three possible events: live birth, spontaneous abortion, or elective termination, yielding a competing risks issue when studying an association between a risk factor and a pregnancy outcome. Cumulative incidences (probabilities to end up with the different outcomes depending on gestational age) can be estimated via the Aalen–Johansen estimate. Another issue is that women are usually not entering such an observational study from the first day of pregnancy, resulting in delayed entries. As in traditional survival analysis, this can be solved by considering “at risk” at a given gestational age only for those women who entered the study before that age. However, the number of women at risk at an early gestational age might be extremely low, such that the estimates of cumulative incidence may increase exaggeratedly at that age because of a single event. One solution to reduce the problem has been recently proposed in the literature, which is to ignore simply those early events, creating a small mean bias but enhancing stability of estimates. In the present paper, we propose an alternative computationally simple approach to tackle this problem that consists to postpone to later gestational ages (rather than to ignore) those early events. The two approaches are compared with respect to bias, stability, and sensitivity on the smoothing parameter via simulations reproducing realistic pregnancy scenarios, and are illustrated with data from a study on the effects of statins on pregnancy outcomes. We also outline that all three approaches are asymptotically equivalent.     

许昌市2009—2013年麻疹流行病学特征和监测系统运转状况分析

目的分析许昌市2009—2013年麻疹流行特征和监测系统运转状况,为加速消除麻疹制定策略及措施提供科学依据。方法利用描述性流行病学方法对许昌市2009—2013年麻疹监测系统资料进行统计分析。结果许昌市2009—2013年累计报告麻疹病例675例,年均报告发病率为3.16/10万。全市8个县、市区均有病例报告,病例数主要集中在禹州市,占总病例数的55.56%;发病呈明显的季节性分布,主要集中在2—5月份,占总病例数的73.48%;病例主要集中于0~6岁儿童,占总病例数的85.63%,其中1岁以下婴幼儿占总病例数的50.22%;8月龄~14岁麻疹病例中有确切免疫史者仅占38.58%。随着监测系统及时性和特异性逐年提高,48 h完整调查率由2009年的88.32%上升至2012年的100%;血标本3 d内送达率由2009年的51.68%上升至2013年的100%;实验室结果 7 d内报告率由2009年的52.80%上升至2013年的100%;血标本采集率从2009年48.86%上升至2013年的100%;暴发血清学确诊率、病原学标本采集率均上升至100%。2009—2013年麻疹监测系统敏感性低,排除病例报告发病率为0.49/10万~1.43/10万。结论 2009—2013年许昌市麻疹发病率下降,小年龄组发病构成增加。监测系统运转综合质量逐年提升,但敏感性低。今后应进一步加强麻疹类疫苗接种与管理,提高人群免疫水平;加强医疗机构传染病报告与管理,提高监测系统敏感性,防止传染源扩散。     

Analysis of longitudinal marginal structural models

In this article we construct and study estimators of the causal effect of a time-dependent treatment on survival in longitudinal studies. We employ a particular marginal structural model (MSM), proposed by Robins (2000), and follow a general methodology for constructing estimating functions in censored data models. The inverse probability of treatment weighted (IPTW) estimator of Robins et al. (2000) is used as an initial estimator and forms the basis for an improved, one-step estimator that is consistent and asymptotically linear when the treatment mechanism is consistently estimated. We extend these methods to handle informative censoring. The proposed methodology is employed to estimate the causal effect of exercise on mortality in a longitudinal study of seniors in Sonoma County. A simulation study demonstrates the bias of naive estimators in the presence of time-dependent confounders and also shows the efficiency gain of the IPTW estimator, even in the absence such confounding. The efficiency gain of the improved, one-step estimator is demonstrated through simulation.     

Analysis of the structural specificity of the lactose permease toward sugars

The sugar specificity properties of the lactose permease were investigated. Free galactose was shown to competitively inhibit the lactose permease yielding a Ki value of 7.4 mM. This value was severalfold higher than the observed Km for lactose (1.3 mM). A variety of other monosaccharides also showed significant inhibition of lactose transport. With regard to -OH groups along the galactose ring it appears that the relative importance is OH-3 greater than OH-4 greater than OH-6 greater than OH-2 greater than OH-1. In general, galactosides with alpha-linkages exhibited significantly higher affinities compared with their beta-linked counterparts. An optimal size for the aglycone portion of the galactoside was reached with aglycones containing hexose residues or a benzene ring. The preferred size of the aglycone appears to be hexose, benzene ring greater than methyl group greater than no aglycone much greater than disaccharide greater than trisaccharide. However, neither the specific structure of the aglycone nor its relative hydrophobicity appeared to be important factors in permease recognition. For example, the hydrophobic beta-nitrophenyl-galactosides had lower affinities compared with lactose (a beta-galactoside), whereas the alpha-nitrophenylgalactosides generally had higher affinities compared with melibiose (an alpha-galactoside). In addition, no consistent preference was seen when considering the location of the nitro group on the benzene ring. From this work, a model is presented which depicts the binding of galactosides to the lactose permease.     

The structural analysis of protein–protein interactions by NMR spectroscopy

A comprehensive understanding of protein–protein interactions is an important next step in our quest to understand how the information contained in a genome is put into action. Although a number of experimental techniques can report on the existence of a protein– protein interaction, very few can provide detailed structural information. NMR spectroscopy is one of these, and in recent years several complementary NMR approaches, including residual dipolar couplings and the use of paramagnetic effects, have been developed that can provide insight into the structure of protein–protein complexes. In this article, we review these approaches and comment on their strengths and weaknesses.     

Analysis of structural robustness of metabolic networks

We study the structural robustness of metabolic networks on the basis of the concept of elementary flux modes. It is shown that the number of elementary modes itself is not an appropriate measure of structural robustness. Instead, we introduce three new robustness measures. These are based on the relative number of elementary modes remaining after the knockout of enzymes. We discuss the relevance of these measures with the help of simple examples, as well as with larger, realistic metabolic networks. Thereby we demonstrate quantitatively that the metabolism of Escherichia coli, which must be able to adapt to varying conditions, is more robust than the metabolism of the human erythrocyte, which lives under much more homeostatic conditions.     

Analysis and predication of structural motifs in the glycolytic enzymes

Protein crystallography has determined the three-dimensional structures of 10 of the 13 enzymes of the glycolytic pathway. Diagrams and details of these enzyme structures are given in the paper. Most of the enzyme domains are variations and extensions of a many (4--9)-stranded, predominantly or totally parallel, beta-sheet that is shielded from solvent by alpha-helices (i.e. alpha/beta structures). There are strong structural similarities between the domains of some, but not all, of the enzymes. In particular the dinucleotide binding fold of lactate dehydrogenase and the beta-barrel of triose phosphate isomerase are found in other domains. General rules governing the topology and packing of alpha-helices against a beta-sheet provide a basis for the combinatorial prediction of the tertiary fold of glycolytic domains from their amino acid sequence and observed secondary structure. The predication algorithm demonstrates that there are severe restrictions on the number of possible structures. However, these restrictions do not fully explain some of the remarkable structural similarities between different enzymes that probably result from evolution from a common ancestor.