Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis

We perform a large-scale study of intrinsically disordered regions in proteins and protein complexes using a non-redundant set of hundreds of different protein complexes. In accordance with the conventional view that folding and binding are coupled, in many of our cases the disorder-to-order transition occurs upon complex formation and can be localized to binding interfaces. Moreover, analysis of disorder in protein complexes depicts a significant fraction of intrinsically disordered regions, with up to one third of all residues being disordered. We find that the disorder in homodimers, especially in symmetrical homodimers, is significantly higher than in heterodimers and offer an explanation for this interesting phenomenon. We argue that the mechanisms of regulation of binding specificity through disordered regions in complexes can be as common as for unbound monomeric proteins. The fascinating diversity of roles of disordered regions in various biological processes and protein oligomeric forms shown in our study may be a subject of future endeavors in this area.     

Structural and Functional Characterization of the Mumps Virus Phosphoprotein

The phosphoprotein (P) is virally encoded by the Rhabdoviridae and Paramyxoviridae in the order Mononegavirales. P is a self-associated oligomer and forms complexes with the large viral polymerase protein (L), the nucleocapsid protein (N), and the assembled nucleocapsid. P from different viruses has shown structural diversities even though their essential functions are the same. We systematically mapped the domains in mumps virus (MuV) P and investigated their interactions with nucleocapsid-like particles (NLPs). Similar to other P proteins, MuV P contains N-terminal, central, and C-terminal domains with flexible linkers between neighboring domains. By pulldown assays, we discovered that in addition to the previously proposed nucleocapsid binding domain (residues 343 to 391), the N-terminal region of MuV P (residues 1 to 194) could also bind NLPs. Further analysis of binding kinetics was conducted using surface plasmon resonance. This is the first observation that both the N- and C-terminal regions of a negative-strand RNA virus P are involved in binding the nucleocapsid. In addition, we defined the oligomerization domain (P_OD) of MuV P as residues 213 to 277 and determined its crystal structure. The tetrameric MuV P_OD is formed by one pair of long parallel α-helices with another pair in opposite orientation. Unlike the parallel orientation of each α-helix in the tetramer of Sendai virus P_OD, this represents a novel orientation of a P_OD where both the N- and the C-terminal domains are at either end of the tetramer. This is consistent with the observation that both the N- and the C-terminal domains are involved in binding the nucleocapsid.     

Edge Length and Surface Area of a Blank: Experimental Assessment of Measures,Size Predictions and Utility

Blank size and form represent one of the main sources of variation in lithic assemblages. They reflect economic properties of blanks and factors such as efficiency and use life. These properties require reliable measures of size, namely edge length and surface area. These measures, however, are not easily captured with calipers. Most attempts to quantify these features employ estimates; however, the efficacy of these estimations for measuring critical features such as blank surface area and edge length has never been properly evaluated. In addition, these parameters are even more difficult to acquire for retouched implements as their original size and hence indication of their previous utility have been lost. It has been suggested, in controlled experimental conditions, that two platform variables, platform thickness and exterior platform angle, are crucial in determining blank size and shape meaning that knappers can control the interaction between size and efficiency by selecting specific core angles and controlling where fracture is initiated. The robustness of these models has rarely been tested and confirmed in context other than controlled experiments. In this paper, we evaluate which currently employed caliper measurement methods result in the highest accuracy of size estimations of blanks, and we evaluate how platform variables can be used to indirectly infer aspects of size on retouched artifacts. Furthermore, we investigate measures of different platform management strategies that control the shape and size of artifacts. To investigate these questions, we created an experimental lithic assemblage, we digitized images to calculate 2D surface area and edge length, which are used as a point of comparison for the caliper measurements and additional analyses. The analysis of aspects of size determinations and the utility of blanks contributes to our understanding of the technological strategies of prehistoric knappers and what economic decisions they made during process of blank production.     

Phosphoprotein analysis: from proteins to proteomes

Characterization of protein modification by phosphorylation is one of the major tasks that have to be accomplished in the post-genomic era. Phosphorylation is a key reversible modification occurring mainly on serine, threonine and tyrosine residues that can regulate enzymatic activity, subcellular localization, complex formation and degradation of proteins. The understanding of the regulatory role played by phosphorylation begins with the discovery and identification of phosphoproteins and then by determining how, where and when these phosphorylation events take place. Because phosphorylation is a dynamic process difficult to quantify, we must at first acquire an inventory of phosphoproteins and characterize their phosphorylation sites. Several experimental strategies can be used to explore the phosphorylation status of proteins from individual moieties to phosphoproteomes. In this review, we will examine and catalogue how proteomics techniques can be used to answer specific questions related to protein phosphorylation. Hence, we will discuss the different methods for enrichment of phospho-proteins and -peptides, and then the various technologies for their identification, quantitation and validation.     

从结构基因组学到功能基因组学

基因组学研究随着模式生物基因组全序列测定的完成由结构基因组学阶段发展到功能基因组学阶段,基因组学成为当今最为活跃、最有影响的前沿学科.以结构基因组学的研究成果为基础,功能基因组学中各学科因其原理不同及其关键技术的特点和优势,具有各自的应用范畴和发展趋势.功能基因组学不断渗透入现代科学的各领域,促成了适用于不同研究目的新兴学科的诞生.     

Diversity of O Antigens within the Genus Cronobacter: from Disorder to Order

Cronobacter species are Gram-negative opportunistic pathogens that can cause serious infections in neonates. The lipopolysaccharides (LPSs) that form part of the outer membrane of such bacteria are possibly related to the virulence of particular bacterial strains. However, currently there is no clear overview of O-antigen diversity within the various Cronobacter strains and links with virulence. In this study, we tested a total of 82 strains, covering each of the Cronobacter species. The nucleotide variability of the O-antigen gene cluster was determined by restriction fragment length polymorphism (RFLP) analysis. As a result, the 82 strains were distributed into 11 previously published serotypes and 6 new serotypes, each defined by its characteristic restriction profile. These new serotypes were confirmed using genomic analysis of strains available in public databases: GenBank and PubMLST Cronobacter. Laboratory strains were then tested using the current serotype-specific PCR probes. The results show that the current PCR probes did not always correspond to genomic O-antigen gene cluster variation. In addition, we analyzed the LPS phenotype of the reference strains of all distinguishable serotypes. The identified serotypes were compared with data from the literature and the MLST database (www.pubmlst.org/cronobacter/). Based on the findings, we systematically classified a total of 24 serotypes for the Cronobacter genus. Moreover, we evaluated the clinical history of these strains and show that Cronobacter sakazakii O2, O1, and O4, C. turicensis O1, and C. malonaticus O2 serotypes are particularly predominant in clinical cases.     

Structural basis of carotenoid cleavage: From bacteria to mammals

Carotenoids and their metabolic derivatives serve critical functions in both prokaryotic and eukaryotic cells, including pigmentation, photoprotection and photosynthesis as well as cell signaling. These organic compounds are also important for visual function in vertebrate and non-vertebrate organisms. Enzymatic transformations of carotenoids to various apocarotenoid products are catalyzed by a family of evolutionarily conserved, non-heme iron-containing enzymes named carotenoid cleavage oxygenases (CCOs). Studies have revealed that CCOs are critically involved in carotenoid homeostasis and essential for the health of organisms including humans. These enzymes typically display a high degree of regio- and stereo-selectivity, acting on specific positions of the polyene backbone located in their substrates. By oxidatively cleaving and/or isomerizing specific double bonds, CCOs generate a variety of apocarotenoid isomer products. Recent structural studies have helped illuminate the mechanisms by which CCOs mobilize their lipophilic substrates from biological membranes to perform their characteristic double bond cleavage and/or isomerization reactions. In this review, we aim to integrate structural and biochemical information about CCOs to provide insights into their catalytic mechanisms.     

Perspectives on Structural Molecular Biology Visualization: From Past to Present

Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged that technology.     

Markov State Model of Lassa Virus Nucleoprotein Reveals Large Structural Changes during the Trimer to Monomer Transition

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From Assessment to Policy: Lessons Learned from the U.S. National Assessment

The process of translating scientific information into timely and useful insights that inform policy and resource management decisions, despite the existence of uncertainties, is a difficult and challenging task. Policy-focused assessment is one approach to achieving this end. It is an ongoing process that engages both researchers and end-users to analyze, evaluate and interpret information from multiple disciplines to draw conclusions that are timely and useful for decision makers. This paper discusses key characteristics of a policy-focused assessment process, including (1) ongoing collaboration between the research, assessment, and stakeholder communities; (2) a focus on stakeholder information needs; (3) multidisciplinary approaches; (4) use of scenarios to deal with uncertainties; and (5) evaluation of risk management options. We illustrate the particular challenge to assessors of providing the specific types of insights stakeholders need to effectively influence policy decisions. And we discuss the role that assessment can play in formulating an agenda for future research. Examples from the U.S. National Assessment of “The Potential Consequences of Climate Variability and Change for the United States” are used to illustrate a policy-focused assessment process. For many of the participants, the first U.S. National Assessment was an extraordinary learning experience about how to develop better ways of conducting assessments.     

When to Ignore Advice: Invasion Predictions and Decision Theory

Organisms generally become pests at a low rate. As a consequence of this low base-rate probability, the large majority of organisms rejected in any random sample of potential introductions would probably be harmless, despite the fairly high accuracy of some recently proposed risk assessment systems for exotic introductions. Here we distinguish between a system's accuracy (the proportion of a group of known pest species that would be correctly identified as pests) and reliability (the rate of false positives and false negatives produced once the base-rate is taken into account). We next adapt a decision theory analysis of earthquake prediction to explore when we would be best advised to ignore the recommendations of a screening system for exotic introductions. In one scenario, we show that a pest risk assessment system with an accuracy of 85% would be better ignored, unless the damage caused by introducing a pest is eight times or more that caused by not introducing a harmless organism that is potentially useful. Furthermore, because of the base-rate effect, in certain situations it may be more efficient to focus on identifying potential invaders from amongst already naturalized species than from amongst species at the importation stage.