Flexible Protein-Protein Docking with SwarmDock.

Methods Mol Biol. 2018;1764:413-428

Authors: Moal IH, Chaleil RAG, Bates PA

Abstract
The atomic structures of protein complexes can provide useful information for drug design, protein engineering, systems biology, and understanding pathology. Obtaining this information experimentally can be challenging. However, if the structures of the subunits are known, then it is often possible to model the complex computationally. This chapter provide practical guidelines for docking proteins using the SwarmDock flexible protein-protein docking method, providing an overview of the factors that need to be considered when deciding whether docking is likely to be successful, the preparation of structural input, generation of docked poses, analysis and ranking of docked poses, and the validation of models using external data.

PMID: 29605931 [PubMed - in process]

Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data.

Methods Mol Biol. 2018;1764:391-399

Authors: Goebels F, Hu L, Bader G, Emili A

Abstract
Biology has amassed a wealth of information about the function of a multitude of protein-coding genes across species. The challenge now is to understand how all these proteins work together to form a living organism, and a crucial step for gaining this knowledge is a complete description of the molecular "wiring circuits" that underlie cellular processes. In this chapter, we describe a general computational framework for predicting multi-protein assemblies from biochemical co-fractionation data.

PMID: 29605929 [PubMed - in process]

Biochemical Identification of Nonmethylated DNA by BioCAP-Seq.

Methods Mol Biol. 2018;1766:15-29

Authors: Long HK, Rose NR, Blackledge NP, Klose RJ

Abstract
CpG islands are regions of vertebrate genomes that often function as gene regulatory elements and are associated with most gene promoters. CpG island elements usually contain nonmethylated CpG dinucleotides, while the remainder of the genome is pervasively methylated. We developed a biochemical approach called biotinylated CxxC affinity purification (BioCAP) to unbiasedly isolate regions of the genome that contain nonmethylated CpG dinucleotides. The resulting highly pure nonmethylated DNA is easily analyzed by quantitative PCR to interrogate specific loci or via massively parallel sequencing to yield genome-wide profiles.

PMID: 29605845 [PubMed - in process]

Trypanosomatids Are Much More than Just Trypanosomes: Clues from the Expanded Family Tree.

Trends Parasitol. 2018 Mar 28;:

Authors: Lukeš J, Butenko A, Hashimi H, Maslov DA, Votýpka J, Yurchenko V

Abstract
Trypanosomes and leishmanias are widely known parasites of humans. However, they are just two out of several phylogenetic lineages that constitute the family Trypanosomatidae. Although dixeny - the ability to infect two hosts - is a derived trait of vertebrate-infecting parasites, the majority of trypanosomatids are monoxenous. Like their common ancestor, the monoxenous Trypanosomatidae are mostly parasites or commensals of insects. This review covers recent advances in the study of insect trypanosomatids, highlighting their diversity as well as genetic, morphological and biochemical complexity, which, until recently, was underappreciated. The investigation of insect trypanosomatids is providing an important foundation for understanding the origin and evolution of parasitism, including colonization of vertebrates and the appearance of human pathogens.

PMID: 29605546 [PubMed - as supplied by publisher]

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

Cell Syst. 2018 Mar 23;:

Authors: Chevrier S, Crowell HL, Zanotelli VRT, Engler S, Robinson MD, Bodenmiller B

Abstract
The advent of mass cytometry increased the number of parameters measured at the single-cell level while decreasing the extent of crosstalk between channels relative to dye-based flow cytometry. Although reduced, spillover still exists in mass cytometry data, and minimizing its effect requires considerable expert knowledge and substantial experimental effort. Here, we describe a novel bead-based compensation workflow and R-based software that estimates and corrects for interference between channels. We performed an in-depth characterization of the spillover properties in mass cytometry, including limitations defined by the linear range of the mass cytometer and the reproducibility of the spillover over time and across machines. We demonstrated the utility of our method in suspension and imaging mass cytometry. To conclude, our approach greatly simplifies the development of new antibody panels, increases flexibility for antibody-metal pairing, opens the way to using less pure isotopes, and improves overall data quality, thereby reducing the risk of reporting cell phenotype artifacts.

PMID: 29605184 [PubMed - as supplied by publisher]

Systematic Evaluation of Molecular Networks for Discovery of Disease Genes.

Cell Syst. 2018 Mar 26;:

Authors: Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T

Abstract
Gene networks are rapidly growing in size and number, raising the question of which networks are most appropriate for particular applications. Here, we evaluate 21 human genome-wide interaction networks for their ability to recover 446 disease gene sets identified through literature curation, gene expression profiling, or genome-wide association studies. While all networks have some ability to recover disease genes, we observe a wide range of performance with STRING, ConsensusPathDB, and GIANT networks having the best performance overall. A general tendency is that performance scales with network size, suggesting that new interaction discovery currently outweighs the detrimental effects of false positives. Correcting for size, we find that the DIP network provides the highest efficiency (value per interaction). Based on these results, we create a parsimonious composite network with both high efficiency and performance. This work provides a benchmark for selection of molecular networks in human disease research.

PMID: 29605183 [PubMed - as supplied by publisher]

Physical-chemical mechanisms of pattern formation during gastrulation.

J Chem Phys. 2018 Mar 28;148(12):123302

Authors: Bozorgui B, Kolomeisky AB, Teimouri H

Abstract
Gastrulation is a fundamental phase during the biological development of most animals when a single layer of identical embryo cells is transformed into a three-layer structure, from which the organs start to develop. Despite a remarkable progress in quantifying the gastrulation processes, molecular mechanisms of these processes remain not well understood. Here we theoretically investigate early spatial patterning in a geometrically confined colony of embryonic stem cells. Using a reaction-diffusion model, a role of Bone-Morphogenetic Protein 4 (BMP4) signaling pathway in gastrulation is specifically analyzed. Our results show that for slow diffusion rates of BMP4 molecules, a new length scale appears, which is independent of the size of the system. This length scale separates the central region of the colony with uniform low concentrations of BMP molecules from the region near the colony edge where the concentration of signaling molecules is elevated. The roles of different components of the signaling pathway are also explained. Theoretical results are consistent with recent in vitro experiments, providing microscopic explanations for some features of early embryonic spatial patterning. Physical-chemical mechanisms of these processes are discussed.

PMID: 29604871 [PubMed - in process]

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