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Table of Contents: February 2017

Kinase activity is frequently regulated by phosphorylation. Enhanced sampling molecular dynamics (MD) methods are used to find structural changes of a specific kinase on phosphorylation of its activation loop. Experimental methods do not currently probe completely the conformational space accessible to the activation loop. MD simulation can then complement and extend hypothesis of the mechanisms of kinase activation based on crystallographic and other methods. The results of this study identify a novel role for specific residues in accelerating phosphotransfer. Karp et al.

Image Credit: Jerome M. Karp

Editorials

Ten Simple Rules on How to Organize a Scientific Retreat

Julia Ponomarenko, Romina Garrido, Roderic Guigó

Ten Simple Rules for Developing a Successful Research Proposal in Brazil

Dyoni M. de Oliveira, Marcos S. Buckeridge, Wanderley D. dos Santos

Research Articles

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The genotype-phenotype map of an evolving digital organism

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Modeling of the axon membrane skeleton structure and implications for its mechanical properties

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Mindboggling morphometry of human brains

Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding

Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert H. Podolsky, Gregory Dyson, Robert P. Hausinger, Gerardo Andrés Cisneros

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald

Two dynamic regimes in the human gut microbiome

Sean M. Gibbons, Sean M. Kearney, Chris S. Smillie, Eric J. Alm

Testing the limits of gradient sensing

Vinal Lakhani, Timothy C. Elston

Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns

Naomi V. Bradbury, William J. M. Probert, Katriona Shea, Michael C. Runge, Christopher J. Fonnesbeck, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley

A mathematical model of calcium dynamics in HSY cells

Jung Min Han, Akihiko Tanimura, Vivien Kirk, James Sneyd

Depth-dependent flow and pressure characteristics in cortical microvascular networks

Franca Schmid, Philbert S. Tsai, David Kleinfeld, Patrick Jenny, Bruno Weber

Conformational diversity analysis reveals three functional mechanisms in proteins

Alexander Miguel Monzon, Diego Javier Zea, María Silvina Fornasari, Tadeo E. Saldaño, Sebastian Fernandez-Alberti, Silvio C. E. Tosatto, Gustavo Parisi

Comparing individual-based approaches to modelling the self-organization of multicellular tissues

James M. Osborne, Alexander G. Fletcher, Joe M. Pitt-Francis, Philip K. Maini, David J. Gavaghan

Computational identification of the selenocysteine tRNA (tRNASec) in genomes

Didac Santesmasses, Marco Mariotti, Roderic Guigó

Spatial separation of two different pathways accounting for the generation of calcium signals in astrocytes

Franziska Oschmann, Konstantin Mergenthaler, Evelyn Jungnickel, Klaus Obermayer

Elucidation of molecular kinetic schemes from macroscopic traces using system identification

Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina

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Vivek Charu, Scott Zeger, Julia Gog, Ottar N. Bjørnstad, Stephen Kissler, Lone Simonsen, Bryan T. Grenfell, Cécile Viboud

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Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

István Bartha, Paul J. McLaren, Chanson Brumme, Richard Harrigan, Amalio Telenti, Jacques Fellay

Representing high throughput expression profiles via perturbation barcodes reveals compound targets

Tracey M. Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor

A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons

Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S. Yen, Chen-Hsiang Yeang

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models

David Henriques, Alejandro F. Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective

Julia Chifman, Seda Arat, Zhiyong Deng, Erica Lemler, James C. Pino, Leonard A. Harris, Michael A. Kochen, Carlos F. Lopez, Steven A. Akman, Frank M. Torti, Suzy V. Torti, Reinhard Laubenbacher

Unifying view of mechanical and functional hotspots across class A GPCRs

Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour

Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C. Coles, Marika C. Kullberg, Jon Timmis

Early and Real-Time Detection of Seasonal Influenza Onset

Miguel Won, Manuel Marques-Pita, Carlota Louro, Joana Gonçalves-Sá

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

Berta Verd, Anton Crombach, Johannes Jaeger

Effects of FGFR2 kinase activation loop dynamics on catalytic activity

Jerome M. Karp, Samuel Sparks, David Cowburn

Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface

Guillaume Lajoie, Nedialko I. Krouchev, John F. Kalaska, Adrienne L. Fairhall, Eberhard E. Fetz

A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations

Christoph Thiel, Henrik Cordes, Lorenzo Fabbri, Hélène Eloise Aschmann, Vanessa Baier, Ines Smit, Francis Atkinson, Lars Mathias Blank, Lars Kuepfer

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Jannis Schuecker, Maximilian Schmidt, Sacha J. van Albada, Markus Diesmann, Moritz Helias