Table of Contents: July 2015

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Ion channels catalyze ionic permeation across membranes via water-filled pores. To understand how changes in intracellular magnesium concentration regulate the influx of Mg2+ into cells, we examine early events in the relaxation of Mg2+ channel CorA toward its open state using massively-repeated molecular dynamics simulations conducted either with or without regulatory ions. The pore of CorA contains a 2-nm-long hydrophobic bottleneck which remained dehydrated in most simulations. However, rapid hydration or "wetting" events concurrent with small-amplitude fluctuations in pore diameter occurred spontaneously and reversibly. In the absence of regulatory ions, wetting transitions are more likely and include a wet state that is significantly more stable and more hydrated. The free energy profile for Mg2+ permeation presents a barrier whose magnitude is anticorrelated to pore diameter and the extent of hydrophobic hydration. These findings support an allosteric mechanism whereby wetting of a hydrophobic gate couples changes in intracellular magnesium concentration to the onset of ionic conduction. Pomès et al.


From “What Is?” to “What Isn't?” Computational Biology

Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns


Research Articles

Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape

César A. Ramírez-Sarmiento, Jeffrey K. Noel, Sandro L. Valenzuela, Irina Artsimovitch

Forecasting Influenza Epidemics in Hong Kong

Wan Yang, Benjamin J. Cowling, Eric H. Y. Lau, Jeffrey Shaman

Fast Simulation of Mechanical Heterogeneity in the Electrically Asynchronous Heart Using the MultiPatch Module

John Walmsley, Theo Arts, Nicolas Derval, Pierre Bordachar, Hubert Cochet, Sylvain Ploux, Frits W. Prinzen, Tammo Delhaas, Joost Lumens

Neutral Models of Microbiome Evolution

Qinglong Zeng, Jeet Sukumaran, Steven Wu, Allen Rodrigo

Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change

Truong D. Nguyen-Huu, Chinmaya Gupta, Bo Ma, William Ott, Krešimir Josić, Matthew R. Bennett

What Can Interaction Webs Tell Us About Species Roles?

Elizabeth L. Sander, J. Timothy Wootton, Stefano Allesina

Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA

Chris Neale, Nilmadhab Chakrabarti, Pawel Pomorski, Emil F. Pai, Régis Pomès

Emergence of Slow-Switching Assemblies in Structured Neuronal Networks

Michael T. Schaub, Yazan N. Billeh, Costas A. Anastassiou, Christof Koch, Mauricio Barahona

Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination

Blake T. Thomas, Davis W. Blalock, William B. Levy

A Developmental Switch for Hebbian Plasticity

Marijn B. Martens, Tansu Celikel, Paul H. E. Tiesinga

Geometry of the Gene Expression Space of Individual Cells

Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi Mayo, Michael E. Rothenberg, Tomer Kalisky, Uri Alon

Evaluating Spatial Interaction Models for Regional Mobility in Sub-Saharan Africa

Amy Wesolowski, Wendy Prudhomme O’Meara, Nathan Eagle, Andrew J. Tatem, Caroline O. Buckee

Genome Modeling System: A Knowledge Management Platform for Genomics

Malachi Griffith, Obi L. Griffith, Scott M. Smith, Avinash Ramu, Matthew B. Callaway, Anthony M. Brummett, Michael J. Kiwala, Adam C. Coffman, Allison A. Regier, Ben J. Oberkfell, Gabriel E. Sanderson, Thomas P. Mooney, Nathaniel G. Nutter, Edward A. Belter, Feiyu Du, Robert L. Long, Travis E. Abbott, Ian T. Ferguson, David L. Morton, Mark M. Burnett, James V. Weible, Joshua B. Peck, Adam Dukes, Joshua F. McMichael, Justin T. Lolofie, Brian R. Derickson, Jasreet Hundal, Zachary L. Skidmore, Benjamin J. Ainscough, Nathan D. Dees, William S. Schierding, Cyriac Kandoth, Kyung H. Kim, Charles Lu, Christopher C. Harris, Nicole Maher, Christopher A. Maher, Vincent J. Magrini, Benjamin S. Abbott, Ken Chen, Eric Clark, Indraniel Das, Xian Fan, Amy E. Hawkins, Todd G. Hepler, Todd N. Wylie, Shawn M. Leonard, William E. Schroeder, Xiaoqi Shi, Lynn K. Carmichael, Matthew R. Weil, Richard W. Wohlstadter, Gary Stiehr, Michael D. McLellan, Craig S. Pohl, Christopher A. Miller, Daniel C. Koboldt, Jason R. Walker, James M. Eldred, David E. Larson, David J. Dooling, Li Ding, Elaine R. Mardis, Richard K. Wilson

Stability of Neuronal Networks with Homeostatic Regulation

Daniel Harnack, Miha Pelko, Antoine Chaillet, Yacine Chitour, Mark C.W. van Rossum

Measuring Asymmetry in Time-Stamped Phylogenies

Bethany L. Dearlove, Simon D. W. Frost

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community

Joshua J. Hamilton, Montserrat Calixto Contreras, Jennifer L. Reed

High Accuracy Decoding of Dynamical Motion from a Large Retinal Population

Olivier Marre, Vicente Botella-Soler, Kristina D. Simmons, Thierry Mora, Gašper Tkačik, Michael J. Berry II

Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments

Tong Li, Malgorzata B. Tracka, Shahid Uddin, Jose Casas-Finet, Donald J. Jacobs, Dennis R. Livesay