Table of Contents

August 2011

A model of the full-length, membrane-bound human cytochrome P450 2C9, an enzyme essential for drug metabolism in the human liver, derived using an approach that combines coarse grained and atomic resolution molecular simulations (see Cojocaru et al., 10.1371/journal.pcbi.1002152). The protein backbone is shown by a green ribbon with two important loops (named "BC" and "FG") highlighted in mauve and blue, whereas the membrane is shown in orange. The lipid head groups are shown with blue and red balls to reveal the position of the positive (blue) and negative (red) charges on the lipids. Three different tunnels from the buried active site to the protein surface are shown by cyan, blue, and red tubes. The proposed substrate access tunnel from the membrane ("2a," cyan) is labeled with yellow arrows pointing towards the inside of the active site while two of the proposed product egress tunnels ("2c," blue; "S," red) are labeled with yellow arrows pointing away from the active site. A substrate molecule (the anti-inflammatory drug flurbiprofen) is overlaid on the membrane at the entrance of the proposed access tunnel, and its product is positioned above the membrane along one of the proposed egress tunnels. The active site is located adjacent to the heme group, shown in ball-and-stick representation colored by atom type. The image was generated with VMD ( and GIMP (

Image Credit: Vlad Cojocaru, MPI for Molecular Biomedicine, Münster, Germany


Biomedical Cloud Computing With Amazon Web Services

Vincent A. Fusaro, Prasad Patil, Erik Gafni, Dennis P. Wall, Peter J. Tonellato


Are There Laws of Genome Evolution?

Eugene V. Koonin

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

Jan Gorodkin, Ivo L. Hofacker

Research Articles

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

Tim D. Williams, Nil Turan, Amer M. Diab, Huifeng Wu, Carolynn Mackenzie, Katie L. Bartie, Olga Hrydziuszko, Brett P. Lyons, Grant D. Stentiford, John M. Herbert, Joseph K. Abraham, Ioanna Katsiadaki, Michael J. Leaver, John B. Taggart, Stephen G. George, Mark R. Viant, Kevin J. Chipman, Francesco Falciani

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

David A. Rasmussen, Oliver Ratmann, Katia Koelle

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

Francisco S. Roque, Peter B. Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas Hansen, Karen Søeby, Søren Bredkjær, Anders Juul, Thomas Werge, Lars J. Jensen, Søren Brunak

Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis

Laia Sadeghi, Carolina Bonilla, Annelie Strålfors, Karl Ekwall, J. Peter Svensson

A Neurocomputational Model of Stimulus-Specific Adaptation to Oddball and Markov Sequences

Robert Mill, Martin Coath, Thomas Wennekers, Susan L. Denham

Binding Free Energy Landscape of Domain-Peptide Interactions

Iskra Staneva, Stefan Wallin

Effective Stimuli for Constructing Reliable Neuron Models

Shaul Druckmann, Thomas K. Berger, Felix Schürmann, Sean Hill, Henry Markram, Idan Segev

Related Articles

Evolutionary Accessibility of Mutational Pathways

Jasper Franke, Alexander Klözer, J. Arjan G. M. de Visser, Joachim Krug

Statistical Inference for Multi-Pathogen Systems

Sourya Shrestha, Aaron A. King, Pejman Rohani

Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks

David N. Adamson, Han N. Lim

Spatial Stereoresolution for Depth Corrugations May Be Set in Primary Visual Cortex

Fredrik Allenmark, Jenny C. A. Read

Alterations in Brain Connectivity Underlying Beta Oscillations in Parkinsonism

Rosalyn J. Moran, Nicolas Mallet, Vladimir Litvak, Raymond J. Dolan, Peter J. Magill, Karl J. Friston, Peter Brown

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9

Vlad Cojocaru, Kia Balali-Mood, Mark S. P. Sansom, Rebecca C. Wade

Boltzmann Energy-based Image Analysis Demonstrates that Extracellular Domain Size Differences Explain Protein Segregation at Immune Synapses

Nigel J. Burroughs, Karsten Köhler, Vladimir Miloserdov, Michael L. Dustin, P. Anton van der Merwe, Daniel M. Davis

Integrating Signals from the T-Cell Receptor and the Interleukin-2 Receptor

Tilo Beyer, Mandy Busse, Kroum Hristov, Slavyana Gurbiel, Michal Smida, Utz-Uwe Haus, Kathrin Ballerstein, Frank Pfeuffer, Robert Weismantel, Burkhart Schraven, Jonathan A. Lindquist

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex

A. Sofia F. Oliveira, António M. Baptista, Cláudio M. Soares