AF-2 domains of nuclear receptors mediate crucial protein–protein interactions with transcriptional coactivators. The AF-2 domains (magenta) of the human nuclear xenobiotic receptor PXR (cyan) were demonstrated using molecular dynamics to move together in an "active-ready" conformation, poised to bind to their cognate protein partners (see Teotico et al. pcbi.1000111). Other nuclear receptors were also shown to follow suit.
Image Credit: Monica Frazier and Matthew Redinbo
Message from ISCB
ISCB Honors David Haussler and Aviv Regev
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000101
Perspectives
Computational Biology Resources Lack Persistence and Usability
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000136
Outlook on Thailand's Genomics and Computational Biology Research and Development
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000115
Review
Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000029
Research Articles
Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis
PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000102
Dynamics of Immune Escape during HIV/SIV Infection
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000103
Circadian Phase Resetting via Single and Multiple Control Targets
PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000104
Local Function Conservation in Sequence and Structure Space
PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000105
Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development
PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000106
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000107
Unraveling Protein Networks with Power Graph Analysis
PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000108
The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000109
The Ascent of the Abundant: How Mutational Networks Constrain Evolution
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000110
Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions
PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000111
Evolution of Evolvability in Gene Regulatory Networks
PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000112
Probing the Extent of Randomness in Protein Interaction Networks
PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000114
Similarity Queries for Temporal Toxicogenomic Expression Profiles
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000116
Related Articles
Intrinsic Gain Modulation and Adaptive Neural Coding
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000119
Using Expression Profiles of Caenorhabditis elegans Neurons To Identify Genes That Mediate Synaptic Connectivity
PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000120
Memory Switches in Chemical Reaction Space
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000122
Emergent Synchronous Bursting of Oxytocin Neuronal Network
PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000123
Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000113
Predicting and Validating Protein Interactions Using Network Structure
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000118
Protein Complex Evolution Does Not Involve Extensive Network Rewiring
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000132
Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000135
Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000126
The Spatiotemporal Pattern of Src Activation at Lipid Rafts Revealed by Diffusion-Corrected FRET Imaging
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000127
Optimal Compensation for Temporal Uncertainty in Movement Planning
PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000130