Table of Contents

July 2010

Despite their lack of permanent tertiary structure, intrinsically disordered regions in proteins carry out a range of important biological functions. By using molecular dynamics simulations and hydration free energy calculations, Awile et al. (doi:10.1371/journal.pcbi.1000854) demonstrate that the intrinsically disordered regions in the enzyme nudix hydrolase from the desiccation- and radiation-resistant bacterium Deinococcus radiodurans may play an important role in keeping this key enzyme hydrated under extreme desiccation. This idealized artistic rendering shows a possible scenario whereby nudix hydrolase remains in a droplet of residual water due to its hydrophilic disordered regions, while other less hydrophilic proteins are forced out of solution.

Image Credit: Omar Awile


The Roots of Bioinformatics in Protein Evolution

Russell F. Doolittle

Research Articles

Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems

Jamie I. MacPherson, Jonathan E. Dickerson, John W. Pinney, David L. Robertson

Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops

Raffaello Potestio, Cristian Micheletti, Henri Orland

A Comprehensive, Quantitative, and Genome-Wide Model of Translation

Marlena Siwiak, Piotr Zielenkiewicz

Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis

Yonghua Wang, Yan Li, Zhi Ma, Wei Yang, Chunzhi Ai

Coding Efficiency of Fly Motion Processing Is Set by Firing Rate, Not Firing Precision

Deusdedit Lineu Spavieri Jr, Hubert Eichner, Alexander Borst

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment

Stephen F. Altschul, John C. Wootton, Elena Zaslavsky, Yi-Kuo Yu

Organization of Cellular Receptors into a Nanoscale Junction during HIV-1 Adhesion

Terrence M. Dobrowsky, Brian R. Daniels, Robert F. Siliciano, Sean X. Sun, Denis Wirtz

Do Humans Optimally Exploit Redundancy to Control Step Variability in Walking?

Jonathan B. Dingwell, Joby John, Joseph P. Cusumano

Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty

Arne J. Nagengast, Daniel A. Braun, Daniel M. Wolpert

Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator

Volkan Sevim, Xinwei Gong, Joshua E. S. Socolar

Avalanches in a Stochastic Model of Spiking Neurons

Marc Benayoun, Jack D. Cowan, Wim van Drongelen, Edward Wallace

Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species

Chrysa Pantzartzi, Elena Drosopoulou, Minas Yiangou, Ignat Drozdov, Sophia Tsoka, Christos A. Ouzounis, Zacharias G. Scouras

Redundancy and the Evolution of Cis-Regulatory Element Multiplicity

Tiago Paixão, Ricardo B. R. Azevedo

Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human

James R. Wagner, Bing Ge, Dmitry Pokholok, Kevin L. Gunderson, Tomi Pastinen, Mathieu Blanchette

A Threshold Equation for Action Potential Initiation

Jonathan Platkiewicz, Romain Brette

Large-Scale Analysis of Network Bistability for Human Cancers

Tetsuya Shiraishi, Shinako Matsuyama, Hiroaki Kitano

Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei

Philippe Andrey, Kiên Kiêu, Clémence Kress, Gaëtan Lehmann, Leïla Tirichine, Zichuan Liu, Eric Biot, Pierre-Gaël Adenot, Cathy Hue-Beauvais, Nicole Houba-Hérin, Véronique Duranthon, Eve Devinoy, Nathalie Beaujean, Valérie Gaudin, Yves Maurin, Pascale Debey

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris

Effects of Macromolecular Crowding on Protein Conformational Changes

Hao Dong, Sanbo Qin, Huan-Xiang Zhou

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

Michael C. Prentiss, David J. Wales, Peter G. Wolynes

Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli

Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hütt

A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature

Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser

Conductance Ratios and Cellular Identity

Amber E. Hudson, Astrid A. Prinz

Dual Coding with STDP in a Spiking Recurrent Neural Network Model of the Hippocampus

Daniel Bush, Andrew Philippides, Phil Husbands, Michael O'Shea

Action Potential Energy Efficiency Varies Among Neuron Types in Vertebrates and Invertebrates

Biswa Sengupta, Martin Stemmler, Simon B. Laughlin, Jeremy E. Niven

Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye

David E. Larson, Ruth I. Johnson, Maciej Swat, Julia B. Cordero, James A. Glazier, Ross L. Cagan

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Augix Guohua Xu, Liu He, Zhongshan Li, Ying Xu, Mingfeng Li, Xing Fu, Zheng Yan, Yuan Yuan, Corinna Menzel, Na Li, Mehmet Somel, Hao Hu, Wei Chen, Svante Pääbo, Philipp Khaitovich