Bi-Weekly Digest 22/02/09

In this Bi-weekly digest, a large scale structural analysis of the human tyrosine phosphatome, a Fas-death domain complex structure, and at least two works concerning calmodulin… 


  • Large-Scale Structural Analysis of the Classical Human Protein Tyrosine Phosphatome. Alastair J. Barr, Emilie Ugochukwu, Wen Hwa Lee, Oliver N.F. King, Panagis Filippakopoulos, Ivan Alfano, Pavel Savitsky, Nicola A. Burgess-Brown, Susanne Müllerand, Stefan Knapp.


  • Visualization of a missing link in retrovirus capsid assembly. Cardone G, Purdy JG, Cheng N, Craven RC, Steven AC.
  • The Fas-FADD death domain complex structure unravels signalling by receptor
    clustering. Scott FL, Stec B, Pop C, Dobaczewska MK, Lee JJ, Monosov E, Robinson H, Salvesen
    GS, Schwarzenbacher R, Riedl SJ.


  • Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin. Swarnendu Tripathi and John J. Portman.
  • The nature of the TRAP–Anti-TRAP complex. Masahiro Watanabe, Jonathan G. Heddle, Kenichi Kikuchi, Satoru Unzai, Satoko Akashi, Sam-Yong Park, and Jeremy R. H. Tam


  • Metal-Binding Dependent Disruption of Membranes by Designed Helices. Rachel S. Signarvic and William F. DeGrado

PLoS Computational Biology:

  • Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests. Mile Sikic, Sanja Tomic, Kristian Vlahovicek.
  • Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, Alessandra Carbone.
  • Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties. Wenxu Tong, Ying Wei, Leonel F. Murga, Mary Jo Ondrechen, Ronald J. Williams.


  • Comprehensive Structural Classification of Ligand-Binding Motifs in Proteins. Akira R. Kinjo, Haruki Nakamura

Nature Structural and Molecular Biology:

  • Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation. Shivani Ahuja, Viktor Hornak, Elsa C Y Yan, Natalie Syrett, Joseph A Goncalves, Amiram Hirshfeld, Martine Ziliox, Thomas P Sakmar, Mordechai Sheves, Philip J Reeves, Steven O Smith and Markus Eilers.
  • Conformational flexibility of metazoan fatty acid synthase enables catalysis. Edward J Brignole, Stuart Smith and Francisco J Asturias.

Biophysical Journal:

  • Blind test of physics-based prediction of protein structures. Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA.
  • Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability. Dixit A, Torkamani A, Schork NJ, Verkhivker G. 
  • Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex. Laine E, Blondel A, Malliavin TE.
  • Thermodynamic effects of noncoded and coded methionine substitutions in calmodulin. Yamniuk AP, Ishida H, Lippert D, Vogel HJ.


  • Computational design of calmodulin mutants with up to 900-fold increase in binding specificity. Yosef E, Politi R, Choi MH, Shifman JM.
  • Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 A Crystal Structure of the Active Form of ScpA. Kagawa TF, O’Connell MR, Mouat P, Paoli M, O’Toole PW, Cooney JC.


  • ProtorP: a protein–protein interaction analysis server. Christopher Reynolds, David Damerell, and Susan Jones.

BMC Bioinformatics:

  • Prediction of protein-protein interaction types using association rule based classification. Park S, Reyes J, Gilbert D, Kim J, Kim S
  • An effective docking strategy for virtual screening based on multi-objective optimization algorithm. Li H, Zhang H, Zheng M, Luo J, Kang L, Liu X, Wang X, Jiang H
  • TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis. Fischer A, Enkler N, Neudert G, Bocola M, Sterner R, Merkl R
  • Motivated Proteins: A web application for studying small three-dimensional protein motifs. Leader DP, Milner-White EJ

Know of any hot literature that’s not here ? Want to hear more about a specific research/field ? Tell us in the comments.

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