Feb
22
2009

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… 

Cell:

  • 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.

Nature:

  • 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.

PNAS:

  • 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

JACS:

  • 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.

Structure:

  • 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.

JMB:

  • 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.

Bioinformatics:

  • 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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