Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example† †This article is part of a Molecular BioSystems themed issue on Computational and Systems Biology.

Structural data, efficient structural comparison algorithms and appropriate datasets and filters can assist in getting an insight into time dimensionality in interaction networks; in predicting which interactions can and cannot co-exist; and in obtaining concrete predictions consistent with experiment.

[1]  R. Russell,et al.  Protein complexes: structure prediction challenges for the 21st century. , 2005, Current opinion in structural biology.

[2]  Ruth Nussinov,et al.  A method for simultaneous alignment of multiple protein structures , 2004, Proteins.

[3]  Wen Tang,et al.  c-Abl tyrosine kinase activates p21 transcription via interaction with p53. , 2007, Journal of biochemistry.

[4]  Paul W Brandt-Rauf,et al.  NMR solution structure of a peptide from the mdm-2 binding domain of the p53 protein that is selectively cytotoxic to cancer cells. , 2004, Biochemistry.

[5]  A. Levine,et al.  Structure of the MDM2 Oncoprotein Bound to the p53 Tumor Suppressor Transactivation Domain , 1996, Science.

[6]  Ozlem Keskin,et al.  Architectures and functional coverage of protein-protein interfaces. , 2008, Journal of molecular biology.

[7]  Jan Vijg,et al.  Ku 80 Deletion Suppresses Spontaneous Tumors and Induces a p 53-Mediated DNA Damage Response , 2008 .

[8]  Hongbo Zhu,et al.  NOXclass: prediction of protein-protein interaction types , 2006, BMC Bioinformatics.

[9]  Jan Vijg,et al.  Ku80 deletion suppresses spontaneous tumors and induces a p53-mediated DNA damage response. , 2008, Cancer research.

[10]  Ruth Nussinov,et al.  BioInfo3D: a suite of tools for structural bioinformatics , 2004, Nucleic Acids Res..

[11]  R Nussinov,et al.  Towards drugs targeting multiple proteins in a systems biology approach. , 2007, Current topics in medicinal chemistry.

[12]  M. Dai,et al.  MDM2 Inhibits PCAF (p300/CREB-binding Protein-associated Factor)-mediated p53 Acetylation* , 2002, The Journal of Biological Chemistry.

[13]  Sophia Tsoka,et al.  Robustness of the p53 network and biological hackers , 2005, FEBS letters.

[14]  P. Andrew Karplus,et al.  Flt3 ligand structure and unexpected commonalities of helical bundles and cystine knots , 2000, Nature Structural Biology.

[15]  Lan V. Zhang,et al.  Evidence for dynamically organized modularity in the yeast protein–protein interaction network , 2004, Nature.

[16]  N. Glansdorff,et al.  Structure of the arginine repressor from Bacillus stearothermophilus , 1999, Nature Structural Biology.

[17]  Ozlem Keskin,et al.  PRISM: protein-protein interaction prediction by structural matching. , 2008, Methods in molecular biology.

[18]  K. Komurov,et al.  Revealing static and dynamic modular architecture of the eukaryotic protein interaction network , 2007, Molecular Systems Biology.

[19]  Gary D Bader,et al.  BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.

[20]  R. Carroll,et al.  Mapping of phosphomonoester and apparent phosphodiester bonds of the oncogene product p53 from simian virus 40-transformed 3T3 cells. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[21]  K. Kohn Molecular interaction map of the mammalian cell cycle control and DNA repair systems. , 1999, Molecular biology of the cell.

[22]  O. Keskina,et al.  Towards Drugs Targeting Multiple Proteins in a Systems Biology Approach , 2008 .

[23]  Gideon Schreiber,et al.  Rational design of faster associating and tighter binding protein complexes , 2000, Nature Structural Biology.

[24]  Gabriele Ausiello,et al.  MINT: the Molecular INTeraction database , 2006, Nucleic Acids Res..

[25]  Geoffrey J. Barton,et al.  PIPs: human protein–protein interaction prediction database , 2008, Nucleic Acids Res..

[26]  P. Bork,et al.  Dynamic Complex Formation During the Yeast Cell Cycle , 2005, Science.

[27]  Ozlem Keskin,et al.  Similar binding sites and different partners: implications to shared proteins in cellular pathways. , 2007, Structure.

[28]  Maria Victoria Schneider,et al.  MINT: a Molecular INTeraction database. , 2002, FEBS letters.

[29]  Ruth Nussinov,et al.  MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions , 2008, Nucleic Acids Res..

[30]  W Eckhart,et al.  Phosphorylation sites in the amino-terminal region of mouse p53. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Ozlem Keskin,et al.  HotSprint: database of computational hot spots in protein interfaces , 2007, Nucleic Acids Res..

[32]  Sudhir Agrawal,et al.  Stabilization of E2F1 protein by MDM2 through the E2F1 ubiquitination pathway , 2005, Oncogene.

[33]  Christina Kiel,et al.  Analyzing protein interaction networks using structural information. , 2008, Annual review of biochemistry.

[34]  Y. Zhang,et al.  IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..

[35]  R. Russell,et al.  Structural systems biology: modelling protein interactions , 2006, Nature Reviews Molecular Cell Biology.

[36]  J. Walker,et al.  Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair , 2001, Nature.

[37]  Tony Kouzarides,et al.  Stimulation of E2F1/DP1 transcriptional activity by MDM2 oncoprotein , 1995, Nature.

[38]  Ken Garber,et al.  Missing the target: ubiquitin ligase drugs stall. , 2005, Journal of the National Cancer Institute.

[39]  Philip M. Kim,et al.  Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.

[40]  D. Meek,et al.  Phosphorylation of p53 in normal and simian virus 40-transformed NIH 3T3 cells , 1988, Molecular and cellular biology.

[41]  Patrick Aloy,et al.  Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Manabu Koike,et al.  Ku80 can translocate to the nucleus independent of the translocation of Ku70 using its own nuclear localization signal , 1999, Oncogene.

[43]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[44]  Michael Berger,et al.  Tyrosine phosphorylation of Mdm2 by c‐Abl: implications for p53 regulation , 2002, The EMBO journal.

[45]  J. Piette,et al.  MDM2: life without p53. , 2001, Trends in genetics : TIG.

[46]  Ozlem Keskin,et al.  PRISM: protein interactions by structural matching , 2005, Nucleic Acids Res..

[47]  W. Sellers,et al.  Interaction between the retinoblastoma protein and the oncoprotein MDM2 , 1995, Nature.

[48]  Ozlem Keskin,et al.  Characterization and prediction of protein interfaces to infer protein-protein interaction networks. , 2008, Current pharmaceutical biotechnology.

[49]  Patrick Aloy,et al.  The third dimension for protein interactions and complexes. , 2002, Trends in biochemical sciences.

[50]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[51]  Peer Bork,et al.  Towards Cellular Systems in 4D , 2005, Cell.

[52]  Michael Schroeder,et al.  Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data , 2007, ISMB/ECCB.

[53]  Andrzej Kloczkowski,et al.  Functional clustering of yeast proteins from the protein-protein interaction network , 2006, BMC Bioinformatics.

[54]  H. Wolfson,et al.  A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.

[55]  Ozlem Keskin,et al.  Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces , 2005, Bioinform..

[56]  Jeong Ho Chang,et al.  Structural basis for the recognition of the E2F transactivation domain by the retinoblastoma tumor suppressor. , 2002, Genes & development.

[57]  Ozlem Keskin,et al.  Topological properties of protein interaction networks from a structural perspective. , 2008, Biochemical Society transactions.

[58]  Joost Schymkowitz,et al.  Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. , 2005, Journal of molecular biology.

[59]  D. Baker,et al.  Computational redesign of protein-protein interaction specificity , 2004, Nature Structural &Molecular Biology.