Molecular principles of the interactions of disordered proteins.

Thorough knowledge of the molecular principles of protein-protein recognition is essential to our understanding of protein function at the cellular level. Whereas interactions of ordered proteins have been analyzed in great detail, complexes of intrinsically unstructured/disordered proteins (IUPs) have hardly been addressed so far. Here, we have collected a database of 39 complexes of experimentally verified IUPs, and compared their interfaces with those of 72 complexes of ordered, globular proteins. The characteristic differences found between the two types of complexes suggest that IUPs represent a distinct molecular implementation of the principles of protein-protein recognition. The interfaces do not differ in size, but those of IUPs cover a much larger part of the surface of the protein than for their ordered counterparts. Moreover, IUP interfaces are significantly more hydrophobic relative to their overall amino acid composition, but also in absolute terms. They rely more on hydrophobic-hydrophobic than on polar-polar interactions. Their amino acids in the interface realize more intermolecular contacts, which suggests a better fit with the partner due to induced folding upon binding that results in a better adaptation to the partner. The two modes of interaction also differ in that IUPs usually use only a single continuous segment for partner binding, whereas the binding sites of ordered proteins are more segmented. Probably, all these features contribute to the increased evolutionary conservation of IUP interface residues. These noted molecular differences are also manifested in the interaction energies of IUPs. Our approximation of these by low-resolution force-fields shows that IUPs gain much more stabilization energy from intermolecular contacts, than from folding, i.e. they use their binding energy for folding. Overall, our findings provide a structural rationale to the prior suggestions that many IUPs are specialized for functions realized by protein-protein interactions.

[1]  Peter B. McGarvey,et al.  UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..

[2]  Patrick Aloy,et al.  Ten thousand interactions for the molecular biologist , 2004, Nature Biotechnology.

[3]  C. Chothia,et al.  The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.

[4]  J. Thornton,et al.  Diversity of protein–protein interactions , 2003, The EMBO journal.

[5]  H. Dyson,et al.  Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.

[6]  R. Nussinov,et al.  Extended disordered proteins: targeting function with less scaffold. , 2003, Trends in biochemical sciences.

[7]  István Simon,et al.  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm035 Structural bioinformatics Local structural disorder imparts plasticity on linear motifs , 2022 .

[8]  P. Tompa.  Intrinsically unstructured proteins. , 2002, Trends in biochemical sciences.

[9]  William I. Weis,et al.  The Structure of the β-Catenin/E-Cadherin Complex and the Molecular Basis of Diverse Ligand Recognition by β-Catenin , 2001, Cell.

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

[11]  H. Dyson,et al.  Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.

[12]  L. Iakoucheva,et al.  Intrinsic Disorder and Protein Function , 2002 .

[13]  P. Tompa.  The interplay between structure and function in intrinsically unstructured proteins , 2005, FEBS letters.

[14]  Philip D. Jeffrey,et al.  Crystal structure of the p27Kip1 cyclin-dependent-kinase inibitor bound to the cyclin A–Cdk2 complex , 1996, Nature.

[15]  Haruki Nakamura,et al.  Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks , 2006, FEBS letters.

[16]  Marc S. Cortese,et al.  Flexible nets , 2005, The FEBS journal.

[17]  Lilia M. Iakoucheva,et al.  Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes , 2006, PLoS Comput. Biol..

[18]  J. Thornton,et al.  Protein–protein interfaces: Analysis of amino acid conservation in homodimers , 2001, Proteins.

[19]  Peter Tompa,et al.  Primary contact sites in intrinsically unstructured proteins: the case of calpastatin and microtubule-associated protein 2. , 2005, Biochemistry.

[20]  A. Dunker,et al.  Disorder and sequence repeats in hub proteins and their implications for network evolution. , 2006, Journal of proteome research.

[21]  V. Uversky,et al.  Why are “natively unfolded” proteins unstructured under physiologic conditions? , 2000, Proteins.

[22]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[23]  Michail Yu. Lobanov,et al.  Prediction of Amyloidogenic and Disordered Regions in Protein Chains , 2006, PLoS Comput. Biol..

[24]  S. Jones,et al.  Principles of protein-protein interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Peter Tompa,et al.  The role of structural disorder in the function of RNA and protein chaperones , 2004, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[26]  A K Dunker,et al.  Protein disorder and the evolution of molecular recognition: theory, predictions and observations. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[27]  Marc S. Cortese,et al.  Coupled folding and binding with α-helix-forming molecular recognition elements , 2005 .

[28]  S. Kanaya,et al.  Large-scale identification of protein-protein interaction of Escherichia coli K-12. , 2006, Genome research.

[29]  Ruth Nussinov,et al.  Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. , 2004, Journal of molecular biology.

[30]  K. Dill,et al.  An iterative method for extracting energy-like quantities from protein structures. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[31]  P. Tompa,et al.  The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. , 2005, Journal of molecular biology.

[32]  Zoran Obradovic,et al.  DisProt: the Database of Disordered Proteins , 2006, Nucleic Acids Res..

[33]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[34]  L. Vassilev,et al.  In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2 , 2004, Science.

[35]  S. Vajda,et al.  Anchor residues in protein-protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Marie-France Carlier,et al.  The β-Thymosin/WH2 Domain Structural Basis for the Switch from Inhibition to Promotion of Actin Assembly , 2004, Cell.

[37]  R. Nussinov,et al.  Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. , 2005, Journal of molecular biology.

[38]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[39]  Marc S. Cortese,et al.  Analysis of molecular recognition features (MoRFs). , 2006, Journal of molecular biology.

[40]  A Keith Dunker,et al.  Characterization of molecular recognition features, MoRFs, and their binding partners. , 2007, Journal of proteome research.

[41]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[42]  E. Guittet,et al.  Coupling of Folding and Binding of Thymosin β4 upon Interaction with Monomeric Actin Monitored by Nuclear Magnetic Resonance* , 2004, Journal of Biological Chemistry.

[43]  István Simon,et al.  Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. , 2004, Journal of molecular biology.

[44]  H. Dyson,et al.  Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. , 1999, Journal of molecular biology.

[45]  Christopher J. Oldfield,et al.  Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling , 2005, Journal of molecular recognition : JMR.

[46]  A. Dunker,et al.  Abundance of intrinsic disorder in protein associated with cardiovascular disease. , 2006, Biochemistry.

[47]  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.

[48]  Seth A. Darst,et al.  Crystal Structure of the Flagellar σ/Anti-σ Complex σ28/FlgM Reveals an Intact σ Factor in an Inactive Conformation , 2004 .

[49]  L. Iakoucheva,et al.  Intrinsic disorder in cell-signaling and cancer-associated proteins. , 2002, Journal of molecular biology.

[50]  Marc S. Cortese,et al.  Rational drug design via intrinsically disordered protein. , 2006, Trends in biotechnology.

[51]  Thomas L. Madden,et al.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.

[52]  P. Tompa,et al.  Prevalent structural disorder in E. coli and S. cerevisiae proteomes. , 2006, Journal of proteome research.

[53]  Ruth Nussinov,et al.  Structural motifs at protein‐protein interfaces: Protein cores versus two‐state and three‐state model complexes , 1997, Protein science : a publication of the Protein Society.

[54]  R. Russell,et al.  Linear motifs: Evolutionary interaction switches , 2005, FEBS letters.