Composition Profiler: a tool for discovery and visualization of amino acid composition differences-2

<p><b>Copyright information:</b></p><p>Taken from "Composition Profiler: a tool for discovery and visualization of amino acid composition differences"</p><p>http://www.biomedcentral.com/1471-2105/8/211</p><p>BMC Bioinformatics 2007;8():211-211.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1914087.</p><p></p>eins shows slight depletion in hydrophilics (cyan) and enrichement in hydrophobics (black) as a general trend, although homodimer interfaces show closer resemblance to the protein surfaces. Composition profile of hub proteins shows a general enrichment in disorder (red) and depletion in order promoting residues (blue)

Composition Profiler: a tool for discovery and visualization of amino acid composition differences-0

<p><b>Copyright information:</b></p><p>Taken from "Composition Profiler: a tool for discovery and visualization of amino acid composition differences"</p><p>http://www.biomedcentral.com/1471-2105/8/211</p><p>BMC Bioinformatics 2007;8():211-211.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1914087.</p><p></p>eins shows slight depletion in hydrophilics (cyan) and enrichement in hydrophobics (black) as a general trend, although homodimer interfaces show closer resemblance to the protein surfaces. Composition profile of hub proteins shows a general enrichment in disorder (red) and depletion in order promoting residues (blue)

Composition Profiler: a tool for discovery and visualization of amino acid composition differences-1

<p><b>Copyright information:</b></p><p>Taken from "Composition Profiler: a tool for discovery and visualization of amino acid composition differences"</p><p>http://www.biomedcentral.com/1471-2105/8/211</p><p>BMC Bioinformatics 2007;8():211-211.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1914087.</p><p></p>lor-coding scheme (flexibility) allows for a direct visual comparison between enrichment and depletion patterns in the three datasets

Conditional probability distributions (TM), (Non-TM) (on the left), and (IU), (Non-IU) (on the right), where is, from top to bottom, polarity, as determined by the Grantham and Zimmerman-Eleizer-Simha scales, bulkiness, and flexibility

TM = transmembrane, IU = intrinsically unstructured. The plots on the left were reproduced with permission from [].<p><b>Copyright information:</b></p><p>Taken from "Investigation of transmembrane proteins using a computational approach"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S7</p><p>BMC Genomics 2008;9(Suppl 1):S7-S7.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386072.</p><p></p

Conditional probability distributions (TM), (Non-TM) (on the left), and (IU), (Non-IU) (on the right), where is hydropathy, as determined by the Kyte-Doolittle, Eisenberg-Schwarz- Komaromy-Wall, Engelman-Steitz-Goldman, and Liu-Deber scales

TM = transmembrane, IU = intrinsi-cally unstructured. The plots on the left were reproduced with permission from [].<p><b>Copyright information:</b></p><p>Taken from "Investigation of transmembrane proteins using a computational approach"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S7</p><p>BMC Genomics 2008;9(Suppl 1):S7-S7.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386072.</p><p></p

Conditional probability distributions (TM), (Non-TM) (on the left), and (IU), (Non-IU) (on the right), where is, from top to bottom, van der Waals volume, polarizability, elec-tronic effects, and helicity

TM = transmembrane, IU = intrinsically unstructured. The plots on the left were reproduced with permission from [].<p><b>Copyright information:</b></p><p>Taken from "Investigation of transmembrane proteins using a computational approach"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S7</p><p>BMC Genomics 2008;9(Suppl 1):S7-S7.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386072.</p><p></p

(A) The C atoms of all residues involved in binding in any of the five peptide bound structures are shown (red) along with the rest of the backbone (light blue ribbon)

(B) The standard deviation in the area bound on complex formation is displayed by coloring the C atoms of peptide binding residues on a gradient, from a standard deviation of 0Å (blue) to 10Å and greater (red). (C) The backbone RMSF of the 14-3-3 domain calculated over C atoms displayed as a color and radius gradient, from an RMSF of 0Å (blue, 0.25Å) to an RMSF of 2.0Å and greater (red, 2.0Å). (D) The side chain RMSF is displayed by coloring the C atoms of peptide binding residues on a gradient, from a RMSF of 0Å (blue) to an RMSF of 0.50Å and greater (red). All parameters were calculated using all five of the peptide-14-3-3 complexes.<p><b>Copyright information:</b></p><p>Taken from "Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S1</p><p>BMC Genomics 2008;9(Suppl 1):S1-S1.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386051.</p><p></p

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners-9

Ons of p53 represented in structure complexes in PDB are represented by horizontal bars, labeled with the name of the binding partner. For the DBD, the extent of the globular domain is indicated by the light grey box, where the internal horizontal bars indicate regions involved in binding to a particular partner. Post translational modifications sites are represented by vertical ticks. Experimentally characterized regions of disorder (red) and order (blue) are indicated by the horizontal bar. Finally, predictions of disorder (scores > 0.5) and order (scores < 0.5) are shown for two PONDR predictors: VLXT (solid line) and VSL2P (dashed line). All, features are presented to scale, as indicated by the horizontal axis. The p53 interaction partners and post translational modification sites have been adapted from Anderson & Appella [].<p><b>Copyright information:</b></p><p>Taken from "Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S1</p><p>BMC Genomics 2008;9(Suppl 1):S1-S1.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386051.</p><p></p

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners-2

Tion between the components of complexes for each residue in the relevant sequence region of p53. The two hatched bars indicate acetylated lysine residues.<p><b>Copyright information:</b></p><p>Taken from "Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S1</p><p>BMC Genomics 2008;9(Suppl 1):S1-S1.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386051.</p><p></p

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners-7

Tion profiles. These are shown aligned with the side chain RMSF (C) and the backbone RMSF (D) calculated from the five structures of bound 14-3-3ζ. Regions of residues that are highly exposed to solvent in all complex structures are indicated by the blue-shaded regions.<p><b>Copyright information:</b></p><p>Taken from "Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners"</p><p>http://www.biomedcentral.com/1471-2164/9/S1/S1</p><p>BMC Genomics 2008;9(Suppl 1):S1-S1.</p><p>Published online 20 Mar 2008</p><p>PMCID:PMC2386051.</p><p></p