Computational Biology, Part 11 Retrieving and Displaying Macromolecular StructuresRetrieving 3D structuresDisplaying StructuresPDB filesSlide 5Example PDB fileSlide 7Cn3D formatExample structure retrieval sessionSlide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 193HHB - all alpha1CD8 - all beta1KFJ - alpha/beta1AL1 - Amphiphilic Alpha HelixStructural homologyFinding proteins with known structures based on sequence homologyFinding proteins with similar structures to a known proteinSlide 27Finding proteins with similar structures to tubulinFinding proteins with structures similar to tubulinSlide 30Slide 311Computational Biology, Part 11Retrieving and Displaying Macromolecular Structures Computational Biology, Part 11Retrieving and Displaying Macromolecular Structures Robert F. MurphyRobert F. MurphyCopyright Copyright  1996, 1999, 2001-2009. 1996, 1999, 2001-2009.All rights reserved.All rights reserved.2Retrieving 3D structuresRetrieving 3D structuresProtein Data Bank (PDB)Protein Data Bank (PDB)home page = http://www.rcsb.org/pdb/home page = http://www.rcsb.org/pdb/NCBINCBIvia Structure Databasevia Structure DatabaseBLASTBLASTvia links following sequence similarity searchesvia links following sequence similarity searches3Displaying StructuresDisplaying StructuresMost web page displays relating to sequences are Most web page displays relating to sequences are two-dimensional and easily interpreted by visual two-dimensional and easily interpreted by visual inspection. Appreciating molecular structures inspection. Appreciating molecular structures requires viewing them from various directions and requires viewing them from various directions and modifying the display to emphasize different modifying the display to emphasize different portions of the moleculeportions of the moleculeTo display 3D structures locally, we can use To display 3D structures locally, we can use programs such as programs such as Cn3D Cn3D oror JMol JMol, public domain , public domain programs available for wide range of computers, programs available for wide range of computers, including MacOS, Windows and Unixincluding MacOS, Windows and Unix4PDB filesPDB filesIn order to optimally display, rotate and In order to optimally display, rotate and color the 3D structure, we need to download color the 3D structure, we need to download a copy of the coordinates for each atom in a copy of the coordinates for each atom in the molecule to our local computerthe molecule to our local computerThe most common format for storage and The most common format for storage and exchange of atomic coordinates for exchange of atomic coordinates for biological molecules is biological molecules is PDB file formatPDB file format5PDB filesPDB filesPDB file format PDB file format is a text (ASCII) format, is a text (ASCII) format, with an extensive header that can be read with an extensive header that can be read and interpreted either by programs or by and interpreted either by programs or by peoplepeopleWe can request either the header only or the We can request either the header only or the entire fileentire file6Example PDB fileExample PDB fileHEADER SYNTHETIC PROTEIN MODEL 02-JUL-90 1AL1 1AL1 2HEADER SYNTHETIC PROTEIN MODEL 02-JUL-90 1AL1 1AL1 2COMPND ALPHA - 1 (AMPHIPHILIC ALPHA HELIX) 1AL1 3COMPND ALPHA - 1 (AMPHIPHILIC ALPHA HELIX) 1AL1 3SOURCE SYNTHETIC 1AL1 4SOURCE SYNTHETIC 1AL1 4AUTHOR C.P.HILL,D.H.ANDERSON,L.WESSON,W.F.DE*GRADO,D.EISENBERG 1AL1 5AUTHOR C.P.HILL,D.H.ANDERSON,L.WESSON,W.F.DE*GRADO,D.EISENBERG 1AL1 5REVDAT 2 15-JAN-95 1AL1A 1 HET 1AL1A 1REVDAT 2 15-JAN-95 1AL1A 1 HET 1AL1A 1REVDAT 1 15-OCT-91 1AL1 0 1AL1 6REVDAT 1 15-OCT-91 1AL1 0 1AL1 6JRNL AUTH C.P.HILL,D.H.ANDERSON,L.WESSON,W.F.DE*GRADO, 1AL1 7JRNL AUTH C.P.HILL,D.H.ANDERSON,L.WESSON,W.F.DE*GRADO, 1AL1 7JRNL AUTH 2 D.EISENBERG 1AL1 8JRNL AUTH 2 D.EISENBERG 1AL1 8JRNL TITL CRYSTAL STRUCTURE OF ALPHA=1=: IMPLICATIONS FOR 1AL1 9JRNL TITL CRYSTAL STRUCTURE OF ALPHA=1=: IMPLICATIONS FOR 1AL1 9JRNL TITL 2 PROTEIN DESIGN 1AL1 10JRNL TITL 2 PROTEIN DESIGN 1AL1 10JRNL REF SCIENCE V. 249 543 1990 1AL1 11JRNL REF SCIENCE V. 249 543 1990 1AL1 11JRNL REFN ASTM SCIEAS US ISSN 0036-8075 038 1AL1 12JRNL REFN ASTM SCIEAS US ISSN 0036-8075 038 1AL1 12REMARK 1 1AL1 13REMARK 1 1AL1 13REMARK 1 REFERENCE 1 1AL1 14REMARK 1 REFERENCE 1 1AL1 14REMARK 1 AUTH D.EISENBERG,W.WILCOX,S.M.ESHITA,P.M.PRYCIAK,S.P.HO 1AL1 15REMARK 1 AUTH D.EISENBERG,W.WILCOX,S.M.ESHITA,P.M.PRYCIAK,S.P.HO 1AL1 15REMARK 1 TITL THE DESIGN, SYNTHESIS, AND CRYSTALLIZATION OF AN 1AL1 16REMARK 1 TITL THE DESIGN, SYNTHESIS, AND CRYSTALLIZATION OF AN 1AL1 16REMARK 1 TITL 2 ALPHA-*HELICAL PEPTIDE 1AL1 17REMARK 1 TITL 2 ALPHA-*HELICAL PEPTIDE 1AL1 17REMARK 1 REF PROTEINS.STRUCT.,FUNCT., V. 1 16 1986 1AL1 18REMARK 1 REF PROTEINS.STRUCT.,FUNCT., V. 1 16 1986 1AL1 18REMARK 1 REF 2 GENET. 1AL1 19REMARK 1 REF 2 GENET. 1AL1 19REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 867 1AL1 20REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 867 1AL1 20REMARK 2 1AL1