Protein Predic+on I for Computer Scien+sts
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1 Protein Predic+on I for Computer Scien+sts Resources June 8 th /20th, Summer Term 2017 Burkhard Rost & Lothar Richter
2 Primary Databases Genbank/EBI/DDBJ: nucleic acid sequences UniprotKB: protein sequences PDB: 3D-structures
3 Growth of GenBank and WGS -doubling approx. every 18 months, diagram for release 207, Apr current version: release 213, Apr. 2016: bases in Genbank, bases in WGS -taken from h[p://
4 Growth of GenBank and WGS -current release 213: sequence in Genbank, sequences in WGS -taken from h[p:// release 207, Apr. 2015
5 UniProtKB: UniProt Components: - UniProtKB/Swiss-Prot - UniProtKB/TrEMBL UniParc: pure sequence archive, no annota+ons UniRef: consists fo three databases of clustered sets of protein sequences (UniRef100, UniRef90, UniRef50) using the CD-HIT algorithm UniMes: data from metagenomic and environmental samples, not in UniProtKB
6 Growth over three years: 2018_4 vs 2017_5 vs 2016_5 vs 2015_5 Protein existence (PE) Entries % 1. Evidence at protein level 98,566 (95,143) (92,536) (85,419) 17,7 (17.2) (16.8) (15.6) 2. Evidence at transcript level 57,060 (57,649) (57,757) (61,814) 10.2 (10.4) (10.5) (11.3) 3. Inferred from homology 386,164 (386,111) (387,589) (387,733) 69.3 (69.6) (70.3) (70.7) 4. Predicted 13,621 (13,751) (11,358) (11,526) 2.4 (2.5) (2.1) (2.1) 5. Uncertain 1864 (1,861) (1,953) (1,962) 0.3 (0.3) (0.4) (0.4)
7 Development taken from h[p://web.expasy.org/docs/relnotes/relstat1.png for release 2017_5
8 More Numbers (rel. 2017_5) Represented species: ( in 2015_5) Top 20 species: 119,149 sequences, i.e. 21.5% of the total number of entries Entries No of Species Entries No of Species 1 5,570 (5,495) (228) 2 1,921 (1,899) (214) 3 1,054 (1,023) (122) (657) (711) (487) (426) (399) (213) (289) > (1.046)
9 Species Representa+on (rel. 2017_5/ 2015_5) Top Frequency Species 1 20,201 (+3) Homo sapiens (Human) 2 16,877 (+166) Mus musculus (Mouse) ,333 (+1,445) Arabidopsis thaliana (Mouse-ear cress) 7,989 (+68) Rattus norvegicus (Rat) 5 6,721 (+3) Saccharomyces cerevisiae (Baker s yest) 6 5,999 (+6) Bos taurus (Bovine) 7 5,141 (+38) Schizosaccheromyces pombe (Fission yeast) 8 4,435 (+2) Escherichia coli K12 9 4,185 (+0) Bacillus subtilis 10 4,134 (+3) Dictyostelium discoideum (Slime mold)
10 Length Distribu+on (rel. 2017_5)
11 Annota+on Phases 1. Sequence cura+on 2. Sequence analysis 3. Literature cura+on 4. Family-based cura+on 5. Evidence a[ribu+on 6. Quality assurance, integra+on and update
12 taken from Figure 1. UniProtKB sequence analysis results displayed in graphical interface
13 Slides by Dr. Schafferhans X-ray Crystallography Crystallize Diffract Ø Measurement shows electron density Ø Not visible: ØH Ø Flexible parts Ø Ambiguity (e.g. NH2 / OH) Build model Images: By Thomas Splettstoesser ( - own work; images were rendered with PyMol ( based on PDB id 1MBO, CC BY-SA 3.0, Public Domain, By Hydrargyrum - Own work, CC BY-SA 3.0, By Jeff Dahl - Own work, CC BY-SA 3.0, By Bassophile 08:00, 25 May 2007 (UTC) - Self made using my own data and PyMol, CC BY 2.5, index.php?curid=
14 Slides by Dr. Schafferhans NMR (Nuclear magnetic resonance) Spinning nucleus absorbs radiation Exact frequency depends on environment chemical shift J-Coupling split Proteins too crowded for normal NMR! Image: By T.vanschaik - Own work, CC BY-SA 3.0,
15 Slides by Dr. Schafferhans Protein NMR Sample preparation (<1 ml, <3 mmol/l) (15N-, 13C-labeled samples help assign residues) Data collection (2D spectra) Resonance assignment Restraint generation Distance (peak intensity) Angle (coupling magnitude) Model building ensemble of solutions No standard quality measures Images: By User:Nonoelmo - English Wikipedia, CC BY-SA 3.0,
16 Slides by Dr. Schafferhans Electron Microscopy Sample preparation (mostly cyro) Measurement: Electron diffraction Electron tomography Model building: Reconstructing electron density Fitting atoms (e.g. from X-ray) No standard quality measures Images: By Claudionico~commonswiki - Own work, CC BY-SA 4.0,
17 Slides by Dr. Schafferhans Images: By D Wells - Own work, CC BY-SA 4.0,
18 Slides by Dr. Schafferhans Protein Data Bank History 1968: Brookhaven RAster Display (BRAD) 1969: Edgar Meyer (Brookhaven National Laboratory): file format for atomic coordinates 1971: Symposium Structure and Function of Proteins at the Three-Dimensional Level 1971: remote access with SEARCH program (Meyer) 1998: transfer to RCSB (Research Collaboratory for Structural Biology) 2003: formation of wwpdb (PDBe, RCSB, PDBj, BMRB)
19 Slides by Dr. Schafferhans Brookhaven RAster Display screen shot
20 Slides by Dr. Schafferhans Current composi+on (2017/05) Experimental Method X-ray diffraction NMR Proteins Nucleic Acids Protein / Nucleic Acid complexes Other Total Hybrid Other Total Electron microscopy Unique chains: 95987
21 Slides by Dr. Schafferhans Tradi+onal: PDB File formats Latest (last) PDB file format version: Contents Guide Version 3.30 (Nov. 21, 2012) 190 pages! Problem: large structures New standard (2104): PDBx/mmCIF see mmcif.wwpdb.org
22 Slides by Dr. Schafferhans PDB file overview Header - Protein informa+on - Cita+on - Details of structure resolu+on Coordinates / Connec+vity
23 Slides by Dr. Schafferhans PDB file format (general) allowed characters: abcdefghijklmnopqrstuvwxyzabcdefg HIJKLMNOPQRSTUVWXYZ :"<>? each line is 80 characters wide including EOL lines self-iden+fying: - col 1-6: record name - col 7: blank Records in defined order Some records are mandatory
24 nomenclature. This nomenclature is described in the Chemical Component Dictionary (ftp://ftp.wwpdb.org/pub/pdb/data/monomers). Slides by Dr. Schafferhans Record Format COLUMNS DATA TYPE FIELD DEFINITION Record name "ATOM " 7-11 Integer serial Atom serial number Atom name Atom name. 17 Character altloc Alternate location indicator Residue name resname Residue name. 22 Character chainid Chain identifier Integer resseq Residue sequence number. 27 AChar icode Code for insertion of residues Real(8.3) x Orthogonal coordinates for X in Angstroms Real(8.3) y Orthogonal coordinates for Y in Angstroms Real(8.3) z Orthogonal coordinates for Z in Angstroms Real(6.2) occupancy Occupancy Real(6.2) tempfactor Temperature factor LString(2) element Element symbol, right-justified LString(2) charge Charge on the atom. PP1CS Details SoSe 18
25 Slides by Dr. Schafferhans Example for Coordinates ATOM 601 N LEU A N ATOM 602 CA LEU A C ATOM 603 C LEU A C ATOM 604 O LEU A O ATOM 605 CB LEU A C TER 606 LEU A 75 ATOM 1185 O LEU B O ATOM 1186 CB LEU B C TER 1187 LEU B 75 HETATM 1188 H2 SRT A H HETATM 1189 HA SRT A H HETATM 1190 H3 SRT A H HETATM 1191 HB SRT A H HETATM 1192 O1 SRT A O ATOM 295 HB2 ALA A H ATOM 296 HB3 ALA A H TER 297 ALA A 18 ENDMDL
26 Slides by Dr. Schafferhans PDBx/mmCIF overview Standard format for PDB since 2014 Originated in the crystallographic community The STAR file: a new format for electronic data transfer and archiving Sydney R. Hall, Journal of Chemical Information and Computer Sciences (2), Advantages of new format: Extensible Flexible with respect to order Few syntax rules Facilitates automatic validation (with mmcif dictionary)
27 Slides by Dr. Schafferhans STAR (PDBx/mmCIF) syntax Data name: any text string starting with an underline (unique) (e.g. _chemical_formula) Data item: any text string not starting with an underline, preceded by data name (e.g. C23 H36 O7 ) Data loop: list of data names, preceded by loop_, followed by repeated data items loop citation_author.citation_id _citation_author.ordinal _citation_author.name primary 1 'Fitzgerald, P.M.D.' primary 2 'McKeever, B.M.' primary 3 'Van Middlesworth, J.F.' " Data block: collection of data, preceded by data_xxx!
28 Slides by Dr. Schafferhans Concepts in mmcif Entity: polymer / non-polymer / water Chemical component: blocks that build entities (e.g. non-standard residue) Structural Component: structural features, e.g. helix Asymmetric Unit Component: (chain), two compontents can refer to same entity Biological Component: sub- and super-components of the structure
29 Chirality (~Handedness)
30 Amino Acids from wiki/amino_acid Schema of an α-amino acid
31 Amino Acids
32 Amino Acids
33 Amino Acids Essential for humans: phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine
34 Protein Sequence / Primary Structure linear sequence of amino acids oriented from N- to C-terminus (typically) always starts with Methionin IMPORTANT: consider the different meanings Coding/Representation Protein Aspects 1D-information: sequence of amino acids as string Primary structure: amino acid sequence 2D-information: 2D-array, contact map Secondary structure: secondary structure elements like helices or sheets,... 3D-information: coordinates or atom couplings Tertiary structure: spatial arrangement of secondary structure elements (incl. amino acids, atoms,...)
35 Secondary Structure local structural elements structural building blocks for higher order structures α-helix, β-sheet, loops stabilized by hydrogen bonds amino acids have preferences for certain secondary structure elements
36 Ter+ary Structure spa+al arrangement of all secondary structure elements of a protein alterna+ve arrangements can exist (conforma+on changes upon substrate binding, or induced fit) can by used to hierarchical organize found protein structures
37 Quarternary Structure forma+on of mul+-protein complexes many cellular processes are carried out by mul+protein complexes: especially for highly coordinated/regulated ac+ons like: - replica+on - transcrip+on - transla+on difficult to determine precisely, some+me visible already in EM
38 Alpha Helix 3.6 amino acids per turn, spiral forming 4-40 residue (mostly 10) stabilized by hydrogen bonds between backbone atoms:
39 Beta Strand/Sheet long range (in terms of involved residues) hydrogen bonds parallel or an+parallel flat
40 Loop/Turn/Coil generally: change of direc+on: alpha (4), beta (3), gamma (2), delta (1), pi (5) omega-loop: catch all term, includes longer stretches, no hydrogen bonding involved connector between be[er defined secondary structure elements or at the end of a polypep+de chain not dis+nguished in 3-state model
41 Random Coil/ Disordered Region no clear secondary structure elements iden+fiable like sta+s+cal distribu+on of shapes biologically: can be used as adapter to different target shapes, i.e. one conforma+on is stabilized upon interac+on with a partner
42 Protein Features surface area hydrophobicity size iso-electric point amino acid composi+on various func+onal or structural mo+fs
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