3D Visualization of Drugs-Protein Complexes
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1 3D Visualization of Drugs-Protein Complexes Goal: Develop better understanding of Protein Database and its entries Plan Introductory information about protein structure database Learn Molsoft-browser for molecular visualization (and/or imolview for portable devices) Learn how to find a drug-protein complex in the database Molecular visualization exercises Contact: Ruben Abagyan : ucsd.edu Website:
2 Molecular Crystals and X-ray diffraction Wilhelm Röntgen Wavelength of X-rays is around 1 Angstrom An X-ray picture (radiograph), taken by Wilhelm Röntgen in 1896, of Albert von Kölliker's hand.
3 From X-ray diffraction spots to 3D structure Each spot needs: 3 coordinates, h,k,l, intensity and phase, F hkl, A hkl To get the electron density map the Fourier transformation is used We need spot intensities and phases, but we only have intensities. Yet another limitation of quality Direct methods Anomalous diffraction (MAD) molecular replacement
4 Drug Targets in PDB Uniprot contains ~20,250 human proteins, with the mean length of 550 and median of 400 amino acids
5 PDB FILE FORMAT PDB Lingo: ATOM HETATM (het) SEQRES HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3I TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE TITLE 2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY)... EXPDTA X-RAY DIFFRACTION AUTHOR R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA, AUTHOR 2 B.BRODSKY,A.ZAGARI,H.M.BERMAN... REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT REMARK 350 BIOMT SEQRES 1 A 9 PRO PRO GLY PRO PRO GLY PRO PRO GLY SEQRES 1 B 6 PRO PRO GLY PRO PRO GLY SEQRES 1 C 6 PRO PRO GLY PRO PRO GLY... ATOM 1 N PRO A N ATOM 2 CA PRO A C ATOM 3 C PRO A C ATOM 4 O PRO A O ATOM 5 CB PRO A C... HETATM 130 C ACY C HETATM 131 O ACY O HETATM 132 OXT ACY O Each atom has X, Y, Z, O, B Occupancy Bfactor, - how smeared the electron density is
6 Difficult cases for crystallography Membrane proteins: only ten GPCRs out of a thousand human ones Fibrils (tubulin, miosin, actin filaments, amyloid) Large particles: ribosomes Flexible multi-domain proteins
7 Unit Cells and Translations Crystals are regular periodic arrays Unit cell is the smallest volume from which the entire crystal can be constructed by translation only Each unit cell contains one or several Asymmetric Units related by crystallographic symmetry (e.g. a mirror plane or a 2-fold rotation axis) a b Unit Cell
8 Unit Cell and Asymmetric Unit One unit cell may contain elements of crystallographic symmetry
9 Asymmetric Unit Asymmetric Unit is the smallest volume from which the unit cell can be constructed by application of the crystallographic symmetry.
10 Asymmetric unit is not unique Two steps: AU is multiplied by the symmetry elements of the cell (unique for each of 230 space groups) Result is translated in 3D
11 Unit Cell and Asymmetric Unit The Unit cell here is one card since by parallel TRANSLATION only the space can be filled The Asymmetric Unit is half a card, related to another half by ROTATION. There are many ways to define that half however. In protein crystals AU does not break proteins Better choice of AU Legal, but poor choice of AU
12 Non-crystallographic symmetry (NCS) An asymmetric unit may still contain several identical molecules or groups of molecules related by LOCAL symmetry Example: a crystal of viral particles, each virus consists of 60 groups of envelope proteins related by local NCS
13 Space Groups 17 groups in 2D 2D group example: p2 230 groups in 3D The most frequent: P P C P C P P1 P2 1
14 Symmetry Group: P Many biomolecules crystallize in P group It has 4 asymmetric units in a unit cell
15 Reconstructing the biological structure from the asymmetric unit Biological protein a part of a biological assembly (oligomer, homo- or hetero-, a complex,..) A structural domain of interest 1,2,.. domains may form an asymmetric unit via NCS Several asymmetric units form a unit cell Unit cells fill space via translation to form a crystal If you are lucky, your space group will be P1 (no internal symmetry), and the asymmetric unit will consist of only your protein
16 Unit Cell Example Transthyretin binds drugs, transports thyroxine (T4). 2flm (1.65A) TTR Amyloid: Familial amyloid polyneuropathy (or cardiomyopathy) Space group P
17 In P there are four dimers in unit cell The biological unit is a HOMOTETRAMER
18 UNLs (unrecognized ligands) From electron density of a protein drug complex to a full atom model Ambiguities and gaps Missing/unclear ligand density Missing/amb. loop or side chains Rotations of Asn, Gln Crystallographic and non-crystallographic symmetry, bio-molecule, water, UNLs Fantasy Heavy Atoms Wrong atoms with full occupancy and low B- factors Protonation and Tautomerization ε and δ Histidines, His rotations, and ligand tautomers protons in His, Asp, Glu,Arg, Lys, Cys Protonation and tautomerization of the ligand 2o5r 2gb 3
19 imolview on Mobiles
20 imolview on Google/Android
21 ICM-Graphics: Mouse Controls Center of the window: left mouse button = rotate middle button = translate right button = menu Left margin: left mouse button = zoom in/out Top margin: left mouse button = Z-rotation Bottom margin: translate With slides: two triangular arrows = switch to next/previous Right Margin: Bottom: front clipping plane Top: back clipping plane
22 Exercise: Finding a PDB By 4-symbol code Every PDB file has a 4-symbol code starting from a digit, e.g. 1crn Try to find code of interest online Type the code in ICM Search panel By text (eg drug name): Type Aspirin into the PDB/Search field Double click on a result row
23 Exercise: Playing with Graphics Search Aspirin via ICM-PDB-search box Choose 1pth Find Aspirin moiety in Workspace Understand all molecules in the structure Select chain B and delete it Center on the Salicylic Acid Find Sites under chain a Select Ser 530 by double clicking on the site and display modified Serine in CPK Make a picture
24 Exercise: Slides and Prepared.icb Go to the site Download prepared Aspirin.icb file Flip through slides using arrows at the bottom margin of the graphics-window Make a picture
25 MolSoft ICM Reference ICM Selections When a 3D structure of a protein, DNA or small molecule is loaded from PDB or other file format into ICM shell, it exists in a data structure that we term as molecular 'object'. Multiple objects may co-exist in ICM. Each object consists of one or more molecules, each molecule of one or more residues and each residue of one or more atoms. Complete atom-level selection constant contains four fields: a_objects.molecules/residues/atoms Example: read pdb 1stp as_graph = a_1stp.a/15/ca The above selects atom ca in residue number 15 of chain 'a' of object '1stp and puts it into a variable called as_graph. This is a graphical selection in the graphics window you will see green crosses on the selected atoms. Selection examples: a_1stp.a/15 # residue number 15 a_1stp.a # molecule chain a a_1stp. # object a_icm. # ICM-type objects a_.a # polypeptide chains in all objects a_1.w # water molecules of the first object a_1.!w # excludes water molecules from 1 st object a_1.* # everything in first object Current Object selections are useful because most operations are performed on the last loaded object a_ #current object, use: set object a_<n>. to reset a_h # heteroatom molecules (ligands, ions etc) in curent object a_/20:30 # residues from 20 to 30 a_/"vta" # consecutive residues matching sequence 'VTA', i.e. val-thr-ala a_/lys,arg,glu,asp # all lysines,arginines,glutamic and aspartic acids a_/sh # residues in Sec.structure Helices a_//c,ca,n # backbone (C,Ca,N atoms) a_//c* # all carbons Basic ICM Commands An instruction one can execute in the ICM-shell interactively or from an ICM script file. Typically a command consists of a verb (like read or delete ) and a bunch of arguments. The word order in the argument list is not important, if arguments have different types. If two or more argument of the same type are present the order becomes important. Example verbs: display,undisplay,color,center, delete, connect Example nouns: wire,cpk,ball,stick,xstick, Surface,skin,ribbon,label,residue,atom Example: read pdb "1crn" display ribbon color ribbon a_/4:8 blue display xstick a_1.1/10 green center display residue label a_/6:12 display string "Crambin" 36 red Write Image write image window=2*view(window) Display Hydrogen Bonds display hbond a_1.* # display all hbonds in object one Superimpose Protein Structures superimpose a_1.1 a_2.1 align minimize ICM Functions ICM functions have the following general format FunctionName(arg1, arg2...). They can return a variety of types. The order of the function arguments is fiexible Example: avb=min( Bfactor(a_//ca) ) show Bfactor(a_//!h*) color a_//* Bfactor(a_//*) color ribbon a_/a Bfactor(a_/A) ICM Macros A Macro is a group of ICM commands in a separate named function with arguments. Convert PDB to ICM Object (convertobject) To display hydrogen bonds display electrostatic or property surfaces then you need to convert a PDB file into an ICM object using the convert command [more]. read pdb "1abe" convertobject a_1,2 yes yes yes no show r_residualrmsd _macro file. A collection of ICM macros. This file contains a set of ICM macros. You can use them, modify them, or browse them to develop your own macros. _macro is downloaded by the call _macro command. ICM-shell Objects The ICM-shell can handle many different types such as integer, (e.g. a=10, b= -3 ) real, (e.g. c = ) string, text in single or double quotes (e.g. d = Hi, guys" ) logical, (e.g. e = (2 > 43); f = yes ) preference, (i.e. fixed multiple choices, try show wirestyle ) iarray, (i.e. integer arrays, g={-2,3,-1} ) rarray, (i.e. real arrays, h={ -2.3, 3.12, -1.} ) sarray, (i.e. string arrays, i={"mek","yerku","erek"} ) parray, including array of 0D,2D or 3D chemicals, e.g. chm = Chemical({"CC","CC(=O)O","C1CC1"}) matrix, (read from a disk file, e.g. read matrix "def.mat" ) sequence, (i.e. amino acid or nucleotide sequences, e.g. a=sequence("asdqwe") alignment, (i.e. pairwise or multiple sequence alignments, read from a file) grob, mesh, surface of shape table, or spreadsheet. Several arrays of the same size are grouped in a table. Table can also have a header with some additional data fields. Tables are essentially simple databases which can be manipulated with, sorted and searched with ICM commands.
26 iphone &ipad
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