Tools for modeling protein 3D structure

Submitted to: Dr. Parveen Pahuja

Submitted by: Priyanka M.Sc Hon’s BT (II) 130181123

Contents

Introduction Tools for modelling protein 3D strucutre1. Swiss Pdb viewer2. Swiss Model3. Cn3D

Introduction Tertiary structure represents spatial arrangement of amino acids that are

far apart in the linear sequence.

It results from interactions between R-groups via vander waal’s , ionic , hydrophobic and hydrogen bonding.

Groupings or arrangement of secondary structure into combinations that are present in a variety of proteins are often described as motifs or domains.

E.g. parallel and anti parallel β-sheets β-ɑ-β motif (can be either two parallel or antiparallel)

Domains

Polypeptide chain of > 200 amino acids that fold into two or more compact globular clusters are called domains.

3 main types of domains:1. ɑ domains are composed of ɑ-helices2. β domains contain anti-parallel β sheets and usually contain two β-sheets

packed against each other.3. ɑ/β domains contain the β-ɑ-β motif of parallel β-sheets.

In the 3-D structure of proteins almost all the hydrophobic side chains are found in the interior of the proteins and almost all the hydrophilic side chains are found in outside of the protein

Tools for modeling protin 3D structure

Deep view (Swiss Pdb Viewer)

Cn3D

Swiss Model

Swiss PDB viewer

An interactive molecular graphics programs for viewing and analyzing protein and nucleic acid structures.

Tightly linked to Swiss-Model, an automated homology modeling server (http:// www.expasy.org/swissmod)

provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.

Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain

Home page of Swiss-Pdb viewer

Visualization of structure in Swiss-Pdb viewer

Working Environment

DeepView can display up to eight interconnected interactive windows.

1. Graphic window2. Control Panel3. Toolbar4. Layers info window5. Alignment window6. Ramachandran plot window7. Surface and cavities window8. Electron Density Map Infos window9. Text window

Deep view working environment

Main windows

Specific windows

DeepView Commands

Accesses all the other window controls

distance angle dihedral angles provenance

Centre Translation tool Zoom tool

Rotation tool

world / local coordinates read PDB file Instructions!

torsiondisplay centre

DeepView: Control Panel

Chain

Current protein

Residue Secondary structure type

Measuring the distances between atoms

•Click the button and follow the instructions that appear in the message space below the toolbar• after picked two atoms on the molecules, the distance is shown, along with a dotted line

Measuring bond angles

•Click the button, and follow the instructions that appear in the message space below the toolbar (1. Pick center atom; 2. Pick 2nd atom; 3. Pick 3rd atom). •After picked three atoms on the model, the angle is shown as a label, along with a dotted line.

Measuring dihedral angles

• Click the button and, following the instructions that appear in the message space below the toolbar, pick one atom.• The values for phi, psi, and omega of the amino acid containing the selected atom are displayed on the message space.

Identifying Group and Atom

•Identifying an atom and the group to which the atom belongs. Click the button and pick one atom. •The atom type (CA, CB, O…) and the group to which it belongs (LYS116, ASN117…) are displayed both on the molecule and on the message space.• In addition, the message space gives the x, y, zatom coordinates and B-factor.

Layer name

aa Amio type

Displaying/selecting groups within a distance of a picked atom

•It allows restricting the display of the molecule on the Graphic window, or the selection of amino acids on the Control Panel, to groups within a distance of a picked atom. •Click the button and, following the instructions that appear in the message space below the toolbar, pick one atom. •The Display Radius dialog box allows entering a distance.

Display Radius dialog box

-Adds to a previous display those groups that are within the entered distance of the picked atom.- Displays groups on the Graphic window that are within the entered distance of the picked atom.- Selects groups on the Control Panel window that are within the entered distance of the picked atom,- Adds to a previous selection those groups that are within the entered distance of the picked atom.

Enter here the distance.If more than one layer was loaded, the Display Radius dialog box lets you enable/disable application of the tool to all layers.

Display only group that are within

Mutating an amino acids

Concept: can mutate an amino acid by first replacing its sidechain, and then browsing a rotamer library (rotolib.aa), which provides the most commonly observed orientations for the new sidechain.

Procedure1. To initiate a mutation, click the mutate tool and, following the instructions that appear

in the message space below, pick the amino acid to be mutated by clicking any of its atoms on the graphic window.

2. A list with the 20 protein amino acids is displayed.3. Chose a new amino acid in the list: the original sidechain of the selected group will be

replaced by the "best" rotamer of the new amino acid. 4. Clicking outside the list or pressing "return" or "enter" will highlight the original amino

acid in the list. 5. Once a mutation is done, the number and the score of the displayed rotamer are shown

in the message space below the tools.6. For example, rotamer: 5/9 score: -4 means that rotamer 5 out of 9 available rotamers is currently on display and scores –4.

Mutating an amino acid

Number corresponding to the displayed rotamer (5) over the number ofavailable rotamers (9).

This score is for evaluating the rotamer: the best rotamer is theone that totalizes the lowestscore.

Use these arrows to cycle through the available rotamers.

Applying torsions

Procedure

Click the Torsion tool and, following the instructions appearing in the message space below, pick one atom belonging to the group (amino acid or

hetero group) to be twisted.

Acting on amino-acids: A number of little arrows will appear below and at the right of the Torsion tool.While changing the dihedral angles will only affect the selected side chain, changing the backbone dihedral angles Phi/Psi will modify the whole protein arrangement.

By default, the C-terminal part of the protein will move. Tool menu (Move C-term part during Phi/Psi Changes), or by clicking the small box [C/N] on the upper left corner of the Ramachandran Plot window

torsion tool: acting on amino acids

From top to bottom, use these arrows to modifyDihedral angles

Use the upper andlower arrows tomodify phi and psirespectively.

Select Menu

The Select menu allows selecting specific groups on the Control Panel on the basis of atom properties, residue properties, structure properties, or other criteria.

Selected groups appear in red on the Control Panel.

If several layers are loaded, shift-clicking a Select option allows extending the selection to all layers.

Selecting group by property

Select> group property command

Subcommand Groups selected

Basic Arg, Lys, His

acidic Asp, Glu

polar Asn, Gln, Ser, Thr, Tyr

Non polar Ala, Cys, Gly, Ile, Leu, Met, Phe, Pro, Trp, Val

Ramachandran plot window

A Ramachandran plot is a graph of φ versus ϕ.

Symbols are colored according to the current backbone color set on the Control Panel.

By default, the N-terminal part of the protein will stay static, while the C-terminal part will move according to the applied change in the backbone angles.

Tools>set omega/phi/psi commandSubcommand ActionAlpha Helix Rebuilds selected amino acids as one long alpha helix (ϕ

= 60°, φ = 40°). The helix is not perfectly straight since only ϕ and φ angles are modified, whereas bond lengths and omega angles of the backbone are not altered.

Beta Sheet Rebuilds selected residues in beta conformation (ϕ = 120°, φ = 120°). Only ϕ and φangles are modified, bond lengths and omega angles of the backbone are not altered.

Other A dialog allows setting numerical ϕ, φ and omega values for selected amino acids (i.e. for one or many residues at once). Setting ϕ and φ to 180 degrees shows the backbone in its most extended form.

Using the Tools menu: For selected residues on the Control Panel window, the Set Omega/Phi/Psi command under the Tools menu offers a submenu that allows altering the values of backbone conformational angles:

•The plot delimits the allowed regions,where most of the amino acids of any given protein should plot:- in yellow: regions of sterically allowed values of PHI and PSI,- in blue: regions of maximum tolerable limits of steric strain•To alter the backbone conformational angles of one residue, click and drag its symbol on the Ramachandran Plot.

Select C or N to letmove on the Graphic window the Cterminal or Nterminal parts of the protein when a dot is dragged on the plot.

Name of thecurrently active layer

Computing Energy Minimisation

Procedure First of all, click Preferences>Energy Minimisation: a dialog lets you

adjust the minimisation parameters.

On the Control Panel, select the residues for which you want to minimize the force field energy, and click Tools>Energy Minimization. The force field of the selected atoms is minimized.

Provided that the Show Energy Report item is checked on the Energy Minimization Preferences dialog, an Energy Report is displayed and, on the Alignment window, the force field graph is plotted.

On the Graphic window, the structure of the minimized molecule is updated.

Enable one, two, or three cycles of n steps of Steepest Descent (currently the only available energy minimization method).

Checkmark the interactions to be considered.- Cutoff: enter a distance (Å) over which non-bonded and electrostatic interactions will not be considered.- Show Energy Report: check this item to obtain an energy report

Enter a value to stop minimization when the checked option is verified (in addition to the default stop after completion of the selected number of cycles).

Molecular Visualization Tool: Cn3D

Cn3D is a helper application for a web browser (i.e. Netscape or Internet Explorer) that allows viewing of 3-dimensional structures from NCBI's structure database.

It is available for free download from the NCBI web site.

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Cn3D is showing a representative protein structure, the family alignment, and annotation panels with information about annotated features of this protein family.

Highlighted in both structure and sequence windows are the conserved residues in a pattern characteristic to this domain.

Features of Cn3D

The Cn3D displays structure-structure alignments along with their structure based sequence alignments to emphasize what regions of a group of related proteins are most conserved in structure and sequence.

Extensive structure and alignment annotation features.

Detailed style control.

High revolution image export

Improved sequence alignment algorithms.

Automatic VAST [Vector alignment search tools] alignment import.

Taxonomy viewer.

Display And Animations:

The view menu options control display style of structures as a whole.

The whole structure can be made larger or smaller with View: Zoom in and View: Zoom out. Zoom in and out can also be done from keyboard shortcuts by using Z and X, respectively.

Animation can also be done via View: Animation menu.

The keyboard shortcuts n and s can also be used to rotate and stop relating the structure in graphic Window.

If there is more than one structure being viewed or if the structure contains

multiple models, then each structure will be assigned its own frame.

The various View: Frame items control the frame which is currently displayed.

Visualization of protien structure

Visual styles – Wireframe

Example: Cysteine Stick/Wireframe: shows individual bonds and corresponding

angles

Without hydrogen atoms With hydrogen atoms

Visual styles - Spacefill Spacefilling:

Spheres represent the electron cloud around nuclei of atoms Relative sizes of atoms and groups show up clearly Merged spheres represent share electrons (covalent bond)

Without hydrogen atoms With hydrogen atoms

Visual style: Ball and Stick

Ball and stick: Allows structure to be seen shows atomic position and bonds, and a portion of volume – small spheres are

centred at the nuclei of atoms

Without hydrogen atoms With hydrogen atoms

Visual style: Backbone

Backbone: Four amino acids shown (Lys, Ala,

Ile, Thr from top to bottom) Green line is a backbone trace: all side

chains removed, rods connect alpha carbon positions (or phosphate atoms)

Backbone does not follow any actual bonds

Right image shows backbone superimposed on tetrapeptide

Visual style: Surface

Shows the surface accessible to water molecules Most useful for studying the properties of the active sites Molecular surface of lysozyme

Active site in a groove Charged, hydrophilic surface

Visual style: Ribbon

Ribbon Smooth ribbon drawn through

peptide units – may either be solid (‘ribbons’) or parallel wires (‘strands’)

Display the fold of a protein Colour schemes shown

by secondary structure by secondary structure succession

- N-terminus blue- C-terminus red

REFERANCES

DeepView homepage http://au.expasy.org/spdbv/

DeepView tutorial http://www.usm.maine.edu/~rhodes/SPVTut/

Klotho - Small molecules in PDB format: http://www.biocheminfo.org/klotho/

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Bioinformatics: Principles and applications by Gosh and Mallik