# Introduction to Structural Bioinformatics: proteins and DNA

Gwenaëlle André-Leroux

► To cite this version:

Gwenaëlle André-Leroux. Introduction to Structural Bioinformatics: proteins and DNA. 3rd cycle. Workshop in Structural bioinformatics (Introduction to Structural bioinformatics), 2015, 60 diapos. hal-02795917

HAL Id: hal-02795917

https://hal.inrae.fr/hal-02795917

Submitted on 5 Jun 2020

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<figure><img src="image_1.png" /></figure>
Introduction to Structural Bioinformatics:
Proteins and DNA

>3CM3:A | PDBID | CHAIN | SEQUENCE
GPEIRMDKKSLYKYLLLRSTGDMHKAKSP
TIMTRVTNNVYLGNYKNAMDAPSSEVKF
KYVLNLTMDKYTLPNSININIIHIPLVDDTTT
DISKYFDDVTAFLSKCDQRNEPVLVHSAA
GVNRSGAMILAYLMSKNKESLPM

<figure><img src="image_2.png" /></figure>

Gwénaëlle André-Leroux
MalAGE

Montevideo december 2015

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Curriculum Vitae

★ 1994 – 1998: PhD in molecular modeling, Inra Nantes, France

★ 1999 – 2000: Visiting Assistant Professor, Cornell University, NY – USA

★ 1998 – 2002: Research assistant, Inra Nantes, BIA

★ 2002 – 2004: Senior researcher, Inra Nantes, BIA

★ 2004 – 2013: Senior researcher at Institut Pasteur, Microbiologie Structurale

★ 2013 – : Senior researcher, Inra Jouy-en-Josas, MaiAGE

<figure><img src="image_7.png" /></figure>

INRA
SCIENCE & IMPACT

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INSTITUT PASTEUR

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Structural biologist and computational scientist
Molecular modeling is dedicated to

★ Visualize

★ Understand

★ Predict

Structural bioinformatics

★ Integrate metaOmics data

★ Develop bioinformatic tools dedicated to analyze 3D fold in metaOmics

<figure><img src="image_11.png" /></figure>

1. Visualize 2. Understand 3. Predict 4. Integrate MetaOmics

« The theoretical in silico prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, and designing new technologies in the life science and material sciences. » A. Kolinski
# Molecular modeling

Introduction, study, expecting in this course

## Introduction to proteins

Tool box: softwares, websites, tricks to study proteins, DNA, RNA and ligands.

Hands on tutorials

### 1. Structures

1.1. Analyse of proteins. Get familiar with PyMOL

1.2. Homology modeling: strategy and use of I-tasser, Phyre2, modeler

1.3. Mutations *in silico*

### 2. Oligomerisation and motion analysis

2.1. Analyse des oligomers with PyMol

2.2. Modeling of oligomers

2.3. Motion and normal mode

Coffee breaks

### 3. Molecular mechanics and docking

3.1. Binding siteidentification and characterization

3.2. Analysis of ligands

3.3. Docking: rigide, flexible

Conclusions, questions, comments

<figure><img src="image_12.png" /></figure>
Introduction : proteins

**Macromolecule** in cell, responsible for metabolism, energy cycle TCA, signaling...

linear repetition of atomic bricks: [amino acid residues linked by peptidic bond](#)

**Fold** (3D space arrangement) is specific and guarantees its function.

From sequence to quaternary arrangement, 4 steps in protein [folding](#)

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

**QUATERNARY STRUCTURE**
**(ASSEMBLY OF INDIVIDUAL PROTEINS INTO A COMPLEX)**
# Proteins: primary structure

It refers to the sequence of amino acids present in the polypeptide chain

Amino acids -called residues- are covalently linked by a peptide bonds

The first is called amino terminal end or N-terminus

The last is called amino carboxy terminal or C-terminus

>3CM3:A|PDBID|CHAIN|SEQUENCE
GPEIRMDKKSLYKYLLLRSTGDMHKAKSPTIMTRV
TNNVYLGNYKNAMDAPSSEVKFKYVLNLTMDKYT
LPNSNINIIHIPLVDDTTTDISKYFDDVTAFLSKCDQ
RNEPVLVHSAAGVNRSGAMILAYLMSKNKESLPM

<figure><img src="image_16.png" /></figure>

Amino acid residue in a peptidic chain

<figure><img src="image_17.png" /></figure>

Each letter refers for an aa residue:

A for Alanine

C for Cysteine ...

R refers to the side chain of the amino acid
Residues: small to large, polar to apolar

<figure><img src="image_18.png" /><figcaption>glycine (G)</figcaption></figure>

<figure><img src="image_19.png" /><figcaption>alanine (A)</figcaption></figure>

<figure><img src="image_20.png" /><figcaption>serine (S)</figcaption></figure>

<figure><img src="image_21.png" /><figcaption>cysteine (C)</figcaption></figure>

<figure><img src="image_22.png" /><figcaption>valine (V)</figcaption></figure>

<figure><img src="image_23.png" /><figcaption>threonine (T)</figcaption></figure>

<figure><img src="image_24.png" /><figcaption>proline (P)</figcaption></figure>

<figure><img src="image_25.png" /><figcaption>isoleucine (I)</figcaption></figure>

<figure><img src="image_26.png" /><figcaption>leucine (L)</figcaption></figure>

<figure><img src="image_27.png" /><figcaption>aspartate (D)</figcaption></figure>

<figure><img src="image_28.png" /><figcaption>asparagine (N)</figcaption></figure>

<figure><img src="image_29.png" /><figcaption>glutamate (E)</figcaption></figure>

<figure><img src="image_30.png" /><figcaption>glutamine (Q)</figcaption></figure>

<figure><img src="image_31.png" /><figcaption>methionine (M)</figcaption></figure>

<figure><img src="image_32.png" /><figcaption>lysine (K)</figcaption></figure>

<figure><img src="image_33.png" /><figcaption>histidine (H)</figcaption></figure>

<figure><img src="image_34.png" /><figcaption>phenylalanine (F)</figcaption></figure>

<figure><img src="image_35.png" /><figcaption>tyrosine (Y)</figcaption></figure>

<figure><img src="image_36.png" /><figcaption>arginine (R)</figcaption></figure>

<figure><img src="image_37.png" /><figcaption>tryptophan (W)</figcaption></figure>
# Proteins: secondary structure

The peptidic chain shows dihedral angles

<figure><img src="image_38.png" /></figure>

Folding patterns into sheets, helix, coils etc ...

Peptidic bond is planar

Consequence: successive plans linked by dihedrals (φ,ψ)
# Proteins: secondary structure

Folding patterns into sheets, helix, coils etc ...

Ramachandran diagram calculates the possible combinaisons of dihedrals (φ,ψ)

<figure><img src="image_39.png" /></figure>

<figure><img src="image_40.png" /></figure>

3 Regions energetically allowed

75% is energetically not favorable

Hélice α : helical periodic structure.

Strand β : flat periodic structure flat.
Assemble into sheets

Turns :
# Proteins: secondary structure

Folding patterns into sheets, helix, coils etc ...

<figure><img src="image_41.png" /></figure>

α Helix: periodic structure.

H bond between –CO from *i* and-NH from *i+4*
# Proteins: secondary structure

Folding patterns into sheets, helix, coils etc ...

<figure><img src="image_42.png" /></figure>

© Georges Dolisi

Strand β: periodic structure extended. Forms β sheets

H bond between–CO et -NH from *i* and *j* -> antiparallel

H bond between–CO et -NH from *i* and *j+2* -> parallel
# Proteins: tertiary structure

Overall 3D structure with a complete folding in 3D space.

**3D structure correlates to function.**

<figure><img src="image_43.png" /></figure>

Several interactions guarantee its fold and its stability

* Covalent bonds (disulfide bridges between cysteine residues)

* Electrostatic bonds (iononic bonds, H-bonds)

* van der Waals interactions

* solvent, ions, lipids interactions
# Proteins: quaternary structure

Assembly of individual proteins (protomers) into a functional complex:
**Either homo-oligomers or hetero-oligomers**

<figure><img src="image_44.png" /></figure>
Protein Structure

1D Sequence

>3CM3:A | PDBID | CHAIN | SEQUENCE
GPEIRMDKKSLYKYLLLLRSTGDMHKAKSPTIMTRVT
NNVYLGNYKNAMDAPSSEVKFKYVLNLTMDKYTL
PNSNINIIHIPLVDDTTTDISKYFDDVTAFLSKCDQR
NEPVLVHSAAGVNRSGAMILAYLMSKNKESLPMLY
FLYVYHSMRDLRGAFVENPSFKRQIIEKYVIDKN

<figure><img src="image_45.png" /></figure>

3D Fold

<figure><img src="image_46.png" /></figure>

<figure><img src="image_47.png" /></figure>

Function

<figure><img src="image_48.png" /></figure>

<figure><img src="image_49.png" /></figure>

Oligomerization

<figure><img src="image_50.png" /></figure>
Protein Structure

1D Sequence

>3CM3:A | PDBID | CHAIN | SEQUENCE
GPEIRMDKKSLYKYLLLLRSTGDMHKAKSPTIMTRVT
NNVYLGNYKNAMDAPSSEVKFKYVLNLTMDKYTL
PNSNINIIHIPLVDDTTTDISKYFDDVTAFLSKCDQR
NEPVLVHSAAGVNRSGAMILAYLMSKNKESLPMLY
FLYVYHSMRDLRGAFVENPSFKRQIIEKYVIDKN

3D Fold

<figure><img src="image_51.png" /></figure>

<figure><img src="image_52.png" /></figure>

Homology modeling

<figure><img src="image_53.png" /></figure>

Function

<figure><img src="image_54.png" /></figure>

Docking

Active site

<figure><img src="image_55.png" /></figure>

Oligomerization

<figure><img src="image_56.png" /></figure>

Interface computation
1D Sequence

>3CM3:A | PDBID | CHAIN | SEQUENCE
GPEIRMDKKSLYKYLLLLRSTGDMHKAKSPTIMTRVT
NNVYLGNYKNAMDAPSSEVKFKYVLNLTMDKYTL
PNSNINIIHIPLVDDTTTDISKYFDDVTAFLSKCDQR
NEPVLVHSAAGVNRSGAMILAYLMSKNKESLPMLY
FLYVYHSMRDLRGAFVENPSFKRQIIEKYVIDKN

<figure><img src="image_57.png" /></figure>

<figure><img src="image_58.png" /></figure>

Why?

How?

Biological consistency?
Protein Structure

double click on PyMol

http://www.pymolwiki.org/index.php/Main_Page
# Analysis of 3CM3.pdb

File /open/3CM3.pdb

<figure><img src="image_59.png" /></figure>

<figure><img src="image_60.png" /></figure>

MATHEMATIQUES ET INFORMATIQUE APPLIQUES

MaiAGE
Analysis of 3CM3.pdb

File /open/3CM3.pdb

<figure><img src="image_61.png" /></figure>

Keywords of 3CM3? Starts at?
Analysis of 3CM3.pdb

File /open/3CM3.pdb

<figure><img src="image_62.png" /></figure>

Starts at SLYK

<figure><img src="image_63.png" /></figure>

MATHEMATIQUES ET INFORMATIQUE APPLIQUES

MaiAGE
Analysis of 3CM3.pdb

File /open/3CM3-basic.pse go to lle 1170 show stick

<figure><img src="image_64.png" /></figure>

<figure><img src="image_65.png" /></figure>
Analysis of 3CM3.pdb

http://www.rcsb.org/pdb/home/home.do

3CM3 download fasta &pdb. Piece of informations?

<figure><img src="image_66.png" /></figure>

<figure><img src="image_67.png" /></figure>

MATHEMATIQUES ET INFORMATIQUE APPLIQUES

MaiAGE
Analysis of 3CM3.pdb

http://www.rcsb.org/pdb/home/home.do

3CM3 download fasta et pdb. Infos?

<figure><img src="image_68.png" /></figure>

<figure><img src="image_69.png" /></figure>

MATHEMATIQUES ET INFORMATIQUE APPLIQUES

MaiAGE
DU GENOME A L'ENVIRONNEMENT
# Analysis of 3CM3.pdb

gedit 3CM3.pdb

<figure><img src="image_70.png" /></figure>
# Analysis of 3CM3.pdb

gedit 3CM3.pdb

<figure><img src="image_71.png" /></figure>

## Crystallization conditions

REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.18
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 62% PEG 400, 0.1M TRIS PH 8,
REMARK 280 BATCH, TEMPERATURE 297K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMPOP SYMMETRY
REMARK 290 NNNMIMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z
REMARK 290 WHERE NNN -> OPERATOR NUMBER

## Sequence

## Hetero atoms

## Space group and unit cell parameters
Analysis of 3CM3.pdb

gedit 3CM3.pdb

<figure><img src="image_72.png" /></figure>

Positions x y z

Occupancy (0<x<1)

B factor

4 parameters per atom:

x,y,z location inside the unit cell

Occupancy

Isotropic B or B factor: atomic displacement that accounts for slightly different positions in each unit cell with average position x,y,z.
Analysis of 3CM3.pdb

gedit 3CM3.pdb

<figure><img src="image_73.png" /></figure>

Positions x y z

Occupancy (0<x<1)

B factor

Go to Ile 1170

Within firefox, go to http://www.ebi.ac.uk/pdbsum/
Then 3CM3.pdb.

Within firefox, go to http://molprobity.biochem.duke.edu/
Then 3CM3.pdb
Analysis of 3CM3.pdb

gedit 3CM3.pdb

<figure><img src="image_74.png" /></figure>

<figure><img src="image_75.png" /></figure>

Positions x y z, facteur d'occupation (0<x<1) et facteur B

Le facteur B reflète l'agitation thermique dans le cristal

Aller de nouveau jusqu'à l'èl 1170

Depuis firefox, taper http://www.ebi.ac.uk/pdbsum/
puis 3CM3.pdb. Voir.

http://molprobity.biochem.duke.edu/
puis éventuellement renseigner 3CM3.pdb sous:
Analysis of 3CM3.pdb

gedit 3CM3.pdb

<figure><img src="image_76.png" /></figure>

<figure><img src="image_77.png" /></figure>

Positions x y z, facteur d'occupation (0<x<1) et facteur B

<figure><img src="image_78.png" /></figure>

Le facteur B reflète l'agitation thermique dans le cristal

Critical to assess the quality of template protein +++
# Homology modeling

**Homology modeling**, also known as **comparative modeling** of protein, refers to constructing an atomic-resolution model of the "query" protein from its amino acid sequence from an experimental three-dimensional structure of an homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that align residues in the query sequence with residues in the template sequence.

*Protein structures are more conserved than protein sequences amongst homologues.*

Sequences falling below a 20% sequence identity can have very different structure. (wiki source)

1. Identification de la/des protéines « templates » de référence

2. Modélisation de la protéine requête « query »

Qualité de l'alignement +++)

http://robetta.bakerlab.org

http://toolkit.tuebingen.mpg.de/hhpred

http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

<figure><img src="image_79.png" /></figure>

<figure><img src="image_80.png" /></figure>

<figure><img src="image_81.png" /></figure>
Homology modeling

http://toolkit.tuebingen.mpg.de/hhpred

<figure><img src="image_82.png" /></figure>

Cliquer pour voir l'alignement 1D /2D

Modeller https://salilab.org/modeller/

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_clustalw.html

Direct link to http://espritp.ibcp.fr/ESPript/cgi-bin/ESPript.cgi

http://www.ebi.ac.uk/Tools/psa/emboss_stretcher/

http://www.ebi.ac.uk/Tools/psa/emboss_water/
Homology modeling

http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

<figure><img src="image_83.png" /></figure>
Homology modeling

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_clustalw.html

Direct link to http://espritp.ibcp.fr/ESPript/cgi-bin/ESPript.cgi

<figure><img src="image_84.png" /></figure>
Homology modeling

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_clustalw.html

Direct link to http://espritp.ibcp.fr/ESPript/cgi-bin/ESPript.cgi

<figure><img src="image_85.png" /></figure>

Renseigner cette partie avec 3CM3.pdb
# 2D alignment of PTP_ORF wt with VH1 from Vaccinia (3CM3) & Vaccinia WR (2Q05)

## Esprit alignment

<figure><img src="image_86.png" /></figure>

<figure><img src="image_87.png" /></figure>

7 residues insertion in Orf virus between α4 & α5 helices

<figure><img src="image_88.png" /></figure>

★ Triade catalytique

7 residues insertion @137 and 143 (PTP orf nb)

## Jalview visualisation

<figure><img src="image_89.png" /></figure>
Homology modeling

Need to convert into.pir alignment. Go back to nps Lyon then ask for a .pir output
Copy/paste/save using gedit/nedit.

Go from 3CM3_2Q05_PTPOrf.pir to aln_modeler_PTP_Orf.pir

NB: PyMol is useful to borne out with residues numbering and chain names

<figure><img src="image_90.png" /></figure>
# Homology modeling

Needs to convert the.pir alignment

Copy/paste/save /with gedit.

Go from `3CM3_2Q05_PTPOrf.pir` to `aln_modeler_PTP_Orf.pir`

Modify now python program

Add alignment, templates, nb modèles etc ...

Launch modeler

Mod9.13 script.py

<figure><img src="image_91.png" /></figure>

```python
from modeller import *
from modeller.automodel import *
log.verbose()  # request verbose output
env = environ()  # create a new MODELLER environment to build this model in
env.io.atom_files_directory = './:/../atom_files'
a = automodel env,
    alnfile = 'aln_VH1_PTPOrf.pir',
    knowns = ('3CM3_A', '2Q05_B'),
    sequence = 'PTP_ORF_WT',
    assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1
a.ending_model = 100
a.make()
```
# Homology modeling

Needs to convert the.pir alignment

Copy/paste/save /with gedit.

Go from `3CM3_2Q05_PTPOrf.pir` to `aln_modeler_PTP_Orf.pir`

Modify now python program

Add alignment, templates, nb modèles etc ...

Launch modeler

Mod9.13 script.py

<figure><img src="image_92.png" /></figure>

https://salilab.org/modeller/

```python
from modeller import *
from modeller.automodel import *
log.verbose()  # request verbose output
env = environ()  # create a new MODELLER environment to build this model in
env.io.atom_files_directory = './:/../atom_files'
a = automodel env,
    alnfile = 'aln_VH1_PTPOrf.pir',
    knowns = ('3CM3_A', '2Q05_B'),
    sequence = 'PTP_ORF_WT',
    assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1
a.ending_model = 100
a.make()
```

ouvrir script.log

Comparison of results: gedit *.log

DOPE score

GABE score

Visualization with PyMOL
# Homology modeling

**Homology modeling**, also known as **comparative modeling** of protein, refers to constructing an atomic-resolution model of the "query" protein from its amino acid sequence from an experimental three-dimensional structure of an homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that align residues in the query sequence with residues in the template sequence.

*Protein structures are more conserved than protein sequences amongst homologues.*

Sequences falling below a 20% sequence identity can have very different structure. (wiki source)

1) Identification of protein(s) as reference « template(s) »

2) Homology modeling of protein « query »

Open PyMol session: compil_Hmodeles.pse
# Mutations

<figure><img src="image_93.png" /></figure>

<figure><img src="image_94.png" /></figure>

## Model the point mutants by substituting residues

1. Modéliser les mutants, les variants pour lesquels on a des données expérimentales.

2. Modifier le site de fixation

3. Vérifier l'accessibilité

4. Analyser l'interface

Pymol/Plugin/PDB Loader Service/ faire la mutation dans 3CM3 S112C
Ouvrir 2Q05

Show sequence. Que voit-on?

Show cartoon/color by chain/ select/action copy to objet/ Wizard ...
Electrostatic profile

<figure><img src="image_95.png" /></figure>

Calcul du profil électrostatique : cartographie des patches hydrophobes/chargés + ou -.
Analyse de la solvatation des systèmes biologiques

1- Simulation des processus de diffusion -> cinétiques de fixation protéine/ligand; protéine/protéine.

2- Modélisation du solvant implicite pour la DM des biomolécules.

3- Solvatation et calcul d'énergie d'affinité et de constantes d'équilibre. Rational drug-design.

4- Etude de titrations des biomolécules.
Electrostatic profile

<figure><img src="image_96.png" /></figure>

Comment? PDB2PQR et APBS Adaptative Poisson-Boltzmann Solver

APBS Adaptative Poisson-Boltzmann Solver dans pymol

PDB2PQR aller à http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
Electrostatic profile

PDB2PQR aller à http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

<figure><img src="image_97.png" /></figure>

<figure><img src="image_98.png" /></figure>
Electrostatic profile

PDB2PQR aller à http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

<figure><img src="image_99.png" /></figure>

<figure><img src="image_100.png" /></figure>
Electrostatic profile

PDB2PQR aller à http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

<figure><img src="image_101.png" /></figure>
Electrostatic profile

PDB2PQR aller à http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/

<table><caption>2Q05_A_Met.pdb</caption><tr><td>ATOM</td><td>1</td><td>N</td><td>MET</td><td>A</td><td>1</td><td>92.038</td><td>61.305</td><td>57.368</td><td>1.00</td><td>0.00</td><td>N</td></tr><tr><td>ATOM</td><td>2</td><td>CA</td><td>MET</td><td>A</td><td>1</td><td>91.096</td><td>61.791</td><td>58.372</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>3</td><td>C</td><td>MET</td><td>A</td><td>1</td><td>91.815</td><td>62.519</td><td>59.482</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>4</td><td>O</td><td>MET</td><td>A</td><td>1</td><td>93.019</td><td>62.442</td><td>59.651</td><td>1.00</td><td>0.00</td><td>O</td></tr><tr><td>ATOM</td><td>5</td><td>CB</td><td>MET</td><td>A</td><td>1</td><td>90.267</td><td>60.604</td><td>58.934</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>6</td><td>CG</td><td>MET</td><td>A</td><td>1</td><td>89.317</td><td>59.911</td><td>57.933</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>7</td><td>SD</td><td>MET</td><td>A</td><td>1</td><td>88.087</td><td>61.085</td><td>57.345</td><td>1.00</td><td>0.00</td><td>S</td></tr><tr><td>ATOM</td><td>8</td><td>CE</td><td>MET</td><td>A</td><td>1</td><td>87.151</td><td>61.276</td><td>58.868</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>9</td><td>N</td><td>ASP</td><td>A</td><td>2</td><td>91.000</td><td>63.233</td><td>60.290</td><td>1.00</td><td>46.15</td><td>N</td></tr><tr><td>ATOM</td><td>10</td><td>CA</td><td>ASP</td><td>A</td><td>2</td><td>91.465</td><td>63.913</td><td>61.491</td><td>1.00</td><td>44.81</td><td>C</td></tr><tr><td>ATOM</td><td>11</td><td>C</td><td>ASP</td><td>A</td><td>2</td><td>92.278</td><td>62.945</td><td>62.353</td><td>1.00</td><td>44.30</td><td>C</td></tr><tr><td>ATOM</td><td>12</td><td>O</td><td>ASP</td><td>A</td><td>2</td><td>91.788</td><td>61.889</td><td>62.768</td><td>1.00</td><td>43.84</td><td>O</td></tr><tr><td>ATOM</td><td>13</td><td>CB</td><td>ASP</td><td>A</td><td>2</td><td>90.268</td><td>64.473</td><td>62.272</td><td>1.00</td><td>44.45</td><td>C</td></tr><tr><td>ATOM</td><td>14</td><td>CG</td><td>ASP</td><td>A</td><td>2</td><td>90.679</td><td>65.206</td><td>63.536</td><td>1.00</td><td>43.48</td><td>C</td></tr><tr><td>ATOM</td><td>15</td><td>OD1</td><td>ASP</td><td>A</td><td>2</td><td>89.901</td><td>65.181</td><td>64.515</td><td>1.00</td><td>42.53</td><td>O</td></tr><tr><td>ATOM</td><td>16</td><td>OD2</td><td>ASP</td><td>A</td><td>2</td><td>91.777</td><td>65.803</td><td>63.555</td><td>1.00</td><td>41.93</td><td>01-</td></tr><tr><td>ATOM</td><td>17</td><td>N</td><td>LYS</td><td>A</td><td>3</td><td>93.518</td><td>63.317</td><td>62.616</td><td>1.00</td><td>0.00</td><td>N</td></tr><tr><td>ATOM</td><td>18</td><td>CA</td><td>LYS</td><td>A</td><td>3</td><td>94.423</td><td>62.396</td><td>63.298</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>19</td><td>C</td><td>LYS</td><td>A</td><td>3</td><td>94.117</td><td>62.330</td><td>64.775</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>20</td><td>O</td><td>LYS</td><td>A</td><td>3</td><td>94.090</td><td>61.225</td><td>65.337</td><td>1.00</td><td>0.00</td><td>O</td></tr><tr><td>ATOM</td><td>21</td><td>CB</td><td>LYS</td><td>A</td><td>3</td><td>95.892</td><td>62.839</td><td>63.054</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>22</td><td>CG</td><td>LYS</td><td>A</td><td>3</td><td>96.937</td><td>61.855</td><td>63.637</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>23</td><td>CD</td><td>LYS</td><td>A</td><td>3</td><td>98.394</td><td>62.301</td><td>63.487</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>24</td><td>CE</td><td>LYS</td><td>A</td><td>3</td><td>98.799</td><td>62.218</td><td>62.010</td><td>1.00</td><td>0.00</td><td>C</td></tr><tr><td>ATOM</td><td>25</td><td>NZ</td><td>LYS</td><td>A</td><td>3</td><td>100.230</td><td>62.544</td><td>61.875</td><td>1.00</td><td>0.00</td><td>N1+</td></tr><tr><td>ATOM</td><td>26</td><td>N</td><td>LYS</td><td>A</td><td>4</td><td>93.866</td><td>63.458</td><td>65.420</td><td>1.00</td><td>43.16</td><td>N</td></tr><tr><td>ATOM</td><td>27</td><td>CA</td><td>LYS</td><td>A</td><td>4</td><td>93.415</td><td>63.466</td><td>66.808</td><td>1.00</td><td>43.30</td><td>C</td></tr></table>

<table><caption>2Q05_A_Met.pqr</caption><tr><td>ATOM</td><td>1</td><td>N</td><td>MET</td><td>A</td><td>1</td><td>92.038</td><td>61.305</td><td>57.368</td><td>-0.3200</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>2</td><td>CA</td><td>MET</td><td>A</td><td>1</td><td>91.096</td><td>61.791</td><td>58.372</td><td>0.3300</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>3</td><td>C</td><td>MET</td><td>A</td><td>1</td><td>91.815</td><td>62.519</td><td>59.482</td><td>0.5500</td><td>1.7000</td><td></td></tr><tr><td>ATOM</td><td>4</td><td>O</td><td>MET</td><td>A</td><td>1</td><td>93.019</td><td>62.442</td><td>59.651</td><td>-0.5500</td><td>1.4000</td><td></td></tr><tr><td>ATOM</td><td>5</td><td>CB</td><td>MET</td><td>A</td><td>1</td><td>90.267</td><td>60.604</td><td>58.934</td><td>0.0000</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>6</td><td>CG</td><td>MET</td><td>A</td><td>1</td><td>89.317</td><td>59.911</td><td>57.933</td><td>0.2650</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>7</td><td>SD</td><td>MET</td><td>A</td><td>1</td><td>88.087</td><td>61.085</td><td>57.345</td><td>-0.5300</td><td>1.8500</td><td></td></tr><tr><td>ATOM</td><td>8</td><td>CE</td><td>MET</td><td>A</td><td>1</td><td>87.151</td><td>61.276</td><td>58.868</td><td>0.2650</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>9</td><td>HE1</td><td>MET</td><td>A</td><td>1</td><td>87.599</td><td>61.954</td><td>59.451</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>10</td><td>HE2</td><td>MET</td><td>A</td><td>1</td><td>86.223</td><td>61.581</td><td>58.652</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>11</td><td>HE3</td><td>MET</td><td>A</td><td>1</td><td>87.112</td><td>60.399</td><td>59.346</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>12</td><td>H2</td><td>MET</td><td>A</td><td>1</td><td>91.895</td><td>61.794</td><td>56.505</td><td>0.3300</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>13</td><td>H3</td><td>MET</td><td>A</td><td>1</td><td>92.977</td><td>61.459</td><td>57.683</td><td>0.3300</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>14</td><td>HG2</td><td>MET</td><td>A</td><td>1</td><td>89.872</td><td>59.548</td><td>57.171</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>15</td><td>HG3</td><td>MET</td><td>A</td><td>1</td><td>88.883</td><td>59.127</td><td>58.400</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>16</td><td>H</td><td>MET</td><td>A</td><td>1</td><td>91.897</td><td>60.324</td><td>57.219</td><td>0.3300</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>17</td><td>HA</td><td>MET</td><td>A</td><td>1</td><td>90.469</td><td>62.439</td><td>57.921</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>18</td><td>HB3</td><td>MET</td><td>A</td><td>1</td><td>89.712</td><td>60.939</td><td>59.712</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>19</td><td>HB2</td><td>MET</td><td>A</td><td>1</td><td>90.906</td><td>59.906</td><td>59.293</td><td>0.0000</td><td>0.0000</td><td></td></tr><tr><td>ATOM</td><td>20</td><td>N</td><td>ASP</td><td>A</td><td>2</td><td>91.000</td><td>63.233</td><td>60.290</td><td>-0.4000</td><td>1.5000</td><td></td></tr><tr><td>ATOM</td><td>21</td><td>CA</td><td>ASP</td><td>A</td><td>2</td><td>91.465</td><td>63.913</td><td>61.491</td><td>-0.0000</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>22</td><td>C</td><td>ASP</td><td>A</td><td>2</td><td>92.278</td><td>62.945</td><td>62.353</td><td>0.5500</td><td>1.7000</td><td></td></tr><tr><td>ATOM</td><td>23</td><td>O</td><td>ASP</td><td>A</td><td>2</td><td>91.788</td><td>61.889</td><td>62.768</td><td>-0.5500</td><td>1.4000</td><td></td></tr><tr><td>ATOM</td><td>24</td><td>CB</td><td>ASP</td><td>A</td><td>2</td><td>90.268</td><td>64.473</td><td>62.272</td><td>0.0000</td><td>2.0000</td><td></td></tr><tr><td>ATOM</td><td>25</td><td>CG</td><td>ASP</td><td>A</td><td>2</td><td>90.679</td><td>65.206</td><td>63.536</td><td>0.1000</td><td>1.7000</td><td></td></tr><tr><td>ATOM</td><td>26</td><td>OD1</td><td>ASP</td><td>A</td><td>2</td><td>89.901</td><td>65.181</td><td>64.515</td><td>-0.5500</td><td>1.4000</td><td></td></tr><tr><td>ATOM</td><td>27</td><td>OD2</td><td>ASP</td><td>A</td><td>2</td><td>91.777</td><td>65.803</td><td>63.555</td><td>-0.5500</td><td>1.4000</td><td></td></tr></table>

Facteur occupation 0< x< 1

Facteur B agitation thermique

Q charge

R rayon

<figure><img src="image_102.png" /></figure>

<figure><img src="image_103.png" /></figure>
<figure><img src="image_104.png" /><figcaption>Mapping of the electrostatic profile</figcaption></figure>
# Oligomerization

<figure><img src="image_105.png" /></figure>

Pourquoi?

Comment?

Pertinence biologique?
Oligomerization

File /open/2Q05.pdb

<figure><img src="image_106.png" /></figure>

PDBePISA : Proteins, Interfaces, Structures and Assemblies is an interactive tool for the exploration of macromolecular interfaces.

http://www.ebi.ac.uk/pdbe/pisa/
Oligomerization

File /open/3CM3.pdb

Action/ remove water

Show cartoon

Action/generate/symetry mates 4A

<figure><img src="image_107.png" /></figure>

Informations on symmetry related mates in crystal packing. Comparison. Computation. Interface profiling.

PDBePISA : Proteins, Interfaces, Structures and Assemblies is an interactive tool for the exploration of macromolecular interfaces.

http://www.ebi.ac.uk/pdbe/pisa/
Normal mode analysis

http://lorentz.dynstr.pasteur.fr/nma/submission.php

Browse 2Q05_AB.pdb keep the selected default parameter then submit

In PyMol: File /open/2Q05_AB.pdb -> arrow below right

<figure><img src="image_108.png" /></figure>
# Docking

Docking is a method which predicts the preferred orientation of one molecule to a second when *bound* to each other to form a stable *complex*.

Knowledge of the preferred orientation in turn may be used to predict the strength of association or *binding affinity* between two molecules using (energy as *scoring functions*).

Docking used to predict the binding orientation of *small molecule drug* candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule.

Docking plays an important role in the *rational design of drugs*. [Wiki site](https://en.wikipedia.org/wiki/Docking)

<figure><img src="image_109.png" /></figure>
# Binding pocket and ligands

## Binding site:

Topology: crevice/groove/funnel/tunnel etc ...: show surface / generate ligand binding site

Electrostatic profile: charged? Polar? Hydrophobic?

Mutants which impede this interaction?

Comparison apo/holo: what are the flexible elements? Color by B-factor?

Accessibility? http://sts.bioe.uic.edu/castp/calculation.php

Druggability? http://pockdrug.rpbs.univ-paris-diderot.fr/cgi-bin/index.py?page=home

## Ligand

Protein: see webservers

ADN/ARN : voir sites web

Ligands : ADT tools/ DiscoveryStudio biovia©

Construction of ligands in mol2 format using PyMol

Prodrg token/free registration mandatory

<figure><img src="image_110.png" /></figure>

## Scoring :

Total potential energy

Intraction energy
# Docking of protein/protein

Rosetta : D. Baker's lab

http://rosie.rosettacommons.org/docking2/submit

http://rosie.rosettacommons.org/

Zdock : Z. Weng's lab

http://zdock.umassmed.edu/

Haddock : A. Bonvin's lab

http://haddock.science.uu.nl/services/HADDOCK2.2/haddock.php

Grammx server : I. A. Vakser's lab

http://vakser.compbio.ku.edu/resources/gramm/grammx/
# Docking of ligands

ADT Auto-dock tools fichier à suivre. Pdf à envoyer

DiscoveryStudio © Biovia ex msi ex Accelrys
# Visualisation for seminars, labmeetings

## « photo »

- Background

- Surface transparancy/fancy helix

- Ray .... Save as png. Insérer une photo png par ppt

## « video »

- Open 3CM3.pdb

- Movie/Program/Camera/X-roll/8seconds

- Play

- Voir pour plus d'informations www.pymolwiki.org/index.php/MovieSchool_1

## « pse »

- Save the PyMol session
Listing non exhaustif

http://toolkit.tuebingen.mpg.de/hhpred

http://molprobity.biochem.duke.edu/

https://salilab.org/modeller/

! Ne pas oublier de les citer dans les publications

http://www.rcsb.org/pdb/home/home.do

http://escript.ibcp.fr/ESScript/cgi-bin/ESScript.cgi

http://www.ebi.ac.uk/pdbsum/

http://www.ebi.ac.uk/services

(...)

http://pockdrug.rpbs.univ-paris-diderot.fr/
# Take home messages

## modélisation par homologie

Passer du temps sur l'analyse de la séquence et la qualité de l'alignement.

## oligomérisation

Compiler données physico-chimiques (UAC, ITC), structurales (RX, RMN, SAXS) et
biochimiques (mutations, tests d'activité). La modélisation seule ne suffit pas.

## docking

L'affinité n'est pas tout, penser à l'accessibilité côté protéine et à la flexibilité côté ligand.

## formation

Sites non exhaustifs. Boîte à outils toujours en évolution.

Gwenaelle.andre-leroux@jouy.inra.fr ou gandre@jouy.inra.fr

Veronique.martin@jouy.inra.fr
A big big big thank to Mabel, Andrea and to you

<figure><img src="image_111.png" /><figcaption>Ribosome
1J5E and 1JJ2</figcaption></figure>

<figure><img src="image_112.png" /><figcaption>Transfer RNA
4TNA</figcaption></figure>

<figure><img src="image_113.png" /><figcaption>Antibody
1IGT</figcaption></figure>

<figure><img src="image_114.png" /><figcaption>Phenylalanyl-tRNA
Synthetase
1EIY</figcaption></figure>

<figure><img src="image_115.png" /><figcaption>Gyrase A Fragment
1AB4</figcaption></figure>

<figure><img src="image_116.png" /><figcaption>Ribisco
1RCX</figcaption></figure>

<figure><img src="image_117.png" /><figcaption>Apoptosome-Procaspase-9
CARD complex
3IZA</figcaption></figure>

<figure><img src="image_118.png" /><figcaption>Simian Virus 40
1SVA</figcaption></figure>

<figure><img src="image_119.png" /><figcaption>Simian Virus 40
Capsid Protein
1SVA</figcaption></figure>

<figure><img src="image_120.png" /><figcaption>Rhodopsin
1F88</figcaption></figure>

<figure><img src="image_121.png" /><figcaption>Prefoldin
1FXK</figcaption></figure>

<figure><img src="image_122.png" /><figcaption>Dehydrofolase
1DHF</figcaption></figure>

<figure><img src="image_123.png" /></figure>

<figure><img src="image_124.png" /><figcaption>Pepsin
5PEP</figcaption></figure>

<figure><img src="image_125.png" /><figcaption>Elon</figcaption></figure>

<figure><img src="image_126.png" /></figure>

<figure><img src="image_127.png" /><figcaption>Hemoglobin
4HHB</figcaption></figure>

<figure><img src="image_128.png" /><figcaption>Myoglobin
1MBD</figcaption></figure>

<figure><img src="image_129.png" /><figcaption>Thermosome
3LOS</figcaption></figure>

acetaldehyde

<figure><img src="image_130.png" /><figcaption>RNA polymerase
3AOH</figcaption></figure>

<figure><img src="image_131.png" /><figcaption>Cyclooxygenase
1PTH</figcaption></figure>

200Å

<figure><img src="image_132.png" /><figcaption>GroEL/GroES chaperonin
1AON</figcaption></figure>

<figure><img src="image_133.png" /><figcaption>Lysozyme
1LZ1</figcaption></figure>

<figure><img src="image_134.png" /><figcaption>Insulin
2HIU</figcaption></figure>

<figure><img src="image_135.png" /><figcaption>Insect Flight Muscle
2W49</figcaption></figure>

<figure><img src="image_136.png" /><figcaption>Adenovirus
Hexon Protein
3IYN</figcaption></figure>
<figure><img src="image_137.png" /></figure>

La nuit n'est jamais complète
Il y a toujours puisque je le dis
Puisque je l'affirme
Au bout du chagrin
une fenêtre ouverte
une fenêtre éclairée
Il y a toujours un rêve qui veille
désir à combler
faim à satisfaire
un cœur généreux
une main tendue
une main ouverte
des yeux attentifs
une vie : la vie à se partager

Paul Eluard

<figure><img src="image_138.png" /></figure>

Pablo Picasso

<figure><img src="image_139.png" /></figure>

Luc Gwiazdzinski