Partial Charges - Docking

Adição de cargas via 

Open BABEL
Não é possível incluir carga nem multiplicidade. Há "atom types" pré definidos para o gasteiger e grupos químicos como O- e metais não estão incluídos. Há outros métodos para atribuir carga que não são adequados para o Autodock.

Antechamber
É possível incluir carga e multiplicidade mas há os mesmos problemas dos "atom types". Há outras opções de cargas que não reconhecem o metal.

MOPAC (Coulson charges)
É possível incluir carga e multiplicidade. Apresenta valores pra energia de ligação (complexo+proteína) na ordem de -6.6 kcal/mol

ESP e RESP
Método mais adequado para o cálculo das cargas parciais mas com resultados incompatíveis para ligantes com metal. Apresenta valores pra energia de ligação (complexo+proteína) na ordem de -5.0 kcal/mol

Autodock (gasteiger)
Não reconhece o metal nem a carga do ligante

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OPEN BABEL:

obabel -L charges

gasteiger    Assign Gasteiger-Marsili sigma partial charges
mmff94       Assign MMFF94 partial charges
qeq    Assign QEq (charge equilibration) partial charges (Rappe and Goddard, 1991)
qtpie    Assign QTPIE (charge transfer, polarization and equilibration) partial charges (Chen and Martinez, 2007)

babel a.pdb a.mol2 --partialcharge mmff94

mmff94: inseriu a carga total do ligante
gasteiger: não acertou a carga

babel Cu.pdb Cu.mol2 --partialcharge qeq

Inseriu carga para o cobre mas inverteu os valores

babel Cu.pdb Cu.mol2 --partialcharge qtpie

Inseriu a carga 1.6 para o cobre mas não forneceu bons resultados de energia do docking

from: 

http://openbabel.org/docs/dev/Command-line_tools/babel.html

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MOPAC

Converter mol2 em formato mopac

babel -imol2 isapnsal.mol2 -omop isa.mop

more Cuisapn+.mop
uhf PM6 doublet charge=1
Cuisapn+  

C   7.76180 1 -1.30940 1 -0.24770 1
C   6.37720 1 -1.13140 1 -0.23890 1
C   5.81970 1  0.14170 1  0.16170 1
C   6.64670 1  1.19420 1  0.56350 1

(...)

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ANTECHAMBER

antechamber -i Cuisapn+.pdb -fi pdb -o Cuisapn+.mol2 -fo mol2 -c bcc -m 2 -nc 1 -s 2 


antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2 -c bcc -m 1 -nc -1 -s 2 


ANTECHAMBER - APENAS O LIGANTE

#Apenas cria um arquivo mol2
antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2

# Gera um arquivo mol2 com as cargas AM1-BCC
antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2 -c bcc -nc -1


# Gera um arquivo mol2 com as cargas GASTEIGER
antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2 -c gas -nc -1

(ERRO PORQUE O MÉTODO NÃO UTILIZA O NUMERO DE ELÉTRONS MAS SIM OS "Atom Types"; Assim este método calcula o ligante com carga total zero que eh errado!!)

# Gera um arquivo mol2 com as cargas de MULLIKEN
antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2 -c mul -nc -1

# ERRO CARGAS CM1 ou CM2
antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2 -c cm1 -nc -1
antechamber -i isapn.pdb -fi pdb -o isapn.mol2 -fo mol2 -c cm2 -nc -1



ANTECHAMBER - TODO O COMPLEXO DE COBRE


antechamber -i Cuisapn.pdb -fi pdb -o Cuisapn.mol2 -fo mol2

# Não reconhece as ligações do cobre com os ligantes. Pode-se inserir a flag -j

# Gera um arquivo mol 2
antechamber -i Cuisapn.pdb -fi pdb -o Cuisapn.mol2 -fo mol2 -j 5


# Gera um arquivo mol2 com as cargas AM1-BCC
antechamber -i Cuisapn.pdb -fi pdb -o Cuisapn.mol2 -fo mol2 -c bcc -nc 1 -m 2 -j 5


# Gera um arquivo mol2 com as cargas de MULLIKEN
antechamber -i Cuisapn.pdb -fi pdb -o Cuisapn.mol2 -fo mol2 -c mul -nc 1 -m 2 -j 5





_________________________________________
cat a.mol2 | awk '{ sum+=$9} END {print sum}'

http://www2.chemie.uni-erlangen.de/software/petra/ (research group of Prof. Dr. J.Gasteiger)

Gaussian input file

# Rodar geometria do checkpoint
$ more zn.com
%chk=znisapn_b3.chk
%NProc=2
%mem=8GB
# bp86/TZVP pop=(ReadRadii,MK) Geom=AllCheckpoint

Cu 1.8

$

Why classify proteins?

Proteins can be classified into groups according to sequence or structural similarity.

Thus, when a novel protein is identified, its functional properties can be proposed based on the group to which it is predicted to belong. 

We will explain how families, domains and sequence features can be defined and used for protein classification.

Lets see how  proteins can be classified into different groups based on:

• the FAMILIES to which they belong

• the DOMAINS they contain

• the SEQUENCE FEATURES they possess

What are protein families?


A protein family is a group of proteins that share a common evolutionary origin, reflected by their related functions and similarities in sequence or structure.

Protein domain

Domains are distinct functional and/or structural units in a protein.
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.

Each domain forms a compact three-dimensional structure and often can be independently stable and folded. 

 Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions




Family- and domain-based protein classification


http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/family-and-domain-based-protei


What are sequence features?


Sequences features are groups of amino acids that confer certain characteristics upon a protein, and may be important for its overall function. Such features include:

• active sites, which contain amino acids involved in catalytic activity. For example, the enzyme lipase, which catalyses the formation and hydrolysis of fats, has two amino acid residues (a histidine followed by a glycine) that are essential for its catalytic activity.
• binding sites, containing amino acids that are directly involved in binding molecules or ions, like the iron-binding site of haemoglobin.
• post-translational modification (PTM) sites, which contain residues known to be chemically modified (phosphorylated, palmitoylated, acetylated, etc) after the process of protein translation.
• repeats, which are typically short amino acid sequences that are repeated within a protein, and may confer binding or structural properties upon it.

From: http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/why-classify-proteins