In sillico Stucture Prediction

Primary structure (Amino acid sequence)

↓ Secondary structure

(α-helix,β-sheet ） ↓

Tertiary structure (Three-dimensional structure formed by assembly of

secondary structures ） ↓ Quaternary structure

(Structure formed by more than one polypeptide chains ）

STRUCTURE PREDICTION• Experimental data

• X-ray crystallography

• NMR spectroscopy

• expensive & time consuming

• Computational methods• Homology/comparative modeling

• Fold recognition (threading)

• Ab initio (de novo, new folds) methods

Homology/comparative modeling• modeling a protein 3D structure using a known

experimentally determined structure of a homologous protein as a template

• usually provides the most reliable result.

• Used when the sequence is similar to a known structure with >30-50% identity).

• two proteins belonging to the same family and sharing similar amino acid sequences, will have similar three-dimensional structures

STEPS INVOLVED;

• template identification

• amino acid sequence alignment (multiple sequence alignment)

• alignment correction

• backbone generation

• generation of loops

• side chain generation & optimization

• ab initio loop building

• overall model optimisation

• model verification. Quality criteria, model quality

• MSA gives an overview of the general features of the protein family, the degree of conservation, the consensus sequence motifs, etc.

• the positions of insertions and deletions should be correct, likewise the conservation of important residues (active site residues)

• The modeling software will thread sequence on the template structure. Creates a preliminary model of protein (backbone generation)

• Building of missing parts, generation of side chains for replaced residues and optimization of side chain conformations.

• At the last step the overall model needs to be optimized followed by verification of model quality.

Softwares used for modeling :

• Swiss Model

• Phyre

• I-tasser

• ROBETTA

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(1)- sequence of the protein to be predicted(2)- MSA(3)- Homologus Template protein(4)- backbone generation(5)- overall model optimization

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Protein threading(fold recognition)

• used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure.

• Fold recognition alignments are quite different from ordinary sequence alignments since they are evaluated from a structural perspective.

• Threading works by using statistical knowledge of the relationship between the structures deposited in the PDB and the sequence of the protein which one wishes to model.

• The prediction is made by "threading" (i.e. placing, aligning) each amino acid in the target sequence to a position in the template structure, and evaluating how well the target fits the template.

Steps involved:

1. The construction of a structure template database:

• Select protein structures from the protein structure databases as structural templates.

• Databases used are PDB, FSSP, SCOP, or CATH

2. The design of the scoring function:

• Design a good scoring function to measure the fitness b/w targetsequences and templates based on the knowledge of the known relationships between the structures and the sequences.

• A good scoring function should contain mutation potential, environment

fitness potential, pairwise potential, secondary structure compatibilities, and gap penalties.

• The quality of the energy function is closely related to the predictionaccuracy, especially the alignment accuracy.

3. Threading alignment:

• Align the target sequence with each of the structure templates by optimizing the designed scoring function.

• This step is one of the major tasks of all threading-based structure prediction programs that take into account the pairwise contact potential; otherwise, a dynamic programming algorithm can fulfill it.

4. Threading prediction:

• Select the threading alignment that is statistically most probable as the threading prediction.

• Then construct a structure model for the target by placing the backbone atoms of the target sequence at their aligned backbone positions of the selected structural template

Protein threading software:

• HHpredis

• RAPTOR

• Phyre

• MUSTER

• SPARKS X.

• BioShell

ab initio method

• means “from the beginning”

• predicts the native fold from amino acid sequence alone

• Methods for ab initio prediction includes;

• Molecular Dynamics (MD) simulations

• Monte Carlo (MC)

• Genetic Algorithms

Softwares used in ab initio methods

• I-TASSER

• ROBETTA

• Abalone

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(1)- protein sequences(2)- suitable folds

Prediction of protein structure from folds