in silico structure prediction
TRANSCRIPT
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In sillico Stucture Prediction
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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 )
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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
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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
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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
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• 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.
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Softwares used for modeling :
• Swiss Model
• Phyre
• I-tasser
• ROBETTA
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(1)
(2)
(1)- sequence of the protein to be predicted(2)- MSA(3)- Homologus Template protein(4)- backbone generation(5)- overall model optimization
(3)
(4)
(5)
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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.
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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.
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• 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
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Protein threading software:
• HHpredis
• RAPTOR
• Phyre
• MUSTER
• SPARKS X.
• BioShell
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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
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Softwares used in ab initio methods
• I-TASSER
• ROBETTA
• Abalone
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(1)
(2)
(1)- protein sequences(2)- suitable folds
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Prediction of protein structure from folds
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