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Protein Modeling. The Outline. Introduction Comparative Modeling Conclusion References. Introduction. 3D Structure of Proteins. T he number of solved 3D structures increases slowly compared to the rate of sequencing DNA. P redictive methods have gained much interest.
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The Outline • Introduction • Comparative Modeling • Conclusion • References
3D Structure of Proteins • The number of solved 3D structures increases slowly compared to the rate of sequencing DNA. • Predictive methods have gained much interest.
The 4 main steps of Comparative Modeling Comparative Modeling Identification of Modeling Templates Aligning the Target Sequence with the Template Sequence Building the Model Accessing the Model
Identification of modeling templates • It requires at least one sequence of known 3D structure with significant similarity to the target sequence. • BLAST, PSI-BLAST, or HHSearch Programs are used.
Identification of modeling templates The Reference = The template with the highest sequence similarity • Maximizing the number of C∞ pairs in the common core while minimizing their relative mean square deviation
Aligning the target sequence with the template sequence • Using the best-scoring diagonals obtained by SIM. • Residues which should not be used for model building will be ignored during the modeling process.
Building the model • Framework Construction Averaging the position of each atom in the target sequence, based on the location of the corresponding atoms in the template
Building the model • Building Non-Conserved Loops WHY? • The accepted "spare parts" are sorted according to their RMSD, and a • Cα framework based on the five best fragments can be added to the model.
Building the model • Completing the Backbone • The co-ordinates of each central tri-peptide are then averaged for each target backbone atom (N, C, O) and added to the model.
Building the model • Adding Side Chains • The number of side chains that need to be built is dictated by the degree of sequence identity between target and template sequences
Building the model • Model Refinement • Idealization of bond geometry and removal of unfavorable non-bonded contacts can be performed by energy minimization with force fields such as CHARMM, AMBER or GROMOS.
Accessing the Model • Removing Errors PS:Error increases rapidly below 30% sequence similarity.
We got to know that Comparative is more accurate…but requires other structures to be known.
References • Baker, D.; Sali, A. Protein Structure Prediction and Structural Genomics.Science 2001, 294, 93-96. • Fiser, A.; Feig, M.; Brooks, C. L.; Sali, A. Evolution and Physics in Comparative Protein Structure Modeling.Acc. Chem. Res. 2002, 35, 413-421. • Peitsch ;Guex.,N. Comparative protein modeling.GlaxoWellcome Experimental Research S.A. 16, chemin des Aulx 1228 Plan-les-Ouates / Switzerland.
