Contents 1. Protein Structure Prediction - Homology Modeling, Threading, Ab Initio Structure Prediction 2. Protein Structure Evaluation - DSSP, PROCHECK, VADAR, Verify 3D 3. Protein Structure Comparison - Structure superposition, RMSD, CATH, SCOP
Protein Structure Prediction 1. Homology Modeling 2. Threading (fold recognition) 3. Ab Initio Structure Prediction
1. Homology Modeling ; The most powerful and accurate approach Predicting three-dimensional structures of proteins based on the coordinates of known homologs founds in PDB. Homology modeling by multi-step process that sequencing alignment, structure modification database searches, energy minimization and structure evaluation to generate a structure. alignment replacing backbone segments replacing side chain validating the model refining the model The most critical step is the first step-alignment Download program : Modeller, DeepView, WHATEIF Web-accessible services : SWISS-MODEL, CPH Models, SDSC1
Human thioredoxin E.Coli thioredoxin 26 % sequence identity
2. Threading ( fold recognition) ; Predicting the structure, or recognizing a common fold in proteins Two approaches to threading exist. - DBM (distance-based method): three-dimensional threading - PBM (prediction-based method): two-dimensional threading Web-accessible services : SAMt99, three-dimensional-PSSM, FUGUE, metaservers 3. Ab Initio Structure Prediction ; Predicting protein structures without prior knowledge of any three-dimensional structure. ab inito structure prediction program : ROSETTA
Threading ( fold recognition) Fig 9.10 A schematic illustration of how threading is performed.
Protein Structure Evaluation ; A high-quality structure can reveal a tremendous amount of biologically important information - Testing new hypotheses on folding or function - The basis to design and construct mutant, or to design new drug How good is this protein structure ? There are some near-universal characteristics to high-quality structures. These observations have led to the development of a number of excellent software programs for automatically evaluating protein structures and protein models
Dictionary of Secondary Structure for Protein A very stringent method to identify hydrogen bonds and hydrogen bonding patterns Determination of the accessible surface area of individual residues using the ANAREA algorithm Protein Structure Evaluation 1. DSSP 2. PROCHECK 3. VADAR 4. Verify 3D
Protein Structure Evaluation 1. DSSP The first quantitative protein structure evaluation program and one of the best available. 2. PROCHECK Accepts PDB coordinate files as input and uses DSSP Most appealing features is its colorful graphical reports along with tables, explanation, and references 3. VADAR 4. Verify 3D
Protein Structure Evaluation 1. DSSP The Volume, Area, Dihedral Angle Reporter is a fully Web-enable protein structure evaluation tool. 2. PROCHECK VADAR uses a more comprehensive approach to identifying secondary structures. VADAR offers a very comprehensive and highly informative picture of protein structure. 3. VADAR 4. Verify 3D
Protein Structure Evaluation 1. DSSP Verify3D uses a form of three-dimensional threading to evaluation protein structure aquality. 2. PROCHECK Verify3D uses a matrix scoring method in which the secondary structure and solvent exposure propensity of each of the 20 a. a was determined statiscally. 3. VADAR Low values ( <0.3) : structure is problem. High values ( >0.5) : structure is good. 4. Verify 3D
Protein Structure Comparison ; Structure comparison can provide tremendous insight into the origin, function, location, interactions, and activity of protein. Structure comparison is a much more computationally difficult process than seq comparison The most common method is called structure superposition. Web server : SuperPose, ProSup PDB coordinate list, information on the alignment, number of equivalent residues, RMSD
RMSD (root mean square deviation) ; In the case of structure comparisons, these are scored using RMSD. RMSD is calculated the same way a standard deviation is calculated. RMSD(Å) = d12+ d22+…/ n
Protein Structure Comparison 1. CATH ; The CATH database can be searched by in a PDB accession number to see the Class, Architecture, Topology, and Homologous superfamily to which a protein belongs. 2. SCOP ; The SCOP database is a similar hierarchically structure database providing a slightly different taxonomic partitioning. (Class, Fold, Family and Superfamily) 3. DALI, CE, VAST ; These servers simply perform strucure comparisons and automatically group structure families using well-defined mathematical criteria.
Figure 9.13 An example of the CATH database description of E.coli thioredoxin.