1. Modelling protein tertiary structure Ram Samudrala University of Washington

2. Outline 1. Introduction to protein structure(15 minutes) - de novo prediction - comparative modelling 2. Introduction to RAMP software (10 minutes) 3. Installation/set up of RAMP software(5 minutes) 4. Comparative modelling using RAMP software(45 minutes) - template selection (web) (10 minutes) - alignment (web) (10 minutes) - scgen_mutate to create initial model (10 minutes) - mcgen_semfold_loop to build loops (10 minutes) - refinement (5 minutes) 5. Ab initio modelling using RAMP software(45 minutes) - secondary structure prediction(5 minutes) - setting up simulation on a cluster(10 minutes) - running the simulation (10-20 minutes) * - break/questions - energy minimisation (5 minutes) - scoring using functions from RAMP (10 minutes) - final selection of native-like conformations (5 minutes)

3. Comparative modelling of protein structure KDHPFGFAVPTKNPDGTMNLMNWECAIP KDPPAGIGAPQDN----QNIMLWNAVIP ** * * * * * * * ** …… scan align refine physical functions build initial model minimum perturbation construct non-conserved side chains and main chains graph theory, semfold

4. De novo prediction of protein structure sample conformational space such that native-like conformations are found astronomically large number of conformations 5 states/100 residues = 5 100 = 10 70 select hard to design functions that are not fooled by non-native conformations (“decoys”)

5. Semi-exhaustive segment-based folding EFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK generate fragments from database 14-state ,  model …… minimise monte carlo with simulated annealing conformational space annealing, GA …… filter all-atom pairwise interactions, bad contacts compactness, secondary structure

6. Ab initio prediction at CASP Consistently predicted correct topology (~ 4 to 6 Å) for 60-100+ residues T172 – 5.9 Å for 74 aaT187 – 5.1 Å for 66 aa T129 – 5.8 Å for 68 aa T170/sfrp3 – 4.8 Å for all 69 aa T138 – 4.6 Å for 84 aaT146 – 5.6 Å for 67 aa

7. Comparative modelling at CASP Overall model accuracy ranging from 1 to 6 Å for 50-10% sequence identity T160 – 2.5 Å (125 aa; 22%)T133 – 6.0 Å (260 aa; 14%) T137 – 1.0 Å (133 aa; 57% id) T185 – 6.0 Å (428 aa; 24% id) T182 – 1.0 Å (249 aa; 41% id)T150 – 2.7 Å (99aa; 32% id)