1. Go MODEL: coarse grained description based on the experimentally determined native structure. Potential energy of the Hamiltonian is given by, Tethering potenital: Potential for the native contacts is given by Lennard-Jones potential Potential for non-native interaction -Purely repulsive  = 5A Theoretical studies of the kinetics of protein folding in off-lattice models encounter a difficulty when deciding at what stage of the temporal evolution from an unfolded state the system can be considered as having reached the native conformation. Simple criteria involve either crossing of the threshold value of the RMSD distance away from the native state or establishing all native contacts. We use Go–like models of proteins and show that both of these simple criteria can result in structures with entire fragments of the resulting conformation having wrong sense of chirality, Fig 1. In order to characterize the geometrical validity of conformation we determine value of the local chirality, Ci. We propose a new simple criterion of folding which is based both on establishing the native value contacts and most of the local chiralities. Ci is considered to be established if it exceeds 50% of its native value. Chirality in Protein Folding Joanna Kwiecinska and Marek Cieplak Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland PROBLEMS WITH THE SIMPLE CRITERIA OF FOLDING Fig. 2 Backbone representaion of the helix from protein 1egj obtained through a folding process in a Go like model. The structure on the left- hand side with C i is obtained when all native contacts are established. The structure on the right when RMSD becomes equal to 2.5. DISTRIBUTION OF LOCAL CHIRALITIES WHEN FOLDING IS DECLARED USING THE SIMPLE CRITERION NEW CRITERION Fig 1. Conformations of crambin in backbone representation. The figure on the left-hand side shows the native structure 1crn. The figure on the right-hand side corresponds to a conforamtion in which all native contacts are established through a folding process in Go-like model, but some of the local chirlaities are non-native. The arrows indicate the sense of chirality in selected places. THE DYNAMICAL ROLE OF CHIRALITY INTRODUCTION The kinetic discrepancy between the simple and compound criteria can be reduced in the Go-like models by providing the Hamiltonian with a term which favours values of the local chirality as introduced in [2]. The effects of the chirality term as a function of term as a function of its amplitude its amplitude CONTACT BASED CRITERION CONTACT AND CHIRALITY Conclusions Considered model with compound criterion helps to obtain structures with all local values of the chirality close to the native ones. If the chirality potential is added to the model it facilities establishing the compound criterion. 1.Abe H, GO N. Biopolymers 1981, 20:1013-1031 2. Cieplak M, Hoang T.X., Robbins M.O. Proteins 2002, 49:104-113 3. Cieplak M and Hoang TX, Biophysical Journal 2003, 475-488 REFERENCES Fig. 3 A number of local deformations with wrong sign of the chirality. Zero in the x-axis corresponds to a number of structures which have all local chiralities of the same sign as native structure. The left panel shows such properties for helix, right panel for hairpin. Fig. The same as Fig. 3 but with a chirality term with k=1 added to the system. 50% of native value -CONSIDERED ESTABLISHED ( k i =1) Fig. 4 Example dependence of C as a function of times for the 8’th residues Number of established native contacts Local chirality K=  k i