Mina Oh KIAS

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• Group 2
• Mina Oh (KIAS)
• Hahnbeom Park (Seoul National Univ.)
• Jae wook Hyun (Kyungwon Univ.)

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• Distance of Ca- Ca3.8 Å
• Bond angles of three consecutive Ca 82-148
• Radius constraints 2.5 Å

Methods
Steric penalty
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Table 1. All geometric properties driven by the
analysis of PDB native structures
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(continues)
Rijk is the radius of a circle drawn through the
C positions of i, j, and k. N is the number of
residues. Each residue is constrained to form no
more than two hydrogen bonds (except the residues
located at the chain termini, which form at most
one hydrogen bond). Applied only when the
corresponding binormal vectors exist. For i 1
andor j N, this is replaced by the constraint
that the connecting vector is making an angle
between 70 and 110 with the extremal peptide
links. The connecting vector, cij rijrij is a
unit vector joining i and j. Applied when at
least one of the two cooperative hydrogen bonds
is nonlocal
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Fig. 1. Tangent, normal, and binormalforming a
right-handed local coordinate system
Cij
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Results and Discussion
Phase diagram from Monte-Carlo simulation using
simulated annealing
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at high temperature (T 0.22)
at folding temperature (T 0.2)
The effective free energy, F(NlNnl,NW)
-lnP(NlNnl,NW)
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Summary

• Geometry and symmetry presculpt the free energy
  landscape of protein
• Determination of free energy minimum by hydrogen
  bonding and hydrophobicity.

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Thank you for your attention!!