Database extraction of residue-specific empirical potentials

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Presentation transcript:

Database extraction of residue-specific empirical potentials building a complete set of energy parameters including distance and angle dependence of inter-residue interactions estimation of secondary structure propensities of amino acids utility in fold recognition, homology modeling and/or threading 11/11/2018

Underlying principle: Inverse Boltzmann law Energies --> Probabilities (Boltzmann) Probabilities --> Energies (inverse Boltzmann) Boltzmann law: Pi ~ exp (-Ei/RT) Inverse Boltzmann: Ei = -RTlnPi + ct

Two types of interaction: Long-range Short-range (close in space, not in sequence) Short-range (sequential neighbors) Long-range are the most important dominant interactions in folding

Residue-specific interactions Interactions of hydrophobic residues Interactions between charged/polar residues

Residue-Residue Interactions (from Protein Structures) Effective solvent-mediated contact potential = exy + e00 – ex0 – eyo

Residue-specific distributions of # of neighbors 0.0 0.1 0.2 0.3 Tot Gly Ala Leu Glu Pro Frequencies 15 10 5 # Neighbors

Short-range (bonded) interactions Coupling between consecutive dihedral angles in the virtual bond model

Abscissa values from helix-coil transition [O'Neil and deGrado (1990)] Comparison of predicted and experimental helical propensities 0.2 0.4 0.6 0.8 -0.2 A M ) (kcal/mol) L Q Y I  F -  F , V  S +  C ( N W A-GLY T - E G -  G (kcal/mol)  Abscissa values from helix-coil transition [O'Neil and deGrado (1990)] For more info... Bahar, Kaplan and Jernigan, Proteins 1998

Experimental (abscissa) values from [Kim and Berg (1993)] Comparison of predicted and experimental b-strand propensities 1 1.5 2 2.5 0.3 0.35 0.4 0.45 0.5 0.55 0.6 E X (  + , - ) = 0.37 + 3.08  G R= 0.90 I V C F )/RT Y L -   , M W  + K T  D ( H A Q - E R N E S A -  G (kcal/mol)  Experimental (abscissa) values from [Kim and Berg (1993)]

Multi-body geometry-dependent interactions? Long distance effects can be taken care by ‘whole sentence exponential model”. Spatial, not sequential, correlations are important in controlling folding, misfolding, interactions. Can we select features/attributes that characterize the 3-d topology of contacts? Multi-body geometry-dependent interactions? Keskin, O. , Bahar, I. , Badredtinov, A., Ptitsyn, O. B., & Jernigan, R. L. Protein Science 7, 2578-2586, 1998.