Folding transition and foldability
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Folding transition and „ foldability ”. The phase transition. Density of water: temperature and pressure dependence. The phase diagram of water. H [J/mol]. C v [J/( mol*K )]. Temperature [ o C]. Temperature [ o C]. Vapor. Liquid water. Ice. „Chemical” view. N. U. Two-state model.

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Folding transition and „ foldability ”

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Folding transition and foldability

Foldingtransition and „foldability”


The phase transition

The phase transition

Density of water: temperature and pressure dependence

The phase diagram of water


Folding transition and foldability

H [J/mol]

Cv [J/(mol*K)]

Temperature [oC]

Temperature [oC]

Vapor

Liquid water

Ice


Folding transition and foldability

„Chemical” view

N

U

Two-state model

N

I

U

Three-state model


Folding transition and foldability

Priovalov and Mathakhadze, Adv. Prot. Chem., 47, 307-425 (1995)


Folding transition and foldability

Wild type

Acid-denaturatedwildtype

L16A mutant

C-terminal peptide

Religa et al., J. Mol. Biol., 333, 977-991 (2003)


Folding transition and foldability

Millet et al.. Biochemistry 41, 321-325 (2002)


Folding transition and foldability

Meersham et al., Biophys. J. 99, 2255–2263 (2010)


Folding transition and foldability

Chodankhar et al., PRAMANA Journal of Physics, 71,1021-1025 (2008)


Folding transition and foldability

Staphylococcal protein A, B-domain (46 residues)

  • UNRES/MREMD simulations

  • Berendsen thermostat

  • 32 temperatures (250 K £T £500 K)

  • 4 trajectories/temperature (a total of 128 trajectories)

  • 28 million MD steps @Dt = 4.9 fs

  • Last 4 million steps for analysis

  • WHAM to compute ensemble averages

Maisuradze et al., J. Am. Chem. Soc. 132,9444–9452 (2010)


Folding transition and foldability

Thermodynamics and ensemble averages


Folding transition and foldability

Experimental structure of 1BDD (red) and most probable conformations (green) at T = 280 K

C

N


Folding transition and foldability

Variation of Ca rmsd distribution with temperature

T = 280 K

T = 300 K

T = 320 K

T = 310 K

T = 315 K

Probability

T = 325 K

T = 350 K

Ca rmsd [Å]


Folding transition and foldability

Protein A @ the folding-transition temperature

Experimental (referemce)

rmsd=8.7 Å

„mirror image” topology

rmsd=9.8 Å

„mirror image” topology

rmsd=5.3 Å

Native topology

rmsd=9.5 Å

Native topology


Folding transition and foldability

Ensemble-averaged contact-probability maps

H-bonding contacts

Experimental (reference)

SC-SC contacts

T=300 K

T=325 K (Tf)

T=350 K


Folding transition and foldability

The folding funnel


Folding transition and foldability

  • Criteria of foldability

  • Gap criterion (Shakhnovich et al., 1994)

  • Large Tf/Tg, (folding to glass-transition temperature) ratio which is the principle of Z-score optimization (Wolynes et al., 1992)

  • Small (Tf-Tq)/Tq ratio (Tq being the hydrophobic collapse temperature; Thirumalai et al., 1996). Inverse proportionality found of the entropy of the excited states to Tf.

  • “Funnel sculpting” (Maritan and Seno, 2003 and Levitt et al., 2003)

  • Hierarchy


Folding transition and foldability

Klimov & Thirumalai, Phys. Rev. Lett., 76, 4070-4073 (1996)


Folding transition and foldability

Energy spectra of a lattice model

level 0 level 1 level 2 native

tf – folding time (MFPT to the native structure)

ts – residence time

tfts

Liwo et al., J. Phys. Chem. B, 108, 16934-16949 (2004)


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