Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

TY - JOUR

T1 - Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

AU - Lindorff-Larsen, Kresten

AU - Kristjansdottir, Sigridur

AU - Teilum, Kaare

AU - Fieber, Wolfgang

AU - Dobson, Christopher M

AU - Poulsen, Flemming Martin

AU - Vendruscolo, Michele

N1 - Keywords: Acyl Coenzyme A; Animals; Carrier Proteins; Cattle; Computer Simulation; Guanidine; Kinetics; Models, Molecular; Monte Carlo Method; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Denaturation; Spin Labels

PY - 2004

Y1 - 2004

N2 - The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.

AB - The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.

U2 - 10.1021/ja039250g

DO - 10.1021/ja039250g

M3 - Journal article

C2 - 15012160

SN - 0002-7863

VL - 126

SP - 3291

EP - 3219

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

IS - 10

ER -