Determination of an Ensemble of Structures Representing the Denatured State of the Bovine Acyl-Coenzyme A Binding Protein

• Published in: Journal of the American Chemical Society Vol. 126; no. 10; pp. 3291 - 3299
• Main Authors: Lindorff-Larsen, Kresten, Kristjansdottir, Sigridur, Teilum, Kaare, Fieber, Wolfgang, Dobson, Christopher M, Poulsen, Flemming M, Vendruscolo, Michele
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 17-03-2004
• Subjects: Acyl Coenzyme A - chemistry; Acyl Coenzyme A - metabolism; Animals; Biological and medical sciences; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Cattle; Computer Simulation; Conformational dynamics in molecular biology; Fundamental and applied biological sciences. Psychology; Guanidine - chemistry; Kinetics; Models, Molecular; Molecular biophysics; Monte Carlo Method; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Denaturation; Spin Labels; Monte Carlo method; Bovine; Conformational dynamics; Molecular dynamics method; Theoretical study; NMR spectrometry; Experimental study; Conformational changes; Denatured state; Binding protein; Vertebrata; Mammalia; Artiodactyla; Ungulata
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja039250g

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.