Kazmirski, S. L. & Daggett, V. Simulations of the structural and dynamical properties of denatured proteins: the 'molten coil' state of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 277, 487-506

Department of Medicinal Chemistry, University of Washington, Seattle WA 98195-7610, USA
Journal of Molecular Biology (Impact Factor: 4.33). 03/1998; 277(2):487-506. DOI: 10.1006/jmbi.1998.1634


The dynamic nature of denatured, unfolded proteins makes it difficult to characterize their structures experimentally. To complement experiment and to obtain more detailed information about the structure and dynamic behavior of the denatured state, we have performed eleven 2.5 ns molecular dynamics simulations of reduced bovine pancreatic trypsin inhibitor (BPTI) at high temperature in water and a control simulation at 298 K, for a total of 30 ns of simulation time. In a neutral pH environment (acidic residues ionized), the unfolded protein structures were compact with an average radius of gyration 9% greater than the native state. The compact conformations resulted from the transient formation of non-native hydrophobic clusters, turns and salt bridges. However, when the acidic residues were protonated, the protein periodically expanded to a radius of gyration of 18 to 20 Å. The early steps in unfolding were similar in the different simulations until passing through the major transition state of unfolding. Afterwards, unfolding proceeded through one of two general pathways with respect to secondary structure: loss of the C-terminal helix followed by loss of β-structure or the opposite. To determine whether the protein preferentially sampled particular conformational substates in the denatured state, pairwise Cα root-mean-square deviations were measured between all structures, but similar structures were found between only two trajectories. Yet, similar composite properties (secondary structure content, side-chain and water contacts, solvent accessible surface area, etc.) were observed for the structures that unfolded through different pathways. Somewhat surprisingly, the unfolded structures are in agreement with both past experiments suggesting that reduced BPTI is a random coil and more recent experiments providing evidence for non-random structure, demonstrating how ensembles of fluctuating structures can give rise to experimental observables that are seemingly at odds.

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    • "These force fields consist of libraries of parameters optimized for different classes of macromolecules (usually proteins or nucleic acids) and for different organic solvent molecules. Commonly used force fields are the following: GROMOS [38] [41], OPLS [42] [43], CHARMM [44] [45] and AMBER [46] [47] [48]. "

    Advances in Protein and Peptide Sciences Volume 1, Bentham e Books edited by Ben M. Dunn, 01/2013: chapter 9: pages 318-381; Bentham Science., ISBN: 978-1-60805-487-9
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    • "Then α1 is added and this helps to form the disulfide bond between residues 5 and 55, and 14 and 38. Our prediction that β1 and β2 interact earlier than the two α-helices is consistent with the result in [53]. "
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