Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion
Literature Information
Jožica Dolenc, Beat H. Meier, Victor H. Rusu, Wilfred F. van Gunsteren
The structural variability of a 16-residue loop (residues 246–261) which is in part disordered and connects two layers of the β-solenoid formed by the prion-form of HET-s and its prion domain HET-s(218–289) is investigated using molecular dynamics computer simulation. A system of three HET-s(218–289) molecules in a β-sheet structure as in the fibril is simulated in aqueous solution. The trajectory structures appear to be consistent with the Cα chemical shift data obtained. In order to delineate the influence of the β-sheet core of the fibril upon the structural variability of the loop, the latter is also simulated without the β-sheet core, but with its N- and C-terminal residues restrained at their positions in the fibril. The analysis of the trajectories shows that the structural variability of the loop is restricted by the β-sheet core, least at its N-terminal end and most in the middle of the trimer.
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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.














