In silico structural and functional analysis of fragments of the ankyrin repeat protein p18(INK4c)

• Published in: Journal of biomolecular structure & dynamics Vol. 27; no. 4; pp. 521 - 540
• Main Authors: Sklenovsý, P, Otyepka, M
• Format: Journal Article
• Language: English
• Published: England 01-02-2010
• Subjects: Ankyrin Repeat; Computational Biology; Crystallography, X-Ray; Cyclin-Dependent Kinase Inhibitor p18 - chemistry; Cyclin-Dependent Kinase Inhibitor p18 - metabolism; Models, Molecular; Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Thermodynamics
• ISSN: 1538-0254
• DOI: 10.1080/07391102.2010.10507336

Ankyrin repeat proteins (ARPs) are ubiquitous proteins that play critical regulatory roles in organisms and consist of repeating motifs (ankyrin repeats) stacked in non-globular, almost linear, "quasi one-dimensional" configurations. They also have highly unusual mechanical properties, notably ARPs can behave as nano-springs. Both their essential cellular functions and distinctive nano-mechanical properties have aroused interest in ARPs for potential applications in medicine and nanotechnology. Further, the modular architecture of ARPs, which lack the long-range contacts that typically stabilize globular proteins, provides a new paradigm for understanding protein stability and folding mechanisms of proteins. In the present study, the stability of ARP p18INK4c (p18) and fifty p18 fragments was investigated by all- atomic molecular dynamics (MD) simulations in explicit water on a ~3.3 micro- seconds timescale. The fragment simulations indicate that p18 alpha-helices are significantly stabilized by tertiary interactions, because in the absence of their native context they readily melt. All single p18 ARs and their structural elements are also unstable outside their native context. The minimal stable motifs are pairs of ARs, implying that inter-repeat contacts are essential for AR stability. Further, pairs of internal ARs are less stable than pairs that include a native capping AR. The MD simulations also provide indications of the functional roles of p18 turns and loops; the turns appear to be essential for the stability of the protein, while the loops both help to stabilize the p18 structure and are involved in recognition processes. Temperature-induced unfolding analysis shows that the p18 melts from the N-terminus to the C- terminus.