In SilicoStructural and Functional Analysis of Fragments of the Ankyrin Repeat Protein p18^INK4c

Abstract

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.

The Pectin Lyases in Arabidopsis thaliana: Evolution, Selection and Expression Profiles

“…Evolutionary relationships between different groups of pectin lyase proteins could not be inferred. By contrast, within each group, strong amino acid sequence and gene organization conservation were evident, suggesting strong evolutionary relationships among subfamily members [24], [25], [26]. Phylogenetic analyses also showed that several pairs of pectin lyase proteins were putative paralogs (Fig.…”

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact

“…All MD simulations were carried out using the AMBER suite of programs with the all-atomic force fields ff99, ff99SB, and ff03 . The simulation protocol, which has been repeatedly shown to perform well for proteins, − was set up as follows. The hydrogen atoms were added by the LEaP module of AMBER.…”

Protein Folding, Binding and Energy Landscape: A Synthesis

“…The statistical result of the lack of preferential interactions between amino acids is based on a large number of already folded protein structures, and therefore it is safe to interpret it as the consequence rather than the cause of protein folding. However, it must be noted that the preferential interactions between amino acids are the basis of the development of knowledge-based potentials, which in turn form the underpinning of protein structure prediction by modeling and simulation (Ji & Liu, 2011a;Rackovsky & Schraga, 2011;Sarma, 2011) that are now routinely performed in many laboratories across the globe (Aman et al, 2010;Sklenovský & Otyepka, 2010;Tao et al, 2010). The lack of preferential interactions between amino acids in a large sample set suggests that the nonpreferential or random inter-residue interactions might maintain the structural stability of the already folded proteins.…”