A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by Quantum mechanics/Molecular mechanics studies

The Ran GTPase protein is a guanine nucleotide-binding protein (GNBP) with an acknowledged profile in cancer onset, progression and metastases. The complex mechanism adopted by GNBPs in exchanging GDP for GTP is an intriguing process and crucial for Ran viability. The successful completion of the process is a fundamental aspect of propagating downstream signalling events. QM/MM molecular dynamics simulations were employed in this study to provide a deeper mechanistic understanding of the initiation of nucleotide exchange in Ran. Results indicate significant disruption of the metal-binding site upon interaction with RCC1 (the Ran guanine nucleotide exchange factor), overall culminating in the prominent shift of the divalent magnesium ion. The observed ion drifting is reasoned to occur as a consequence of the complex formation between Ran and RCC1 and is postulated to be a critical factor in the exchange process adopted by Ran. This is the first report to observe and detail such intricate dynamics for a protein in Ras superfamily.

Estimating quantum chromatic numbers

We develop further the new versions of quantum chromatic numbers of graphs introduced by the first and fourth authors. We prove that the problem of computation of the commuting quantum chromatic number of a graph is solvable by an SDP algorithm and describe an hierarchy of variants of the commuting quantum chromatic number which converge to it. We introduce the tracial rank of a graph, a parameter that gives a lower bound for the commuting quantum chromatic number and parallels the projective rank, and prove that it is multiplicative. We describe the tracial rank, the projective rank and the fractional chromatic numbers in a unified manner that clarifies their connection with the commuting quantum chromatic number, the quantum chromatic number and the classical chromatic number, respectively. Finally, we present a new SDP algorithm that yields a parameter larger than the Lovász number and is yet a lower bound for the tracial rank of the graph. We determine the precise value of the tracial rank of an odd cycle.