Abstract
Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells.
Highlights
Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations
It becomes clear that in order to understand and appreciate the choreography of a living cell and its interactions with its surroundings, dynamic information at the molecular and atomic level is essential. This is the territory of nuclear magnetic resonance (NMR) and of simulations of molecular structures, in particular molecular dynamics (MD), because of their ability to describe both structure and dynamics with atomic resolution in timescales ranging from ns to ms and longer
The examples we discuss below are aimed at the atomic-level exploration of the conformational landscapes of both folded proteins and intrinsically disordered proteins (IDPs) relating to catalysis, binding and signaling, allostery, folding, and aggregation
Summary
Signal transduction is firmly rooted in the interactions of proteins with diverse ligands, and in the molecular consequences of these interactions. An intriguing consequence of the paradigm of population shift is that all that is needed for signal transmission is to select the appropriate conformations of the receptor and the ligand; the affinity controls the lifetime of the complex, not the message that is sent (Nussinov and Ma, 2012) Proteins emerge from these analyses as integrators of signals (Nussinov and Tsai, 2014a), where their non-linear output depends on the order and location in which ligands and/or PTMs are bound or acquired, becoming logical gates as part of the complex circuitry of life (Nussinov et al, 2013). The examples we discuss below are aimed at the atomic-level exploration of the conformational landscapes of both folded proteins and IDPs relating to catalysis, binding and signaling, allostery, folding, and aggregation
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