Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used hereto provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
Bacteria frequently need to adapt to altered environmental conditions. Adaptation requires changes in gene expression, often mediated by global regulators of transcription. The nucleoid-associated protein H-NS is a key global regulator in Gram-negative bacteria and is believed to be a crucial player in bacterial chromatin organization via its DNA-bridging activity. H-NS activity in vivo is modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. Mechanistically, it is unclear how functional modulation of H-NS by such factors is achieved. Here, we show that a diverse spectrum of H-NS modulators alter the DNA-bridging activity of H-NS. Changes in monovalent and divalent ion concentrations drive an abrupt switch between a bridging and non-bridging DNA-binding mode. Similarly, synergistic and antagonistic co-regulators modulate the DNA-bridging efficiency. Structural studies suggest a conserved mechanism: H-NS switches between a ‘closed’ and an ‘open’, bridging competent, conformation driven by environmental cues and interaction partners.
We have used dissipative particle dynamics (DPD) to simulate surfactant monolayers on the interface between oil and water. With a simple surfactant model, we investigate how variations in size and structure of surfactants influence their ability to reduce the interfacial tension. In particular, we studied the effect of branching of the hydrophobic tail. We found that branched surfactants are more efficient at the interface than linear ones only if the head groups are sufficiently hydrophilic to prevent the molecules from staggering. By combining DPD with a Monte Carlo method, we have imposed constant surfactant chemical potential and (normal) pressure in separate simulations of bulk and interface. From this, we can determine the bulk concentration needed to obtain a given interfacial tension. We found that higher concentrations of branched surfactants are required to obtain the same reduction of the interfacial tension. We argue that the stronger excluded volume interactions which make branched surfactants more efficient at the interface compared to their linear isomers at the same time make them less inclined to adsorb at the interface.
Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the α-helical region 43-51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge that is part of the N-terminal domain. Additional molecular dynamics simulations indicate that the exposure of the chromophore does not result in a productive pathway. We discuss several possibilities for experimental validation of these predictions. Our results open the way for studying millisecond conformational changes in other medium-sized (signaling) proteins. molecular dynamics | protein unfolding mechanism | transition path sampling | transition state ensemble | committor analysis I nvestigation of the dynamics of large conformational changes in proteins leads to a better understanding of their functioning. Molecular simulation can complement experiments by modeling the dynamical time evolution of biomolecular systems in atomistic detail. Yet, even though straightforward all-atom molecular dynamics (MD) can now access the microsecond regime, simulating the kinetics of folding and other large conformational changes in proteins at ambient conditions has been limited to relatively small (model) proteins (1). Here we show how the transition path sampling technique enables investigation of the atomistic dynamical pathways for the millisecond timescale partial unfolding transition in a biologically relevant signaling protein, the photoactive yellow protein (PYP). Moreover, analysis of the ensembles of unbiased molecular trajectories allows the extraction of the (possibly complex) reaction coordinates.PYP is a water soluble blue-light photo receptor from Halorhodospira halophila (2, 3) composed of 125 amino acids and a covalently bound chromophore (para-coumaric acid, pCA) (4). The protein folds into a Per-Arnt-Sim core capped by an Nterminal domain (5, 6). Upon the absorption of a blue-light photon, PYP undergoes many different conformational rearrangements, culminating in the formation of the signaling state. The first steps in signaling state formation are the isomerization of pCA, on a picosecond timescale (7), followed by a proton transfer, taking place within microseconds (8, 9). These reactions result in an intermediate pB 0 with pCA in a strained configuration and a negative charge on a buried glutamate (Glu46) (10, 11). As a consequence, the protein partially unfolds to expose pCA and Glu46 to bulk water (12-14), completing ...
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