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Carbon monoxide has been recognized relatively recently as signaling molecule, and only very few dedicated natural CO sensor proteins have been identified so far. These include in particular heme-based transcription factors: the bacterial sensor proteins CooA and RcoM. In these 6-coordinated systems, exchange between an internal protein residue and CO as a heme ligand in the sensor domain affects the properties of the DNA-binding domain. Using light to dissociate heme-ligand bonds can in principle initiate this switching process. We review the efforts to use this method to investigate early processes in ligand switching and signaling, with an emphasis on the CO-"trappingˮ properties of the heme cavity. These features are unusual for most heme proteins, but common for heme-based CO sensors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Vos, Salman and Liebl.)

The dynamic interactions of enzymes and substrates underpins catalysis, yet few techniques can interrogate the dynamics of protein-bound ligands. Here we describe the use of field cycling NMR relaxometry to measure the dynamics of enzyme-bound substrates and cofactors in catalytically competent complexes of GMP reductase. These studies reveal new binding modes unanticipated by x-ray crystal structures and reaction-specific dynamic networks. Importantly, this work demonstrates that distal interactions not usually considered part of the reaction coordinate can play an active role in catalysis. The commercialization of shuttling apparatus will make field cycling relaxometry more accessible and expand its use to additional nuclei, promising more intriguing findings to come., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Roberts and Hedstrom.)

Nanocrystal surfaces are commonly populated by organic ligands, which play a determining role in the optical, electronic, thermal, and catalytic properties of the individual nanocrystals and their assemblies. Understanding the bonding of ligands to nanocrystal surfaces and their dynamics is therefore important for the optimization of nanocrystals for different applications. In this study, we use temperature-dependent, quasi-elastic neutron scattering (QENS) to investigate the dynamics of different surface bound alkanethiols in lead sulfide nanocrystal solids. We select alkanethiols with mono- and dithiol terminations, as well as different backbone types and lengths. QENS spectra are collected both on a time-of-flight spectrometer and on a backscattering spectrometer, allowing us to investigate ligand dynamics in a time range from a few picoseconds to nanoseconds. Through model-based analysis of the QENS data, we find that ligands can either (1) precess around a central axis, while simultaneously rotating around their own molecular axis, or (2) only undergo uniaxial rotation with no precession. We establish the percentage of ligands undergoing each type of motion, the average relaxation times, and activation energies for these motions. We determine, for example, that dithiols which link facets of neighboring nanocrystals only exhibit uniaxial rotation and that longer ligands have higher activation energies and show smaller opening angles of precession due to stronger ligand-ligand interactions. Generally, this work provides insight into the arrangement and dynamics of ligands in nanocrystal solids, which is key to understanding their mechanical and thermal properties, and, more generally, highlights the potential of QENS for studying ligand behavior.

Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein-ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein-ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and R free values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail., (open access.)

The interfacial adsorption, desorption, and exchange behaviors of thiolated ligands on nanotextured Au nanoparticle surfaces exhibit phenomenal site-to-site variations essentially dictated by the local surface curvatures, resulting in heterogeneous thermodynamic and kinetic profiles remarkably more sophisticated than those associated with the self-assembly of organothiol ligand monolayers on atomically flat Au surfaces. Here we use plasmon-enhanced Raman scattering as a spectroscopic tool combining time-resolving and molecular fingerprinting capabilities to quantitatively correlate the ligand dynamics with detailed molecular structures in real time under a diverse set of ligand adsorption, desorption, and exchange conditions at both equilibrium and nonequilibrium states, which enables us to delineate the effects of nanoscale surface curvature on the binding affinity, cooperativity, structural ordering, and the adsorption/desorption/exchange kinetics of organothiol ligands on colloidal Au nanoparticles. This work provides mechanistic insights on the key thermodynamic, kinetic, and geometric factors underpinning the surface curvature-dependent interfacial ligand behaviors, which serve as a central knowledge framework guiding the site-selective incorporation of desired surface functionalities into individual metallic nanoparticles for specific applications.

Surface ligand dynamics of colloidal quantum dots (QDs) has been revealed as an important issue for determining QDs performance in their synthesis and postsynthesis treatment, such as ligand-related photoluminescence, colloidal stability, and so forth. However, this issue is less associated with the preparation of highly luminescent nanocomposites, which usually leads to poor performance and repeatability. In this work, on the basis of the studies about surface ligand dynamics of aqueous QDs, highly luminescent QDs-cellulose composites are prepared and employed to fabricate high color purity light-emitting diodes (LEDs). Detailed investigations indicate that the species of QD capping ligands and in particular the temperature are the key for controlling the ligand dynamics. The preparation of nanocomposites using less dynamic ligand-modified QDs at low temperature overcomes the conventional problems of QD aggregation, low QD content, luminescence quenching and shift, thus producing highly luminescent QDs-cellulose composites. This protocol is available for a variety of aqueous QDs, such as CdS, CdSe, CdTe, and CdSe(x)Te(1-x), which permits the design and fabrication of QD-based LEDs using the nanocomposites as color conversion layer on a blue emitting InGaN chip.

Background: The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled., Methods: All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics., Results: Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites., Conclusions: Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion., General Significance: Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics., (Copyright © 2014 Elsevier B.V. All rights reserved.)

The catalytic site of heme-copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the CuB atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems., (Copyright © 2014 Elsevier B.V. All rights reserved.)