In this study, we investigated the stability of the fully activated conformation of the orexin receptor 2 (OX2R) embedded in a pure POPC bilayer using MD simulations. Various thermodynamic ensembles (i.e., NPT, NVT, NVE, NPAT, μVT, and NPγT) were employed to explore the dynamical heterogeneity of the system in a comprehensive way. In addition, informational similarity metrics (e.g., Jensen-Shannon divergence) as well as Markov state modeling approaches were utilized to elucidate the receptor kinetics. Special attention was paid to assessing surface tension within the simulation box, particularly under NPγT conditions, where 21 nominal surface tension constants were evaluated. Our findings suggest that traditional thermodynamic ensembles such as NPT may not adequately control physical properties of the POPC membrane, impacting the plausibility of the OX2R model. In general, the performed study underscores the importance of employing the NPγT ensemble for computational investigations of membrane-embedded receptors, as it effectively maintains zero surface tension in the simulated system. These results offer valuable insights for future research aimed at understanding receptor dynamics and designing targeted therapeutics.
The hippocampus (HPC) is essential for navigation and memory, tracking environmental continuity and change, including navigation relative to moving targets. CA1 ensembles expressing immediate-early gene (IEG) Arc and Homer1a RNA are contextually specific. While IEG expression correlates with HPC-dependent task demands, the effects of behavioral demands on IEG-expressing ensembles remain unclear. In three experiments, we investigated the effects of context switch, sustained presence, and task demands on dorso-proximal CA1 IEG+ ensembles in rats. Experiment 1 showed that the size of IEG+ (Arc, Homer1a RNA) ensembles dropped to baseline during uninterrupted 30-min exploration, reflecting familiarization, unless a context switch was present. Context-specificity of the ensembles depended on both environment identity and timing of the context switch. Experiment 2 found no effect of HPC-dependent mobile robot avoidance or HPC-independent avoidance of a stationary robot on IEG+ ensembles beyond mere exploration. Experiment 3 replicated these findings for c-Fos protein. The data suggest that IEG+ ensembles are driven by a context switch and shrink over time during sustained presence in the same environment. We found no evidence of task demands or their change affecting the size, stability over time, or task-specificity of IEG+ ensembles. These results shed light on the temporal dynamics of CA1 IEG+ ensembles, and their control by contextual and behavioral factors.
- MeSH
- Behavior, Animal physiology MeSH
- Cytoskeletal Proteins genetics metabolism MeSH
- CA1 Region, Hippocampal * metabolism physiology MeSH
- Homer Scaffolding Proteins * metabolism genetics MeSH
- Rats MeSH
- Genes, Immediate-Early * physiology MeSH
- Rats, Long-Evans * MeSH
- Nerve Tissue Proteins genetics metabolism MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
BACKGROUND: The chromodomain (CD) of HP1 proteins is an established H3K9me3 reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARKme3S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging. METHODS: We acquired ~350 μs of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields. RESULTS: The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K0me3 and A-2 target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the -3 position. The Q-4 residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATKme3A motif, for which no structure is available, is predicted. CONCLUSIONS: The CD reads a longer target segment than previously thought, ranging from positions -7 to +3. The CD anionic clamp can be neutralized not only by the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. GENERAL SIGNIFICANCE: Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.
- MeSH
- Chromosomal Proteins, Non-Histone chemistry metabolism MeSH
- Histocompatibility Antigens metabolism MeSH
- Histone-Lysine N-Methyltransferase metabolism MeSH
- Histones metabolism MeSH
- Protein Interaction Domains and Motifs MeSH
- Humans MeSH
- Lysine metabolism MeSH
- Methylation MeSH
- Protein Processing, Post-Translational MeSH
- Amino Acid Sequence MeSH
- Molecular Dynamics Simulation MeSH
- Protein Binding MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Several small-molecule ligands specifically bind and stabilize G-quadruplex (G4) nucleic acid structures, which are considered to be promising therapeutic targets. G4s are polymorphic structures of varying stability, and their formation is dynamic. Here, we investigate the mechanisms of ligand binding to dynamically populated human telomere G4 DNA by using the bisquinolinium based ligand Phen-DC3 and a combination of single-molecule FRET microscopy, ensemble FRET and CD spectroscopies. Different cations are used to tune G4 polymorphism and folding dynamics. We find that ligand binding occurs to pre-folded G4 structures and that Phen-DC3 also induces G4 formation in unfolded single strands. Following ligand binding to dynamically populated G4s, the DNA undergoes pronounced conformational redistributions that do not involve direct ligand-induced G4 conformational interconversion. On the contrary, the redistribution is driven by ligand-induced G4 folding and trapping of dynamically populated short-lived conformation states. Thus, ligand-induced stabilization does not necessarily require the initial presence of stably folded G4s.
- MeSH
- Quinolines chemistry metabolism MeSH
- G-Quadruplexes * MeSH
- Nucleic Acid Conformation MeSH
- Humans MeSH
- Ligands * MeSH
- Fluorescence Resonance Energy Transfer MeSH
- Molecular Dynamics Simulation MeSH
- Telomere chemistry MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
... 1.Introduction -- 2.Numerical Integrators -- 3.Analyzing Geometric Integrators -- 4.The Stability Threshold ...
Interdisciplinary Applied Mathematics, ISSN 0939-6047 39
1st edition XXII, 443 stran : ilustrace ; 24 cm
- MeSH
- Mathematics MeSH
- Molecular Dynamics Simulation MeSH
- Publication type
- Monograph MeSH
- Conspectus
- Matematika
- NML Fields
- přírodní vědy
We study the folding of the designed hairpin chignolin, using simulations with four different force fields. Interestingly, we find a misfolded, out-of-register, structure comprising 20-50% of the ordered structures with three force fields, but not with a fourth. A defining feature of the misfold is that Gly-7 adopts a β(PR) conformation rather than α(L). By reweighting, we show that differences between the force fields can mostly be attributed to differences in glycine properties. Benchmarking against NMR data suggests that the preference for β(PR) is not a force-field artifact. For chignolin, we show that including the misfold in the ensemble results in back-recalculated NMR observables in slightly better agreement with experiment than parameters calculated from a folded ensemble only. For comparison, we show by NMR and circular dichroism spectroscopy that the G7K mutant of chignolin, in which formation of this misfold is impossible, is well folded with stability similar to the wild-type and does not populate the misfolded state in simulation. Our results highlight the complexity of interpreting NMR data for small, weakly structured, peptides in solution, as well as the importance of accurate glycine parameters in force fields, for a correct description of turn structures.
... Contractile Force Is Produced by Cross Bridges 678 -- Noncontractile Components in Muscle Fibers Provide Stability ... ... Vestibular Stimulation 806 -- Meničre Disease Affects the Vestibular Labyrinth 807 -- Vestibular Reflexes Stabilize ... ... Volitional Control 822 -- Vestibulospinal and Cervicospinal Reflexes Collaborate in Maintaining Postural Stability ... ... Brain Stem Deviates From the Organization of the Spinal Cord in Two Important Ways 885 -- Neuronal Ensembles ...
4th ed. xxxiii, 1414 s. : il., tab., grafy ; 30 cm
- MeSH
- Behavior MeSH
- Molecular Biology MeSH
- Nervous System Diseases MeSH
- Nervous System MeSH
- Neurochemistry MeSH
- Neurophysiology MeSH
- Neurons MeSH
- Neurosciences MeSH
- Publication type
- Monograph MeSH
- Conspectus
- Fyziologie člověka a srovnávací fyziologie
- NML Fields
- neurovědy
- biologie
