scholarly journals Sodium Binding Stabilizes the Outward-Open State of SERT by Limiting Bundle Domain Motions

Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 255
Author(s):  
Dániel Szöllősi ◽  
Thomas Stockner
Keyword(s):  
Substrate Binding ◽  
Chloride Ion ◽  
Synaptic Cleft ◽  
High Concentration ◽  
Neurologic Diseases ◽  
Presynaptic Nerve Terminal ◽  
Access Path ◽  
Outer Vestibule ◽  
Dynamics Simulations ◽  
Domain Motions

The human serotonin transporter (hSERT) removes the neurotransmitter serotonin from the synaptic cleft by reuptake into the presynaptic nerve terminal. A number of neurologic diseases are associated with dysfunction of the hSERT, and several medications for their treatment are hSERT blockers, including citalopram, fluoxetine, and paroxetine. The substrate transport is energized by the high concentration of external NaCl. We showed through molecular dynamics simulations that the binding of NaCl stabilized the hSERT in the substrate-binding competent conformation, which was characterized by an open access path to the substrate-binding site through the outer vestibule. Importantly, the binding of NaCl reduced the dynamics of the hSERT by decreasing the internal fluctuations of the bundle domain as well as the movement of the bundle domain relative to the scaffold domain. In contrast, the presence of only the bound chloride ion did not reduce the high domain mobility of the apo state.

Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽  
2021 ◽  
Author(s):  
Margrethe Gaardløs ◽  
Sergey A Samsonov ◽  
Marit Sletmoen ◽  
Maya Hjørnevik ◽  
Gerd Inger Sætrom ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
Substrate Binding ◽  
Interdisciplinary Approach ◽  
Product Formation ◽  
Titration Calorimetry ◽  
Binding Groove ◽  
Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

Directional manipulation of diffusio-osmosis flow by design of solute-wall and solvent-wall interactions

2021 ◽  
Author(s):  
Xin Wang ◽  
Dengwei Jing
Keyword(s):  
Critical Role ◽  
Liquid Interface ◽  
High Concentration ◽  
Interfacial Layers ◽  
Fluidic Devices ◽  
Wall Interaction ◽  
Dynamics Simulations ◽  
External Forces ◽  
Solid Liquid Interface ◽  
Solid Liquid

Abstract Understanding of the diffusio-osmosis, the flow induced by a solute gradient acting in narrow interfacial layers at nanoscale solid-liquid interface, is of great value in view of the increasing importance of micro- and nano-fluidic devices and self-propelling particle. Here, using molecular dynamics simulations, we develop a numerical method for direct simulation of diffusio-osmosis flows mimicking the realistic experiment without any assumed external forces. It allows us to obtain reliable flow details which is however hard to get in experiments. We found that the solvent-wall interaction, previously overlooked in classical paradigm, plays a critical role in diffusio-osmosis process. In particular, diffusio-osmosis is controlled by the interaction difference between solute-wall and solvent-wall. When solute-than solvent-wall, a surface excess (depletion) of solute particles on solid-liquid interface is formed which induces diffusio-osmosis flow towards low (high) concentration. We modified the classical Derjaguin expression to include the effect of nanoscale hydrodynamics boundary conditions for the accurate prediction of diffusio-osmosis characteristics. Overall, our results provide the clear guidance for controlling fluids flow and manipulating motion of colloids under tunable solute concentrations.

scholarly journals The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release

2018 ◽  
Vol 293 (21) ◽  
pp. 7969-7981 ◽  
Author(s):  
Thomas E. Bohl ◽  
Pek Ieong ◽  
John K. Lee ◽  
Thomas Lee ◽  
Jayakanth Kankanala ◽  
...  
Keyword(s):  
Rational Design ◽  
Substrate Binding ◽  
Flexible Substrate ◽  
Binding Mode ◽  
Antibiotic Development ◽  
Product Release ◽  
Outer Leaflet ◽  
Hydrogen Deuterium ◽  
Dynamics Simulations ◽  
Secondary Membrane

Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen–deuterium exchange MS provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic, thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1

2018 ◽  
Vol 20 (9) ◽  
pp. 6409-6420 ◽  
Author(s):  
Juan Duan ◽  
Chuncai Hu ◽  
Jiafan Guo ◽  
Lianxian Guo ◽  
Jia Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
New Delhi ◽  
Binding Process ◽  
Dynamics Simulations

We have investigated the substrate-binding pathways of NDM-1 via unbiased molecular dynamics simulations and metadynamics.

scholarly journals Understanding the Role of Diffusion in Synaptic Transmission through Inquiry-Based Learning & Quantitative Reasoning

2019 ◽  
Vol 81 (6) ◽  
pp. 435-441
Author(s):  
Günther K. H. Zupanc
Keyword(s):  
Synaptic Transmission ◽  
Synaptic Cleft ◽  
Quantitative Reasoning ◽  
Synaptic Delay ◽  
Structural Components ◽  
High Concentration ◽  
Undergraduate Biology ◽  
Inquiry Based Learning ◽  
History Of

The elucidation of the principal features of chemical synaptic transmission has been one of the great achievements in the history of neuroscience, yet students have significant difficulties developing a deeper understanding of the underlying concept. This is particularly true for the role that diffusion of neurotransmitters across the synaptic cleft plays in this process. At least part of the learning problem is due to an erroneous view of diffusion as a slow process, and to an inability to apply the concepts of size and scale to the synapse and its structural components. To overcome these difficulties, a structured/guided inquiry activity, combined with quantitative reasoning tasks, is described for teaching chemical synaptic transmission as part of undergraduate biology or neuroscience courses. Through this activity, students familiarize themselves with the absolute and relative dimensions of the structural components of synapses; use data from morphometric and schematic models of synapses to estimate the time it takes a neurotransmitter to diffuse across the synaptic cleft; and evaluate how this process relates to synaptic delay and generation of a sufficiently high concentration of transmitter molecules for activation of postsynaptic receptors.

Limits to the Development of Fast Neuromuscular Transmission in Zebrafish

2001 ◽  
Vol 86 (6) ◽  
pp. 2951-2956 ◽  
Author(s):  
Pierre Drapeau ◽  
Robert R. Buss ◽  
Declan W. Ali ◽  
Pascal Legendre ◽  
Richard L. Rotundo
Keyword(s):  
Time Course ◽  
Neuromuscular Junctions ◽  
Synaptic Cleft ◽  
Muscle Membrane ◽  
High Concentration ◽  
Limited Region ◽  
Neuromuscular Synapses ◽  
Transmission Electron ◽  
Order Of Magnitude ◽  
High Concentrations

Zebrafish embryos have small and slow miniature end-plate currents (mEPCs), whereas only a few days later larval mEPCs are an order of magnitude larger and faster, being among the fastest of all neuromuscular synapses. To identify the bases for these changes we compared, in embryos and larvae, the properties and distributions of acetylcholine (ACh) receptors (AChRs) and acetylcholinesterase (AChE) as well as the ultrastructure of the developing neuromuscular junctions (NMJs). To mimic synaptic release, patches of muscle membrane were exposed briefly (for 1 ms) to a saturating concentration (10 mM) of ACh. The AChR deactivation kinetics were twice as slow in embryos compared with larvae. In both embryos and larvae, AChRs demonstrated open channel block by millimolar ACh, and this was detected during mEPCs, indicating that a high concentration of ACh is released at immature and mature NMJs. AChR and AChE distributions were compared using the selective fluorescently conjugated labels α-bungarotoxin and fasciculin 2, respectively. In larvae, punctate AChR clusters were detected whereas junctional AChE staining was less intense than that found at adult NMJs. Transmission electron microscopy revealed immature nerve endings in embryos that were closely juxtaposed to the surrounding muscle cells, whereas mature larval NMJs had a wider synaptic cleft with a conspicuous basal lamina over a limited region of synaptic contact. Our results indicate that ACh is released at high concentrations at immature NMJs, but its clearance is prolonged and the AChRs are dispersed, resulting in a slow mEPC time course until a mature cleft appears with densely packed faster AChRs and abundant AChE.

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