scholarly journals A sulfur-aromatic gate latch is essential for opening of the Orai1 channel pore

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Priscilla S-W Yeung ◽  
Christopher E Ing ◽  
Megumi Yamashita ◽  
Régis Pomès ◽  
Murali Prakriya
Keyword(s):  
Metal Ion ◽  
Mutational Analysis ◽  
Hydrophobic Interactions ◽  
Protein Structures ◽  
Experimental Studies ◽  
Functional Roles ◽  
Methionine Residue ◽  
Aromatic Interactions ◽  
Additional Stabilization ◽  
Dynamics Simulations

Sulfur-aromatic interactions occur in the majority of protein structures, yet little is known about their functional roles in ion channels. Here, we describe a novel molecular motif, the M101 gate latch, which is essential for gating of human Orai1 channels via its sulfur-aromatic interactions with the F99 hydrophobic gate. Molecular dynamics simulations of different Orai variants reveal that the gate latch is mostly engaged in open but not closed channels. In experimental studies, we use metal-ion bridges to show that promoting an M101-F99 bond directly activates Orai1, whereas disrupting this interaction triggers channel closure. Mutational analysis demonstrates that the methionine residue at this position has a unique combination of length, flexibility, and chemistry to act as an effective latch for the phenylalanine gate. Because sulfur-aromatic interactions provide additional stabilization compared to purely hydrophobic interactions, we infer that the six M101-F99 pairs in the hexameric channel provide a substantial energetic contribution to Orai1 activation.

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

2015 ◽  
Vol 71 (4) ◽  
pp. 779-789 ◽  
Author(s):  
Zhiming Wang ◽  
Zhu Qiao ◽  
Sheng Ye ◽  
Rongguang Zhang
Keyword(s):  
Bound States ◽  
Hydrophobic Interactions ◽  
Crystal Packing ◽  
Protein Structures ◽  
Structural Basis ◽  
Phosphagen Kinase ◽  
Domain Arrangement ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Shaped Domain

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

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.

scholarly journals Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Renu Wadhwa ◽  
Neetu Singh Yadav ◽  
Shashank P. Katiyar ◽  
Tomoko Yaguchi ◽  
Chohee Lee ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Bilayer Membrane ◽  
Withaferin A ◽  
Head Group ◽  
Polar Head Group ◽  
Natural Drugs ◽  
Dynamics Simulations

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs—withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.

Possible Mechanisms for Thermal Conductivity Enhancement in Nanofluids

2006 ◽  
Author(s):  
Amit Gupta ◽  
Xuan Wu ◽  
Ranganathan Kumar
Keyword(s):  
Heat Transfer ◽  
Thermal Conductivity ◽  
Brownian Motion ◽  
Brownian Dynamics ◽  
Lattice Vibration ◽  
Experimental Studies ◽  
High Heat ◽  
Conductivity Enhancement ◽  
High Heat Transfer ◽  
Dynamics Simulations

This study discusses the merits of various physical mechanisms that are responsible for enhancing the heat transfer in nanofluids. Experimental studies have cemented the claim that ‘seeding’ liquids with nanoparticles can increase the thermal conductivity of the nanofluid by up to 40% for metallic and oxide nanoparticles dispersed in a base liquid. Experiments have also shown that the rise in conductivity of the nanofluid is highly dependent on the size and concentration of the nanoparticles. On the theoretical side, traditional models like Maxwell or Hamilton-Crosser models cannot explain this unusually high heat transfer. Several mechanisms have been postulated in the literature such as Brownian motion, thermal diffusion in nanoparticles and thermal interaction of nanoparticles with the surrounding fluid, the formation of an ordered liquid layer on the surface of the nanoparticle and microconvection. This study concentrates on 3 possible mechanisms: Brownian dynamics, microconvection and lattice vibration of nanoparticles in the fluid. By considering two nanofluids, copper particles dispersed in ethylene glycol, and silica in water, it is determined that translational Brownian motion of the nanoparticles, presence of an interparticle potential and the microconvection heat transfer are mechanisms that play only a smaller role in the enhancement of thermal conductivity. On the other hand, the lattice vibrations, determined by molecular dynamics simulations show a great deal of promise in increasing the thermal conductivity by as much as 23%. In a simplistic sense, the lattice vibration can be regarded as a means to simulate the phononic transport from solid to liquid at the interface.

Oxidative Modification of Fibrinogen Affects Its Binding Activity to Glycoprotein (GP) IIb/IIIa

2009 ◽  
Vol 16 (1) ◽  
pp. 51-59 ◽  
Author(s):  
Sermin Tetik ◽  
Kurtulus Kaya ◽  
M. Demir ◽  
Emel Eksioglu-Demiralp ◽  
Turay Yardimci
Keyword(s):  
Metal Ion ◽  
Degradation Products ◽  
Binding Capacity ◽  
Protein Structures ◽  
Human Platelets ◽  
Binding Activity ◽  
Oxidative Modification ◽  
Oxidized Fibrinogen ◽  
Protein Functions

Aim: Proteins are sensitive biomarkers of human diease condition associated with oxidative stress. Alteration of protein structures by oxidants may result in partial or complete loss of protein functions. We have investigated the effect of structural modifications induced by metal ion catalyzed oxidation of fibrinogen on its binding capacity to glycoprotein IIb/IIIa (GpIIb/IIIa) and human platelets. Methods: We identified and quantified of binding capacity of native and oxidized fibrinogen to its receptor in vitro by flow cytometer. Dityrosine formation on oxidized fibrinogen were detected spectrophotometrically. Elevated degradation products of fibrinogen after oxidation were revealed in the HPLC analysis. The native and oxidized fibrinogen were analyzed on mass spectrum upon digestion with tyripsin. Results: Oxidatively modified fibrinogen showed less binding activity than native fibrinogen to GpIIb/IIIa coated micro beads and human platelets whereas slightly higher binding capaticity to ADP induced stimulated platelets. Formation of dityrosines in the amino acid side chains of fibrinogen were observed upon oxidation. Decreased binding capacity of oxidized fibrinogen correlated with intensities of dityrosine formation. Oxidized fibrinogen had more ion-mass intensities at higher than native fibrinogen. Clinical implications: Important point is decreased of binding capacity of the oxidized fibrinogen to own receptor. The decreased rate of binding, leading to effect in the diseases of clot formation may acount for the association between oxidation of fibrinogen and the incidence of effect in human diseases.

scholarly journals Equilibrium modeling of mono and binary sorption of Cu(II) and Zn(II) onto chitosan gel beads

2016 ◽  
Vol 37 (4) ◽  
pp. 485-501 ◽  
Author(s):  
Józef Nastaj ◽  
Małgorzata Tuligłowicz ◽  
Konrad Witkiewicz
Keyword(s):  
Metal Ion ◽  
Ph Value ◽  
Experimental Studies ◽  
Process Conditions ◽  
Optimal Process ◽  
Sorption Data ◽  
Gel Beads ◽  
Two Component ◽  
Equilibrium Data ◽  
Chitosan Gel

Abstract The objective of the work are in-depth experimental studies of Cu(II) and Zn(II) ion removal on chitosan gel beads from both one- and two-component water solutions at the temperature of 303 K. The optimal process conditions such as: pH value, dose of sorbent and contact time were determined. Based on the optimal process conditions, equilibrium and kinetic studies were carried out. The maximum sorption capacities equaled: 191.25 mg/g and 142.88 mg/g for Cu(II) and Zn(II) ions respectively, when the sorbent dose was 10 g/L and the pH of a solution was 5.0 for both heavy metal ions. One-component sorption equilibrium data were successfully presented for six of the most useful three-parameter equilibrium models: Langmuir-Freundlich, Redlich-Peterson, Sips, Koble-Corrigan, Hill and Toth. Extended forms of Langmuir-Freundlich, Koble-Corrigan and Sips models were also well fitted to the two-component equilibrium data obtained for different ratios of concentrations of Cu(II) and Zn(II) ions (1:1, 1:2, 2:1). Experimental sorption data were described by two kinetic models of the pseudo-first and pseudo-second order. Furthermore, an attempt to explain the mechanisms of the divalent metal ion sorption process on chitosan gel beads was undertaken.

scholarly journals Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

2021 ◽  
Vol 17 (5) ◽  
pp. e1008988
Author(s):  
Nikolina ŠoŠtarić ◽  
Vera van Noort
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Protein Structures ◽  
Cellular Protein ◽  
Free Energy Calculations ◽  
Protein Protein Interactions ◽  
Post Translational Modifications ◽  
Protein Properties ◽  
Dynamics Simulations

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.

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