scholarly journals Molecular Properties of Ca2+ Transport Through TRPV2 Channel: A Molecular Dynamic Simulations Study

2021 ◽  
Author(s):  
Mozhgan Alipour ◽  
Behnam Hajipour-Verdom ◽  
Parviz Abdolmaleki ◽  
Mohammad Javan
Keyword(s):  
Calcium Ions ◽  
Electrostatic Interactions ◽  
Potential Of Mean Force ◽  
Divalent Ions ◽  
Energy Fluctuation ◽  
Dynamic Simulations ◽  
Nonselective Cation Channels ◽  
Trpv Channels ◽  
Calculation Results ◽  
Smd Simulations

Abstract TRPV channels are a category of nonselective cation channels that activated by heat and ligands, and permeate monovalent and divalent ions. The mechanism of Ca2+ transfer through TRPV2 channel is not well known. Here, we investigated the reaction coordination and energy fluctuation of Ca2+ transition in TRPV2 channel by steered molecular dynamics (SMD) simulations and potential of mean force (PMF) calculation. Results showed that electrostatic interactions between Ca2+ and residues of the first and second gates had main roles in ions transfer through the channel, and also, we recognized important amino acids in this path. Moreover, results indicated that enter and exit of calcium ions needed to overcome barrier energies in first and second gates.

Acetylcholine activates nonselective cation channels in guinea pig ileum through a G protein

1990 ◽  
Vol 258 (6) ◽  
pp. C1173-C1178 ◽  
Author(s):  
R. Inoue ◽  
G. Isenberg
Keyword(s):  
G Protein ◽  
Calcium Ions ◽  
Voltage Dependence ◽  
Sodium Ions ◽  
Nonselective Cation Channel ◽  
Guinea Pig Ileum ◽  
Channel Activation ◽  
Present Evidence ◽  
Nonselective Cation Channels ◽  
Gamma S

Acetylcholine (ACh) depolarizes the membrane of mammalian intestinal myocytes by activating a nonselective cation channel (G. D. Benham, T. B. Bolton, and R. J. Lang. Nature Lond. 316: 345-347, 1985; R. Inoue, K. Kitamura, and H. Kuriyama. Pfluegers Arch. 410: 69-74, 1987). Here, we present evidence that occupation of the muscarinic receptor by ACh couples to channel activation via a G protein; the coupling can be blocked by pertussis toxin or by intracellular guanosine 5'-O-(2-thio-diphosphate) (GDP beta S), whereas intracellular guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) activates the channel in the absence of ACh. The currents, activated by either ACh or GTP gamma S, are nonadditive, conduct sodium ions, and are similar in their voltage dependence and facilitation by submicromolar calcium ions in the cytosol.

scholarly journals Coarse-grained dynamic RNA titration simulations

2019 ◽  
Vol 9 (3) ◽  
pp. 20180066 ◽  
Author(s):  
S. Pasquali ◽  
E. Frezza ◽  
F. L. Barroso da Silva
Keyword(s):  
Electrostatic Interactions ◽  
Molecular Organization ◽  
Coarse Grained ◽  
Solution Ph ◽  
Dynamic Simulations ◽  
Rna Molecules ◽  
Coarse Grained Model ◽  
Constant Ph ◽  
Conformational Plasticity ◽  
And Function

Electrostatic interactions play a pivotal role in many biomolecular processes. The molecular organization and function in biological systems are largely determined by these interactions. Owing to the highly negative charge of RNA, the effect is expected to be more pronounced in this system. Moreover, RNA base pairing is dependent on the charge of the base, giving rise to alternative secondary and tertiary structures. The equilibrium between uncharged and charged bases is regulated by the solution pH, which is therefore a key environmental condition influencing the molecule’s structure and behaviour. By means of constant-pH Monte Carlo simulations based on a fast proton titration scheme, coupled with the coarse-grained model HiRE-RNA, molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local p K a values for each nucleotide.

Interaction of neutrophil elastase with hydrophobic polyanionic chelators

1991 ◽  
Vol 69 (9) ◽  
pp. 624-629 ◽  
Author(s):  
Suresh C. Tyagi ◽  
Sanford R. Simon
Keyword(s):  
Calcium Ions ◽  
Neutrophil Elastase ◽  
Metal Ion ◽  
Electrostatic Interactions ◽  
Enzyme Inhibitor ◽  
Human Neutrophil Elastase ◽  
Tetraacetic Acid ◽  
Fura 2 ◽  
A Site ◽  
Substrate Binding Domain

The polyanionic calcium chelators, ethylenediamine-tetraacetic acid (EDTA), ethylene-bis-(oxyethylenenitrilo)-tetraacetic acid (EGTA), [bis-(O-aminophenoxy)-ethane-N,N,N′,N′-tetraacetic acid (BAPTA), 1-[2-amino-5-(6-carboxy-indol-2-yl)phenoxyl]-2-(2′-amino-5′-methylphenoxy)ethane- N,N,N′,N′-tetraacetic acid (INDO-1), 1-[2-(5-carboxyoxazol-2yl)-6-phenoxyl]-2-(2′-amino-5′-methylphenoxy)ethane-N,N,N′,N′-tetraacetic acid (FURA-2), and 2-{[2-bis-(carboxymethyl)-amino-5-methylphenoxy]-methyl}-6-methyl-8-bis-(bis-(carboxymethyl)-aminoquinoline (QUIN-2), are all inhibitors of amidolytic activity of human neutrophil elastase (HNE). With MeOSuc-Ala-Ala-Pro-Val-pNA as substrate, these chelators all display mixed partial competitive and partial noncompetitive inhibition, but with the smaller substrate, pGlu-Pro-Val-pNA, only the noncompetitive component persists. The most effective inhibitor is FURA-2, with an apparent Ki of 0.5–0.7 mM. QUIN-2 is somewhat less effective, with a Ki of 2 mM, while EDTA is much less effective, with a Ki of 7 mM. In general, the more hydrophobic chelators are the best inhibitors, although INDO-1, which is about the same size as FURA-2, is surprisingly ineffective as an inhibitor. The chelators no longer function as effective inhibitors if their carboxyl groups are blocked by esterification with acetoxymethyl groups or by complexation with calcium ions, indicating that their binding to HNE is mediated in part through electrostatic interactions with a center of positive charge on the protein. The excitation spectrum of the complex of FURA-2 with HNE differs from that of the chelator with calcium ions, indicating that the structure of the enzyme-inhibitor complex is not like that of the coordination complex of the chelator with the metal ion. The inhibitory capacity of FURA-2 apparently arises from binding to a site that is in the vicinity of the S4 and S5 subsites of the extended substrate binding domain on HNE through a combination of hydrophobic and electrostatic interactions with the enzyme.Key words: elastase, protease inhibitors, chelators, poly anions, calcium.

Measurements of cell adhesion

Development ◽  
1973 ◽  
Vol 30 (2) ◽  
pp. 511-518
Author(s):  
Janet E. Hornby
Keyword(s):  
Cell Adhesion ◽  
Calcium Ions ◽  
Limb Bud ◽  
Magnesium Ions ◽  
Divalent Ions

The forces of interaction found for 5-day chick limb-bud cells in media containing different divalent ions (magnesium, calcium, strontium or barium) show that the cells are most adhesive in the presence of magnesium ions, then calcium and strontium, then barium. When magnesium and calcium ions are present together at similar concentrations the calcium ions modify the action of the magnesium ions. The importance of magnesium ions in cell adhesion is discussed.

The Effects of Prolactin and Divalent Ions on the Permeability to Water of Fundulus Kansae

1970 ◽  
Vol 53 (2) ◽  
pp. 317-327 ◽  
Author(s):  
W. T. W. POTTS ◽  
W. R. FLEMING
Keyword(s):  
Fresh Water ◽  
Calcium Ions ◽  
Sea Water ◽  
Tritiated Water ◽  
Low Doses ◽  
Divalent Ions ◽  
Water Turnover ◽  
Drinking Rate ◽  
Low Concentration ◽  
Ovine Prolactin

1. Measurements have been made of the rate of exchange of tritiated water in both intact and hypophysectomized Fundulus kansae in a variety of media. 2. Hypophysectomy reduces the rate of exchange in fresh water. 3. Low doses (30 mu) of ovine prolactin stimulate water turnover in hypophysectomized fish in fresh water. 4. The rate of exchange declines in both intact and hypophysectomized animals with increasing salinity. 5. Experiments with synthetic solutions show that the decline in the rate of exchange in sea water and in higher salinities is due mainly to the effects of calcium ions. 6. Fishes maintained in synthetic sea water containing a low concentration of calcium have both a higher rate of exchange of tritiated water and a higher drinking rate than fish in normal sea water.

scholarly journals Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

RSC Advances ◽  
2018 ◽  
Vol 8 (61) ◽  
pp. 34867-34876 ◽  
Author(s):  
S. Tolosa ◽  
J. A. Sansón ◽  
A. Hidalgo
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Theoretical Study ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Cytosine Deamination ◽  
Energy Profiles ◽  
Free Energy Profiles ◽  
Hydrolytic Deamination ◽  
Smd Simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

Multiparticle Models of Brownian Dynamics for the Description of Photosynthetic Electron Transfer Involving Protein Mobile Carriers

2019 ◽  
Vol 9 (1) ◽  
pp. 1-19 ◽  
Author(s):  
Galina Yurjevna Riznichenko ◽  
Ilya Kovalenko
Keyword(s):  
Electron Transfer ◽  
Conformational Changes ◽  
Brownian Dynamics ◽  
Electrostatic Interactions ◽  
State University ◽  
Protein Diffusion ◽  
Photosynthetic Membrane ◽  
Dynamic Simulations ◽  
Model Combining ◽  
Biological Faculty

The article presents a review of modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The authors used multiparticle Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational changes in the transfer of an electron from the cytochrome complex to the molecule of the mobile carrier plastocyanin in plants, green algae, and cianobacteria. Taking into account the interior of photosynthetic membrane, they developed the model, combining events of protein diffusion along the thylakoid membrane, electrostatic interactions between proteins and the proteins with the membrane charges, formation of a multiprotein complex, electron transfer within a complex, and complex dissociation. They have also developed multiparticle models of competitive interactions between electron acceptors ferredoxin.

scholarly journals Interactions of Peptide Coated Gold Nanoparticles with Spike Protein of the SARS-CoV-2: A Basis for Design of a Simple and Rapid Detection Tool

2020 ◽  
Author(s):  
Nitu Verma ◽  
Yogesh Badhe ◽  
Rakesh Gupta ◽  
Auhin Maparu ◽  
Beena Rai
Keyword(s):  
Gold Nanoparticles ◽  
Host Cell ◽  
Potential Of Mean Force ◽  
Spike Protein ◽  
Coarse Grained ◽  
Dynamic Simulations ◽  
Host Cell Membrane ◽  
Preferential Binding ◽  
Set Up ◽  
Force Calculation

<p>The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic which not only created a situation of dealing with public health emergency but also triggered the financial crisis of international concern. The current situation demands rapid, convenient and reliable diagnosis of the disease to downregulate its spread. Primary method of diagnosis presently being used, such as nucleic acid testing (RT-PCR), CT scans etc. involve time-consuming advanced machinery for imaging/ RNA replication and highly skilled technicians which could be only done in a laboratory set-up. A rapid, simple yet selective naked eye detection methodology that does not require any advanced instrumental techniques is highly desirable. </p> <p>In this study, we report computational results which could form the basis of a simple and rapid strategy for the detection of SARS-Cov-2 using peptide (screened from angiotensin-converting enzyme 2 (ACE2) receptor of host cell) functionalized gold nanoparticles (GNPs). This is based on the preferential binding of viral spike (S) protein to ACE2 receptor situated on the surface of the host cell membrane by which the virus gains access to the host cell. The interaction of peptide coated GNPs with spike protein has been investigated using coarse grained molecular dynamic simulations. The potential of mean force calculation of spike protein confirmed strong binding between peptide and receptor binding domain (RBD) of spike protein. The results presented here demonstrate the potential of this peptide coated GNPs-based system in the development of convenient sensors for the clinical diagnosis. </p>

scholarly journals Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations

2019 ◽  
Vol 20 (15) ◽  
pp. 3780 ◽  
Author(s):  
Ting Yang ◽  
Wenying Zhang ◽  
Jie Cheng ◽  
Yanhong Nie ◽  
Qi Xin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Binding Sites ◽  
Electrostatic Interactions ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Cationic Channel ◽  
Dynamics Simulations

Channelrhodopsin-2 (ChR2) is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light. Although ChR2 has been extensively used as an optogenetic tool in neuroscience research, the molecular mechanism of cation channel formation following retinal photoisomerization in ChR2 is not well understood. In this paper, studies of the closed and opened state ChR2 structures are presented. The formation of the cationic channel is elucidated in atomic detail using molecular dynamics simulations on the all-trans-retinal (ChR2-trans) configuration of ChR2 and its isomerization products, 13-cis-retinal (ChR2-cis) configuration, respectively. Photoisomerization of the retinal-chromophore causes the destruction of interactions among the crucial residues (e.g., E90, E82, N258, and R268) around the channel and the extended H-bond network mediated by numerous water molecules, which opens the pore. Steering molecular dynamics (SMD) simulations show that the electrostatic interactions at the binding sites in intracellular gate (ICG) and central gate (CG) can influence the transmembrane transport of Na+ in ChR2-cis obviously. Potential of mean force (PMF) constructed by SMD and umbrella sampling also found the existing energy wells at these two binding sites during the transportation of Na+. These wells partly hinder the penetration of Na+ into cytoplasm through the ion channel. This investigation provides a theoretical insight on the formation mechanism of ion channels and the mechanism of ion permeation.

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