scholarly journals A Network of Phosphatidylinositol 4,5-bisphosphate Binding Sites Regulate Gating of the Ca2+-activated Cl− Channel ANO1 (TMEM16A)

2019 ◽  
Author(s):  
Kuai Yu ◽  
Tao Jiang ◽  
YuanYuan Cui ◽  
Emad Tajkhorshid ◽  
H. Criss Hartzell
Keyword(s):  
Molecular Dynamics ◽  
Protein Interactions ◽  
Binding Sites ◽  
Protein Function ◽  
Computational Study ◽  
Channel Gating ◽  
Fluid Secretion ◽  
Hydroxyl Groups ◽  
Binding Modes ◽  
Cytoplasmic Extension

AbstractANO1 (TMEM16A) is a Ca2+-activated Cl− channel that regulates diverse cellular functions including fluid secretion, neuronal excitability, and smooth muscle contraction. ANO1 is activated by elevation of cytosolic Ca2+ and modulated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). Here we describe a closely concerted experimental and computational study, including electrophysiology, mutagenesis, functional assays, and extended sampling of lipid-protein interactions with molecular dynamics (MD) to characterize PI(4,5)P2 binding modes and sites on ANO1. ANO1 currents in excised inside-out patches activated by 270 nM Ca2+ at +100 mV are increased by exogenous PI(4,5)P2 with an EC50 = 1.24 µM. The effect of PI(4,5)P2 is dependent on membrane voltage and Ca2+ and is explained by a stabilization of the ANO1 Ca2+-bound open state. Unbiased atomistic MD simulations with 1.4 mol% PI(4,5)P2 in a phosphatidylcholine bilayer identified 8 binding sites with significant probability of binding PI(4,5)P2. Three of these sites captured 85% of all ANO1 - PI(4,5)P2 interactions. Mutagenesis of basic amino acids near the membrane-cytosol interface found three regions of ANO1 critical for PI(4,5)P2 regulation that correspond to the same three sites identified by MD. PI(4,5)P2 is stabilized by hydrogen bonding between amino acid sidechains and phosphate/hydroxyl groups on PI(4,5)P2. Binding of PI(4,5)P2 alters the position of the cytoplasmic extension of TM6, which plays a crucial role in ANO1 channel gating, and increases the accessibility of the inner vestibule to Cl−ions. We propose a model consisting of a network of three PI(4,5)P2 binding sites at the cytoplasmic face of the membrane allosterically regulating ANO1 channel gating.Significance statementMembrane proteins dwell in a sea of phospholipids that not only structurally stabilize the proteins by providing a hydrophobic environment for their transmembrane segments, but also dynamically regulate protein function. While many cation channels are known to be regulated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), relatively little is known about anion channel regulation by phosphoinositides. Using a combination of patch clamp electrophysiology and atomistic molecular dynamics simulations, we have identified several PI(4,5)P2 binding sites in ANO1 (TMEM16A), a Cl− channel that performs myriad physiological functions from epithelial fluid secretion to regulation of electrical excitability. These binding sites form a band at the cytosolic interface of the membrane that we propose constitute a network to dynamically regulate this highly allosteric protein.

scholarly journals A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca2+-activated Cl− channel ANO1 (TMEM16A)

2019 ◽  
Vol 116 (40) ◽  
pp. 19952-19962 ◽  
Author(s):  
Kuai Yu ◽  
Tao Jiang ◽  
YuanYuan Cui ◽  
Emad Tajkhorshid ◽  
H. Criss Hartzell
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Neuronal Excitability ◽  
Computational Study ◽  
Channel Gating ◽  
Md Simulations ◽  
Fluid Secretion ◽  
Hydroxyl Groups ◽  
Binding Modes ◽  
Cytoplasmic Extension

ANO1 (TMEM16A) is a Ca2+-activated Cl− channel that regulates diverse cellular functions including fluid secretion, neuronal excitability, and smooth muscle contraction. ANO1 is activated by elevation of cytosolic Ca2+ and modulated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Here, we describe a closely concerted experimental and computational study, including electrophysiology, mutagenesis, functional assays, and extended sampling of lipid–protein interactions with molecular dynamics (MD) to characterize PI(4,5)P2 binding modes and sites on ANO1. ANO1 currents in excised inside-out patches activated by 270 nM Ca2+ at +100 mV are increased by exogenous PI(4,5)P2 with an EC50 = 1.24 µM. The effect of PI(4,5)P2 is dependent on membrane voltage and Ca2+ and is explained by a stabilization of the ANO1 Ca2+-bound open state. Unbiased atomistic MD simulations with 1.4 mol% PI(4,5)P2 in a phosphatidylcholine bilayer identified 8 binding sites with significant probability of binding PI(4,5)P2. Three of these sites captured 85% of all ANO1–PI(4,5)P2 interactions. Mutagenesis of basic amino acids near the membrane–cytosol interface found 3 regions of ANO1 critical for PI(4,5)P2 regulation that correspond to the same 3 sites identified by MD. PI(4,5)P2 is stabilized by hydrogen bonding between amino acid side chains and phosphate/hydroxyl groups on PI(4,5)P2. Binding of PI(4,5)P2 alters the position of the cytoplasmic extension of TM6, which plays a crucial role in ANO1 channel gating, and increases the accessibility of the inner vestibule to Cl− ions. We propose a model consisting of a network of 3 PI(4,5)P2 binding sites at the cytoplasmic face of the membrane allosterically regulating ANO1 channel gating.

scholarly journals The Phosphorylated Estrogen Receptor α (ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2

2018 ◽  
Vol 39 (3) ◽  
Author(s):  
Kyle T. Helzer ◽  
Mary Szatkowski Ozers ◽  
Mark B. Meyer ◽  
Nancy A. Benkusky ◽  
Natalia Solodin ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Transcription Factor ◽  
Dna Binding ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Binding Sites ◽  
Protein Function ◽  
Estrogen Receptor Α ◽  
Binding Activity

ABSTRACT Posttranslational modifications are key regulators of protein function, providing cues that can alter protein interactions and cellular location. Phosphorylation of estrogen receptor α (ER) at serine 118 (pS118-ER) occurs in response to multiple stimuli and is involved in modulating ER-dependent gene transcription. While the cistrome of ER is well established, surprisingly little is understood about how phosphorylation impacts ER-DNA binding activity. To define the pS118-ER cistrome, chromatin immunoprecipitation sequencing was performed on pS118-ER and ER in MCF-7 cells treated with estrogen. pS118-ER occupied a subset of ER binding sites which were associated with an active enhancer mark, acetylated H3K27. Unlike ER, pS118-ER sites were enriched in GRHL2 DNA binding motifs, and estrogen treatment increased GRHL2 recruitment to sites occupied by pS118-ER. Additionally, pS118-ER occupancy sites showed greater enrichment of full-length estrogen response elements relative to ER sites. In an in vitro DNA binding array of genomic binding sites, pS118-ER was more commonly associated with direct DNA binding events than indirect binding events. These results indicate that phosphorylation of ER at serine 118 promotes direct DNA binding at active enhancers and is a distinguishing mark for associated transcription factor complexes on chromatin.

scholarly journals Deprotonation of resorcinarenes and novel ammonium salt complexes

2014 ◽  
Vol 70 (a1) ◽  
pp. C678-C678
Author(s):  
Ngong Beyeh ◽  
Arto Valkonen ◽  
Fanfang Pan ◽  
Kari Rissanen
Keyword(s):  
Hydrogen Bonds ◽  
Binding Sites ◽  
Molecular Complexes ◽  
Ammonium Salts ◽  
Hydroxyl Groups ◽  
Binding Modes ◽  
Intermolecular Hydrogen Bonds ◽  
Guest Molecules ◽  
Cone Conformation ◽  
Intramolecular Hydrogen

The bowl shape cavity of resorcinarenes usually stabilized by four intramolecular hydrogen bonds offers an interesting array of binding modes such as C–H...π and cation...π interactions to recognize a variety of guests. The multiple hydroxyl groups can participate in a series of intermolecular hydrogen bonds with guest molecules. This unique cone conformation of resorcinarenes has led to the synthesis of many receptors with convergent arrangement of binding sites suitable for molecular recognition in many applications. Unfunctionalized resorcinarenes are known to easily form molecular complexes with guests of varying shapes and sizes. Amines are very common bases used in many catalytic processes. A good example is the use of amines as bases in the alkylation and acylation of resorcinarenes leading to cavitands, carcerands, hemicarcerands and velcrands. The use of amines in such reactions is to deprotonate the resorcinarene hydroxyl groups, hence facilitating the alkylation and acylation processes. The subsequently protonated ammonium cation then forms interesting supramolecular complexes with the anionic and dianionic resorcinarenes. Furthermore, secondary and tertiary ammonium salts possess hydrogen bond donating -NH2 and -NH respectively and these can further enhance their complexation through intermolecular hydrogen bonds. Here we present our recent examples of supramolecular assemblies resulting from the deprotonation of resorcinarenes by mono- and dibasic amines. Also, our latest supramolecular co-crystals between resorcinarenes as the receptors and a series of secondary and tertiary mono- and diammonium cations are illustrated.

scholarly journals Design of heparin oligosaccharide based molecules for inhibition of Alzheimer amyloid beta (Aβ40) aggregation

2016 ◽  
Vol 94 (12) ◽  
pp. 1090-1098 ◽  
Author(s):  
Thomas J. Paul ◽  
Harvey Kelly ◽  
Joshua Zuchniarz ◽  
Tahir Ahmed ◽  
Rajeev Prabhakar
Keyword(s):  
Molecular Dynamics ◽  
Amyloid Beta ◽  
Binding Sites ◽  
Md Simulation ◽  
Computational Study ◽  
The Other ◽  
Therapeutic Interventions ◽  
Simulation Techniques ◽  
Deadly Disease ◽  
Monomeric And Aggregated Forms

In this computational study, we have combined molecular docking and molecular dynamics (MD) simulation techniques to explore interactions of monomeric and aggregated forms of Alzheimer’s amyloid beta (Aβ40) with seven chemically distinct heparin derived glycoaminoglycans (GAGs) referred to as ADC, SDC, DC, V1, V2, V3, and V4. The docking procedure proposed two major binding sites, i.e., one present at the top of the fibril (site A), and the other located in the hairpin region (site B). Due to its position, site B offers an interesting target to design molecules with anti-aggregation properties. Our results predicted that out of seven GAGs, only three of them (ADC, SDC, and DC) bind to site B. The identification of these molecules can advance our efforts to develop therapeutic interventions for this deadly disease.

A computational study of the adsorption of the isomers of butanol on silicalite and H-ZSM-5

1994 ◽  
Vol 446 (1928) ◽  
pp. 411-427 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Energy Minimization ◽  
Computational Study ◽  
Hydroxyl Groups ◽  
Confinement Effects ◽  
Surface Hydroxyl ◽  
Ambient Temperatures ◽  
Surface Hydroxyl Groups ◽  
Minimization Procedure

We have studied the adsorption of the four isomers of butanol on silicalite and on H-ZSM-5 using an energy minimization procedure supplemented by a Monte Carlo/molecular dynamics algorithm to assist in the location of minima. The energetics and the geometries of adsorption of the butanol isomers in the pores of silicalite and H-ZSM-5 are reported. The effect of the relaxation of both the adsorbent framework and of the adsorbate molecule is investigated. Significant changes in the direction of the surface hydroxyl groups at certain crystallographic positions are induced by alcohol physisorption. For both silicalite and H-ZSM-5, similar energy values were obtained for each butanol isomer sorbed at a number of different crystallographic positions. We therefore predict that there are a range of physisorbed states for all butanols at ambient temperatures. The small variations in the adsorption energetics and sites between isomers may be explained in the terms of pore-confinement effects on the adsorption of molecules with dimensions similar to those of pentasil channels.

scholarly journals Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

2016 ◽  
Author(s):  
Ralph Patrick ◽  
Coralie Horin ◽  
Bostjan Kobe ◽  
Kim-Anh Lê Cao ◽  
Mikael Bodén
Keyword(s):  
Protein Interactions ◽  
Binding Sites ◽  
Protein Function ◽  
Computational Prediction ◽  
Alternative Methods ◽  
Integrative Model ◽  
Model Organisms ◽  
Phosphorylation Sites ◽  
Nuclear Localisation ◽  
Cellular Context

AbstractThe identification of kinase substrates and the specific phosphorylation sites they regulate is an important factor in understanding protein function regulation and signalling pathways. Computational prediction of kinase targets – assigning kinases to putative substrates, and selecting from protein sequence the sites that kinases can phosphorylate – requires the consideration of both the cellular context that kinases operate in, as well as their binding affinity. This consideration enables investigation of how phosphorylation influences a range of biological processes.We report here a novel probabilistic model for the classification of kinase-specific phosphorylation sites from sequence across three model organisms: human, mouse and yeast. The model incorporates position-specific amino acid frequencies, and counts of co-occurring amino acids from kinase binding sites in a kinase‐ and family-specific manner. We show how this model can be seamlessly integrated with protein interactions and cell-cycle abundance profiles. When evaluating the prediction accuracy of our method, PhosphoPICK, on an independent hold-out set of kinase-specific phosphorylation sites, we found it achieved an average specificity of 97% while correctly predicting 32% of true positives. We also compared PhosphoPICK’s ability, through cross-validation, to predict kinase-specific phosphorylation sites with alternative methods, and found that at high levels of specificity PhosphoPICK outperforms alternative methods for most comparisons made.We investigated the relationship between experimentally confirmed phosphorylation sites and predicted nuclear localisation signals by predicting the most likely kinases to be regulating the phosphorylated residues immediately upstream or downstream from the localisation signal. We show that kinases PKA, Akt1 and AurB have an over-representation of predicted binding sites at particular positions downstream from predicted nuclear localisation signals, demonstrating an important role for these kinases in regulating the nuclear import of proteins.PhosphoPICK is freely available online as a web-service at http://bioinf.scmb.uq.edu.au/phosphopick.

Exploration of human serum albumin binding sites by docking and molecular dynamics flexible ligand–protein interactions

Biopolymers ◽  
2010 ◽  
Vol 93 (2) ◽  
pp. 161-170 ◽  
Author(s):  
Omar Deeb ◽  
Martha Cecilia Rosales-Hernández ◽  
Carlos Gómez-Castro ◽  
Ramón Garduño-Juárez ◽  
José Correa-Basurto
Keyword(s):  
Molecular Dynamics ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Protein Interactions ◽  
Binding Sites ◽  
Albumin Binding ◽  
Human Serum Albumin Binding

Probing the binding mechanism of novel dual NF-κB/AP-1 inhibitors by 3D-QSAR, docking and molecular dynamics simulations

RSC Advances ◽  
2015 ◽  
Vol 5 (99) ◽  
pp. 81523-81532 ◽  
Author(s):  
Shaojie Ma ◽  
Shepei Tan ◽  
Danqing Fang ◽  
Rong Zhang ◽  
Shengfu Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Computational Study ◽  
3D Qsar ◽  
Structural Features ◽  
Binding Mechanism ◽  
Interaction Mechanisms ◽  
Dynamics Simulations

Potent dual NF-κB/AP-1 inhibitors could effectively treat immunoinflammatory diseases. An integrated computational study was carried out to identify the most favourable binding sites, the structural features and the interaction mechanisms.

scholarly journals A Comparative Study of Binding of Different Drugs on gp120: Insight from Molecular Dynamics Simulation Study

2018 ◽  
Vol 34 (6) ◽  
pp. 2954-2962
Author(s):  
Vishnudatt Pandey ◽  
Gargi Tiwari ◽  
Rajendra Prasad Ojha
Keyword(s):  
Molecular Dynamics ◽  
Protein Interactions ◽  
Binding Sites ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Receptor Protein ◽  
Contact Points ◽  
Gp120 Binding ◽  
Cd4 Binding Site ◽  
Dynamics Simulations

HIV-I cellular infection triggered by CD4 receptor protein and viral envelop glycoprotein gp120 binding event. CD4:gp120 surface is directed by the contact points of a hydrophobic gp120 cavity capped by Phe43CD4 and ionic bonds residues Arg59CD4 and Asp368gp120. The binding sites originated by gp120 and CD4 interaction leads to the entry of HIV-I into the host membrane, where, gp120 and a CD4 binding site becomes the main mark for plenty of drug uncovering program. Here, we took the crystal structure of small-molecule of gp120 in a complex that concurrently pursues both of the hotspots of gp120 binding sites. All ligands in our study are small molecules that are able to obstruct the protein-protein interactions between CD4 and gp120. This study aims at the thermodynamical insights of the ligand binding in CD4 binding sites using Molecular Dynamics Simulations Study and calculation of binding free energy. The physical of binding of drugs distinctly indicates a hydrophobic and electrostatics interaction motivated binding of ligands which explicitly mark CD4 binding sites.

scholarly journals N-glycosylation blocks and simultaneously fosters different receptor-ligand binding sites: the chameleonic CD44–hyaluronan interaction

2020 ◽  
Author(s):  
Joni Vuorio ◽  
Jana Škerlová ◽  
Milan Fábry ◽  
Václav Veverka ◽  
Ilpo Vattulainen ◽  
...  
Keyword(s):  
Protein Structure ◽  
Binding Site ◽  
Binding Sites ◽  
Protein Function ◽  
Protein Structure Determination ◽  
Host Protein ◽  
Cell Surface Receptor ◽  
Binding Modes ◽  
Surface Receptor ◽  
First Time

ABSTRACTWhile DNA encodes protein structure, glycans provide a complementary layer of information to protein function. As a prime example of the significance of glycans, the ability of the cell surface receptor CD44 to bind its ligand, hyaluronan, is modulated by N-glycosylation. However, the details of this modulation remain unclear. Based on atomistic simulations and NMR, we provide evidence that CD44 has multiple distinct binding sites for hyaluronan, and that N-glycosylation modulates their respective roles. We find that non-glycosylated CD44 favors the canonical sub-micromolar binding site, while glycosylated CD44 binds hyaluronan with an entirely different micromolar binding site. Our findings show (for the first time) how glycosylation can alter receptor affinity by shielding specific regions of the host protein, thereby promoting weaker binding modes. The mechanism revealed in this work emphasizes the importance of glycosylation in protein function and poses a challenge for protein structure determination where glycosylation is usually neglected.

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