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Article ; Online: Molecular Dynamics Refinement of Open State Serotonin 5-HT

Li, Zoe / Chan, Kevin C / Nickels, Jonathan D / Cheng, Xiaolin

Journal of chemical information and modeling

2023 Volume 63, Issue 4, Page(s) 1196–1207

Abstract: Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5- ... ...

Abstract	Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT
MeSH term(s)	Molecular Dynamics Simulation ; Serotonin/chemistry ; Serotonin/metabolism ; Cryoelectron Microscopy ; Protein Structure, Secondary ; Ion Transport ; Receptors, Serotonin, 5-HT3/chemistry ; Receptors, Serotonin, 5-HT3/metabolism
Chemical Substances	Serotonin (333DO1RDJY) ; Receptors, Serotonin, 5-HT3
Language	English
Publishing date	2023-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.2c01441
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Article ; Online: Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein.

Li, Zoe / Chan, Kevin C / Nickels, Jonathan D / Cheng, Xiaolin

The journal of physical chemistry. B

2022 Volume 126, Issue 43, Page(s) 8669–8679

Abstract: Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the ... ...

Abstract	Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
MeSH term(s)	Nicotine/chemistry ; Nicotine/metabolism ; Acetylcholine/chemistry ; Ligands ; Carrier Proteins/chemistry ; Static Electricity ; Tryptophan/chemistry ; Models, Molecular ; Receptors, Nicotinic/chemistry ; Binding Sites ; Protein Binding
Chemical Substances	Nicotine (6M3C89ZY6R) ; Acetylcholine (N9YNS0M02X) ; Ligands ; Carrier Proteins ; Tryptophan (8DUH1N11BX) ; Receptors, Nicotinic
Language	English
Publishing date	2022-10-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c04641
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Article: Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations.

Yang, Rui / Wu, Sijin / Wang, Shen / Rubino, Grace / Nickels, Jonathan D / Cheng, Xiaolin

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 1027223

Abstract: COVID-19 has become an unprecedented threat to human health. The SARS-CoV-2 envelope (E) protein plays a critical role in the viral maturation process and pathogenesis. Despite intensive investigation, its structure in physiological conditions remains ... ...

Abstract	COVID-19 has become an unprecedented threat to human health. The SARS-CoV-2 envelope (E) protein plays a critical role in the viral maturation process and pathogenesis. Despite intensive investigation, its structure in physiological conditions remains mysterious: no high-resolution full-length structure is available and only an NMR structure of the transmembrane (TM) region has been determined. Here, we present a refined E protein structure, using molecular dynamics (MD) simulations to investigate its structure and dynamics in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system. Our initial homology model based upon the SARS-CoV E protein structure is shown to be unstable in the lipid bilayer, and the H3 helices tend to move away from the membrane center to the membrane-water interface. A more stable model was developed by replacing all H3 helices with the fully equilibrated H3 structure sampled in the MD simulations. This refined model exhibited more favorable contacts with lipids and water than the original homology model and induced local membrane curvature, decreasing local lipid order. Interestingly, the pore radius profiles showed that the channel in both homology and refined models remained in a closed state throughout the simulations. We also demonstrated the utility of this structure to develop anti-SARS-CoV-2 drugs by docking a library of FDA-approved, investigational, and experimental drugs to the refined E protein structure, identifying 20 potential channel blockers. This highlights the power of MD simulations to refine low-resolution structures of membrane proteins in a native-like membrane environment, shedding light on the structural features of the E protein and providing a platform for the development of novel antiviral treatments.
Language	English
Publishing date	2022-10-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.1027223
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Article: Transition between Different Diffusion Regimes and Its Relationship with Structural Properties in Nafion by High Field Diffusion NMR in Combination with Small-Angle X-ray and Neutron Scattering

Berens, Samuel J / Yahya, Ahmad / Fang, Junchuan / Angelopoulos, Anastasios / Nickels, Jonathan D / Vasenkov, Sergey

Journal of physical chemistry. 2020 Sept. 15, v. 124, no. 40

2020

Abstract: Pulsed field gradient (PFG) NMR at high field was utilized to directly observe a transition between two different diffusion regimes in a Nafion 117 membrane loaded with water and acetone. Although water self-diffusivity at small water loadings was ... ...

Abstract	Pulsed field gradient (PFG) NMR at high field was utilized to directly observe a transition between two different diffusion regimes in a Nafion 117 membrane loaded with water and acetone. Although water self-diffusivity at small water loadings was observed to be diffusion time-independent in the limit of small and large diffusion times, it showed a significant decrease with increasing diffusion time at intermediate times corresponding to root mean square displacements on the order of several microns. Under our experimental conditions, no self-diffusivity dependence on diffusion time was found for water at large water loadings and for acetone at all studied acetone loadings. The diffusion time-dependent self-diffusivity at small water concentration is explained by the existence of finite domains of interconnected water channels with sizes in the range of several microns that form in Nafion in the presence of acetone. The domain sizes and permeance of transport barriers separating adjacent domains are estimated based on the measured PFG NMR data. At large water concentrations, the water channels form a fully interconnected network, resulting in time-independent self-diffusivity. The absence of such a percolation-like transition with increasing molecular concentration for acetone is attributed to a difference in the regions available for water and acetone diffusion in Nafion. The diffusion data are correlated with and supported by structural data obtained using small-angle X-ray and neutron scattering techniques. These techniques reveal distinct water channels with radial dimensions in the nanometer range increasing upon water addition, while acetone appears to be in an interfacial perfluoroether region, reducing the size of the radial channel dimension.
Keywords	acetone ; neutrons ; physical chemistry ; small-angle X-ray scattering
Language	English
Dates of publication	2020-0915
Size	p. 8943-8950.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ISSN	1520-5207
DOI	10.1021/acs.jpcb.0c07249
Database	NAL-Catalogue (AGRICOLA)

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Article: Improved chemical and isotopic labeling of biomembranes in

Nickels, Jonathan D / Bonifer, Kyle S / Tindall, Rachel R / Yahya, Ahmad / Tan, Luoxi / Do, Changwoo / Davison, Brian H / Elkins, James G

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 1011981

Abstract: Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. ...

Abstract	Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure-and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct
Language	English
Publishing date	2022-10-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.1011981
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Article ; Online: Influence of vanillic acid immobilization in Nafion membranes on intramembrane diffusion and structural properties.

Trusty, Blake / Berens, Samuel / Yahya, Ahmad / Fang, Junchuan / Barber, Sarah / Angelopoulos, Anastasios P / Nickels, Jonathan D / Vasenkov, Sergey

Physical chemistry chemical physics : PCCP

2022 Volume 24, Issue 17, Page(s) 10069–10078

Abstract: Pulsed field gradient (PFG) NMR in combination with quasielastic neutron scattering (QENS) was used to investigate self-diffusion of water and acetone in Nafion membranes with and without immobilized vanillic acid (VA). Complementary characterization of ... ...

Abstract	Pulsed field gradient (PFG) NMR in combination with quasielastic neutron scattering (QENS) was used to investigate self-diffusion of water and acetone in Nafion membranes with and without immobilized vanillic acid (VA). Complementary characterization of these membranes was performed by small angle X-ray scattering (SAXS) and NMR relaxometry. This study was motivated by the recent data showing that an organic acid, such as VA, in Nafion can preserve its catalytic activity in the presence of water even at high intra-polymer water concentrations corresponding up to 100% ambient relative humidity. However, there is currently no clear understanding of how immobilized organic acid molecules influence the microscopic transport properties and related structural properties of Nafion. Microscopic diffusion data measured by PFG NMR and QENS are compared for Nafion with and without VA. For displacements smaller than the micrometer-sized domains previously reported for Nafion, the VA addition was not observed to lead to any significant changes in the water and/or acetone self-diffusivity measured by each technique inside Nafion. However, the reported PFG NMR data present evidence of a different influence of acetone concentration in the membranes with and without VA on the water permeance of the interfaces between neighboring micrometer-sized domains. The reported diffusion data are correlated with the results of SAXS structural characterization and NMR relaxation data for water and acetone.
MeSH term(s)	Acetone ; Fluorocarbon Polymers ; Scattering, Small Angle ; Vanillic Acid ; Water/chemistry ; X-Ray Diffraction
Chemical Substances	Fluorocarbon Polymers ; Water (059QF0KO0R) ; Acetone (1364PS73AF) ; perfluorosulfonic acid (39464-59-0) ; Vanillic Acid (GM8Q3JM2Y8)
Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d2cp01125e
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Article: Water and Lipid Bilayers.

Nickels, Jonathan D / Katsaras, John

Sub-cellular biochemistry

2015 Volume 71, Page(s) 45–67

Abstract: Water is crucial to the structure and function of biological membranes. In fact, the membrane's basic structural unit, i.e. the lipid bilayer, is self-assembled and stabilized by the so-called hydrophobic effect, whereby lipid molecules unable to ... ...

Abstract	Water is crucial to the structure and function of biological membranes. In fact, the membrane's basic structural unit, i.e. the lipid bilayer, is self-assembled and stabilized by the so-called hydrophobic effect, whereby lipid molecules unable to hydrogen bond with water aggregate in order to prevent their hydrophobic portions from being exposed to water. However, this is just the beginning of the lipid-bilayer-water relationship. This mutual interaction defines vesicle stability in solution, controls small molecule permeation, and defines the spacing between lamella in multi-lamellar systems, to name a few examples. This chapter will describe the structural and dynamical properties central to these, and other water- lipid bilayer interactions.
MeSH term(s)	Lipid Bilayers/chemistry ; Water/chemistry
Chemical Substances	Lipid Bilayers ; Water (059QF0KO0R)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ISSN	0306-0225 ; 0096-8757
ISSN	0306-0225 ; 0096-8757
DOI	10.1007/978-3-319-19060-0_3
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Article ; Online: Branched-Chain Fatty Acid Content Modulates Structure, Fluidity, and Phase in Model Microbial Cell Membranes.

Mostofian, Barmak / Zhuang, Tony / Cheng, Xiaolin / Nickels, Jonathan D

The journal of physical chemistry. B

2019 Volume 123, Issue 27, Page(s) 5814–5821

Abstract: Recent progress in understanding the importance and origins of lipid rafts in microbial cell membranes has focused attention on membranes containing branched-chain fatty acids. The working hypothesis is that branched fatty acids increase the fluidity of ... ...

Abstract	Recent progress in understanding the importance and origins of lipid rafts in microbial cell membranes has focused attention on membranes containing branched-chain fatty acids. The working hypothesis is that branched fatty acids increase the fluidity of the bilayer, analogous to unsaturated fatty acids in membranes of higher organisms. Here, we perform a series of 7 μs long atomistic simulations on biomimetic, branched-chain lipid containing bilayer patches, systematically varying the amount of the straight-chain fatty acid component,
MeSH term(s)	Cell Membrane/chemistry ; Cell Membrane/metabolism ; Fatty Acids/chemistry ; Fatty Acids/metabolism ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Membrane Fluidity ; Models, Molecular ; Molecular Structure ; Staphylococcus aureus/cytology ; Staphylococcus aureus/metabolism
Chemical Substances	Fatty Acids ; Lipid Bilayers
Language	English
Publishing date	2019-06-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.9b04326
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Article ; Online: Transition between Different Diffusion Regimes and Its Relationship with Structural Properties in Nafion by High Field Diffusion NMR in Combination with Small-Angle X-ray and Neutron Scattering.

Berens, Samuel J / Yahya, Ahmad / Fang, Junchuan / Angelopoulos, Anastasios / Nickels, Jonathan D / Vasenkov, Sergey

The journal of physical chemistry. B

2020 Volume 124, Issue 40, Page(s) 8943–8950

Abstract	Pulsed field gradient (PFG) NMR at high field was utilized to directly observe a transition between two different diffusion regimes in a Nafion 117 membrane loaded with water and acetone. Although water self-diffusivity at small water loadings was observed to be diffusion time-independent in the limit of small and large diffusion times, it showed a significant decrease with increasing diffusion time at intermediate times corresponding to root mean square displacements on the order of several microns. Under our experimental conditions, no self-diffusivity dependence on diffusion time was found for water at large water loadings and for acetone at all studied acetone loadings. The diffusion time-dependent self-diffusivity at small water concentration is explained by the existence of finite domains of interconnected water channels with sizes in the range of several microns that form in Nafion in the presence of acetone. The domain sizes and permeance of transport barriers separating adjacent domains are estimated based on the measured PFG NMR data. At large water concentrations, the water channels form a fully interconnected network, resulting in time-independent self-diffusivity. The absence of such a percolation-like transition with increasing molecular concentration for acetone is attributed to a difference in the regions available for water and acetone diffusion in Nafion. The diffusion data are correlated with and supported by structural data obtained using small-angle X-ray and neutron scattering techniques. These techniques reveal distinct water channels with radial dimensions in the nanometer range increasing upon water addition, while acetone appears to be in an interfacial perfluoroether region, reducing the size of the radial channel dimension.
Language	English
Publishing date	2020-09-25
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c07249
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Branched-Chain Fatty Acid Content Modulates Structure, Fluidity, and Phase in Model Microbial Cell Membranes

Mostofian, Barmak / Zhuang, Tony / Cheng, Xiaolin / Nickels, Jonathan D

Journal of physical chemistry. 2019 June 17, v. 123, no. 27

2019

Abstract	Recent progress in understanding the importance and origins of lipid rafts in microbial cell membranes has focused attention on membranes containing branched-chain fatty acids. The working hypothesis is that branched fatty acids increase the fluidity of the bilayer, analogous to unsaturated fatty acids in membranes of higher organisms. Here, we perform a series of 7 μs long atomistic simulations on biomimetic, branched-chain lipid containing bilayer patches, systematically varying the amount of the straight-chain fatty acid component, n16:0, from 7.0 to 47.3 mol %. The simulations reveal thickening and ordering of the bilayer as well as higher bilayer viscosity and bending modulus with increasing n16:0 content, thus providing quantitative support that branched fatty acids increase the bilayer fluidity. A sharp transition in these properties is observed at ∼20% n16:0 content, resembling a phase change. The simulations provide the first access to ordered and disordered phases in a bacterial cell membrane mimic containing branched-chain lipids. Granted several assumptions, a comparison of these phases provides estimates of physical properties such as hydrophobic mismatch (∼1.2 Å), difference in bending moduli (∼15.7 kBT), and the line tension (∼0.6 pN) for a putative lipid raft in the cell membrane of an organism such as Bacillus subtilis or Staphylococcus aureus.
Keywords	Bacillus subtilis ; Staphylococcus aureus ; bacteria ; biomimetics ; branched chain fatty acids ; cell membranes ; fatty acid composition ; hydrophobicity ; models ; phase transition ; unsaturated fatty acids ; viscosity
Language	English
Dates of publication	2019-0617
Size	p. 5814-5821.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.9b04326
Database	NAL-Catalogue (AGRICOLA)

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