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189 results on '"Nickels, Jonathan D."'

1. Lipid Rafts in Bacteria: Structure and Function

Author

Nickels, Jonathan D., Hogg, Jacob, Cordner, Destini, Katsaras, John, Timmis, Kenneth N., Editor-in-Chief, Boll, Matthias, Series Editor, Geiger, Otto, Series Editor, Goldfine, Howard, Series Editor, Krell, Tino, Series Editor, Lee, Sang Yup, Series Editor, McGenity, Terry J., Series Editor, Rojo, Fernando, Series Editor, Sousa, Diana Z., Series Editor, Stams, Alfons J. M., Series Editor, Steffan, Robert J., Series Editor, and Wilkes, Heinz, Series Editor

Published
2020
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7. Amphiphilic Co-Solvents Modulate the Structure of Membrane Domains

Author

Tan, Luoxi, primary, Scott, Haden L., additional, Smith, Micholas Dean, additional, Pingali, Sai Venkatesh, additional, O’Neill, Hugh M., additional, Morrell-Falvey, Jennifer L., additional, Katsaras, John, additional, Smith, Jeremy C., additional, Davison, Brian H., additional, Elkins, James G., additional, and Nickels, Jonathan D., additional

Published
2023
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20. Toxic Effects of Butanol in the Plane of the Cell Membrane

Author

Tan, Luoxi, Scott, Haden L., Smith, Micholas Dean, Pingali, Sai Venkatesh, Cheng, Xiaolin, O’Neill, Hugh M., Katsaras, John, Smith, Jeremy C., Elkins, James G., Davison, Brian H., and Nickels, Jonathan D.

Abstract

Solvent toxicity limits n-butanol fermentation titer, increasing the cost and energy consumption for subsequent separation processes and making biobased production more expensive and energy-intensive than petrochemical approaches. Amphiphilic solvents such as n-butanol partition into the cell membrane of fermenting microorganisms, thinning the transverse structure, and eventually causing a loss of membrane potential and cell death. In this work, we demonstrate the deleterious effects of n-butanol partitioning upon the lateral dimension of the membrane structure, called membrane domains or lipid rafts. Lipid rafts are regions of the cell membrane enriched with certain lipids, providing a reservoir of high melting temperature lipids and a platform for membrane protein partitioning and oligomerization. Neutron scattering experiments and molecular dynamics simulations revealed that n-butanol increased the size of the lipid domains in a model membrane system. The data showed that n-butanol partitions more into the disordered lipid regions than into the raft-like phase, leading to a differential thinning of these coexisting phases in the plane of the membrane and increasing the hydrophobic mismatch. The resulting increase in line tension at the interface favors domain coalescence to minimize the ratio of the interfacial length to domain area. A detailed computational investigation of the lipid domain interface identifies the boundary as a site of membrane disorder and thinning due to an accumulation of n-butanol. Solvent-induced changes to domain morphology and membrane instability at the domain interface are unrecognized modes of solvent-induced stress to fermenting microbes, representing targets for new solvent tolerance strategies to increase the n-butanol titer.

Published
2025
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21. Molecular Dynamics Refinement of Open State Serotonin 5-HT3AReceptor Structures

Author

Li, Zoe, Chan, Kevin C., Nickels, Jonathan D., and Cheng, Xiaolin

Abstract

Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT3receptors are a clinical target for treating nausea and vomiting associated with chemotherapy and radiation therapy (Thompson and Lummis, 2006). Multiple cryo-electron microscopy (cryo-EM) structures of 5-HT3receptors have been determined in distinct functional states (e.g., open, closed, etc.) (Basak et al., 2018; Basak et al., 2018; Polovinkin et al., 2018; Zhang et al., 2015). However, recent work has shown that the transmembrane pores of the open 5-HT3receptor structures rapidly collapse and become artificially asymmetric in molecular dynamics (MD) simulations. To avoid this hydrophobic collapse, Dämgen and Biggin developed an equilibration protocol that led to a stable open state structure of the glycine receptor in MD simulations (Dämgen and Biggin, 2020). However, the protocol failed to yield open-like structures of the 5-HT3receptor in our simulations. Here, we present a refined equilibration protocol that involves the rearrangement of the transmembrane helices to achieve stable open state structures of the 5-HT3receptor that allow both water and ion permeation through the channel. Notably, channel gating is mediated through collective movement of the transmembrane helices, involving not only pore lining M2 helices but also their cross-talk with the adjacent M1 and M3 helices. Thus, the successful application of our refined equilibration protocol underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like structures of the 5-HT3receptor.

Published
2023
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25. Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome

Author

Nickels, Jonathan D., primary, Poudel, Suresh, additional, Chatterjee, Sneha, additional, Farmer, Abigail, additional, Cordner, Destini, additional, Campagna, Shawn R., additional, Giannone, Richard J., additional, Hettich, Robert L., additional, Myles, Dean A. A., additional, Standaert, Robert F., additional, Katsaras, John, additional, and Elkins, James G., additional

Published
2020
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26. Molecular origins of bulk viscosity in liquid water

Author

Yahya, Ahmad, primary, Tan, Luoxi, additional, Perticaroli, Stefania, additional, Mamontov, Eugene, additional, Pajerowski, Daniel, additional, Neuefeind, Joerg, additional, Ehlers, Georg, additional, and Nickels, Jonathan D., additional

Published
2020
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27. Solvent-induced membrane stress in biofuel production: molecular insights from small-angle scattering and all-atom molecular dynamics simulations

Author

Smith, Micholas Dean, primary, Pingali, Sai Venkatesh, additional, Elkins, James G., additional, Bolmatov, Dima, additional, Standaert, Robert F., additional, Nickels, Jonathan D., additional, Urban, Volker S., additional, Katsaras, John, additional, Davison, Brian H., additional, Smith, Jeremy C., additional, and Petridis, Loukas, additional

Published
2020
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29. Cannabinoid Receptor CB2 Oligomerization in a Lipid Matrix

Author

Yeliseev, Alexei, primary, Nickels, Jonathan D., additional, Hines, Kirk G., additional, Zoubak, Lioudmila, additional, Teague, Walter E., additional, Lynch, Diane L., additional, Hurst, Dow P., additional, Weiss, Kevin L., additional, Katsaras, John, additional, Reggio, Patricia H., additional, and Gawrisch, Klaus, additional

Published
2019
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30. Lipid Rafts: Buffers of Cell Membrane Physical Properties

Author

Nickels, Jonathan D., primary, Smith, Micholas Dean, additional, Alsop, Richard J., additional, Himbert, Sebastian, additional, Yahya, Ahmad, additional, Cordner, Destini, additional, Zolnierczuk, Piotr, additional, Stanley, Christopher B., additional, Katsaras, John, additional, Cheng, Xiaolin, additional, and Rheinstädter, Maikel C., additional

Published
2019
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31. Molecular origins of bulk viscosity in liquid water.

Author

Yahy, Ahmad, Tan, Luoxi, Perticaroli, Stefania, Mamontov, Eugene, Pajerowski, Daniel, Neuefeind, Joerg, Ehlers, Georg, and Nickels, Jonathan D.

Abstract

The rapid equilibrium fluctuations of water molecules are intimately connected to the rheological response; molecular motions resetting the local structure and stresses seen as flow and volume changes. In the case of water or hydrogen bonding liquids generally, the relationship is a non-trivial consideration due to strong directional interactions complicating theoretical models and necessitating clear observation of the timescale and nautre of the associated equilibrium motions. Recent work has illustrated a coincidence of timescales for short range sub-picosecond motions and the implied timescale for the shear viscosity response in liquid water. Here, neutron and light scattering methods are used to experimentally illustrate the timescale of bulk viscosity and provide a description of the associated molecular relaxation. Brillouin scattering has been used to establish the timescale of bulk viscosity; and borrowing the Maxwell approach, the ratio of the bulk viscosity, ζ, to the bulk modulus, K, yields a relaxation time, τB, which emerges on the order of 1–2 ps in the 280 K to 303 K temperature range. Inelastic neutron scattering is subsequently used to describe the motions of water and heavy water at the molecular scale, providing both coherent and incoherent scattering data. A rotational (alternatively described as localized) motion of water protons on the 1–2 ps timescale is apparent in the incoherent scattering spectra of water, while the coherent spectra from D2O on the length scale of the first sharp diffraction peak, describing the microscopic density fluctuations of water, confirms the relaxation of water structure at a comparable timescale of 1–2 ps. The coincidence of these three timescales provides a mechanistic description of the bulk viscous response, with the local structure resetting due to rotational/localized motions on the order of 1–2 ps, approximately three times slower than the relaxations associated with shear viscosity. In this way we show that the shear viscous response is most closely associated with changes in water network connectivity, while the bulk viscous response is associated with local density fluctuations. [ABSTRACT FROM AUTHOR]

Published
2020
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32. Neutron scattering in the biological sciences: progress and prospects

Author

Ashkar, Rana, primary, Bilheux, Hassina Z., additional, Bordallo, Heliosa, additional, Briber, Robert, additional, Callaway, David J. E., additional, Cheng, Xiaolin, additional, Chu, Xiang-Qiang, additional, Curtis, Joseph E., additional, Dadmun, Mark, additional, Fenimore, Paul, additional, Fushman, David, additional, Gabel, Frank, additional, Gupta, Kushol, additional, Herberle, Frederick, additional, Heinrich, Frank, additional, Hong, Liang, additional, Katsaras, John, additional, Kelman, Zvi, additional, Kharlampieva, Eugenia, additional, Kneller, Gerald R., additional, Kovalevsky, Andrey, additional, Krueger, Susan, additional, Langan, Paul, additional, Lieberman, Raquel, additional, Liu, Yun, additional, Losche, Mathias, additional, Lyman, Edward, additional, Mao, Yimin, additional, Marino, John, additional, Mattos, Carla, additional, Meilleur, Flora, additional, Moody, Peter, additional, Nickels, Jonathan D., additional, O'Dell, William B., additional, O'Neill, Hugh, additional, Perez-Salas, Ursula, additional, Peters, Judith, additional, Petridis, Loukas, additional, Sokolov, Alexei P., additional, Stanley, Christopher, additional, Wagner, Norman, additional, Weinrich, Michael, additional, Weiss, Kevin, additional, Wymore, Troy, additional, Zhang, Yang, additional, and Smith, Jeremy C., additional

Published
2018
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33. Neutron scattering in the biological sciences:progress and prospects

Author

Ashkar, Rana, Bilheux, Hassina Z., Bordallo, Heliosa, Briber, Robert, Callaway, David J. E., Cheng, Xiaolin, Chu, Xiang-Qiang, Curtis, Joseph E., Dadmun, Mark, Fenimore, Paul, Fushman, David, Gabel, Frank, Gupta, Kushol, Herberle, Frederick, Heinrich, Frank, Hong, Liang, Katsaras, John, Kelman, Zvi, Kharlampieva, Eugenia, Kneller, Gerald R., Kovalevsky, Andrey, Krueger, Susan, Langan, Paul, Lieberman, Raquel, Liu, Yun, Losche, Mathias, Lyman, Edward, Mao, Yimin, Marino, John, Mattos, Carla, Meilleur, Flora, Moody, Peter, Nickels, Jonathan D., O'Dell, William B., O'Neill, Hugh, Perez-Salas, Ursula, Peters, Judith, Petridis, Loukas, Sokolov, Alexei P., Stanley, Christopher, Wagner, Norman, Weinrich, Michael, Weiss, Kevin, Wymore, Troy, Zhang, Yang, Smith, Jeremy C., Ashkar, Rana, Bilheux, Hassina Z., Bordallo, Heliosa, Briber, Robert, Callaway, David J. E., Cheng, Xiaolin, Chu, Xiang-Qiang, Curtis, Joseph E., Dadmun, Mark, Fenimore, Paul, Fushman, David, Gabel, Frank, Gupta, Kushol, Herberle, Frederick, Heinrich, Frank, Hong, Liang, Katsaras, John, Kelman, Zvi, Kharlampieva, Eugenia, Kneller, Gerald R., Kovalevsky, Andrey, Krueger, Susan, Langan, Paul, Lieberman, Raquel, Liu, Yun, Losche, Mathias, Lyman, Edward, Mao, Yimin, Marino, John, Mattos, Carla, Meilleur, Flora, Moody, Peter, Nickels, Jonathan D., O'Dell, William B., O'Neill, Hugh, Perez-Salas, Ursula, Peters, Judith, Petridis, Loukas, Sokolov, Alexei P., Stanley, Christopher, Wagner, Norman, Weinrich, Michael, Weiss, Kevin, Wymore, Troy, Zhang, Yang, and Smith, Jeremy C.

Published
2018

34. G Protein-GPCR Interaction Studied by SANS

Author

Soubias, Olivier, primary, Nickels, Jonathan D., additional, Yeliseev, Alexei, additional, Hines, Kirk G., additional, Teague, Walter E., additional, Northup, John, additional, Katsaras, John, additional, and Gawrisch, Klaus, additional

Published
2018
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35. Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane

Author

Nickels, Jonathan D., primary, Chatterjee, Sneha, additional, Mostofian, Barmak, additional, Stanley, Christopher B., additional, Ohl, Michael, additional, Zolnierczuk, Piotr, additional, Schulz, Roland, additional, Myles, Dean A. A., additional, Standaert, Robert F., additional, Elkins, James G., additional, Cheng, Xiaolin, additional, and Katsaras, John, additional

Published
2017
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37. Description of Hydration Water in Protein (GFP) Solution

Author

Perticaroli, Stefania, primary, Ehlers, Georg, additional, Stanley, Christopher, additional, Mamontov, Eugene, additional, O'Neill, Hugh, additional, Zhang, Qui, additional, Cheng, Xiaolin, additional, Myles, Dean A.A., additional, Katsaras, John, additional, and Nickels, Jonathan D., additional

Published
2017
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42. Subnanometer Structure of an Asymmetric Model Membrane: Interleaflet Coupling Influences Domain Properties

Author

Heberle, Frederick A., primary, Marquardt, Drew, additional, Doktorova, Milka, additional, Geier, Barbara, additional, Standaert, Robert F., additional, Heftberger, Peter, additional, Kollmitzer, Benjamin, additional, Nickels, Jonathan D., additional, Dick, Robert A., additional, Feigenson, Gerald W., additional, Katsaras, John, additional, London, Erwin, additional, and Pabst, Georg, additional

Published
2016
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43. Dynamics in Protein Powders on the Nanosecond–Picosecond Time Scale Are Dominated by Localized Motions

Author

Nickels, Jonathan D., García Sakai, Victoria, and Sokolov, Alexei P.

Abstract

We present analysis of nanosecond-picosecond dynamics of Green Fluorescence Protein (GFP) using neutron scattering data obtained on three spectrometers. GFP has a β-barrel structure that differs significantly from the structure of other globular proteins and is thought to result in a more rigid local environment. Despite this difference, our analysis reveals that the dynamics of GFP are similar to dynamics of other globular proteins such as lysozyme and myoglobin. We suggest that the same general concept of protein dynamics may be applicable to all these proteins. The dynamics of dry protein are dominated by methyl group rotations, while hydration facilitates localized diffusion-like motions in the protein. The latter has an extremely broad relaxation spectrum. The nanosecond–picosecond dynamics of both dry and hydrated GFP are localized to distances of ∼1–3.5 Å, in contrast to the longer range diffusion of hydration water.

Published
2024
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45. Mechanical Properties of Nanoscopic Lipid Domains

Author

Nickels, Jonathan D., primary, Cheng, Xiaolin, additional, Mostofian, Barmak, additional, Stanley, Christopher, additional, Lindner, Benjamin, additional, Heberle, Frederick A., additional, Perticaroli, Stefania, additional, Feygenson, Mikhail, additional, Egami, Takeshi, additional, Standaert, Robert F., additional, Smith, Jeremy C., additional, Myles, Dean A. A., additional, Ohl, Michael, additional, and Katsaras, John, additional

Published
2015
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48. Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid.

Author

PerticaroliCurrent affiliation: The Procter & Gamble Company Research and Development Mason OH 45040 USA. E-mail: perticaroli.s@pg.com, Stefania, Mostofian, Barmak, Ehlers, Georg, Neuefeind, Joerg C., Diallo, Souleymane O., Stanley, Christopher B., Daemen, Luke, Egami, Takeshi, Katsaras, John, Cheng, Xiaolin, and Nickels, Jonathan D.

Abstract

In liquids, the ability of neighboring molecules to rearrange and jostle past each other is directly related to viscosity, the property which describes the propensity to flow. The presence of hydrogen bonds (H-bonds) complicates the molecular scale picture of viscosity. H-Bonds are attractive, directional interactions between molecules which, in some cases, result in transient network structures. In this work, we use experimental and computational methods to demonstrate that the timescale of H-bond network reorganization is the dominant dynamical timescale associated with viscosity for the case of the model H-bonding liquid n-methylacetamide (NMA). This molecule is a peptide analog which forms a transient linear H-bond network. Individual H-bond lifetimes and dynamical fluctuations were observed on the timescale of 1.5 ps, while collective motions and the longest lived population of H-bond partner lifetimes were observed on the order of 20 ps, in agreement with the Maxwell relaxation time. This identifies a mechanism which may aid in understanding the emergence of various complex phenomena arising from transient molecular structures, with implications ranging from the internal dynamics of proteins, to the glass transition, to better understanding the origins of the unique properties of H-bonding liquids. [ABSTRACT FROM AUTHOR]

Published
2017
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