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Journal articles on the topic 'Crowded lipid membrane biophysics'

Author: Grafiati

Published: 6 September 2023

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1

Erwin, Nelli, Satyajit Patra, Mridula Dwivedi, Katrin Weise, and Roland Winter. "Influence of isoform-specific Ras lipidation motifs on protein partitioning and dynamics in model membrane systems of various complexity." Biological Chemistry 398, no. 5-6 (May 1, 2017): 547–63. http://dx.doi.org/10.1515/hsz-2016-0289.

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Abstract The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid mixtures, heterogeneous raft model membranes up to complex native-like lipid mixtures (GPMVs) in the absence and presence of integral membrane proteins have been explored in the last decade in a combined chemical-biological and biophysical approach. These studies have revealed pronounced isoform-specific differences regarding the lateral distribution in membranes and formation of protein-rich membrane domains. In this context, we will also discuss the effects of lipid head group structure and charge density on the partitioning behavior of the lipoproteins. Moreover, the dynamic properties of N-Ras and K-Ras4B have been studied in different model membrane systems and native-like crowded milieus. Addition of crowding agents such as Ficoll and its monomeric unit, sucrose, gradually favors clustering of Ras proteins in forming small oligomers in the bulk; only at very high crowder concentrations association is disfavored.

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2

Arnarez, C., S. J. Marrink, and X. Periole. "Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes." Chemical Science 7, no. 7 (2016): 4435–43. http://dx.doi.org/10.1039/c5sc04664e.

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We reveal the molecular mechanism by which cardiolipin glues respiratory complexes into supercomplexes. This mechanism defines a new biophysico-chemical pathway of protein–lipid interplay, with broad general implications for the dynamic organization of crowded cell membranes.

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3

Kessler, Michael S., and Susan Gillmor. "Lipid Membrane Phase Dynamics." Biophysical Journal 104, no. 2 (January 2013): 248a. http://dx.doi.org/10.1016/j.bpj.2012.11.1398.

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4

Nawrocki, Grzegorz, Wonpil Im, Yuji Sugita, and Michael Feig. "Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending." Proceedings of the National Academy of Sciences 116, no. 49 (November 18, 2019): 24562–67. http://dx.doi.org/10.1073/pnas.1910771116.

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Atomistic molecular dynamics simulations of concentrated protein solutions in the presence of a phospholipid bilayer are presented to gain insights into the dynamics and interactions at the cytosol–membrane interface. The main finding is that proteins that are not known to specifically interact with membranes are preferentially excluded from the membrane, leaving a depletion zone near the membrane surface. As a consequence, effective protein concentrations increase, leading to increased protein contacts and clustering, whereas protein diffusion becomes faster near the membrane for proteins that do occasionally enter the depletion zone. Since protein–membrane contacts are infrequent and short-lived in this study, the structure of the lipid bilayer remains largely unaffected by the crowded protein solution, but when proteins do contact lipid head groups, small but statistically significant local membrane curvature is induced, on average.

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5

Fischer, Wolfgang B. "Assembling Within The Lipid Membrane: Viral Membrane Proteins." Biophysical Journal 96, no. 3 (February 2009): 338a—339a. http://dx.doi.org/10.1016/j.bpj.2008.12.3823.

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6

Mitchison-Field, Lorna MY, and Brittany J. Belin. "Bacterial lipid biophysics and membrane organization." Current Opinion in Microbiology 74 (August 2023): 102315. http://dx.doi.org/10.1016/j.mib.2023.102315.

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7

Ho, Chian Sing, Nawal K. Khadka, Fengyu She, Jianfeng Cai, and Jianjun Pan. "Polyglutamine aggregates impair lipid membrane integrity and enhance lipid membrane rigidity." Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, no. 4 (April 2016): 661–70. http://dx.doi.org/10.1016/j.bbamem.2016.01.016.

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8

Wang, Hongyin, Kandice R. Levental, Joseph H. Lorent, Adhvikaa A. Revathi, and Ilya Levental. "Lipid scrambling facilitates membrane vesiculation through decreasing membrane stiffness." Biophysical Journal 122, no. 3 (February 2023): 22a—23a. http://dx.doi.org/10.1016/j.bpj.2022.11.347.

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9

Hoopes, Matthew I., Roland Faller, and Marjorie L. Longo. "Membrane Curvature Modeling and Lipid Organization in Supported Lipid Bilayers." Biophysical Journal 98, no. 3 (January 2010): 78a—79a. http://dx.doi.org/10.1016/j.bpj.2009.12.445.

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10

Sodt, Alexander J., Olivier Soubias, Klaus Gawrisch, and Richard W. Pastor. "Lipid-Lipid Coupling to Membrane Curvature by Simulation and NMR." Biophysical Journal 110, no. 3 (February 2016): 243a. http://dx.doi.org/10.1016/j.bpj.2015.11.1340.

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11

Ericsson, Maria, Victoria von Saucken, Andrew J. Newman, Lena Doehr, Camilla Hoesch, Tae-Eun Kim, and Ulf Dettmer. "Crowded organelles, lipid accumulation, and abnormal membrane tubulation in cellular models of enhanced α-synuclein membrane interaction." Brain Research 1758 (May 2021): 147349. http://dx.doi.org/10.1016/j.brainres.2021.147349.

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12

Duncan, Anna L., Heidi Koldsø, Tyler Reddy, Jean Helie, and Mark S. P. Sansom. "Lipid Composition Modulates Membrane Protein Clustering." Biophysical Journal 110, no. 3 (February 2016): 81a. http://dx.doi.org/10.1016/j.bpj.2015.11.499.

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13

Sapp, Kayla, and Alexander J. Sodt. "Analyzing membrane mechanics and lipid dynamics using lateral lipid density fluctuations." Biophysical Journal 122, no. 3 (February 2023): 362a. http://dx.doi.org/10.1016/j.bpj.2022.11.2002.

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14

Snead, Wilton T., Wade F. Zeno, Grace Kago, Ryan W. Perkins, J. Blair Richter, Chi Zhao, Eileen M. Lafer, and Jeanne C. Stachowiak. "BAR scaffolds drive membrane fission by crowding disordered domains." Journal of Cell Biology 218, no. 2 (November 30, 2018): 664–82. http://dx.doi.org/10.1083/jcb.201807119.

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Cellular membranes are continuously remodeled. The crescent-shaped bin-amphiphysin-rvs (BAR) domains remodel membranes in multiple cellular pathways. Based on studies of isolated BAR domains in vitro, the current paradigm is that BAR domain–containing proteins polymerize into cylindrical scaffolds that stabilize lipid tubules. But in nature, proteins that contain BAR domains often also contain large intrinsically disordered regions. Using in vitro and live cell assays, here we show that full-length BAR domain–containing proteins, rather than stabilizing membrane tubules, are instead surprisingly potent drivers of membrane fission. Specifically, when BAR scaffolds assemble at membrane surfaces, their bulky disordered domains become crowded, generating steric pressure that destabilizes lipid tubules. More broadly, we observe this behavior with BAR domains that have a range of curvatures. These data suggest that the ability to concentrate disordered domains is a key driver of membrane remodeling and fission by BAR domain–containing proteins.

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15

Chawla, Udeep, Suchithranga M. D. C. Perera, Adam A. Wallace, James W. Lewis, Blake Mertz, and Michael F. Brown. "Membrane Bilayer Environment Influences Thermodynamics of Rhodopsin Membrane Protein-Lipid Interactions." Biophysical Journal 104, no. 2 (January 2013): 434a. http://dx.doi.org/10.1016/j.bpj.2012.11.2413.

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16

Hwang, Hyeondo (Luke), Peter J. Chung, Alessandra Leong, and Ka Yee C. Lee. "Understanding How Alpha-Synuclein Modifies Steric Interactions of Silica Supported Lipid Bilayers in Crowded Environments." Biophysical Journal 116, no. 3 (February 2019): 509a. http://dx.doi.org/10.1016/j.bpj.2018.11.2745.

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17

Cooke, Ira R., and Markus Deserno. "Coupling between Lipid Shape and Membrane Curvature." Biophysical Journal 91, no. 2 (July 2006): 487–95. http://dx.doi.org/10.1529/biophysj.105.078683.

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18

Edidin, Michael. "Switching Sides: The Actin/Membrane Lipid Connection." Biophysical Journal 91, no. 11 (December 2006): 3963. http://dx.doi.org/10.1529/biophysj.106.094078.

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19

Ho, C., and C. D. Stubbs. "Hydration at the membrane protein-lipid interface." Biophysical Journal 63, no. 4 (October 1992): 897–902. http://dx.doi.org/10.1016/s0006-3495(92)81671-5.

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20

Camp, Philip, Jacek Biernat, Eckhard Mandelkow, Jaroslaw Majewski, and Eva Y. Chi. "Lipid-Membrane Mediated Tau Misfolding and Aggregation." Biophysical Journal 98, no. 3 (January 2010): 239a—240a. http://dx.doi.org/10.1016/j.bpj.2009.12.1300.

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21

Ranganathan, Radha, and Jasmeet Singh. "Characterization of Membrane Bound Phospholipase-Lipid Complex." Biophysical Journal 98, no. 3 (January 2010): 448a—449a. http://dx.doi.org/10.1016/j.bpj.2009.12.2439.

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22

Lai, Alex L., and David S. Cafiso. "Synaptotagmin Perturbs Lipid Structure of Membrane Bilayers." Biophysical Journal 98, no. 3 (January 2010): 483a. http://dx.doi.org/10.1016/j.bpj.2009.12.2629.

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23

Rostovtseva, Tatiana K., Michael Weinrich, Meng-Yang Chen, Kely L. Sheldon, and Sergey M. Bezrukov. "Membrane Lipid Composition Regulates Tubulin-VDAC Interaction." Biophysical Journal 100, no. 3 (February 2011): 42a. http://dx.doi.org/10.1016/j.bpj.2010.12.429.

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24

Last, Julie A., Tina A. Waggoner, and Darryl Y. Sasaki. "Lipid Membrane Reorganization Induced by Chemical Recognition." Biophysical Journal 81, no. 5 (November 2001): 2737–42. http://dx.doi.org/10.1016/s0006-3495(01)75916-4.

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25

Ohki, Shinpei, and Yoichi Takato. "A Molecular Mechanism of Lipid Membrane Fusion." Biophysical Journal 104, no. 2 (January 2013): 92a. http://dx.doi.org/10.1016/j.bpj.2012.11.550.

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26

Marte, Joseph A., Dalia Hassan, and Frank X. Vazquez. "Dynamin pH Domain Interactions with Lipid Membrane." Biophysical Journal 116, no. 3 (February 2019): 203a. http://dx.doi.org/10.1016/j.bpj.2018.11.1124.

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27

Dietel, Lisa, Louma Kalie, and Heiko Heerklotz. "Lipid Scrambling Induced by Membrane-Active Substances." Biophysical Journal 119, no. 4 (August 2020): 767–79. http://dx.doi.org/10.1016/j.bpj.2020.07.004.

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28

Izumi, Kayano, Keisuke Shimizu, and Ryuji Kawano. "Lipid Membrane Deformation Induced by Transmembrane Peptides." Biophysical Journal 118, no. 3 (February 2020): 231a. http://dx.doi.org/10.1016/j.bpj.2019.11.1368.

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29

Disalvo, E. Anibal, A. Sebastian Rosa, Jimena P. Cejas, and María de los A. Frias. "Water as a Link between Membrane and Colloidal Theories for Cells." Molecules 27, no. 15 (August 5, 2022): 4994. http://dx.doi.org/10.3390/molecules27154994.

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This review is an attempt to incorporate water as a structural and thermodynamic component of biomembranes. With this purpose, the consideration of the membrane interphase as a bidimensional hydrated polar head group solution, coupled to the hydrocarbon region allows for the reconciliation of two theories on cells in dispute today: one considering the membrane as an essential part in terms of compartmentalization, and another in which lipid membranes are not necessary and cells can be treated as a colloidal system. The criterium followed is to describe the membrane state as an open, non-autonomous and responsive system using the approach of Thermodynamic of Irreversible Processes. The concept of an open/non-autonomous membrane system allows for the visualization of the interrelationship between metabolic events and membrane polymorphic changes. Therefore, the Association Induction Hypothesis (AIH) and lipid properties interplay should consider hydration in terms of free energy modulated by water activity and surface (lateral) pressure. Water in restricted regions at the lipid interphase has thermodynamic properties that explain the role of H-bonding networks in the propagation of events between membrane and cytoplasm that appears to be relevant in the context of crowded systems.

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30

Marassi, Francesca M. "NMR Structural Studies of Membrane Proteins in Lipid Micelles and Lipid Bilayers." Biophysical Journal 98, no. 3 (January 2010): 209a. http://dx.doi.org/10.1016/j.bpj.2009.12.1123.

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31

Weber, Florian, Herbert Stangl, Taras Synch, Birgit Plochberger, and Erdinc Sezgin. "HDL-membrane-interactions are highly influenced by the target membrane-lipid composition." Biophysical Journal 122, no. 3 (February 2023): 222a. http://dx.doi.org/10.1016/j.bpj.2022.11.1320.

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32

Mukhin, Sergei I., and Boris B. Kheyfets. "Inter-Domain Line Tension Induced by Hydrophobic Lipid Tails in a Lipid Membrane." Biophysical Journal 100, no. 3 (February 2011): 493a. http://dx.doi.org/10.1016/j.bpj.2010.12.2890.

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33

Sandberg, Jesse, and Grace H. Brannigan. "Coronavirus Envelope Protein: Lipid Sensitivity and Membrane Bending." Biophysical Journal 120, no. 3 (February 2021): 227a. http://dx.doi.org/10.1016/j.bpj.2020.11.1513.

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34

Nylander, Tommy, Viveka Alfredsson, Pierandrea Lo Nostro, and Barry Ninham. "Morphologies and structure of brain lipid membrane dispersions." Biophysical Journal 121, no. 3 (February 2022): 216a. http://dx.doi.org/10.1016/j.bpj.2021.11.1659.

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35

Morgenstein, Lion, Merav Tsubary, Ayelet Atkins, Asaf Grupi, and Shimon Weiss. "Controlled membrane interactions by lipid coated quantum dots." Biophysical Journal 121, no. 3 (February 2022): 73a. http://dx.doi.org/10.1016/j.bpj.2021.11.2335.

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36

Hager-Barnard, Elizabeth A., Benjamin D. Almquist, and Nicholas A. Melosh. "Lipid Membrane Penetration Forces from AFM Force Spectroscopy." Biophysical Journal 96, no. 3 (February 2009): 389a. http://dx.doi.org/10.1016/j.bpj.2008.12.2909.

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37

Fiedler, Steven L., and Angela Violi. "Simulation of Nanoparticle Permeation through a Lipid Membrane." Biophysical Journal 99, no. 1 (July 2010): 144–52. http://dx.doi.org/10.1016/j.bpj.2010.03.039.

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38

Heimburg, Thomas. "The Physics of Nerves and Lipid Membrane Channels." Biophysical Journal 100, no. 3 (February 2011): 4a. http://dx.doi.org/10.1016/j.bpj.2010.11.072.

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39

Gopalakrishnan, Gopakumar, Patricia T. Yam, Isabelle Rouiller, David R. Colman, and R. Bruce Lennox. "Lipid Membrane Domains Promote In-Vitro Presynapse Formation." Biophysical Journal 100, no. 3 (February 2011): 507a. http://dx.doi.org/10.1016/j.bpj.2010.12.2966.

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40

Kurad, Dieter, Gunnar Jeschke, and Derek Marsh. "Lipid Membrane Polarity Profiles by High-Field EPR." Biophysical Journal 85, no. 2 (August 2003): 1025–33. http://dx.doi.org/10.1016/s0006-3495(03)74541-x.

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41

Goose, Joseph E., Matthieu Chavent, and Mark S. P. Sansom. "How Instantaneous Lipid Flows Influence Membrane Protein Diffusion." Biophysical Journal 104, no. 2 (January 2013): 426a. http://dx.doi.org/10.1016/j.bpj.2012.11.2372.

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42

Maftouni, Negin, Mehryar Amininassab, and Mansour Vali. "Physical Properties of an Asymmetric Nanobio Lipid Membrane." Biophysical Journal 104, no. 2 (January 2013): 80a. http://dx.doi.org/10.1016/j.bpj.2012.11.485.

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43

Kelley, Elizabeth G., Moritz P. K. Frewein, Georg Pabst, and Michihiro Nagao. "Nanoscale membrane dynamics in chain asymmetric lipid bilayers." Biophysical Journal 122, no. 3 (February 2023): 22a. http://dx.doi.org/10.1016/j.bpj.2022.11.346.

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44

Kim, Siyoung. "Lipid backmapping and its application to membrane builder." Biophysical Journal 122, no. 3 (February 2023): 422a. http://dx.doi.org/10.1016/j.bpj.2022.11.2287.

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45

Rachid Thiam, Abdou. "Regulation of Lipid Droplet Formation by Membrane Tension." Biophysical Journal 114, no. 3 (February 2018): 562a—563a. http://dx.doi.org/10.1016/j.bpj.2017.11.3076.

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46

Amos, Sarah-Beth, Antreas C. Kalli, Jiye Shi, and Mark S. P. Sansom. "Multiscale Simulations of Membrane Recognition by Lipid Kinases." Biophysical Journal 114, no. 3 (February 2018): 613a. http://dx.doi.org/10.1016/j.bpj.2017.11.3753.

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47

Li, Feng, R. Venkat Kalyana Sundaram, Jeff Coleman, Shyam S. Krishnakumar, Frederic Pincet, and James Rothman. "Munc13 Clusters Capture Vesicles to Lipid Bilayer Membrane." Biophysical Journal 118, no. 3 (February 2020): 344a. http://dx.doi.org/10.1016/j.bpj.2019.11.1990.

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48

Munguía, Irene Jiménez, Arsenii Fedorov, Ivan Meshkov, Yuri Ermakov, Yulia Gorbunova, and Valerij Sokolov. "Adsorption and Permeation of Porphyrins through Lipid Membrane." Biophysical Journal 118, no. 3 (February 2020): 78a. http://dx.doi.org/10.1016/j.bpj.2019.11.598.

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49

Drolle, Elizabeth, Norbert Kučerka, Youngjik Choi, John Katsaras, and Zoya Leonenko. "Melatonin Counteracts Cholesterol's Effects on Lipid Membrane Structure." Biophysical Journal 104, no. 2 (January 2013): 182a. http://dx.doi.org/10.1016/j.bpj.2012.11.1022.

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50

Hagerty, Nicholas, Edwin Li, and Kalina Hristova. "Integration of Plasma Membrane in Supported Lipid Bilayers." Biophysical Journal 96, no. 3 (February 2009): 329a. http://dx.doi.org/10.1016/j.bpj.2008.12.1656.

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