1
|
Gamage YI, Wadumesthri Y, Gutiérrez HR, Voronine DV, Pan J. The impact of transmembrane peptides on lipid bilayer structure and mechanics: A study of the transmembrane domain of the influenza A virus M2 protein. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184373. [PMID: 39047857 DOI: 10.1016/j.bbamem.2024.184373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/15/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Transmembrane peptides play important roles in many biological processes by interacting with lipid membranes. This study investigates how the transmembrane domain of the influenza A virus M2 protein, M2TM, affects the structure and mechanics of model lipid bilayers. Atomic force microscopy (AFM) imaging revealed small decreases in bilayer thickness with increasing peptide concentrations. AFM-based force spectroscopy experiments complemented by theoretical model analysis demonstrated significant decreases in bilayer's Young's modulus (E) and lateral area compressibility modulus (KA). This suggests that M2TM disrupts the cohesive interactions between neighboring lipid molecules, leading to a decrease in both the bilayer's resistance to indentation (E) and its ability to resist lateral compression/expansion (KA). The large decreases in bilayer elastic parameters (i.e., E and KA) contrast with small changes in bilayer thickness, implying that bilayer mechanics are not solely dictated by bilayer thickness in the presence of transmembrane peptides. The observed significant reduction in bilayer mechanical properties suggests a softening effect on the bilayer, potentially facilitating membrane curvature generation, a crucial step for M2-mediated viral budding. In parallel, our Raman spectroscopy revealed small but statistically significant changes in hydrocarbon chain vibrational dynamics, indicative of minor disordering in lipid chain conformation. Our findings provide useful insights into the complex interplay between transmembrane peptides and lipid bilayers, highlighting the significance of peptide-lipid interactions in modulating membrane structure, mechanics, and molecular dynamics.
Collapse
Affiliation(s)
| | - Yasinthara Wadumesthri
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | | | - Dmitri V Voronine
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America.
| |
Collapse
|
2
|
Lin G, Rennie M, Adeeko A, Scarlata S. The role of calcium in neuronal membrane tension and synaptic plasticity. Biochem Soc Trans 2024; 52:937-945. [PMID: 38533899 DOI: 10.1042/bst20231518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024]
Abstract
Calcium is a primary second messenger that plays a role in cellular functions including growth, movement and responses to drugs. The role that calcium plays in mediating communication between neurons by synaptic vesicle release is well established. This review focuses on the dependence of the physical properties of neuronal plasma membranes on calcium levels. After describing the key features of synaptic plasticity, we summarize the general role of calcium in cell function and the signaling pathways responsible for intracellular increase in calcium levels. We then present findings showing that increases in intracellular calcium levels cause neurites to contract and break synaptic connections by changes in membrane tension.
Collapse
Affiliation(s)
- Guanyu Lin
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA 01609, U.S.A
| | - Madison Rennie
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA 01609, U.S.A
| | - Ayobami Adeeko
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA 01609, U.S.A
| | - Suzanne Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA 01609, U.S.A
| |
Collapse
|
3
|
Kharche S, Yadav M, Hande V, Prakash S, Sengupta D. Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model. J Chem Inf Model 2024; 64:837-850. [PMID: 38291973 DOI: 10.1021/acs.jcim.3c00802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The Martini coarse-grain force-field has emerged as an important framework to probe cellular processes at experimentally relevant time- and length-scales. However, the recently developed version, the Martini3 force-field with the implemented Go̅ model (Martini3Go̅), as well as previous variants of the Martini model have not been benchmarked and rigorously tested for globular proteins. In this study, we consider three globular proteins, ubiquitin, lysozyme, and cofilin, and compare protein dynamics and hydration with observables from experiments and all-atom simulations. We show that the Martini3Go̅ model is able to accurately model the structural and dynamic features of small globular proteins. Overall, the structural integrity of the proteins is maintained, as validated by contact maps, radii of gyration (Rg), and SAXS profiles. The chemical shifts predicted from the ensemble sampled in the simulations are consistent with the experimental data. Further, a good match is observed in the protein-water interaction energetics, and the hydration levels of the residues are similar to atomistic simulations. However, the protein-water interaction dynamics is not accurately represented and appears to depend on the protein structural complexity, residue specificity, and water dynamics. Our work is a step toward testing and assessing the Martini3Go̅ model and provides insights into future efforts to refine Martini models with improved solvation effects and better correspondence to the underlying all-atom systems.
Collapse
Affiliation(s)
- Shalmali Kharche
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Manjul Yadav
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Vrushali Hande
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shikha Prakash
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
4
|
Cieślak D, Kabelka I, Bartuzi D. Molecular Dynamics Simulations in Protein-Protein Docking. Methods Mol Biol 2024; 2780:91-106. [PMID: 38987465 DOI: 10.1007/978-1-0716-3985-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Concerted interactions between all the cell components form the basis of biological processes. Protein-protein interactions (PPIs) constitute a tremendous part of this interaction network. Deeper insight into PPIs can help us better understand numerous diseases and lead to the development of new diagnostic and therapeutic strategies. PPI interfaces, until recently, were considered undruggable. However, it is now believed that the interfaces contain "hot spots," which could be targeted by small molecules. Such a strategy would require high-quality structural data of PPIs, which are difficult to obtain experimentally. Therefore, in silico modeling can complement or be an alternative to in vitro approaches. There are several computational methods for analyzing the structural data of the binding partners and modeling of the protein-protein dimer/oligomer structure. The major problem with in silico structure prediction of protein assemblies is obtaining sufficient sampling of protein dynamics. One of the methods that can take protein flexibility and the effects of the environment into account is Molecular Dynamics (MD). While sampling of the whole protein-protein association process with plain MD would be computationally expensive, there are several strategies to harness the method to PPI studies while maintaining reasonable use of resources. This chapter reviews known applications of MD in the PPI investigation workflows.
Collapse
Affiliation(s)
- Dominika Cieślak
- Laboratory of Plant Protein Phosphorylation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ivo Kabelka
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Damian Bartuzi
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland.
| |
Collapse
|
5
|
Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
Collapse
Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
6
|
Ma L, Li X, Petersen RB, Peng A, Huang K. Probing the interactions between amyloidogenic proteins and bio-membranes. Biophys Chem 2023; 296:106984. [PMID: 36889133 DOI: 10.1016/j.bpc.2023.106984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.
Collapse
Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China; Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China.
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
7
|
Biochemical and Biophysical Characterization of the Caveolin-2 Interaction with Membranes and Analysis of the Protein Structural Alteration by the Presence of Cholesterol. Int J Mol Sci 2022; 23:ijms232315203. [PMID: 36499524 PMCID: PMC9736327 DOI: 10.3390/ijms232315203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Caveolin-2 is a protein suitable for the study of interactions of caveolins with other proteins and lipids present in caveolar lipid rafts. Caveolin-2 has a lower tendency to associate with high molecular weight oligomers than caveolin-1, facilitating the study of its structural modulation upon association with other proteins or lipids. In this paper, we have successfully expressed and purified recombinant human caveolin-2 using E. coli. The structural changes of caveolin-2 upon interaction with a lipid bilayer of liposomes were characterized using bioinformatic prediction models, circular dichroism, differential scanning calorimetry, and fluorescence techniques. Our data support that caveolin-2 binds and alters cholesterol-rich domains in the membranes through a CARC domain, a type of cholesterol-interacting domain in its sequence. The far UV-CD spectra support that the purified protein keeps its folding properties but undergoes a change in its secondary structure in the presence of lipids that correlates with the acquisition of a more stable conformation, as shown by differential scanning calorimetry experiments. Fluorescence experiments using egg yolk lecithin large unilamellar vesicles loaded with 1,6-diphenylhexatriene confirmed that caveolin-2 adsorbs to the membrane but only penetrates the core of the phospholipid bilayer if vesicles are supplemented with 30% of cholesterol. Our study sheds light on the caveolin-2 interaction with lipids. In addition, we propose that purified recombinant caveolin-2 can provide a new tool to study protein-lipid interactions within caveolae.
Collapse
|
8
|
Gupta S, Mandal T. Simulation study of domain formation in a model bacterial membrane. Phys Chem Chem Phys 2022; 24:18133-18143. [PMID: 35856570 DOI: 10.1039/d2cp01873j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental studies revealed that functional membrane microdomains (FMMs) are formed in prokaryotic cells which are structurally and functionally similar to the lipid rafts formed in eukaryotic cells. In this study, we employ coarse-grained molecular dynamics simulations to investigate the mechanism of domain formation and its physiochemical properties in a model methicillin-resistant staphylococcus aureus (MRSA) cell membrane. We find that domains are formed through lateral segregation of staphyloxanthin (STX), a carotenoid which shields the bacteria from the host's immune because of its antioxidant nature. Simulation results suggest that membrane integrity increases with the size of the domain, which is assessed by computing bond order parameter of the lipid tails, membrane expansion modulus and water permeability across the membrane. Various membrane domain proteins such as flotillin-like protein floA and penicillin binding protein (PBP2a) preferentially bind with the STX and accumulate in the membrane domain which is consistent with the recent experimental results.
Collapse
Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| |
Collapse
|
9
|
Lavagna E, Bochicchio D, De Marco AL, Güven ZP, Stellacci F, Rossi G. Ion-bridges and lipids drive aggregation of same-charge nanoparticles on lipid membranes. NANOSCALE 2022; 14:6912-6921. [PMID: 35451442 PMCID: PMC9109710 DOI: 10.1039/d1nr08543c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/14/2022] [Indexed: 05/19/2023]
Abstract
The control of the aggregation of biomedical nanoparticles (NP) in physiological conditions is crucial as clustering may change completely the way they interact with the biological environment. Here we show that Au nanoparticles, functionalized by an anionic, amphiphilic shell, spontaneously aggregate in fluid zwitterionic lipid bilayers. We use molecular dynamics and enhanced sampling techniques to disentangle the short-range and long-range driving forces of aggregation. At short inter-particle distances, ion-mediated, charge-charge interactions (ion bridging) stabilize the formation of large NP aggregates, as confirmed by cryo-electron microscopy. Lipid depletion and membrane curvature are the main membrane deformations driving long-range NP-NP attraction. Ion bridging, lipid depletion, and membrane curvature stem from the configurational flexibility of the nanoparticle shell. Our simulations show, more in general, that the aggregation of same-charge membrane inclusions can be expected as a result of intrinsically nanoscale effects taking place at the NP-NP and NP-bilayer soft interfaces.
Collapse
Affiliation(s)
- Enrico Lavagna
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| | - Davide Bochicchio
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| | - Anna L De Marco
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| | - Zekiye P Güven
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Bioengineering Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giulia Rossi
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| |
Collapse
|
10
|
Hao B, Zhou W, Theg SM. Hydrophobic mismatch is a key factor in protein transport across lipid bilayer membranes via the Tat pathway. J Biol Chem 2022; 298:101991. [PMID: 35490783 PMCID: PMC9207671 DOI: 10.1016/j.jbc.2022.101991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022] Open
Abstract
The twin-arginine translocation (Tat) pathway transports folded proteins across membranes in bacteria, thylakoids, plant mitochondria, and archaea. In most species, the active Tat machinery consists of three independent subunits: TatA, TatB, and TatC. TatA and TatB possess short transmembrane alpha helices (TMHs), both of which are only 15 residues long in Escherichia coli. Such short TMHs cause a hydrophobic mismatch between Tat subunits and the membrane bilayer, although the functional significance of this mismatch is unclear. Here, we sought to address the functional importance of the hydrophobic mismatch in the Tat transport mechanism in E. coli. We conducted three different assays to evaluate the effect of TMH length mutants on Tat activity and observed that the TMHs of TatA and TatB appear to be evolutionarily tuned to 15 amino acids, with activity dropping off following any modification of this length. Surprisingly, TatA and TatB with as few as 11 residues in their TMHs can still insert into the membrane bilayer, albeit with a decline in membrane integrity. These findings support a model of Tat transport utilizing localized toroidal pores that form when the membrane bilayer is thinned to a critical threshold. In this context, we conclude that the 15-residue length of the TatA and TatB TMHs can be seen as a compromise between the need for some hydrophobic mismatch to allow the membrane to reversibly reach the threshold thinness required for toroidal pore formation and the permanently destabilizing effect of placing even shorter helices into these energy-transducing membranes.
Collapse
Affiliation(s)
- Binhan Hao
- Plant Biology Department, University of California, Davis, CA 95616
| | - Wenjie Zhou
- Plant Biology Department, University of California, Davis, CA 95616
| | - Steven M Theg
- Plant Biology Department, University of California, Davis, CA 95616.
| |
Collapse
|
11
|
Gong Y, Cao Z, Zhang Z, Liu R, Zhang F, Wei J, Yang Z. Chirality Inversion in Self-Assembled Nanocomposites Directed by Curvature-Mediated Interactions. Angew Chem Int Ed Engl 2022; 61:e202117406. [PMID: 34981650 DOI: 10.1002/anie.202117406] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Indexed: 11/05/2022]
Abstract
Nanoscale curvature-dependent interactions are of paramount importance in biological systems. Here, we report that nanoscale curvature plays an important role in regulating the chirality of self-assembled nanocomposites from chiral organic molecules and achiral nanoparticles. Specifically, we show that the supramolecular chirality of the nanocomposites markedly depends on the nanoparticle curvature, where small-sized nanoparticles of high curvature and large-sized nanoparticles of low curvature lead to nanocomposites with opposite chirality. Quantitative kinetic experiments and molecular dynamics simulations reveal that nanoparticle curvature plays a key role in promoting the pre-nucleation oligomerization of chiral molecules, which consequently regulates the supramolecular chirality of the nanocomposites. We anticipate that this study will aid in rational design of an artificial cooperative system giving rise to emergent assembling phenomena that can be surprisingly rich and often cannot be understood by studying the conventional noncooperative systems.
Collapse
Affiliation(s)
- Yanjun Gong
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| | - Zhaozhen Cao
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| | - Zongze Zhang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| | - Rongjuan Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| | - Fenghua Zhang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| | - Zhijie Yang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of MOE, Shandong University, Jinan, 250100, P. R. China
| |
Collapse
|
12
|
Kluge C, Pöhnl M, Böckmann RA. Spontaneous local membrane curvature induced by transmembrane proteins. Biophys J 2022; 121:671-683. [PMID: 35122737 PMCID: PMC8943716 DOI: 10.1016/j.bpj.2022.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/13/2022] [Accepted: 01/28/2022] [Indexed: 11/26/2022] Open
Abstract
The (local) curvature of cellular membranes acts as a driving force for the targeting of membrane-associated proteins to specific membrane domains, as well as a sorting mechanism for transmembrane proteins, e.g., by accumulation in regions of matching spontaneous curvature. The latter measure was previously experimentally employed to study the curvature induced by the potassium channel KvAP and by aquaporin AQP0. However, the direction of the reported spontaneous curvature levels as well as the molecular driving forces governing the membrane curvature induced by these integral transmembrane proteins could not be addressed experimentally. Here, using both coarse-grained and atomistic molecular dynamics (MD) simulations, we report induced spontaneous curvature values for the homologous potassium channel Kv 1.2/2.1 Chimera (KvChim) and AQP0 embedded in unrestrained lipid bicelles that are in very good agreement with experiment. Importantly, the direction of curvature could be directly assessed from our simulations: KvChim induces a strong positive membrane curvature (≈0.036 nm-1) whereas AQP0 causes a comparably small negative curvature (≈-0.019 nm-1). Analyses of protein-lipid interactions within the bicelle revealed that the potassium channel shapes the surrounding membrane via structural determinants. Differences in shape of the protein-lipid interface of the voltage-gating domains between the extracellular and cytosolic membrane leaflets induce membrane stress and thereby promote a protein-proximal membrane curvature. In contrast, the water pore AQP0 displayed a high structural stability and an only faint effect on the surrounding membrane environment that is connected to its wedge-like shape.
Collapse
Affiliation(s)
- Christoph Kluge
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Matthias Pöhnl
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany,National Center for High-Performance Computing Erlangen (NHR@FAU), Erlangen, Germany,Corresponding author
| |
Collapse
|
13
|
Gong Y, Cao Z, Zhang Z, Liu R, Zhang F, Wei J, Yang Z. Chirality Inversion in Self‐Assembled Nanocomposites Directed by Curvature‐Mediated Interactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yanjun Gong
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| | - Zhaozhen Cao
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| | - Zongze Zhang
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| | - Rongjuan Liu
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| | - Fenghua Zhang
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| | - Zhijie Yang
- School of Chemistry and Chemical Engineering Key Laboratory of Colloid and Interface Chemistry of MOE Shandong University Jinan 250100 P. R. China
| |
Collapse
|
14
|
Muscolino E, Luoto LM, Brune W. Viral Induced Protein Aggregation: A Mechanism of Immune Evasion. Int J Mol Sci 2021; 22:ijms22179624. [PMID: 34502533 PMCID: PMC8431809 DOI: 10.3390/ijms22179624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 12/20/2022] Open
Abstract
Various intrinsic and extrinsic factors can interfere with the process of protein folding, resulting in protein aggregates. Usually, cells prevent the formation of aggregates or degrade them to prevent the cytotoxic effects they may cause. However, during viral infection, the formation of aggregates may serve as a cellular defense mechanism. On the other hand, some viruses are able to exploit the process of aggregate formation and removal to promote their replication or evade the immune response. This review article summarizes the process of cellular protein aggregation and gives examples of how different viruses exploit it. Particular emphasis is placed on the ribonucleotide reductases of herpesviruses and how their additional non-canonical functions in viral immune evasion are closely linked to protein aggregation.
Collapse
Affiliation(s)
- Elena Muscolino
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (E.M.); (L.-M.L.)
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Laura-Marie Luoto
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (E.M.); (L.-M.L.)
| | - Wolfram Brune
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (E.M.); (L.-M.L.)
- Correspondence: ; Tel.: +49-40-48051351
| |
Collapse
|
15
|
Marx DC, Fleming KG. Local Bilayer Hydrophobicity Modulates Membrane Protein Stability. J Am Chem Soc 2021; 143:764-772. [DOI: 10.1021/jacs.0c09412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Dagan C. Marx
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Karen G. Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
16
|
Gastaldo IP, Himbert S, Ram U, Rheinstädter MC. The Effects of Resveratrol, Caffeine, β-Carotene, and Epigallocatechin Gallate (EGCG) on Amyloid- β 25 -- 35 Aggregation in Synthetic Brain Membranes. Mol Nutr Food Res 2020; 64:e2000632. [PMID: 32981185 DOI: 10.1002/mnfr.202000632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 01/08/2023]
Abstract
SCOPE Alzheimer's disease is a neurodegenerative condition marked by the formation and aggregation of amyloid-β (Aβ) peptides. There exists, to this day, no cure or effective prevention for the disease; however, there is evidence that a healthy diet and certain food products can slow down first occurrence and progression. To investigate if food ingredients can interact with peptide aggregates, synthetic membranes that contained aggregates consisting of cross-β sheets of the membrane active fragment A β 25 -- 35 are prepared. METHODS AND RESULTS The impact of resveratrol, found in grapes, caffeine, the main active ingredient in coffee, β-carotene, found in orange fruits and vegetables, and epigallocatechin gallate (EGCG), a component of green tea, on the size and volume fraction of Aβ aggregates is studied using optical and fluorescence microscopy, X-ray diffraction, UV-vis spectroscopy, and molecular dynamics simulations. All compounds are membrane active and spontaneously partitioned in the synthetic brain membranes. While resveratrol and caffeine lead to membrane thickening and reduced membrane fluidity, β-carotene and EGCG preserve or increase fluidity. CONCLUSION Resveratrol and caffeine do not reduce the volume fraction of peptide aggregates while β-carotene significantly reduces plaque size. Interestingly, EGCG dissolves peptide aggregates and significantly decreases the corresponding cross-β and β-sheet signals.
Collapse
Affiliation(s)
- Isabella P Gastaldo
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, L8S 4M1, Canada.,Origins Institute, McMaster University, Hamilton, Ontario, L8S 4M1, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4M1, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, L8S 4M1, Canada.,Origins Institute, McMaster University, Hamilton, Ontario, L8S 4M1, Canada
| | - Udbhav Ram
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, L8S 4M1, Canada.,Origins Institute, McMaster University, Hamilton, Ontario, L8S 4M1, Canada
| | - Maikel C Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, L8S 4M1, Canada.,Origins Institute, McMaster University, Hamilton, Ontario, L8S 4M1, Canada
| |
Collapse
|
17
|
Direct and indirect cholesterol effects on membrane proteins with special focus on potassium channels. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158706. [DOI: 10.1016/j.bbalip.2020.158706] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022]
|
18
|
Highlighting the effect of amyloid beta assemblies on the mechanical properties and conformational stability of cell membrane. J Mol Graph Model 2020; 100:107670. [PMID: 32711259 DOI: 10.1016/j.jmgm.2020.107670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/05/2023]
Abstract
Alzheimer disease (AD) is the most common cause of dementia, characterized by a progressive decline in cognitive function due to the abnormal aggregation and deposition of Amyloid beta (Aβ) fibrils in the brain of patients. In this context, the molecular mechanisms of protein misfolding and aggregation that are known to induce significant biophysical alterations in cells, including destabilization of plasma membranes, remain partially unclear. Physical interaction between the Aβ assemblies and the membrane leads to the disruption of the cell membrane in multiple ways including, surface carpeting, generation of transmembrane channels and detergent-like membrane dissolution. Understanding the impact of amyloidogenic protein in different stages of aggregation with the plasma membrane, plays a crucial role to fully elucidate the pathological mechanisms of AD. Within this framework, computer simulations represent a powerful tool able to shed lights on the interactions governing the structural influence of Aβ proteins on biological membrane. In this study, molecular dynamics (MD) simulations have been performed in order to characterize how POPC bilayer conformational and mechanical properties are affected by the interaction with Aβ11-42 peptide, oligomer and fibril.
Collapse
|
19
|
Nyenhuis DA, Nilaweera TD, Niblo JK, Nguyen NQ, DuBay KH, Cafiso DS. Evidence for the Supramolecular Organization of a Bacterial Outer-Membrane Protein from In Vivo Pulse Electron Paramagnetic Resonance Spectroscopy. J Am Chem Soc 2020; 142:10715-10722. [PMID: 32452197 DOI: 10.1021/jacs.0c01754] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the outer membrane of Gram-negative bacteria, membrane proteins are thought to be organized into domains or islands that play a role in the segregation, movement, and turnover of membrane components. However, there is presently limited information on the structure of these domains or the molecular interactions that mediate domain formation. In the present work, the Escherichia coli outer membrane vitamin B12 transporter, BtuB, was spin-labeled, and double electron-electron resonance was used to measure the distances between proteins in intact cells. These data together with Monte Carlo simulations provide evidence for the presence of specific intermolecular contacts between BtuB monomers that could drive the formation of string-like oligomers. Moreover, the EPR data provide evidence for the location of the interacting interfaces and indicate that lipopolysaccharide mediates the contacts between BtuB monomers.
Collapse
|
20
|
Lavagna E, Barnoud J, Rossi G, Monticelli L. Size-dependent aggregation of hydrophobic nanoparticles in lipid membranes. NANOSCALE 2020; 12:9452-9461. [PMID: 32328605 DOI: 10.1039/d0nr00868k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aggregation of nanoparticles affects their reactivity, transport across biological membranes, uptake into cells, toxicity, and fate in the environment. In the case of membrane-embedded, hydrophobic nanoparticles the relationship between size and aggregation pattern is not well understood. Here, we explore this relationship for the case of spherically symmetrical nanoparticles using the MARTINI coarse-grained force field. We find that the free energy of dimerization depends strongly on nanoparticle size: the smallest molecules (mimicking C60 fullerene) aggregate only weakly, the largest ones form large three-dimensional aggregates causing major deformations in the host membrane, and the intermediate-sized particles show a tendency to form linear aggregates. Suppressing membrane undulations reduces very significantly aggregation, and substantially abolishes linear aggregation, suggesting a relationship between membrane curvature and aggregation geometry. At low concentration, when placed on membranes of variable curvature, the intermediate size nanoparticles move rapidly to high curvature regions - suggesting that they can sense membrane curvature. At high concentration, the same nanoparticles induce massive membrane deformations, without affecting the mechanical stability of the membrane - suggesting that they can generate membrane curvature.
Collapse
Affiliation(s)
- Enrico Lavagna
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy.
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Giulia Rossi
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy.
| | - Luca Monticelli
- Univ Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France.
| |
Collapse
|
21
|
Noh SY, Nash A, Notman R. The aggregation of striped nanoparticles in mixed phospholipid bilayers. NANOSCALE 2020; 12:4868-4881. [PMID: 31916561 DOI: 10.1039/c9nr07106g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The unique and adjustable properties of nanoparticles present enormous opportunities for their use as targeted drug delivery vectors. For example, nanoparticles functionalized with key surface ligands have been shown to pass through phospholipid bilayers without causing localised disruption. However, the further effects nanoparticles have on multi-component phospholipid bilayers remain unclear. We use coarse-grained computational models to investigate the structural properties of mixed phospholipid bilayers in the presence of ligand-functionalized nanoparticles. Model bilayers are composed of DPPC, DUPC, DFPC and cholesterol, and the nanoparticles are striped with a hydrophobic-ligand band and charged-ligand spherical caps. Our results show that nanoparticles aggregate near unsaturated phospholipid regions, phospholipid bilayer phase-separation is promoted in the presence of nanoparticles, and the heterogeneous components of a phospholipid bilayer play a significant role in the lateral organization of nanoparticles. This study highlights the need for considering the complexity of realistic phospholipid bilayers when optimising ligand functionalized nanoparticles for efficient drug delivery vectors.
Collapse
Affiliation(s)
- Sang Young Noh
- Department of Chemistry, University of Warwick, Coventry, UK.
| | - Anthony Nash
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Coventry, UK.
| |
Collapse
|
22
|
Jefferies D, Khalid S. Atomistic and coarse-grained simulations of membrane proteins: A practical guide. Methods 2020; 185:15-27. [PMID: 32084518 DOI: 10.1016/j.ymeth.2020.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are amphipathic macromolecules whose exposed hydrophobic surfaces promote interactions with lipid membranes. Membrane proteins are remarkably diverse in terms of chemical composition and correspondingly, their biological functions and general biophysical behavior. Conventional experimental techniques provide an approach to study specific properties of membrane proteins e.g. their surface features, the nature and abundance of stabilizing intramolecular forces, preferred bilayer orientation, and the characteristics of their annular lipid shells. Molecular modeling software-and in particular, the suite of molecular dynamics algorithms-enables a more comprehensive exploration of dynamic membrane protein behavior. Molecular dynamics methods enable users to produce stepwise trajectories of proteins on arbitrary spatiotemporal scales that enable the easy identification of dynamic interactions that are beyond the scope of conventional analytical techniques. This article explains the molecular dynamics theoretical framework and popular step-by-step approaches for simulating membrane proteins in planar, and to a lesser extent, nonplanar lipid geometries. We detail popular procedures and computational tools that produce well-packed configurations of lipids and proteins and additionally, the efficient molecular dynamics simulation algorithms that reproduce their dynamic interactions.
Collapse
Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK.
| |
Collapse
|
23
|
Rajagopal N, Irudayanathan FJ, Nangia S. Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface. Int J Mol Sci 2019; 20:E5583. [PMID: 31717316 PMCID: PMC6888702 DOI: 10.3390/ijms20225583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.
Collapse
Affiliation(s)
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
| |
Collapse
|
24
|
Grasso G, Leanza L, Morbiducci U, Danani A, Deriu MA. Aminoacid substitutions in the glycine zipper affect the conformational stability of amyloid beta fibrils. J Biomol Struct Dyn 2019; 38:3908-3915. [PMID: 31543007 DOI: 10.1080/07391102.2019.1671224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The aggregation of amyloid-beta peptides is associated with the pathogenesis of Alzheimer's disease. The hydrophobic core of the amyloid beta sequence contains a GxxxG repeated motif, called glycine zipper, which involves crucial residues for assuring stability and promoting the process of fibril formation. Mutations in this motif lead to a completely different oligomerization pathway and rate of fibril formation. In this work, we have tested G33L and G37L residue substitutions by molecular dynamics simulations. We found that both protein mutations may lead to remarkable changes in the fibril conformational stability. Results suggest the disruption of the glycine zipper as a possible strategy to reduce the aggregation propensity of amyloid beta peptides. On the basis of our data, further investigations may consider this key region as a binding site to design/discover novel effective inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Applied Sciences of Southern Switzerland (SUPSI), University of Italian Switzerland (USI), Manno, Switzerland
| | - Luigi Leanza
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
| | - Umberto Morbiducci
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Applied Sciences of Southern Switzerland (SUPSI), University of Italian Switzerland (USI), Manno, Switzerland
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
| |
Collapse
|
25
|
Nilaweera TD, Nyenhuis DA, Nakamoto RK, Cafiso DS. Disulfide Chaperone Knockouts Enable In Vivo Double Spin Labeling of an Outer Membrane Transporter. Biophys J 2019; 117:1476-1484. [PMID: 31582182 DOI: 10.1016/j.bpj.2019.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022] Open
Abstract
Recent advances in the application of electron paramagnetic resonance spectroscopy have demonstrated that it is possible to obtain structural information on bacterial outer membrane (OM) proteins in intact cells from extracellularly labeled cysteines. However, in the Escherichia coli OM B12 transport protein, BtuB, the double labeling of many cysteine pairs is not possible in a wild-type K12-derived E. coli strain. It has also not yet been possible to selectively label single or paired cysteines that face the periplasmic space. Here, we demonstrate that the inability to produce reactive cysteine residues in pairs is a result of the disulfide bond formation system, which functions to oxidize pairs of free-cysteine residues. Mutant strains that are dsbA or dsbB null facilitate labeling pairs of cysteines. Moreover, we demonstrate that the double labeling of sites on the periplasmic-facing surface of BtuB is possible using a dsbA null strain. BtuB is found to exhibit different structures and structural changes in the cell than it does in isolated OMs or reconstituted systems, and the ability to label and perform electron paramagnetic resonance in cells is expected to be applicable to a range of other bacterial OM proteins.
Collapse
Affiliation(s)
- Thushani D Nilaweera
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David A Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
| |
Collapse
|
26
|
Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G. Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nat Commun 2019; 10:2370. [PMID: 31147549 PMCID: PMC6542808 DOI: 10.1038/s41467-019-10345-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
FAM134B/RETREG1 is a selective ER-phagy receptor that regulates the size and shape of the endoplasmic reticulum. The structure of its reticulon-homology domain (RHD), an element shared with other ER-shaping proteins, and the mechanism of membrane shaping remain poorly understood. Using molecular modeling and molecular dynamics (MD) simulations, we assemble a structural model for the RHD of FAM134B. Through MD simulations of FAM134B in flat and curved membranes, we relate the dynamic RHD structure with its two wedge-shaped transmembrane helical hairpins and two amphipathic helices to FAM134B functions in membrane-curvature induction and curvature-mediated protein sorting. FAM134B clustering, as expected to occur in autophagic puncta, amplifies the membrane-shaping effects. Electron microscopy of in vitro liposome remodeling experiments support the membrane remodeling functions of the different RHD structural elements. Disruption of the RHD structure affects selective autophagy flux and leads to disease states. FAM134B/RETREG1 is a selective ER-phagy receptor that regulates the size and shape of the endoplasmic reticulum. Here authors use molecular modeling and molecular dynamics simulations to assemble a structural model for the reticulon-homology domain of FAM134B.
Collapse
Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Paolo Grumati
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Javier Garcia-Pardo
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology, Division for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Sissy Kalayil
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Wenbo Chen
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Mikhail Kudryashev
- Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.,Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theoder-Stern-Kai 7, 60590, Frankfurt am Main, Germany. .,Buchmann Institute of Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Straße 15, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438, Frankfurt am Main, Germany. .,Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| |
Collapse
|
27
|
Kahraman O, Haselwandter CA. Supramolecular organization of membrane proteins with anisotropic hydrophobic thickness. SOFT MATTER 2019; 15:4301-4310. [PMID: 31070658 DOI: 10.1039/c9sm00358d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Experiments have revealed that membrane proteins often self-assemble into locally ordered clusters. Such membrane protein lattices can play key roles in the functional organization of cell membranes. Membrane protein organization can be driven, at least in part, by bilayer-mediated elastic interactions between membrane proteins. For membrane proteins with anisotropic hydrophobic thickness, bilayer-mediated protein interactions are inherently directional. Here we establish general relations between anisotropy in membrane protein hydrophobic thickness and supramolecular membrane protein organization. We show that protein symmetry is distinctively reflected in the energy landscape of bilayer-mediated protein interactions, favoring characteristic lattice architectures of membrane protein clusters. We find that, in the presence of thermal fluctuations, anisotropy in protein hydrophobic thickness can induce membrane proteins to form mesh-like structures dividing the membrane into compartments. Our results help to elucidate the physical principles and mechanisms underlying the functional organization of cell membranes.
Collapse
Affiliation(s)
- Osman Kahraman
- Department of Physics & Astronomy and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | |
Collapse
|
28
|
Masone D, Bustos DM. Transmembrane domain dimerization induces cholesterol rafts in curved lipid bilayers. Phys Chem Chem Phys 2019; 21:268-274. [DOI: 10.1039/c8cp06783j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Are the dimerization of transmembrane (TM) domains and the reorganization of the lipid bilayer two independent events?
Collapse
Affiliation(s)
- Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ingeniería
| | - Diego M. Bustos
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Universidad Nacional de Cuyo (UNCuyo)
- Mendoza
- Argentina
- Facultad de Ciencias Exactas y Naturales
| |
Collapse
|
29
|
Ramakrishnan N, Bradley RP, Tourdot RW, Radhakrishnan R. Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:273001. [PMID: 29786613 PMCID: PMC6066392 DOI: 10.1088/1361-648x/aac702] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.
Collapse
Affiliation(s)
- N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | | | | | | |
Collapse
|
30
|
Spangler EJ, Kumar PBS, Laradji M. Stability of membrane-induced self-assemblies of spherical nanoparticles. SOFT MATTER 2018; 14:5019-5030. [PMID: 29855646 DOI: 10.1039/c8sm00537k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The self-assembly of spherical nanoparticles, resulting from their adhesion on tensionless lipid membranes, is investigated through molecular dynamics simulations of a coarse-grained implicit-solvent model. Our simulations indicate that, with increasing adhesion strength, while reshaping the membrane, the nanoparticles aggregate into a sequence of self-assemblies corresponding to in-plane chains, two-row tubular (bitube) chains, annular (ring) chains, and single-row tubular (tube) chains. Annealing scans, with respect to adhesion strength, show that the transitions between the various phases are highly first-order with significant hystereses. Free energy calculations indicate that the gas and single-row tubular chains are stable over wide ranges of adhesion strength. In contrast, the in-plane chains are only stable for small aggregates of NPs, and the bitube and ring chains are long-lived metastable states over a wide range of adhesion strength.
Collapse
Affiliation(s)
- Eric J Spangler
- Department of Biomedical Engineering, The University of Memphis, Memphis, TN 38152, USA
| | | | | |
Collapse
|
31
|
Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition. Sci Rep 2018; 8:5080. [PMID: 29572541 PMCID: PMC5865177 DOI: 10.1038/s41598-018-22912-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/02/2018] [Indexed: 12/11/2022] Open
Abstract
The oligomeric state of membrane proteins has recently emerged in many cases as having an effect on their function. However, the intrinsic dynamics of their spatial organization in cells and model systems makes it challenging to characterize. Here we use molecular dynamics (MD) simulations at multiple resolutions to determine the dimer conformation of the human serotonin transporter (hSERT). From self-assembly simulations we predict dimer candidates and subsequently quantify their relative strength. We use umbrella sampling (US) replica exchange MD simulations for which we present extensive analysis of their efficiency and improved sampling compared to regular US MD simulations. The data shows that the most stable hSERT dimer interface is symmetrical and involves transmembrane helix 12 (TM12), similar to the crystal structure of the bacterial homologue LeuT, but with a slightly different orientation. We also describe the supramolecular organization of hSERT from a 250 μs self-assembly simulation. Finally, the effects of the presence of phosphatidylinositol bisphosphate or cholesterol in the membrane model has been quantified for the TM12-TM12 predicted interface. Collectively, the presented data bring new insight to the area of protein and lipid interplay in biological membranes.
Collapse
|
32
|
Abstract
Besides direct protein-protein interactions, indirect interactions mediated by membranes play an important role for the assembly and cooperative function of proteins in membrane shaping and adhesion. The intricate shapes of biological membranes are generated by proteins that locally induce membrane curvature. Indirect curvature-mediated interactions between these proteins arise because the proteins jointly affect the bending energy of the membranes. These curvature-mediated interactions are attractive for crescent-shaped proteins and are a driving force in the assembly of the proteins during membrane tubulation. Membrane adhesion results from the binding of receptor and ligand proteins that are anchored in the apposing membranes. The binding of these proteins strongly depends on nanoscale shape fluctuations of the membranes, leading to a fluctuation-mediated binding cooperativity. A length mismatch between receptor-ligand complexes in membrane adhesion zones causes repulsive curvature-mediated interactions that are a driving force for the length-based segregation of proteins during membrane adhesion.
Collapse
Affiliation(s)
- Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany;
| |
Collapse
|
33
|
Liu Y, Ren B, Zhang Y, Sun Y, Chang Y, Liang G, Xu L, Zheng J. Molecular simulation aspects of amyloid peptides at membrane interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1906-1916. [PMID: 29421626 DOI: 10.1016/j.bbamem.2018.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
The interactions of amyloid peptides with cell membranes play an important role in maintaining the integrity and functionality of cell membrane. A thorough molecular-level understanding of the structure, dynamics, and interactions between amyloid peptides and cell membranes is critical to amyloid aggregation and toxicity mechanisms for the bench-to-bedside applications. Here we review the most recent computational studies of amyloid peptides at model cell membranes. Different mechanisms of action of amyloid peptides on/in cell membranes, targeted by different computational techniques at different lengthscales and timescales, are rationally discussed. Finally, we have proposed some new insights into the remaining challenges and perspectives for future studies to improve our understanding of the activity of amyloid peptides associated with protein-misfolding diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
Collapse
Affiliation(s)
- Yonglan Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yung Chang
- R&D Center for Membrane Technology and Department of Chemical EngineeringChung Yuan Christian University, Chung-Li, Taoyuan 320, Taiwan
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Lijian Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
| |
Collapse
|
34
|
Excessive aggregation of membrane proteins in the Martini model. PLoS One 2017; 12:e0187936. [PMID: 29131844 PMCID: PMC5683612 DOI: 10.1371/journal.pone.0187936] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 11/19/2022] Open
Abstract
The coarse-grained Martini model is employed extensively to study membrane protein oligomerization. While this approach is exceptionally promising given its computational efficiency, it is alarming that a significant fraction of these studies demonstrate unrealistic protein clusters, whose formation is essentially an irreversible process. This suggests that the protein-protein interactions are exaggerated in the Martini model. If this held true, then it would limit the applicability of Martini to study multi-protein complexes, as the rapidly clustering proteins would not be able to properly sample the correct dimerization conformations. In this work we first demonstrate the excessive protein aggregation by comparing the dimerization free energies of helical transmembrane peptides obtained with the Martini model to those determined from FRET experiments. Second, we show that the predictions provided by the Martini model for the structures of transmembrane domain dimers are in poor agreement with the corresponding structures resolved using NMR. Next, we demonstrate that the first issue can be overcome by slightly scaling down the Martini protein-protein interactions in a manner, which does not interfere with the other Martini interaction parameters. By preventing excessive, irreversible, and non-selective aggregation of membrane proteins, this approach renders the consideration of lateral dynamics and protein-lipid interactions in crowded membranes by the Martini model more realistic. However, this adjusted model does not lead to an improvement in the predicted dimer structures. This implicates that the poor agreement between the Martini model and NMR structures cannot be cured by simply uniformly reducing the interactions between all protein beads. Instead, a careful amino-acid specific adjustment of the protein-protein interactions is likely required.
Collapse
|
35
|
Kong X, Zhao Z, Jiang J. Dipeptides Embedded in a Lipid Bilayer Membrane as Synthetic Water Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11490-11495. [PMID: 28732442 DOI: 10.1021/acs.langmuir.7b02060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water channels are essential to life sciences and many biological processes. We report a molecular simulation study on dipeptides embedded in a lipid (dipalmitoylphosphatidylcholine) membrane as synthetic water channels. Five dipeptides are examined including FF, FL, LF, and LL (with hydrophilic channels) and AV (with hydrophobic channel). It is found that AV is unstable in the lipid membrane due to incompatible interaction between the hydrophilic external surface of AV and the hydrophobic lipid tails; whereas FF, FL, LF, and LL with hydrophobic external surface exhibit good stability. In the four hydrophilic channels FF, FL, LF, and LL, water chains are formed; the number of chains ranges from multiple, two to one depending on channel diameter; moreover, water undergoes single-file diffusion and the mobility is enhanced with increasing channel diameter. The permeation rate of water in the FF channel is 9.20/ns, about three times that in aquaporin; however, the rate in FL, LF, and LL is much slower. Intriguingly, the rate can be tuned by a lateral stress/strain on the lipid membrane. The simulation study provides fundamental understanding on the stability of dipeptide channels embedded in a lipid membrane, quantitatively characterizing water structure, dynamics, and permeation in the channels. These microscopic insights are useful for the development of new water channels.
Collapse
Affiliation(s)
- Xian Kong
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 117576, Singapore
| | - Zeyu Zhao
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 117576, Singapore
| | - Jianwen Jiang
- Department of Chemical and Biomolecular Engineering, National University of Singapore , 117576, Singapore
| |
Collapse
|
36
|
Mikucki M, Zhou YC. CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE. SIAM JOURNAL ON APPLIED MATHEMATICS 2017; 77:1587-1605. [PMID: 29056778 PMCID: PMC5650120 DOI: 10.1137/16m1076551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization.
Collapse
Affiliation(s)
- Michael Mikucki
- Department of Applied Mathematics & Statistics, Colorado School of Mines, Golden, Colorado, 80401-1887
| | - Y C Zhou
- Department of Mathematics, Colorado State University, Fort Collins, Colorado, 80523-1874
| |
Collapse
|
37
|
Boyd KJ, Alder NN, May ER. Buckling Under Pressure: Curvature-Based Lipid Segregation and Stability Modulation in Cardiolipin-Containing Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6937-6946. [PMID: 28628337 PMCID: PMC5654595 DOI: 10.1021/acs.langmuir.7b01185] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Mitochondrial metabolic function is affected by the morphology and protein organization of the mitochondrial inner membrane. Cardiolipin (CL) is a unique tetra-acyl lipid that is involved in the maintenance of the highly curved shape of the mitochondrial inner membrane as well as spatial organization of the proteins necessary for respiration and oxidative phosphorylation. Cardiolipin has been suggested to self-organize into lipid domains due to its inverted conical molecular geometry, though the driving forces for this organization are not fully understood. In this work, we use coarse-grained molecular dynamics simulations to study the mechanical properties and lipid dynamics in heterogeneous bilayers both with and without CL, as a function of membrane curvature. We find that incorporation of CL increases bilayer deformability and that CL becomes highly enriched in regions of high negative curvature. We further show that another mitochondrial inverted conical lipid, phosphatidylethanolamine (PE), does not partition or increase the deformability of the membrane in a significant manner. Therefore, CL appears to possess some unique characteristics that cannot be inferred simply from molecular geometry considerations.
Collapse
|
38
|
Abstract
To study integral membrane proteins, one has to extract them from the membrane—the step that is typically achieved by the application of detergents. In this mini-review, we summarize the top 10 detergents used for the structural analysis of membrane proteins based on the published results. The aim of this study is to provide the reader with an overview of the main properties of available detergents (critical micelle concentration (CMC) value, micelle size, etc.) and provide an idea of what detergents to may merit further study. Furthermore, we briefly discuss alternative solubilization and stabilization agents, such as polymers.
Collapse
|
39
|
A distinct function of the retinoblastoma protein in the control of lipid composition identified by lipidomic profiling. Oncogenesis 2017. [PMID: 28650445 PMCID: PMC5519198 DOI: 10.1038/oncsis.2017.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Here, by combining lipidomics with transcriptome analysis, we demonstrate that Rb depletion in mouse embryonic fibroblastss induces significant alterations in their lipid composition. We discovered that Rb depletion induced increase in lysophosphatidylserine, diacylglycerol (DAG), fatty acid (FA), acylcarnitine, phosphatidylcholine (PC), arachidonoyl ethanolamine, and decrease in phosphatidylglycerol, monoacylglycerol, without change in total lipid per protein levels. Analysis of the acyl chain composition of DAG, PC and phosphatidylserine revealed increase of saturated and mono-unsaturated acyl chains with specific carbon chain length. Consistently, we observed that Rb depletion increased the levels of fatty acids with the corresponding carbon chain length and number of carbon-carbon double bondssuch as myristic acid (14:0), palmitic acid (16:0), stearic acid (18:0) and all forms of FA 18:1. Microarray analysis revealed that Rb depletion induced significant upregulation of enzymes involved in elongation and desaturation of fatty acids. Among these, we found that elongation of long chain fatty acid family member 6 (Elovl6) and stearoyl-CoA desaturase 1 (Scd1) are the most robustly controlled by Rb possibly through E2F and sterol regulatory element-binding protein transcription factors. Depletion of Elovl6 or Scd1 significantly suppressed colony formation, sphere formation and xenograft tumor growth of Rb-deficient tumor cells. Suppression of self-renewal by the SCD1 inhibitor was rescued upon supplementation of the mono-unsaturated fatty acids generated by this enzyme. This study suggests a novel role for Rb in suppressing the malignant progression of tumors by controlling the lipid composition.
Collapse
|
40
|
Sun F, Chen L, Wei P, Chai M, Ding X, Xu L, Luo SZ. Dimerization and Structural Stability of Amyloid Precursor Proteins Affected by the Membrane Microenvironments. J Chem Inf Model 2017; 57:1375-1387. [DOI: 10.1021/acs.jcim.7b00196] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fude Sun
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Long Chen
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Wei
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengya Chai
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiufang Ding
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lida Xu
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of
Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
41
|
Herzog FA, Braun L, Schoen I, Vogel V. Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes. J Phys Chem B 2017; 121:3523-3535. [DOI: 10.1021/acs.jpcb.6b09349] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Florian A. Herzog
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Lukas Braun
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Ingmar Schoen
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| | - Viola Vogel
- Laboratory of Applied
Mechanobiology,
Department of Health Sciences and Technology, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
42
|
|
43
|
Periole X. Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. Chem Rev 2016; 117:156-185. [PMID: 28073248 DOI: 10.1021/acs.chemrev.6b00344] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G protein-coupled receptors (GPCRs) are central to many fundamental cellular signaling pathways. They transduce signals from the outside to the inside of cells in physiological processes ranging from vision to immune response. It is extremely challenging to look at them individually using conventional experimental techniques. Recently, a pseudo atomistic molecular model has emerged as a valuable tool to access information on GPCRs, more specifically on their interactions with their environment in their native cell membrane and the consequences on their supramolecular organization. This approach uses the Martini coarse grain (CG) model to describe the receptors, lipids, and solvent in molecular dynamics (MD) simulations and in enough detail to allow conserving the chemical specificity of the different molecules. The elimination of unnecessary degrees of freedom has opened up large-scale simulations of the lipid-mediated supramolecular organization of GPCRs. Here, after introducing the Martini CGMD method, we review these studies carried out on various members of the GPCR family, including rhodopsin (visual receptor), opioid receptors, adrenergic receptors, adenosine receptors, dopamine receptor, and sphingosine 1-phosphate receptor. These studies have brought to light an interesting set of novel biophysical principles. The insights range from revealing localized and heterogeneous deformations of the membrane bilayer at the surface of the protein, specific interactions of lipid molecules with individual GPCRs, to the effect of the membrane matrix on global GPCR self-assembly. The review ends with an overview of the lessons learned from the use of the CGMD method, the biophysical-chemical findings on lipid-protein interplay.
Collapse
Affiliation(s)
- Xavier Periole
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747AG Groningen, The Netherlands
| |
Collapse
|
44
|
Musiani F, Giorgetti A. Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:49-77. [PMID: 28109331 DOI: 10.1016/bs.ircmb.2016.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment.
Collapse
Affiliation(s)
- F Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Bologna, Italy.
| | - A Giorgetti
- Applied Bioinformatics Group, University of Verona, Verona, Italy.
| |
Collapse
|
45
|
Fowler PW, Hélie J, Duncan A, Chavent M, Koldsø H, Sansom MSP. Membrane stiffness is modified by integral membrane proteins. SOFT MATTER 2016; 12:7792-7803. [PMID: 27722554 PMCID: PMC5314686 DOI: 10.1039/c6sm01186a] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/25/2016] [Indexed: 05/12/2023]
Abstract
The ease with which a cell membrane can bend and deform is important for a wide range of biological functions. Peripheral proteins that induce curvature in membranes (e.g. BAR domains) have been studied for a number of years. Little is known, however, about the effect of integral membrane proteins on the stiffness of a membrane (characterised by the bending rigidity, Kc). We demonstrate by computer simulation that adding integral membrane proteins at physiological densities alters the stiffness of the membrane. First we establish that the coarse-grained MARTINI forcefield is able to accurately reproduce the bending rigidity of a small patch of 1500 phosphatidyl choline lipids by comparing the calculated value to both experiment and an atomistic simulation of the same system. This enables us to simulate the dynamics of large (ca. 50 000 lipids) patches of membrane using the MARTINI coarse-grained description. We find that altering the lipid composition changes the bending rigidity. Adding integral membrane proteins to lipid bilayers also changes the bending rigidity, whilst adding a simple peripheral membrane protein has no effect. Our results suggest that integral membrane proteins can have different effects, and in the case of the bacterial outer membrane protein, BtuB, the greater the density of protein, the larger the reduction in stiffness.
Collapse
Affiliation(s)
- Philip W Fowler
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Anna Duncan
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK.
| |
Collapse
|
46
|
Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes. Proc Natl Acad Sci U S A 2016; 113:E5117-24. [PMID: 27531962 DOI: 10.1073/pnas.1605259113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present coarse-grained molecular dynamics simulations of the epsin N-terminal homology domain interacting with a lipid bilayer and demonstrate a rigorous theoretical formalism and analysis method for computing the induced curvature field in varying concentrations of the protein in the dilute limit. Our theory is based on the description of the height-height undulation spectrum in the presence of a curvature field. We formulated an objective function to compare the acquired undulation spectrum from the simulations to that of the theory. We recover the curvature field parameters by minimizing the objective function even in the limit where the protein-induced membrane curvature is of the same order as the amplitude due to thermal undulations. The coupling between curvature and undulations leads to significant predictions: (i) Under dilute conditions, the proteins can sense a site of spontaneous curvature at distances much larger than their size; (ii) as the density of proteins increases the coupling focuses and stabilizes the curvature field to the site of the proteins; and (iii) the mapping of the protein localization and the induction of a stable curvature is a cooperative process that can be described through a Hill function.
Collapse
|
47
|
Holdbrook DA, Huber RG, Piggot TJ, Bond PJ, Khalid S. Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition. PLoS One 2016; 11:e0156963. [PMID: 27310814 PMCID: PMC4910979 DOI: 10.1371/journal.pone.0156963] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/22/2016] [Indexed: 11/22/2022] Open
Abstract
The bacterial cell envelope is composed of a mixture of different lipids and proteins, making it an inherently complex organelle. The interactions between integral membrane proteins and lipids are crucial for their respective spatial localization within bacterial cells. We have employed microsecond timescale coarse-grained molecular dynamics simulations of vesicles of varying sizes and with a range of protein and lipid compositions, and used novel approaches to measure both local and global system dynamics, the latter based on spherical harmonics analysis. Our results suggest that both hydrophobic mismatch, enhanced by embedded membrane proteins, and curvature based sorting, due to different modes of undulation, may drive assembly in vesicular systems. Interestingly, the modes of undulation of the vesicles were found to be altered by the specific protein and lipid composition of the vesicle. Strikingly, lipid dynamics were shown to be coupled to proteins up to 6 nm from their surface, a substantially larger distance than has previously been observed, resulting in multi-layered annular rings enriched with particular types of phospholipid. Such large protein-lipid complexes may provide a mechanism for long-range communication. Given the complexity of bacterial membranes, our results suggest that subtle changes in lipid composition may have major implications for lipid and protein sorting under a curvature-based membrane-sorting model.
Collapse
Affiliation(s)
- Daniel A. Holdbrook
- Bioinformatics Institute (A*STAR), 30 Biopolis Str, #07–01 Matrix, Singapore 138671, Singapore
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Roland G. Huber
- Bioinformatics Institute (A*STAR), 30 Biopolis Str, #07–01 Matrix, Singapore 138671, Singapore
| | - Thomas J. Piggot
- The Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Peter J. Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis Str, #07–01 Matrix, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| |
Collapse
|
48
|
Ackerman DG, Feigenson GW. Effects of Transmembrane α-Helix Length and Concentration on Phase Behavior in Four-Component Lipid Mixtures: A Molecular Dynamics Study. J Phys Chem B 2016; 120:4064-77. [PMID: 27081858 DOI: 10.1021/acs.jpcb.6b00611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We used coarse-grained molecular dynamics simulations to examine the effects of transmembrane α-helical WALP peptides on the behavior of four-component lipid mixtures. These mixtures contain a high-melting temperature (high-Tm) lipid, a nanodomain-inducing low-Tm lipid, a macrodomain-inducing low-Tm lipid and cholesterol to model the outer leaflet of cell plasma membranes. In a series of simulations, we incrementally replace the nanodomain-inducing low-Tm lipid by the macrodomain-inducing low-Tm lipid and measure how lipid and phase properties are altered by the addition of WALPs of different length. Regardless of the ratio of the two low-Tm lipids, shorter WALPs increase domain size and all WALPs increase domain alignment between the two leaflets. These effects are smallest for the longest WALP tested, and increase with increasing WALP concentration. Thus, our simulations explain the experimental observation that WALPs induce macroscopic domains in otherwise nanodomain-forming lipid-only mixtures (unpublished). Since the cell plasma membrane contains a large fraction of transmembrane proteins, these findings link the behavior of lipid-only model membranes in vitro to phase behavior in vivo.
Collapse
Affiliation(s)
- David G Ackerman
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States
| | - Gerald W Feigenson
- Department of Molecular Biology and Genetics, Cornell University , Ithaca, New York 14853, United States
| |
Collapse
|
49
|
Kahraman O, Koch PD, Klug WS, Haselwandter CA. Bilayer-thickness-mediated interactions between integral membrane proteins. Phys Rev E 2016; 93:042410. [PMID: 27176332 DOI: 10.1103/physreve.93.042410] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Indexed: 12/14/2022]
Abstract
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane environments provided by living cells.
Collapse
Affiliation(s)
- Osman Kahraman
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Peter D Koch
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| | - Christoph A Haselwandter
- Department of Physics & Astronomy and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| |
Collapse
|
50
|
Rossi G, Monticelli L. Gold nanoparticles in model biological membranes: A computational perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2380-2389. [PMID: 27060434 DOI: 10.1016/j.bbamem.2016.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 01/15/2023]
Abstract
The electronic, optical, catalytic, and magnetic properties of metal nanoparticles (NPs) make them extremely interesting for biomedical applications. In this rapidly moving field, monolayer-protected gold nanoparticles emerge both as a reference system and as promising candidates for drug and gene delivery, photothermal treatment, and imaging applications. Despite the technological relevance, there is still poor understanding of the molecular processes driving the interactions of metal nanoparticles with cells, and with cell membranes in particular. In this paper we review molecular-level computational studies of the interaction between monolayer-protected gold NPs and model lipid membranes. Our review comprises a brief description of the most relevant experimental results in this field and of the questions they raised, followed by a description of the computational achievements reported so far. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
Affiliation(s)
- Giulia Rossi
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy.
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS UMR 5086, 7 Passage du Vercors, 69007 Lyon, France.
| |
Collapse
|