1
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Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nat Commun 2024; 15:1848. [PMID: 38418487 PMCID: PMC10901782 DOI: 10.1038/s41467-024-46027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1's structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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2
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Banerjee S, Smith IM, Hengen AC, Stroka KM. Methods for studying mammalian aquaporin biology. Biol Methods Protoc 2023; 8:bpad031. [PMID: 38046463 PMCID: PMC10689382 DOI: 10.1093/biomethods/bpad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
Aquaporins (AQPs), transmembrane water-conducting channels, have earned a great deal of scrutiny for their critical physiological roles in healthy and disease cell states, especially in the biomedical field. Numerous methods have been implemented to elucidate the involvement of AQP-mediated water transport and downstream signaling activation in eliciting whole cell, tissue, and organ functional responses. To modulate these responses, other methods have been employed to investigate AQP druggability. This review discusses standard in vitro, in vivo, and in silico methods for studying AQPs, especially for biomedical and mammalian cell biology applications. We also propose some new techniques and approaches for future AQP research to address current gaps in methodology.
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Affiliation(s)
- Shohini Banerjee
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Ian M Smith
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Autumn C Hengen
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Kimberly M Stroka
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore MD 21201, United States
- Biophysics Program, University of Maryland, MD 20742, United States
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland, Baltimore MD 21201, United States
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3
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Ozu M, Galizia L, Alvear-Arias JJ, Fernández M, Caviglia A, Zimmermann R, Guastaferri F, Espinoza-Muñoz N, Sutka M, Sigaut L, Pietrasanta LI, González C, Amodeo G, Garate JA. Mechanosensitive aquaporins. Biophys Rev 2023; 15:497-513. [PMID: 37681084 PMCID: PMC10480384 DOI: 10.1007/s12551-023-01098-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/04/2023] [Indexed: 09/09/2023] Open
Abstract
Cellular systems must deal with mechanical forces to satisfy their physiological functions. In this context, proteins with mechanosensitive properties play a crucial role in sensing and responding to environmental changes. The discovery of aquaporins (AQPs) marked a significant breakthrough in the study of water transport. Their transport capacity and regulation features make them key players in cellular processes. To date, few AQPs have been reported to be mechanosensitive. Like mechanosensitive ion channels, AQPs respond to tension changes in the same range. However, unlike ion channels, the aquaporin's transport rate decreases as tension increases, and the molecular features of the mechanism are unknown. Nevertheless, some clues from mechanosensitive ion channels shed light on the AQP-membrane interaction. The GxxxG motif may play a critical role in the water permeation process associated with structural features in AQPs. Consequently, a possible gating mechanism triggered by membrane tension changes would involve a conformational change in the cytoplasmic extreme of the single file region of the water pathway, where glycine and histidine residues from loop B play a key role. In view of their transport capacity and their involvement in relevant processes related to mechanical forces, mechanosensitive AQPs are a fundamental piece of the puzzle for understanding cellular responses.
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Affiliation(s)
- Marcelo Ozu
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luciano Galizia
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan José Alvear-Arias
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Miguel Fernández
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Agustín Caviglia
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rosario Zimmermann
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Florencia Guastaferri
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Present Address: Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Nicolás Espinoza-Muñoz
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Moira Sutka
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lorena Sigaut
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lía Isabel Pietrasanta
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carlos González
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
- Department of Physiology and Biophysics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
- Present Address: Molecular Bioscience Department, University of Texas, Austin, TX 78712 USA
| | - Gabriela Amodeo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - José Antonio Garate
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia y Vida, Universidad San Sebastián, 7750000 Santiago, Chile
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4
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Wang L, Zhang J, Wang D, Song C. Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins. PLoS Comput Biol 2022; 18:e1009972. [PMID: 35353812 PMCID: PMC9000120 DOI: 10.1371/journal.pcbi.1009972] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/11/2022] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
Abstract
One of the unique traits of membrane proteins is that a significant fraction of their hydrophobic amino acids is exposed to the hydrophobic core of lipid bilayers rather than being embedded in the protein interior, which is often not explicitly considered in the protein structure and function predictions. Here, we propose a characteristic and predictive quantity, the membrane contact probability (MCP), to describe the likelihood of the amino acids of a given sequence being in direct contact with the acyl chains of lipid molecules. We show that MCP is complementary to solvent accessibility in characterizing the outer surface of membrane proteins, and it can be predicted for any given sequence with a machine learning-based method by utilizing a training dataset extracted from MemProtMD, a database generated from molecular dynamics simulations for the membrane proteins with a known structure. As the first of many potential applications, we demonstrate that MCP can be used to systematically improve the prediction precision of the protein contact maps and structures. The distribution of residues on protein surfaces is largely determined by the surrounding environment. For soluble proteins, most of the residues on the outer surface are hydrophilic, and people use the quantity “solvent accessibility” to describe and predict these surface residues. In contrast, for membrane proteins that are embedded in a lipid bilayer, many of their surface residues are hydrophobic and membrane-contacting, but there is yet a widely-accepted quantity for the description or prediction of this characteristic property. Here, we propose a new quantity termed “membrane contact probability (MCP)”, which can be used to describe and predict the membrane-contacting surface residues of proteins. We also propose a machine learning-based method to predict MCP from protein sequences, utilizing the dataset generated by physics-based computer simulations. We demonstrate that a quantity such as MCP is helpful for protein structure prediction, and we believe that it will find broad applications in the structure and function studies of membrane proteins.
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Affiliation(s)
- Lei Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
| | - Jiangguo Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Dali Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail:
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5
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Behera BK, Parhi J, Dehury B, Rout AK, Khatei A, Devi AL, Mandal SC. Molecular characterization and structural dynamics of Aquaporin1 from walking catfish in lipid bilayers. Int J Biol Macromol 2021; 196:86-97. [PMID: 34914911 DOI: 10.1016/j.ijbiomac.2021.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 01/17/2023]
Abstract
Aquaporin's (AQPs) are the major superfamily of small integral membrane proteins that facilitates transportation of water, urea, ammonia, glycerol and ions across biological cell membranes. Despite of recent advancements made in understanding the biology of Aquaporin's, only few isoforms of aquaporin 1 (AQP1) some of the teleost fish species have been characterized at molecular scale. In this study, we made an attempt to elucidate the molecular mechanism of water transportation in AQP1 from walking catfish (Clarias batrachus), a model species capable of breathing in air and inhabits in challenging environments. Using state-of-the-art computational modelling and all-atoms molecular dynamics simulation, we explored the structural dynamics of full-length aquaporin 1 from walking catfish (CbAQP1) in lipid mimetic bilayers. Unlike AQP1 of human and bovine, structural ensembles of CbAQP1 from MD revealed discrete positioning of pore lining residues at the intracellular end. Snapshots from MD simulation displayed differential dynamics of aromatic/arginine (ar/R) filter and extracellular loop C bridging transmembrane (TM) helix H3 and H4. Distinct conformation of large extracellular loops, loop bridging TM2 domain and HB helix along with positioning of selectivity filter lining residues controls the permeability of water across the bilayer. Moreover, the identified unique and conserved lipid binding sites with 100% lipid occupancy signifies lipid mediated structural dynamics of CbAQP1. All-together, this is the first ever report on structural-dynamics of aquaporin 1 in walking catfish which will be useful to understand the molecular basis of transportation of water and other small molecules under varying degree of hyperosmotic environment.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India.
| | - Janmejay Parhi
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
| | - Budheswar Dehury
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India; Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - Ananya Khatei
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
| | - Asem Lembika Devi
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
| | - Sagar Chandra Mandal
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
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6
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Pluhackova K, Horner A. Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity. BMC Biol 2021; 19:4. [PMID: 33441107 PMCID: PMC7807449 DOI: 10.1186/s12915-020-00936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments. RESULTS To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly. CONCLUSIONS The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.
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Affiliation(s)
- Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule (ETH) Zürich, Mattenstr. 26, Basel, 4058, Switzerland.
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
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7
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Pannuzzo M, Szała B, Raciti D, Raudino A, Ferrarini A. Helical Inclusions in Phospholipid Membranes: Lipid Adaptation and Chiral Order. J Phys Chem Lett 2019; 10:5629-5633. [PMID: 31487187 DOI: 10.1021/acs.jpclett.9b02252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid bilayer is a flexible matrix that is able to adapt in response to the perturbation induced by inclusions, such as peptides and proteins. Here we use molecular dynamics simulations with a coarse-grained model to investigate the effect of a helical inclusion on a lipid bilayer in the liquid disordered phase. We show that the helical inclusion induces a collective tilt of acyl chains, with a small, yet unambiguous difference between a right- and a left-handed inclusion. This behavior is rationalized using the elastic continuum theory: The magnitude of the chiral (twist) deformation of the bilayer is determined by the interaction at the lipid/inclusion interface, and the decay length is controlled by the elastic properties of the bilayer. The lipid reorganization can thus be identified as a generic mechanism that, together with specific interactions, contributes to chiral recognition in phospholipid bilayers. An enhanced response is expected in highly ordered environments, such as rafts in biomembranes, with a potential impact on membrane-mediated interactions between inclusions.
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Affiliation(s)
- Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine , Fondazione Istituto Italiano di Tecnologia , via Morego, 30 , 16163 Genova , Italy
| | - Beata Szała
- Department of Chemical Sciences , University of Padova , via Marzolo 1 , 35131 Padova , Italy
- Faculty of Chemistry , Adam Mickiewicz University in Poznań , Umultowska 89b , 61-614 Poznań , Poland
| | - Domenica Raciti
- Department of Chemical Sciences , University of Catania , Viale A. Doria, 6 , 95125 Catania , Italy
| | - Antonio Raudino
- Department of Chemical Sciences , University of Catania , Viale A. Doria, 6 , 95125 Catania , Italy
| | - Alberta Ferrarini
- Department of Chemical Sciences , University of Padova , via Marzolo 1 , 35131 Padova , Italy
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8
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Corey RA, Vickery ON, Sansom MSP, Stansfeld PJ. Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations. J Chem Theory Comput 2019; 15:5727-5736. [PMID: 31476127 PMCID: PMC6785801 DOI: 10.1021/acs.jctc.9b00548] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Integral membrane proteins are regulated
by specific interactions
with lipids from the surrounding bilayer. The structures of protein–lipid
complexes can be determined through a combination of experimental
and computational approaches, but the energetic basis of these interactions
is difficult to resolve. Molecular dynamics simulations provide the
primary computational technique to estimate the free energies of these
interactions. We demonstrate that the energetics of protein–lipid
interactions may be reliably and reproducibly calculated using three
simulation-based approaches: potential of mean force calculations,
alchemical free energy perturbation, and well-tempered metadynamics.
We employ these techniques within the framework of a coarse-grained
force field and apply them to both bacterial and mammalian membrane
protein–lipid systems. We demonstrate good agreement between
the different techniques, providing a robust framework for their automated
implementation within a pipeline for annotation of newly determined
membrane protein structures.
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Affiliation(s)
- Robin A Corey
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Owen N Vickery
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Mark S P Sansom
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Phillip J Stansfeld
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
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9
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Machado MR, Zeida A, Darré L, Pantano S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019; 9:20180085. [PMID: 31065347 PMCID: PMC6501346 DOI: 10.1098/rsfs.2018.0085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
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Affiliation(s)
- Matías R. Machado
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Institut Pasteur de Montevideo, Functional Genomics Unit, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
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10
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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11
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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12
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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13
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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14
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Hall JE, Freites JA, Tobias DJ. Experimental and Simulation Studies of Aquaporin 0 Water Permeability and Regulation. Chem Rev 2019; 119:6015-6039. [PMID: 31026155 DOI: 10.1021/acs.chemrev.9b00106] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We begin with the history of aquaporin zero (AQP0), the most prevalent membrane protein in the eye lens, from the early days when AQP0 was a protein of unknown function known as Major Intrinsic Protein 26. We progress through its joining the aquaporin family as a water channel in its own right and discuss how regulation of its water permeability by pH and calcium came to be discovered experimentally and linked to lens homeostasis and development. We review the development of molecular dynamics (MD) simulations of lipid bilayers and membrane proteins, including aquaporins, with an emphasis on simulation studies that have elucidated the mechanisms of water conduction, selectivity, and proton exclusion by aquaporins in general. We also review experimental and theoretical progress toward understanding why mammalian AQP0 has a lower water permeability than other aquaporins and the evolution of our present understanding of how its water permeability is regulated by pH and calcium. Finally, we discuss how MD simulations have elucidated the nature of lipid interactions with AQP0.
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16
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Newport TD, Sansom MS, Stansfeld PJ. The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. Nucleic Acids Res 2019; 47:D390-D397. [PMID: 30418645 PMCID: PMC6324062 DOI: 10.1093/nar/gky1047] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/05/2018] [Accepted: 10/16/2018] [Indexed: 12/19/2022] Open
Abstract
Integral membrane proteins fulfil important roles in many crucial biological processes, including cell signalling, molecular transport and bioenergetic processes. Advancements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins. Yet, these structures are rarely resolved in complex with membrane lipids. In 2015, the MemProtMD pipeline was developed to allow the automated lipid bilayer assembly around new membrane protein structures, released from the Protein Data Bank (PDB). To make these data available to the scientific community, a web database (http://memprotmd.bioch.ox.ac.uk) has been developed. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualizations of the assembled bilayer and 2D visualizations of lipid contact data and membrane protein topology. In addition, ensemble analyses are performed to detail conserved lipid interaction information across proteins, families and for the entire database of 3506 PDB entries. Proteins may be searched using keywords, PDB or Uniprot identifier, or browsed using classification systems, such as Pfam, Gene Ontology annotation, mpstruc or the Transporter Classification Database. All files required to run further molecular simulations of proteins in the database are provided.
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Affiliation(s)
- Thomas D Newport
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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17
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Overduin M, Esmaili M. Memtein: The fundamental unit of membrane-protein structure and function. Chem Phys Lipids 2019; 218:73-84. [DOI: 10.1016/j.chemphyslip.2018.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 12/14/2022]
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18
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Briones R, Blau C, Kutzner C, de Groot BL, Aponte-Santamaría C. GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations. Biophys J 2018; 116:4-11. [PMID: 30558883 DOI: 10.1016/j.bpj.2018.11.3126] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022] Open
Abstract
We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics simulations. GROmaρs efficiently computes density maps by fast multi-Gaussian spreading of atomic densities onto a three-dimensional grid. It complements existing map-based tools by enabling spatial inspection of atomic average localization during the simulations. Most importantly, it allows the comparison between computed and reference maps (e.g., experimental) through calculation of difference maps and local and time-resolved global correlation. These comparison operations proved useful to quantitatively contrast perturbed and control simulation data sets and to examine how much biomolecular systems resemble both synthetic and experimental density maps. This was especially advantageous for multimolecule systems in which standard comparisons like RMSDs are difficult to compute. In addition, GROmaρs incorporates absolute and relative spatial free-energy estimates to provide an energetic picture of atomistic localization. This is an open-source GROMACS-based toolset, thus allowing for static or dynamic selection of atoms or even coarse-grained beads for the density calculation. Furthermore, masking of regions was implemented to speed up calculations and to facilitate the comparison with experimental maps. Beyond map comparison, GROmaρs provides a straightforward method to detect solvent cavities and average charge distribution in biomolecular systems. We employed all these functionalities to inspect the localization of lipid and water molecules in aquaporin systems, the binding of cholesterol to the G protein coupled chemokine receptor type 4, and the identification of permeation pathways through the dermicidin antimicrobial channel. Based on these examples, we anticipate a high applicability of GROmaρs for the analysis of molecular dynamics simulations and their comparison with experimentally determined densities.
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Affiliation(s)
- Rodolfo Briones
- Computational Neurophysiology Group, Institute of Complex Systems 4, Forschungszentrum Jülich, Jülich, Germany
| | - Christian Blau
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholms Universitet, Stockholm, Sweden
| | - Carsten Kutzner
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
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19
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Ozu M, Galizia L, Acuña C, Amodeo G. Aquaporins: More Than Functional Monomers in a Tetrameric Arrangement. Cells 2018; 7:E209. [PMID: 30423856 PMCID: PMC6262540 DOI: 10.3390/cells7110209] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/27/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
Aquaporins (AQPs) function as tetrameric structures in which each monomer has its own permeable pathway. The combination of structural biology, molecular dynamics simulations, and experimental approaches has contributed to improve our knowledge of how protein conformational changes can challenge its transport capacity, rapidly altering the membrane permeability. This review is focused on evidence that highlights the functional relationship between the monomers and the tetramer. In this sense, we address AQP permeation capacity as well as regulatory mechanisms that affect the monomer, the tetramer, or tetramers combined in complex structures. We therefore explore: (i) water permeation and recent evidence on ion permeation, including the permeation pathway controversy-each monomer versus the central pore of the tetramer-and (ii) regulatory mechanisms that cannot be attributed to independent monomers. In particular, we discuss channel gating and AQPs that sense membrane tension. For the latter we propose a possible mechanism that includes the monomer (slight changes of pore shape, the number of possible H-bonds between water molecules and pore-lining residues) and the tetramer (interactions among monomers and a positive cooperative effect).
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Affiliation(s)
- Marcelo Ozu
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
| | - Luciano Galizia
- Instituto de investigaciones Médicas A. Lanari, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1427ARO, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Buenos Aires C1427ARO, Argentina.
| | - Cynthia Acuña
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
| | - Gabriela Amodeo
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428EGA CABA, Argentina.
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20
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Goossens K, De Winter H. Molecular Dynamics Simulations of Membrane Proteins: An Overview. J Chem Inf Model 2018; 58:2193-2202. [PMID: 30336018 DOI: 10.1021/acs.jcim.8b00639] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulations of membrane proteins have been rising in popularity in the past decade. Advancements in technology and force fields made it possible to simulate behavior of membrane proteins. Membrane protein simulations can now be used as supporting evidence for experimental findings, for elucidating protein mechanisms, and validating protein crystal structures. Unrelated to experimental data, these simulations can also serve to investigate larger scale processes like protein sorting, protein-membrane interactions, and more. In this review, the history as well as the state-of-the-art methodologies in membrane protein simulations will be summarized. An emphasis will be put on how to set up the system and on the current models for the different components of the simulation system. An overview of the available tools for membrane protein simulation will be given, and current limitations and prospects will also be discussed.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
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21
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Kalli AC, Reithmeier RAF. Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen. PLoS Comput Biol 2018; 14:e1006284. [PMID: 30011272 PMCID: PMC6080803 DOI: 10.1371/journal.pcbi.1006284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/07/2018] [Accepted: 06/08/2018] [Indexed: 11/29/2022] Open
Abstract
The Band 3 (AE1, SLC4A1) membrane protein is found in red blood cells and in kidney where it functions as an electro-neutral chloride/bicarbonate exchanger. In this study, we have used molecular dynamics simulations to provide the first realistic model of the dimeric membrane domain of human Band 3 in an asymmetric lipid bilayer containing a full complement of phospholipids, including phosphatidylinositol 4,5–bisphosphate (PIP2) and cholesterol, and its partner membrane protein Glycophorin A (GPA). The simulations show that the annular layer in the inner leaflet surrounding Band 3 was enriched in phosphatidylserine and PIP2 molecules. Cholesterol was also enriched around Band 3 but also at the dimer interface. The interaction of these lipids with specific sites on Band 3 may play a role in the folding and function of this anion transport membrane protein. GPA associates with Band 3 to form the Wright (Wr) blood group antigen, an interaction that involves an ionic bond between Glu658 in Band 3 and Arg61 in GPA. We were able to recreate this complex by performing simulations to allow the dimeric transmembrane portion of GPA to interact with Band 3 in a model membrane. Large-scale simulations showed that the GPA dimer can bridge Band 3 dimers resulting in the dynamic formation of long strands of alternating Band 3 and GPA dimers. Human Band 3 (AE1, SLC4A1), an abundant 911 amino acid glycoprotein, catalyzes the exchange of bicarbonate and chloride across the red blood cell membrane, a process necessary for efficient respiration. Malfunction of Band 3 leads to inherited diseases such as Southeast Asian Ovalocytosis, hereditary spherocytosis and distal renal tubular acidosis. Despite much available structural and functional data about Band 3, key questions about the conformational changes associated with transport and the molecular details of its interaction with lipids and other proteins remain unanswered. In this study, we have used computer simulations to investigate the dynamics of Band 3 in lipid bilayers that resemble the red blood cell plasma membrane. Our results suggest that negatively charged phospholipids and cholesterol interact strongly with Band 3 forming an annulus around the protein. Glycophorin A (GPA) interacts with Band 3 to form the Wright (Wr) blood group antigen. We were able to recreate this complex and show that GPA promotes the clustering of Band 3 in red blood cell membranes. Understanding the molecular details of the interaction of Band 3 with GPA has provided new insights into the nature of the Wright blood group antigen.
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Affiliation(s)
- Antreas C. Kalli
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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22
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Computational studies of membrane proteins: from sequence to structure to simulation. Curr Opin Struct Biol 2017; 45:133-141. [DOI: 10.1016/j.sbi.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/19/2022]
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23
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Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Sci Rep 2017; 7:4016. [PMID: 28638135 PMCID: PMC5479825 DOI: 10.1038/s41598-017-04180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
Regulation of aquaporins is a key process of living organisms to counteract sudden osmotic changes. Aqy1, which is a water transporting aquaporin of the yeast Pichia pastoris, is suggested to be gated by chemo-mechanical stimuli as a protective regulatory-response against rapid freezing. Here, we tested the influence of temperature by determining the X-ray structure of Aqy1 at room temperature (RT) at 1.3 Å resolution, and by exploring the structural dynamics of Aqy1 during freezing through molecular dynamics simulations. At ambient temperature and in a lipid bilayer, Aqy1 adopts a closed conformation that is globally better described by the RT than by the low-temperature (LT) crystal structure. Locally, for the blocking-residue Tyr31 and the water molecules inside the pore, both LT and RT data sets are consistent with the positions observed in the simulations at room-temperature. Moreover, as the temperature was lowered, Tyr31 adopted a conformation that more effectively blocked the channel, and its motion was accompanied by a temperature-driven rearrangement of the water molecules inside the channel. We therefore speculate that temperature drives Aqy1 from a loosely- to a tightly-blocked state. This analysis provides high-resolution structural evidence of the influence of temperature on membrane-transport channels.
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Affiliation(s)
- Camilo Aponte-Santamaría
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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24
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Goldman RP, Jozefkowicz C, Canessa Fortuna A, Sutka M, Alleva K, Ozu M. Tonoplast (BvTIP1;2) and plasma membrane (BvPIP2;1) aquaporins show different mechanosensitive properties. FEBS Lett 2017; 591:1555-1565. [PMID: 28486763 DOI: 10.1002/1873-3468.12671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/01/2017] [Accepted: 05/04/2017] [Indexed: 12/22/2022]
Abstract
Previous works proposed that aquaporins behave as mechanosensitive channels. However, principal issues about mechanosensitivity of aquaporins are not known. In this work, we characterized the mechanosensitive properties of the water channels BvTIP1;2 (TIP1) and BvPIP2;1 (PIP2) from red beet (Beta vulgaris). We simultaneously measured the mechanical behavior and the water transport rates during the osmotic response of emptied-out oocytes expressing TIP1 or PIP2. Our results indicate that TIP1 is a mechanosensitive aquaporin, whereas PIP2 is not. We found that a single exponential function between the osmotic permeability coefficient and the volumetric elastic modulus governs the mechanosensitivity of TIP1. Finally, homology modeling analysis indicates that putative residues involved in mechanosensitivity show different quantity and distribution in TIP1 and PIP2.
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Affiliation(s)
- Ramiro P Goldman
- Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Medicina, Instituto de Fisiología y Biofísica (IFIBIO Houssay), Laboratorio de Biomembranas, Universidad de Buenos Aires, Argentina
| | - Cintia Jozefkowicz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Fisicomatemática, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
| | - Agustina Canessa Fortuna
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Fisicomatemática, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
| | - Moira Sutka
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Karina Alleva
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Fisicomatemática, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina
| | - Marcelo Ozu
- Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Medicina, Instituto de Fisiología y Biofísica (IFIBIO Houssay), Laboratorio de Biomembranas, Universidad de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
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25
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Briones R, Aponte-Santamaría C, de Groot BL. Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects. Front Physiol 2017; 8:124. [PMID: 28303107 PMCID: PMC5332469 DOI: 10.3389/fphys.2017.00124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution. To understand the role of temperature, lipid phase, and protein mobility in the localization and ordering of AQP0-lipids, we used MD simulations of an AQP0-DMPC bilayer system. Simulations were performed at physiological and at DMPC gel-phase temperatures. To decouple the protein and lipid mobility effects, we induced gel-phase in the lipids or restrained the protein. We monitored the lipid ordering effects around the protein. Reducing the system temperature or inducing lipid gel-phase had a marginal effect on the annular lipid localization. However, restraining the protein mobility increased the annular lipid localization around the whole AQP0 surface, resembling EC. The distribution of the inter-phosphate and hydrophobic thicknesses showed that stretching of the DMPC annular layer around AQP0 surface is the mechanism that compensates the hydrophobic mismatch in this system. The distribution of the local area-per-lipid and the acyl-chain order parameters showed particular fluid- and gel-like areas that involved several lipid layers. These areas were in contact with the surfaces of higher and lower protein mobility, respectively. We conclude that the AQP0 surfaces induce specific fluid- and gel-phase prone areas. The presence of these areas might guide the AQP0 lipid sorting interactions with other membrane components, and is compatible with the squared array oligomerization of AQP0 tetramers separated by a layer of annular lipids.
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Affiliation(s)
- Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
| | - Camilo Aponte-Santamaría
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies and Interdisciplinary Center for Scientific Computing Heidelberg, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
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26
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Padhi S, Priyakumar UD. Microsecond simulation of human aquaporin 2 reveals structural determinants of water permeability and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:10-16. [DOI: 10.1016/j.bbamem.2016.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 02/06/2023]
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27
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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.
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Affiliation(s)
- Xavier Periole
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747AG Groningen, The Netherlands
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28
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Hedger G, Rouse SL, Domański J, Chavent M, Koldsø H, Sansom MSP. Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes. Biochemistry 2016; 55:6238-6249. [PMID: 27786441 PMCID: PMC5120876 DOI: 10.1021/acs.biochem.6b00751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
The exchange of ADP
and ATP across the inner mitochondrial membrane
is a fundamental cellular process. This exchange is facilitated by
the adenine nucleotide translocase, the structure and function of
which are critically dependent on the signature phospholipid of mitochondria,
cardiolipin (CL). Here we employ multiscale molecular dynamics simulations
to investigate CL interactions within a membrane environment. Using
simulations at both coarse-grained and atomistic resolutions, we identify
three CL binding sites on the translocase, in agreement with those
seen in crystal structures and inferred from nuclear magnetic resonance
measurements. Characterization of the free energy landscape for lateral
lipid interaction via potential of mean force calculations demonstrates
the strength of interaction compared to those of binding sites on
other mitochondrial membrane proteins, as well as their selectivity
for CL over other phospholipids. Extending the analysis to other members
of the family, yeast Aac2p and mouse uncoupling protein 2, suggests
a degree of conservation. Simulation of large patches of a model mitochondrial
membrane containing multiple copies of the translocase shows that
CL interactions persist in the presence of protein–protein
interactions and suggests CL may mediate interactions between translocases.
This study provides a key example of how computational microscopy
may be used to shed light on regulatory lipid–protein interactions.
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Affiliation(s)
- George Hedger
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Sarah L Rouse
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,Department of Life Sciences, Imperial College London , London SW7 2AZ, U.K
| | - Jan Domański
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K.,D. E. Shaw Research , 120 West 45th Street, 39th Floor, New York, New York 10036, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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29
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Duneau JP, Khao J, Sturgis JN. Lipid perturbation by membrane proteins and the lipophobic effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:126-134. [PMID: 27794424 DOI: 10.1016/j.bbamem.2016.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 11/26/2022]
Abstract
Understanding how membrane proteins interact with their environment is fundamental to the understanding of their structure, function and interactions. We have performed coarse-grained molecular dynamics simulations on a series of membrane proteins in a membrane environment to examine the perturbations of the lipids by the presence of protein. We analyze these perturbations in terms of elastic membrane deformations and local lipid protein interactions. However these two factors are insufficient to describe the variety of effects that we observe and the changes caused by membranes proteins to the structure and dynamics of their lipid environment. Other factors that change the conformation available to lipid molecules are evident and are able to modify lipid structure far from the protein surface, and thus mediate long-range interactions between membrane proteins. We suggest that these multiple modifications to lipid behavior are responsible, at the molecular level, for the lipophobic effect we have proposed to account for our observations of membrane protein organization.
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Affiliation(s)
- Jean-Pierre Duneau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
| | - Jonathan Khao
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France
| | - James N Sturgis
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
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30
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Chavent M, Duncan AL, Sansom MS. Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. Curr Opin Struct Biol 2016; 40:8-16. [PMID: 27341016 PMCID: PMC5404110 DOI: 10.1016/j.sbi.2016.06.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 11/21/2022]
Abstract
Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Sp Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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31
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Wang S, Ing C, Emami S, Jiang Y, Liang H, Pomès R, Brown LS, Ladizhansky V. Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics. J Phys Chem B 2016; 120:9887-902. [DOI: 10.1021/acs.jpcb.6b06731] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shenlin Wang
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Christopher Ing
- Molecular
Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Sanaz Emami
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Yunjiang Jiang
- Department
of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department
of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Régis Pomès
- Molecular
Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Leonid S. Brown
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Vladimir Ladizhansky
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
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32
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Landreh M, Marty MT, Gault J, Robinson CV. A sliding selectivity scale for lipid binding to membrane proteins. Curr Opin Struct Biol 2016; 39:54-60. [PMID: 27155089 PMCID: PMC5287393 DOI: 10.1016/j.sbi.2016.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/11/2016] [Accepted: 04/20/2016] [Indexed: 01/24/2023]
Abstract
Biological membranes form barriers that are essential for cellular integrity and compartmentalisation. Proteins in the membrane have co-evolved with their hydrophobic lipid environment, which serves as a solvent for proteins with very diverse requirements. As a result, their interactions range from non-selective to highly discriminating. Mass spectrometry enables us to monitor how lipids interact with membrane proteins and assess their effects on structure and dynamics. Recent studies illustrate the ability to differentiate specific lipid binding, preferential interactions with lipid subsets, and nonselective annular contacts. Here, we consider the biological implications of different lipid-binding scenarios and propose that binding occurs on a sliding selectivity scale, in line with the view of biological membranes as facilitators of dynamic protein and lipid organization.
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Affiliation(s)
- Michael Landreh
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Michael T Marty
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Joseph Gault
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Carol V Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom.
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33
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Klein N, Hellmann N, Schneider D. Anionic Lipids Modulate the Activity of the Aquaglyceroporin GlpF. Biophys J 2016; 109:722-31. [PMID: 26287624 DOI: 10.1016/j.bpj.2015.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023] Open
Abstract
The structure and composition of a biological membrane can severely influence the activity of membrane-embedded proteins. Here, we show that the E. coli aquaglyceroporin GlpF has only little activity in lipid bilayers formed from native E. coli lipids. Thus, at first glance, GlpF appears to not be optimized for its natural membrane environment. In fact, we found that GlpF activity was severely affected by negatively charged lipids regardless of the exact chemical nature of the lipid headgroup, whereas GlpF was not sensitive to changes in the lateral membrane pressure. These observations illustrate a potential mechanism by which the activity of an α-helical membrane protein is modulated by the negative charge density around the protein.
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Affiliation(s)
- Noreen Klein
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Nadja Hellmann
- Institut für Molekulare Biophysik, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg Universität Mainz, Mainz, Germany.
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34
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Hedger G, Shorthouse D, Koldsø H, Sansom MSP. Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor. J Phys Chem B 2016; 120:8154-63. [PMID: 27109430 PMCID: PMC5002933 DOI: 10.1021/acs.jpcb.6b01387] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Lipid molecules can
bind to specific sites on integral membrane
proteins, modulating their structure and function. We have undertaken
coarse-grained simulations to calculate free energy profiles for glycolipids
and phospholipids interacting with modulatory sites on the transmembrane
helix dimer of the EGF receptor within a lipid bilayer environment.
We identify lipid interaction sites at each end of the transmembrane
domain and compute interaction free energy profiles for lipids with
these sites. Interaction free energies ranged from ca. −40
to −4 kJ/mol for different lipid species. Those lipids (glycolipid
GM3 and phosphoinositide PIP2) known to modulate EGFR function
exhibit the strongest binding to interaction sites on the EGFR, and
we are able to reproduce the preference for interaction with GM3 over
other glycolipids suggested by experiment. Mutation of amino acid
residues essential for EGFR function reduce the binding free energy
of these key lipid species. The residues interacting with the lipids
in the simulations are in agreement with those suggested by experimental
(mutational) studies. This approach provides a generalizable tool
for characterizing the interactions of lipids that bind to specific
sites on integral membrane proteins.
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Affiliation(s)
- George Hedger
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - David Shorthouse
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.,MRC Cancer Unit, University of Cambridge , MRC Research Centre, Box 197, Cambridge CB2 0X1, United Kingdom
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom.,D. E. Shaw Research , 120 West 45th Street, 39th floor, New York, New York 10036, United States
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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35
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Hanson SM, Newstead S, Swartz KJ, Sansom MSP. Capsaicin interaction with TRPV1 channels in a lipid bilayer: molecular dynamics simulation. Biophys J 2016; 108:1425-1434. [PMID: 25809255 PMCID: PMC4375533 DOI: 10.1016/j.bpj.2015.02.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/29/2015] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
Transient receptor potential vanilloid subtype 1 (TRPV1) is a heat-sensitive ion channel also involved in pain sensation, and is the receptor for capsaicin, the active ingredient of hot chili peppers. The recent structures of TRPV1 revealed putative ligand density within the S1 to S4 voltage-sensor-like domain of the protein. However, questions remain regarding the dynamic role of the lipid bilayer in ligand binding to TRPV1. Molecular dynamics simulations were used to explore behavior of capsaicin in a 1-palmitoyl-2-oleoyl phosphatidylcholine bilayer and with the target S1–S4 transmembrane helices of TRPV1. Equilibrium simulations reveal a preferred interfacial localization for capsaicin. We also observed a capsaicin molecule flipping from the extracellular to the intracellular leaflet, and subsequently able to access the intracellular TRPV1 binding site. Calculation of the potential of mean force (i.e., free energy profile) of capsaicin along the bilayer normal confirms that it prefers an interfacial localization. The free energy profile indicates that there is a nontrivial but surmountable barrier to the flipping of capsaicin between opposing leaflets of the bilayer. Molecular dynamics of the S1–S4 transmembrane helices of the TRPV1 in a lipid bilayer confirm that Y511, known to be crucial to capsaicin binding, has a distribution along the bilayer normal similar to that of the aromatic group of capsaicin. Simulations were conducted of the TRPV1 S1–S4 transmembrane helices in the presence of capsaicin placed in the aqueous phase, in the lipid, or docked to the protein. No stable interaction between ligand and protein was seen for simulations initiated with capsaicin in the bilayer. However, interactions were seen between TRPV1 and capsaicin starting from the cytosolic aqueous phase, and capsaicin remained stable in the majority of simulations from the docked pose. We discuss the significance of capsaicin flipping from the extracellular to the intracellular leaflet and mechanisms of binding site access by capsaicin.
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Affiliation(s)
- Sonya M Hanson
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York; Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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36
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Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2390-2400. [PMID: 26946244 DOI: 10.1016/j.bbamem.2016.02.037] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 11/22/2022]
Abstract
Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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37
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Ternary structure reveals mechanism of a membrane diacylglycerol kinase. Nat Commun 2015; 6:10140. [PMID: 26673816 PMCID: PMC4703834 DOI: 10.1038/ncomms10140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/09/2015] [Indexed: 11/24/2022] Open
Abstract
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution. Diacylglycerol kinase is a small bacterial membrane-bound trimer that catalyses diacylglycerol conversion to phosphatidic acid. Here, the authors solve the crystal structure of the kinase bound to a lipid substrate and an ATP analogue, and show that the active site arose through convergent evolution.
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38
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Koldsø H, Sansom MSP. Organization and Dynamics of Receptor Proteins in a Plasma Membrane. J Am Chem Soc 2015; 137:14694-704. [PMID: 26517394 DOI: 10.1021/jacs.5b08048] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interactions of membrane proteins are influenced by their lipid environment, with key lipid species able to regulate membrane protein function. Advances in high-resolution microscopy can reveal the organization and dynamics of proteins and lipids within living cells at resolutions <200 nm. Parallel advances in molecular simulations provide near-atomic-resolution models of the dynamics of the organization of membranes of in vivo-like complexity. We explore the dynamics of proteins and lipids in crowded and complex plasma membrane models, thereby closing the gap in length and complexity between computations and experiments. Our simulations provide insights into the mutual interplay between lipids and proteins in determining mesoscale (20-100 nm) fluctuations of the bilayer, and in enabling oligomerization and clustering of membrane proteins.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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Molecular simulations of glycolipids: Towards mammalian cell membrane models. Biochimie 2015; 120:105-9. [PMID: 26427555 PMCID: PMC4710579 DOI: 10.1016/j.biochi.2015.09.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 09/25/2015] [Indexed: 12/19/2022]
Abstract
Glycolipids are key components of mammalian cell membranes, influencing a diverse range of cellular functions. For example, a number of receptor tyrosine kinases, including the epidermal growth factor receptor (EGFR), are allosterically regulated by the glycolipid monosialodihexosylganglioside (GM3). Recent advances in molecular dynamics methods, especially the development of coarse-grained models, have enabled simulations of increasingly complex models of cell membranes. We demonstrate these methodological developments via a case study of a coarse-grained model for the ganglioside GM3. This glycolipid is included in simulations of a mixed lipid bilayer model reflecting the compositional complexity of a mammalian cell membrane. The resultant membrane model is used to simulate the interactions of GM3 with the transmembrane domain of the EGFR. We review recent progress in molecular dynamics simulations of glycolipids. A coarse-grained model of the ganglioside GM3 is described. The GM3 model is used in coarse-grained simulations of a mammalian cell membrane. We describe the interactions of GM3 with the transmembrane domain of the EGFR.
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40
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Wojdyla JA, Cutts E, Kaminska R, Papadakos G, Hopper JTS, Stansfeld PJ, Staunton D, Robinson CV, Kleanthous C. Structure and function of the Escherichia coli Tol-Pal stator protein TolR. J Biol Chem 2015; 290:26675-87. [PMID: 26354441 PMCID: PMC4646322 DOI: 10.1074/jbc.m115.671586] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 12/31/2022] Open
Abstract
TolR is a 15-kDa inner membrane protein subunit of the Tol-Pal complex in Gram-negative bacteria, and its function is poorly understood. Tol-Pal is recruited to cell division sites where it is involved in maintaining the integrity of the outer membrane. TolR is related to MotB, the peptidoglycan (PG)-binding stator protein from the flagellum, suggesting it might serve a similar role in Tol-Pal. The only structure thus far reported for TolR is of the periplasmic domain from Haemophilus influenzae in which N- and C-terminal residues had been deleted (TolR(62–133), Escherichia coli numbering). H. influenzae TolR(62–133) is a symmetrical dimer with a large deep cleft at the dimer interface. Here, we present the 1.7-Å crystal structure of the intact periplasmic domain of E. coli TolR (TolR(36–142)). E. coli TolR(36–142) is also dimeric, but the architecture of the dimer is radically different from that of TolR(62–133) due to the intertwining of its N and C termini. TolR monomers are rotated ∼180° relative to each other as a result of this strand swapping, obliterating the putative PG-binding groove seen in TolR(62–133). We found that removal of the strand-swapped regions (TolR(60–133)) exposes cryptic PG binding activity that is absent in the full-length domain. We conclude that to function as a stator in the Tol-Pal complex dimeric TolR must undergo large scale structural remodeling reminiscent of that proposed for MotB, where the N- and C-terminal sequences unfold in order for the protein to both reach and bind the PG layer ∼90 Å away from the inner membrane.
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Affiliation(s)
- Justyna A Wojdyla
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Erin Cutts
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Renata Kaminska
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Grigorios Papadakos
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Jonathan T S Hopper
- the Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Phillip J Stansfeld
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - David Staunton
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Carol V Robinson
- the Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Colin Kleanthous
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
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Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MSP. MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure 2015; 23:1350-61. [PMID: 26073602 PMCID: PMC4509712 DOI: 10.1016/j.str.2015.05.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/24/2015] [Accepted: 05/02/2015] [Indexed: 01/26/2023]
Abstract
There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein. A simulation pipeline for predicting the location of a membrane protein in a bilayer A protocol for identifying novel membrane protein structures in the PDB Analysis of lipid binding sites and local bilayer deformation by membrane proteins Functional implications from enhanced understanding of local membrane environments
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Affiliation(s)
- Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph E Goose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Caffrey
- Schools of Medicine and Biochemistry & Immunology, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Cordeiro RM. Molecular dynamics simulations of the transport of reactive oxygen species by mammalian and plant aquaporins. Biochim Biophys Acta Gen Subj 2015; 1850:1786-94. [PMID: 25982446 DOI: 10.1016/j.bbagen.2015.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Aquaporins are responsible for water transport across lipid membranes. They are also able to transport reactive oxygen species, playing an important role in redox signaling. Certain plant aquaporins have even the ability to be regulated by oxidative stress. However, the underlying mechanisms are still not fully understood. METHODS Here, molecular dynamics simulations were employed to determine the activation free energies related to the transport of reactive oxygen species through both mammalian and plant aquaporin models. RESULTS AND CONCLUSIONS Both aquaporins may transport hydrogen peroxide (H2O2) and the protonated form of superoxide radicals (HO2). The solution-to-pore transfer free energies were low for small oxy-radicals, suggesting that even highly reactive hydroxyl radicals (HO) might have access to the pore interior and oxidize amino acids responsible for channel selectivity. In the plant aquaporin, no significant change in water permeability was observed upon oxidation of the solvent-exposed disulfide bonds at the extracellular region. During the simulated time scale, the existence of a direct oxidative gating mechanism involving these disulfide bonds could not be demonstrated. GENERAL SIGNIFICANCE Simulation results may improve the understanding of redox signaling mechanisms and help in the interpretation of protein oxidative labeling experiments.
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Affiliation(s)
- Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580, Santo André, SP, Brazil.
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Zakhvataev VE. Tidal variations of radon activity as a possible factor synchronizing biological processes. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915010273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kalli AC, Sansom MSP, Reithmeier RAF. Molecular dynamics simulations of the bacterial UraA H+-uracil symporter in lipid bilayers reveal a closed state and a selective interaction with cardiolipin. PLoS Comput Biol 2015; 11:e1004123. [PMID: 25729859 PMCID: PMC4346270 DOI: 10.1371/journal.pcbi.1004123] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/09/2015] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a “proton trap” that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane. Symporters are proteins that are responsible for the co-transport of ions and small molecule solutes across cell membranes. UraA is an example of a symporter, and is responsible for the proton-driven uptake of uracil in bacteria like E. coli. Despite its importance as a member of a large family of nucleobase/ascorbate transporters (NAT) and the existence of structural and functional data, the mechanism by which UraA transports uracil across the bacterial membrane, and in particular the role of its diverse and complex lipid environment in the transport mechanism, remains elusive. In this study, we have used a multiscale computational methodology to examine the dynamics of UraA and to elucidate its interactions with lipids that resemble its native environment in the bacterial inner membrane. Our results demonstrate that negatively-charged lipids in the membrane (phosphatidylglycerol and cardiolipin) associate preferentially with UraA and may play a role in its function. Additionally, our simulations resulted in a closed state of UraA, a likely intermediate in the transport mechanism that may not be readily accessible by experimental methods.
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Affiliation(s)
- Antreas C. Kalli
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Ma X, Shatil-Cohen A, Ben-Dor S, Wigoda N, Perera IY, Im YJ, Diminshtein S, Yu L, Boss WF, Moshelion M, Moran N. Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway? PLANTA 2015; 241:741-55. [PMID: 25486887 DOI: 10.1007/s00425-014-2216-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/25/2014] [Indexed: 05/07/2023]
Abstract
MAIN CONCLUSION Enhancing the membrane content of PtdInsP 2 , the already-recognized protein-regulating lipid, increased the osmotic water permeability of tobacco protoplasts, apparently by increasing the abundance of active aquaporins in their membranes. While phosphoinositides are implicated in cell volume changes and are known to regulate some ion channels, their modulation of aquaporins activity has not yet been reported for any organism. To examine this, we compared the osmotic water permeability (P f) of protoplasts isolated from tobacco (Nicotiana tabacum) cultured cells (NT1) with different (genetically lowered or elevated relative to controls) levels of inositol trisphosphate (InsP3) and phosphatidyl inositol [4,5] bisphosphate (PtdInsP2). To achieve this, the cells were transformed with, respectively, the human InsP3 5-phosphatase ('Ptase cells') or human phosphatidylinositol (4) phosphate 5-kinase ('PIPK cells'). The mean P f of the PIPK cells was several-fold higher relative to that of controls and Ptase cells. Three results favor aquaporins over the membrane matrix as underlying this excessive P f: (1) transient expression of the maize aquaporin ZmPIP2;4 in the PIPK cells increased P f by 12-30 μm s(-1), while in the controls only by 3-4 μm s(-1). (2) Cytosol acidification-known to inhibit aquaporins-lowered the P f in the PIPK cells down to control levels. (3) The transcript of at least one aquaporin was elevated in the PIPK cells. Together, the three results demonstrate the differences between the PIPK cells and their controls, and suggest a hitherto unobserved regulation of aquaporins by phosphoinositides, which could occur through direct interaction or indirect phosphoinositides-dependent cellular effects.
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Affiliation(s)
- Xiaohong Ma
- The Robert H. Smith Faculty of Agriculture Food and Environment, The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
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Gu Y, Stansfeld PJ, Zeng Y, Dong H, Wang W, Dong C. Lipopolysaccharide is inserted into the outer membrane through an intramembrane hole, a lumen gate, and the lateral opening of LptD. Structure 2015; 23:496-504. [PMID: 25684578 PMCID: PMC4353691 DOI: 10.1016/j.str.2015.01.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 11/25/2022]
Abstract
Lipopolysaccharide (LPS) is essential for the vitality of most Gram-negative bacteria and plays an important role in bacterial multidrug resistance. The LptD/E translocon inserts LPS into the outer leaflet, the mechanism of which is poorly understood. Here, we report mutagenesis, functional assays, and molecular dynamics simulations of the LptD/E complex, which suggest two distinct pathways for the insertion of LPS. The N-terminal domain of LptD comprises a hydrophobic slide that injects the acyl tails of LPS directly into the outer membrane through an intramembrane hole, while the core oligosaccharide and O-antigen pass a lumen gate that triggers the unzipping of the lateral opening between strands β1C and β26C of the barrel of LptD, to finalize LPS insertion. Mutation of the LPS transport related residues or block of the LPS transport pathways results in the deaths of Escherichia coli. These findings are important for the development of novel antibiotics. Hydrophobic residues at the N-terminal domain are essential for LPS transport A hydrophobic intramembrane hole of LptD is critical for LPS insertion A lumenal gate of LptD is important for translocation of LPS
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Affiliation(s)
- Yinghong Gu
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Yi Zeng
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Haohao Dong
- Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - Wenjian Wang
- Laboratory of Department of Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080, China.
| | - Changjiang Dong
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
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Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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Trick JL, Wallace EJ, Bayley H, Sansom MSP. Designing a hydrophobic barrier within biomimetic nanopores. ACS NANO 2014; 8:11268-11279. [PMID: 25317664 DOI: 10.1021/nn503930p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nanopores in membranes have a range of potential applications. Biomimetic design of nanopores aims to mimic key functions of biological pores within a stable template structure. Molecular dynamics simulations have been used to test whether a simple β-barrel protein nanopore can be modified to incorporate a hydrophobic barrier to permeation. Simulations have been used to evaluate functional properties of such nanopores, using water flux as a proxy for ionic conductance. The behavior of these model pores has been characterized as a function of pore size and of the hydrophobicity of the amino acid side chains lining the narrow central constriction of the pore. Potential of mean force calculations have been used to calculate free energy landscapes for water and for ion permeation in selected models. These studies demonstrate that a hydrophobic barrier can indeed be designed into a β-barrel protein nanopore, and that the height of the barrier can be adjusted by modifying the number of consecutive rings of hydrophobic side chains. A hydrophobic barrier prevents both water and ion permeation even though the pore is sterically unoccluded. These results both provide insights into the nature of hydrophobic gating in biological pores and channels, and furthermore demonstrate that simple design features may be computationally transplanted into β-barrel membrane proteins to generate functionally complex nanopores.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
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Klein N, Neumann J, O'Neil JD, Schneider D. Folding and stability of the aquaglyceroporin GlpF: Implications for human aqua(glycero)porin diseases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:622-33. [PMID: 25462169 DOI: 10.1016/j.bbamem.2014.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 01/22/2023]
Abstract
Aquaporins are highly selective polytopic transmembrane channel proteins that facilitate the permeation of water across cellular membranes in a large diversity of organisms. Defects in aquaporin function are associated with common diseases, such as nephrogenic diabetes insipidus, congenital cataract and certain types of cancer. In general, aquaporins have a highly conserved structure; from prokaryotes to humans. The conserved structure, together with structural dynamics and the structural framework for substrate selectivity is discussed. The folding pathway of aquaporins has been a topic of several studies in recent years. These studies revealed that a conserved protein structure can be reached by following different folding pathways. Based on the available data, we suggest a complex folding pathway for aquaporins, starting from the insertion of individual helices up to the formation of the tetrameric aquaporin structure. The consequences of some known mutations in human aquaporin-encoding genes, which most likely affect the folding and stability of human aquaporins, are discussed.
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Affiliation(s)
- Noreen Klein
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Jennifer Neumann
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Joe D O'Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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