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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: 156] [Impact Index Per Article: 31.2] [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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Menozzi I, Polverini E, Berni R. Deciphering protein dynamics changes along the pathway of retinol uptake by cellular retinol-binding proteins 1 and 2. Arch Biochem Biophys 2018; 645:107-116. [PMID: 29567208 DOI: 10.1016/j.abb.2018.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/12/2018] [Accepted: 03/18/2018] [Indexed: 12/11/2022]
Abstract
Four Cellular Retinol-binding Proteins (CRBP 1, 2, 3, 4) are encoded in the human genome. CRBP 1 and 2, sharing a 56% amino acid sequence identity, exhibit the highest binding affinities for retinol. Previous NMR studies provided some insights into the mechanism of retinol uptake, but details of such mechanism remain to be elucidated. Herein, the results of molecular dynamics simulations for the uptake of retinol by CRBP 1 and 2 are consistent with the presence of two different retinol entry points, both involving the 'cap region' (α-helices I and II and neighboring loops). We observed that a hydrophobic patch at the surface of the 'portal region' (α-helix II, CD and EF loops) of CRBP 1 attracts retinol, which accesses the binding cavity through an opening generated by the concerted movements of Arg58 and Phe57, present in the CD loop. In CRBP 2 a different distribution of the surface residues of the 'cap region' allows retinol to access the binding cavity by sinking in a hydrophobic matrix between the two α-helices. Polar interactions mainly affect retinol movements inside the β-barrel cavities of both CRBPs. The interaction energy profiles are in agreement with the different behavior of the two protein systems.
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Affiliation(s)
- Ilaria Menozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze, 23/A, University of Parma, 43124 Parma, Italy
| | - Eugenia Polverini
- Department of Mathematical, Physical and Computer Sciences, Parco Area delle Scienze, 7/A, University of Parma, 43124 Parma, Italy.
| | - Rodolfo Berni
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze, 23/A, University of Parma, 43124 Parma, Italy.
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3
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Kaieda S, Halle B. Time Scales of Conformational Gating in a Lipid-Binding Protein. J Phys Chem B 2015; 119:7957-67. [DOI: 10.1021/acs.jpcb.5b03214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuji Kaieda
- Department of Biophysical
Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Department of Biophysical
Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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4
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Li Y, Li X, Dong Z. Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations. Biochemistry 2014; 53:6409-17. [PMID: 25231537 PMCID: PMC4196735 DOI: 10.1021/bi500374t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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In this work, we investigate the
dynamic motions of fatty acid
binding protein 4 (FABP4) in the absence and presence of a ligand
by explicitly solvated all-atom molecular dynamics simulations. The
dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is
compared via multiple 1.2 μs simulations. In our simulations,
the protein interconverts between the open and closed states. Ligand-free
FABP4 prefers the closed state, whereas ligand binding induces a conformational
transition to the open state. Coupled with opening and closing of
FABP4, the ligand adopts distinct binding modes, which are identified
and compared with crystal structures. The concerted dynamics of protein
and ligand suggests that there may exist multiple FABP4–ligand
binding conformations. Thus, this work provides details about how
ligand binding affects the conformational preference of FABP4 and
how ligand binding is coupled with a conformational change of FABP4
at an atomic level.
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Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota , Austin, Minnesota 55912, United States
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5
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Esteves A, Paulino Zunini M. In silicostudies ofEchinococcus granulosusFABPs. J Biomol Struct Dyn 2013; 31:224-39. [DOI: 10.1080/07391102.2012.698246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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6
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Paramo T, Garzón D, Holdbrook DA, Khalid S, Bond PJ. The simulation approach to lipid-protein interactions. Methods Mol Biol 2013; 974:435-455. [PMID: 23404287 DOI: 10.1007/978-1-62703-275-9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.
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Affiliation(s)
- Teresa Paramo
- Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK
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7
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Adeli M, Kalantari M, Parsamanesh M, Sadeghi E, Mahmoudi M. Synthesis of new hybrid nanomaterials: promising systems for cancer therapy. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2011; 7:806-17. [PMID: 21419867 DOI: 10.1016/j.nano.2011.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/18/2010] [Accepted: 02/19/2011] [Indexed: 10/18/2022]
Abstract
UNLABELLED Polyrotaxanes consisting of cyclodextrin rings, polyethylene glycol axes and quantum dot (QD) stoppers were synthesized and characterized. The molecular self-assembly of polyrotaxanes led to spindlelike nano-objects whose shape, size and position were dominated by QD stoppers. Due to their well-defined molecular self-assemblies, carbohydrate backbone, high functionality and several types of functional groups together with the high luminescence yield, synthesized hybrid nanostructures were recognized as promising candidates for biomedical applications. The potential applications of the molecular self-assemblies as drug-delivery systems was investigated by conjugation of doxorubicin (DOX) to their functional groups and then release the drug inside the cancer cells in mouse tissue connective fibroblast adhesive cell line L929. It was found that the molecular self-assemblies quickly transfer through the cell membrane and slowly release the drug into the intracellular environment. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and cell cycle assays showed that the molecular self-assemblies degrade back into individual molecules that can be broken down by the cell metabolically, confirming that they can be used as new drug-delivery systems with high treatment efficacy and minimum side effects for future cancer therapy, thus forming a firm foundation for further study and improvement. FROM THE CLINICAL EDITOR This study investigates polyrotaxanes consisting of cyclodextrin rings, polyethylene glycol axes and quantum dot (QD) stoppers as promising candidates for biomedical applications, including cancer therapy.
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Affiliation(s)
- Mohsen Adeli
- Department of Chemistry, Faculty of Science, Lorestan University, Khoramabad, Iran.
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8
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Marom M, Safonov R, Amram S, Avneon Y, Nachliel E, Gutman M, Zohary K, Azem A, Tsfadia Y. Interaction of the Tim44 C-Terminal Domain with Negatively Charged Phospholipids. Biochemistry 2009; 48:11185-95. [DOI: 10.1021/bi900998v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Milit Marom
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roman Safonov
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shay Amram
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoav Avneon
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Esther Nachliel
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Menachem Gutman
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Keren Zohary
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Abdussalam Azem
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yossi Tsfadia
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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9
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Insight into the interaction sites between fatty acid binding proteins and their ligands. J Mol Model 2009; 16:929-38. [DOI: 10.1007/s00894-009-0599-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/20/2009] [Indexed: 10/20/2022]
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