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Hilpert C, Beranger L, Souza PCT, Vainikka PA, Nieto V, Marrink SJ, Monticelli L, Launay G. Facilitating CG Simulations with MAD: The MArtini Database Server. J Chem Inf Model 2023; 63:702-710. [PMID: 36656159 DOI: 10.1021/acs.jcim.2c01375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.
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Affiliation(s)
- Cécile Hilpert
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Louis Beranger
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Paulo C T Souza
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Vincent Nieto
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Luca Monticelli
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Guillaume Launay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
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2
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Kok ZY, Stoddart LA, Mistry SJ, Mocking TAM, Vischer HF, Leurs R, Hill SJ, Mistry SN, Kellam B. Optimization of Peptide Linker-Based Fluorescent Ligands for the Histamine H 1 Receptor. J Med Chem 2022; 65:8258-8288. [PMID: 35734860 PMCID: PMC9234962 DOI: 10.1021/acs.jmedchem.2c00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histamine H1 receptor (H1R) has recently been implicated in mediating cell proliferation and cancer progression; therefore, high-affinity H1R-selective fluorescent ligands are desirable tools for further investigation of this behavior in vitro and in vivo. We previously reported a H1R fluorescent ligand, bearing a peptide-linker, based on antagonist VUF13816 and sought to further explore structure-activity relationships (SARs) around the linker, orthostere, and fluorescent moieties. Here, we report a series of high-affinity H1R fluorescent ligands varying in peptide linker composition, orthosteric targeting moiety, and fluorophore. Incorporation of a boron-dipyrromethene (BODIPY) 630/650-based fluorophore conferred high binding affinity to our H1R fluorescent ligands, remarkably overriding the linker SAR observed in corresponding unlabeled congeners. Compound 31a, both potent and subtype-selective, enabled H1R visualization using confocal microscopy at a concentration of 10 nM. Molecular docking of 31a with the human H1R predicts that the optimized peptide linker makes interactions with key residues in the receptor.
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Affiliation(s)
- Zhi Yuan Kok
- Division of Biomolecular Science and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, U.K.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, the Midlands, Nottingham NG7 2UH, U.K
| | - Leigh A Stoddart
- Division of Physiology, Pharmacology & Neuroscience, Medical School, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, U.K.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, the Midlands, Nottingham NG7 2UH, U.K
| | - Sarah J Mistry
- Division of Biomolecular Science and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, U.K.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, the Midlands, Nottingham NG7 2UH, U.K
| | - Tamara A M Mocking
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelean 1083, 1083 HV Amsterdam, The Netherlands
| | - Henry F Vischer
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelean 1083, 1083 HV Amsterdam, The Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelean 1083, 1083 HV Amsterdam, The Netherlands
| | - Stephen J Hill
- Division of Physiology, Pharmacology & Neuroscience, Medical School, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, U.K.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, the Midlands, Nottingham NG7 2UH, U.K
| | - Shailesh N Mistry
- Division of Biomolecular Science and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, U.K
| | - Barrie Kellam
- Division of Biomolecular Science and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, University Park, Nottingham NG7 2RD, U.K.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, the Midlands, Nottingham NG7 2UH, U.K
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3
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Lim TKY, Ruthazer ES. Microglial trogocytosis and the complement system regulate axonal pruning in vivo. eLife 2021; 10:e62167. [PMID: 33724186 PMCID: PMC7963485 DOI: 10.7554/elife.62167] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 02/28/2021] [Indexed: 12/14/2022] Open
Abstract
Partial phagocytosis-called trogocytosis-of axons by microglia has been documented in ex vivo preparations but has not been directly observed in vivo. The mechanisms that modulate microglial trogocytosis of axons and its function in neural circuit development remain poorly understood. Here, we directly observe axon trogocytosis by microglia in vivo in the developing Xenopus laevis retinotectal circuit. We show that microglia regulate pruning of retinal ganglion cell axons and are important for proper behavioral response to dark and bright looming stimuli. Using bioinformatics, we identify amphibian regulator of complement activation 3, a homolog of human CD46, as a neuronally expressed synapse-associated complement inhibitory molecule that inhibits trogocytosis and axonal pruning. Using a membrane-bound complement C3 fusion protein, we demonstrate that enhancing complement activity enhances axonal pruning. Our results support the model that microglia remodel axons via trogocytosis and that neurons can control this process through expression of complement inhibitory proteins.
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Affiliation(s)
- Tony KY Lim
- Department of Neurology & Neurosurgery, Montreal Neurological Institute-Hospital, McGill UniversityMontrealCanada
| | - Edward S Ruthazer
- Department of Neurology & Neurosurgery, Montreal Neurological Institute-Hospital, McGill UniversityMontrealCanada
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Marchetto A, Si Chaib Z, Rossi CA, Ribeiro R, Pantano S, Rossetti G, Giorgetti A. CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations. Molecules 2020; 25:E5934. [PMID: 33333836 PMCID: PMC7765266 DOI: 10.3390/molecules25245934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/28/2020] [Indexed: 12/17/2022] Open
Abstract
Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.
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Affiliation(s)
- Alessandro Marchetto
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Carlo Alberto Rossi
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
| | - Rui Ribeiro
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay;
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (A.M.); (C.A.R.); (R.R.)
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany;
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5
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Wu C, Liu S, Zhang S, Yang Z. Molcontroller: A VMD Graphical User Interface Featuring Molecule Manipulation. J Chem Inf Model 2020; 60:5126-5131. [DOI: 10.1021/acs.jcim.0c00754] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- ChenChen Wu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shitong Zhang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu 215123, China
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Damre M, Marchetto A, Giorgetti A. MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. Nucleic Acids Res 2020; 47:W456-W461. [PMID: 31106328 PMCID: PMC6602572 DOI: 10.1093/nar/gkz416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 01/06/2023] Open
Abstract
Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories.
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Affiliation(s)
- Mangesh Damre
- Neurobiology, International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy.,Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy
| | - Alessandro Marchetto
- Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy.,Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany
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Xia Q, Zhang Y, Li Z, Hou X, Feng N. Red blood cell membrane-camouflaged nanoparticles: a novel drug delivery system for antitumor application. Acta Pharm Sin B 2019; 9:675-689. [PMID: 31384529 PMCID: PMC6663920 DOI: 10.1016/j.apsb.2019.01.011] [Citation(s) in RCA: 333] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/30/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Erythrocytes (red blood cells, RBCs) are the most abundant circulating cells in the blood and have been widely used in drug delivery systems (DDS) because of their features of biocompatibility, biodegradability, and long circulating half-life. Accordingly, a "camouflage" comprised of erythrocyte membranes renders nanoparticles as a platform that combines the advantages of native erythrocyte membranes with those of nanomaterials. Following injection into the blood of animal models, the coated nanoparticles imitate RBCs and interact with the surroundings to achieve long-term circulation. In this review, the biomimetic platform of erythrocyte membrane-coated nano-cores is described with regard to various aspects, with particular focus placed on the coating mechanism, preparation methods, verification methods, and the latest anti-tumor applications. Finally, further functional modifications of the erythrocyte membranes and attempts to fuse the surface properties of multiple cell membranes are discussed, providing a foundation to stimulate extensive research into multifunctional nano-biomimetic systems.
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Key Words
- ABC, accelerated blood clearance
- APCs, antigen presenting cells
- Antitumor
- AuNCs, gold nanocages
- AuNPs, gold nanoparticles
- Biomimetic nanoparticles
- C8bp, C8 binding protein
- CR1, complement receptor 1
- DAF, decay accelerating factor
- DDS, drug delivery systems
- DLS, dynamic light scattering
- Dox, doxorubicin
- Drug delivery
- ECM, extracellular matrix
- EPR, enhanced permeability and retention
- ETA, endothelin A
- EpCam, epithelial cell adhesion molecule
- FA, folic acid
- GA, gambogic acid
- H&E, hematoxylin and eosin
- HRP, homologous restriction protein
- MCP, membrane cofactor protein
- MNCs, magnetic nanoclusters
- MNs, magnetic nanoparticles
- MPS, mononuclear phagocyte system
- MRI, magnetic resonance imaging
- MSNs, mesoporous silica nanoparticles
- Membrane
- NIR, near-infrared radiation
- Nanoparticles
- PAI, photoacoustic imaging
- PBS, phosphate buffered saline
- PCL, poly(caprolactone)
- PDT, photodynamic therapy
- PEG, polyethylene glycol
- PFCs, perfluorocarbons
- PLA, poly(lactide acid)
- PLGA, poly(d,l-lactide-co-glycolide)
- PPy, polypyrrole
- PS, photosensitizers
- PTT, photothermal therapy
- PTX, paclitaxel
- RBCM-NPs, RBCM-coated nanoparticles
- RBCMs, RBC membranes
- RBCs, red blood cells
- RES, reticuloendothelial system
- ROS, reactive oxygen species
- RVs, RBCM-derived vesicles
- Red blood cells
- SEM, scanning electron microscopy
- SIRPα, signal-regulatory protein alpha
- TEM, transmission electron microscopy
- TEMPO, 2,2,6,6-tetramethylpiperidin-1-yl oxyl
- TPP, triphenylphosphonium
- UCNPs, upconversion nanoparticles
- UV, ultraviolet
- rHuPH20, recombinant hyaluronidase, PH20
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Affiliation(s)
| | | | | | | | - Nianping Feng
- Department of Pharmaceutical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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8
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Cacciotto P, Ramaswamy VK, Malloci G, Ruggerone P, Vargiu AV. Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters. Methods Mol Biol 2018; 1700:179-219. [PMID: 29177832 DOI: 10.1007/978-1-4939-7454-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Efflux pumps of the resistance nodulation division (RND) superfamily are among the major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural information on AcrAB-TolC and MexAB-OprM, major efflux pumps of Escherichia coli and Pseudomonas aeruginosa respectively, boosted intensive research aimed at understanding the molecular mechanisms ruling the active extrusion processes. In particular, several studies were devoted to the understanding of the determinants behind the extraordinary broad specificity of the RND transporters AcrB and MexB. In this chapter, we discuss the ever-growing role computational methods have been playing in deciphering key structural and dynamical features of these transporters and of their interaction with substrates and inhibitors. We further discuss and illustrate examples from our lab of how molecular docking, homology modeling, all-atom molecular dynamics simulations and in silico free energy estimations can all together give precious insights into the processes of recognition and extrusion of substrates, as well as on the possible inhibition strategies.
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Affiliation(s)
- Pierpaolo Cacciotto
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Venkata K Ramaswamy
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy.
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Abstract
Most interfacial enzymes undergo activation upon membrane binding. Interfacial activation is determined not only by the binding strength but also by the specific mode of protein-membrane interactions, including the angular orientation and membrane insertion of the enzymes. This chapter describes biophysical techniques to quantitatively evaluate membrane binding, orientation, membrane insertion, and activity of secreted phospholipase A2 (PLA2) and lipoxygenase (LO) enzymes. Procedures for recombinant production and purification of human pancreatic PLA2 and human 5-lipoxygenase (5-LO) are also presented. Several methods for measurements of membrane binding of peripheral proteins are described, i.e., fluorescence resonance energy transfer (FRET) from tryptophan or tyrosine residues of the protein to a fluorescent lipid in vesicles, changes in fluorescence of an environment-sensitive fluorescent lipid upon binding of proteins to membranes, and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. These methods produce the apparent binding constant, the protein-to-lipid binding stoichiometry, and the Hill cooperativity coefficient. Experimental procedures for segmental isotope labeling of proteins and determination of the orientation of membrane-bound proteins by polarized ATR-FTIR spectroscopy are described. Furthermore, evaluation of membrane insertion of peripheral proteins by a fluorescence quenching technique is outlined. Combination of the orientation and membrane insertion provides a unique configuration of the protein-membrane complex and hence elucidates certain details of the enzyme function, such as the modes of acquisition of a membrane-residing substrate and product release. Finally, assays for determination of the activities of secreted PLA2, soybean LO, and human 5-LO are described.
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Affiliation(s)
- S A Tatulian
- College of Sciences, University of Central Florida, Orlando, FL, United States.
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10
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Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Sci Rep 2016; 6:23249. [PMID: 26988596 PMCID: PMC4796874 DOI: 10.1038/srep23249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/03/2016] [Indexed: 11/30/2022] Open
Abstract
Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.
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11
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Javanainen M, Martinez-Seara H. Efficient preparation and analysis of membrane and membrane protein systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2468-2482. [PMID: 26947184 DOI: 10.1016/j.bbamem.2016.02.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/25/2022]
Abstract
Molecular dynamics (MD) simulations have become a highly important technique to consider lipid membrane systems, and quite often they provide considerable added value to laboratory experiments. Rapid development of both software and hardware has enabled the increase of time and size scales reachable by MD simulations to match those attainable by several accurate experimental techniques. However, until recently, the quality and maturity of software tools available for building membrane models for simulations as well as analyzing the results of these simulations have seriously lagged behind. Here, we discuss the recent developments of such tools from the end-users' point of view. In particular, we review the software that can be employed to build lipid bilayers and other related structures with or without embedded membrane proteins to be employed in MD simulations. Additionally, we provide a brief critical insight into force fields and MD packages commonly used for membrane and membrane protein simulations. Finally, we list analysis tools that can be used to study the properties of membrane and membrane protein systems. In all these points we comment on the respective compatibility of the covered tools. We also share our opinion on the current state of the available software. We briefly discuss the most commonly employed tools and platforms on which new software can be built. We conclude the review by providing a few ideas and guidelines on how the development of tools can be further boosted to catch up with the rapid pace at which the field of membrane simulation progresses. This includes improving the compatibility between software tools and promoting the openness of the codes on which these applications rely. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Matti Javanainen
- Department of Physics, Tampere University of Technology, Tampere, Finland.
| | - Hector Martinez-Seara
- Department of Physics, Tampere University of Technology, Tampere, Finland; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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12
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Keller RCA. The role and significance of potential lipid-binding regions in the mitochondrial protein import motor: an in-depth in silico study. 3 Biotech 2015; 5:1041-1051. [PMID: 28324412 PMCID: PMC4624131 DOI: 10.1007/s13205-015-0310-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/12/2015] [Indexed: 12/05/2022] Open
Abstract
Over the last two decades, an impressive progress has been made in the identification of novel factors in the translocation machineries of the mitochondrial protein import and their possible roles. The role of lipids and possible protein–lipids interactions remains a relatively unexplored territory. Investigating the role of potential lipid-binding regions in the sub-units of the mitochondrial motor might help to shed some more light in our understanding of protein–lipid interactions mechanistically. Bioinformatics results seem to indicate multiple potential lipid-binding regions in each of the sub-units. The subsequent characterization of some of those regions in silico provides insight into the mechanistic functioning of this intriguing and essential part of the protein translocation machinery. Details about the way the regions interact with phospholipids were found by the use of Monte Carlo simulations. For example, Pam18 contains one possible transmembrane region and two tilted surface bound conformations upon interaction with phospholipids. The results demonstrate that the presented bioinformatics approach might be useful in an attempt to expand the knowledge of the possible role of protein–lipid interactions in the mitochondrial protein translocation process.
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Affiliation(s)
- Rob C A Keller
- Section Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ, Nijmegen, The Netherlands.
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13
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Determining the N-terminal orientations of recombinant transmembrane proteins in the Escherichia coli plasma membrane. Sci Rep 2015; 5:15086. [PMID: 26462555 PMCID: PMC4604451 DOI: 10.1038/srep15086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022] Open
Abstract
In silico algorithms have been the common approach for transmembrane (TM) protein topology prediction. However, computational tools may produce questionable results and experimental validation has proven difficult. Although biochemical strategies are available to determine the C-terminal orientation of TM proteins, experimental strategies to determine the N-terminal orientation are still limited but needed because the N-terminal end is essential for membrane targeting. Here, we describe a new and easy method to effectively determine the N-terminal orientation of the target TM proteins in Escherichia coli plasma membrane environment. D94N, the mutant of bacteriorhodopsin from Haloarcula marismortui, can be a fusion partner to increase the production of the target TM proteins if their N-termini are in cytoplasm (Nin orientation). To create a suitable linker for orientating the target TM proteins with the periplasmic N-termini (Nout orientation) correctly, we designed a three-TM-helix linker fused at the C-terminus of D94N fusion partner (termed D94N-3TM) and found that D94N-3TM can specifically improve the production of the Nout target TM proteins. In conclusion, D94N and D94N-3TM fusion partners can be applied to determine the N-terminal end of the target TM proteins oriented either Nin or Nout by evaluating the net expression of the fusion proteins.
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Homeyer N, Gohlke H. Extension of the free energy workflow FEW towards implicit solvent/implicit membrane MM-PBSA calculations. Biochim Biophys Acta Gen Subj 2014; 1850:972-982. [PMID: 25450172 DOI: 10.1016/j.bbagen.2014.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 10/13/2014] [Accepted: 10/14/2014] [Indexed: 01/12/2023]
Abstract
BACKGROUND The number of high-resolution structures of pharmacologically relevant membrane proteins has been strongly increasing. This makes computing relative affinities of chemically similar compounds binding to a membrane protein possible in order to guide decision making in drug design. However, the preparation step of such calculations is time-consuming and complex. METHODS We extended the free energy workflow tool FEW, available in AMBER, towards facilitating the setup of molecular dynamics simulations with explicit membrane, and the setup and execution of effective binding energy calculations according to a 1-trajectory implicit solvent/implicit membrane MM-PBSA approach for multiple ligands binding to the same membrane protein. RESULTS We validated the implemented protocol initially on two model systems, a sodium ion in the presence of an implicit membrane slab and a proton traversing the M2 proton-channel of the influenza A virus. For the latter, we found a good agreement for several important events along the proton pathway with those obtained in a recent computational study. Finally, we performed a case study on effective binding energy calculations for a set of inhibitors binding to the M2 proton-channel. CONCLUSIONS From the case study, we estimate a considerable speed up in the setup and analysis times for implicit solvent/implicit membrane MM-PBSA calculations by the extended version of FEW compared to a manual preparation. GENERAL SIGNIFICANCE Together with the overall runtime and the analysis results, this suggests that such type of calculations can be valuable in later stages of drug design projects on membrane proteins. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Nadine Homeyer
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany.
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