1
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Marsch P, Rajagopal N, Nangia S. Biophysics of claudin proteins in tight junction architecture: Three decades of progress. Biophys J 2024:S0006-3495(24)00393-X. [PMID: 38859584 DOI: 10.1016/j.bpj.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/19/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024] Open
Abstract
Tight junctions are cell-cell adhesion complexes that act as gatekeepers of the paracellular space. Formed by several transmembrane proteins, the claudin family performs the primary gate-keeping function. The claudin proteins form charge and size-selective diffusion barriers to maintain homeostasis across endothelial and epithelial tissue. Of the 27 known claudins in mammals, some are known to seal the paracellular space, while others provide selective permeability. The differences in permeability arise due to the varying expression levels of claudins in each tissue. The tight junctions are observed as strands in freeze-fracture electron monographs; however, at the molecular level, tight junction strands form when multiple claudin proteins assemble laterally (cis assembly) within a cell and head-on (trans assembly) with claudins of the adjacent cell in a zipper-like architecture, closing the gap between the neighboring cells. The disruption of tight junctions caused by changing claudin expression levels or mutations can lead to diseases. Therefore, knowledge of the molecular architecture of the tight junctions and how that is tied to tissue-specific function is critical for fighting diseases. Here, we review the current understanding of the tight junctions accrued over the last three decades from experimental and computational biophysics perspectives.
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Affiliation(s)
- Patrick Marsch
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York
| | - Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York.
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2
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Pierce M, Ji J, Novak SX, Sieburg MA, Nangia S, Nangia S, Hougland JL. Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization. J Chem Inf Model 2023; 63:7159-7170. [PMID: 37939203 PMCID: PMC10685452 DOI: 10.1021/acs.jcim.3c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023]
Abstract
Membrane proteins are difficult to isolate and purify due to their dependence on the surrounding lipid membrane for structural stability. Detergents are often used to solubilize these proteins, with this approach requiring a careful balance between protein solubilization and denaturation. Determining which detergent is most appropriate for a given protein has largely been done empirically through screening, which requires large amounts of membrane protein and associated resources. Here, we describe an alternative to conventional detergent screening using a computational modeling approach to identify the most likely candidate detergents for solubilizing a protein of interest. We demonstrate our approach using ghrelin O-acyltransferase (GOAT), a member of the membrane-bound O-acyltransferase family of integral membrane enzymes that has not been solubilized or purified in active form. A computationally derived GOAT structural model provides the only structural information required for this approach. Using computational analysis of detergent ability to penetrate phospholipid bilayers and stabilize the GOAT structure, a panel of common detergents were rank-ordered for their proposed ability to solubilize GOAT. The simulations were performed at all-atom resolution for a combined simulation time of 24 μs. Independently, we biologically screened these detergents for their solubilization of fluorescently tagged GOAT constructs. We found computational prediction of protein structural stabilization was the better predictor of detergent solubilization ability, but neither approach was effective for predicting detergents that would support GOAT enzymatic function. The current rapid expansion of membrane protein computational models lacking experimental structural information and our computational detergent screening approach can greatly improve the efficiency of membrane protein detergent solubilization, supporting downstream functional and structural studies.
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Affiliation(s)
- Mariah
R. Pierce
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Sadie X. Novak
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Michelle A. Sieburg
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shivangi Nangia
- Department
of Chemistry, University of Hartford, West Hartford, Connecticut 06117, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse, New York 13244, United States
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
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3
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Raya-Sandino A, Lozada-Soto KM, Rajagopal N, Garcia-Hernandez V, Luissint AC, Brazil JC, Cui G, Koval M, Parkos CA, Nangia S, Nusrat A. Claudin-23 reshapes epithelial tight junction architecture to regulate barrier function. Nat Commun 2023; 14:6214. [PMID: 37798277 PMCID: PMC10556055 DOI: 10.1038/s41467-023-41999-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 09/26/2023] [Indexed: 10/07/2023] Open
Abstract
Claudin family tight junction proteins form charge- and size-selective paracellular channels that regulate epithelial barrier function. In the gastrointestinal tract, barrier heterogeneity is attributed to differential claudin expression. Here, we show that claudin-23 (CLDN23) is enriched in luminal intestinal epithelial cells where it strengthens the epithelial barrier. Complementary approaches reveal that CLDN23 regulates paracellular ion and macromolecule permeability by associating with CLDN3 and CLDN4 and regulating their distribution in tight junctions. Computational modeling suggests that CLDN23 forms heteromeric and heterotypic complexes with CLDN3 and CLDN4 that have unique pore architecture and overall net charge. These computational simulation analyses further suggest that pore properties are interaction-dependent, since differently organized complexes with the same claudin stoichiometry form pores with unique architecture. Our findings provide insight into tight junction organization and propose a model whereby different claudins combine to form multiple distinct complexes that modify epithelial barrier function by altering tight junction structure.
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Affiliation(s)
- Arturo Raya-Sandino
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA
| | | | - Anny-Claude Luissint
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jennifer C Brazil
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Guiying Cui
- Department of Pediatrics, Emory + Children's Center for Cystic Fibrosis and Airways Disease Research, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael Koval
- Departments of Medicine and Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Charles A Parkos
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA.
| | - Asma Nusrat
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
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4
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Berselli A, Alberini G, Benfenati F, Maragliano L. The impact of pathogenic and artificial mutations on Claudin-5 selectivity from molecular dynamics simulations. Comput Struct Biotechnol J 2023; 21:2640-2653. [PMID: 37138900 PMCID: PMC10149405 DOI: 10.1016/j.csbj.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Tight-junctions (TJs) are multi-protein complexes between adjacent endothelial or epithelial cells. In the blood-brain-barrier (BBB), they seal the paracellular space and the Claudin-5 (Cldn5) protein forms their backbone. Despite the fundamental role in brain homeostasis, little is known on Cldn5-based TJ assemblies. Different structural models were suggested, with Cldn5 protomers generating paracellular pores that restrict the passage of ions and small molecules. Recently, the first Cldn5 pathogenic mutation, G60R, was identified and shown to induce Cl--selective channels and Na+ barriers in BBB TJs, providing an excellent opportunity to validate the structural models. Here, we used molecular dynamics to study the permeation of ions and water through two distinct G60R-Cldn5 paracellular architectures. Only the so-called Pore I reproduces the functional modification observed in experiments, displaying a free energy (FE) minimum for Cl- and a barrier for Na+ consistent with anionic selectivity. We also studied the artificial Q57D and Q63D mutations in the constriction region, Q57 being conserved in Cldns except for cation permeable homologs. In both cases, we obtain FE profiles consistent with facilitated passage of cations. Our calculations provide the first in-silico description of a Cldn5 pathogenic mutation, further assessing the TJ Pore I model and yielding new insight on BBB's paracellular selectivity.
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Affiliation(s)
- Alessandro Berselli
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- Department of Experimental Medicine, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132, Genova, Italy
| | - Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132, Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, 16132, Genova, Italy
- Corresponding authors at: Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Corresponding authors at: Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, 16132 Genova, Italy.
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5
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Berselli A, Benfenati F, Maragliano L, Alberini G. Multiscale modelling of claudin-based assemblies: a magnifying glass for novel structures of biological interfaces. Comput Struct Biotechnol J 2022; 20:5984-6010. [DOI: 10.1016/j.csbj.2022.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/03/2022] Open
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6
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Rajagopal N, Nangia S. Unique structural features of claudin‐5 and claudin‐15 lead to functionally distinct tight junction strand architecture. Ann N Y Acad Sci 2022; 1517:225-233. [DOI: 10.1111/nyas.14891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering Syracuse University Syracuse New York USA
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering Syracuse University Syracuse New York USA
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7
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Berselli A, Alberini G, Benfenati F, Maragliano L. Computational Assessment of Different Structural Models for Claudin-5 Complexes in Blood-Brain Barrier Tight Junctions. ACS Chem Neurosci 2022; 13:2140-2153. [PMID: 35816296 PMCID: PMC9976285 DOI: 10.1021/acschemneuro.2c00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The blood-brain barrier (BBB) strictly regulates the exchange of ions and molecules between the blood and the central nervous system. Tight junctions (TJs) are multimeric structures that control the transport through the paracellular spaces between the adjacent brain endothelial cells of the BBB. Claudin-5 (Cldn5) proteins are essential for TJ formation and assemble into multiprotein complexes via cis-interactions within the same cell membrane and trans-interactions across two contiguous cells. Despite the relevant biological function of Cldn5 proteins and their role as targets of brain drug delivery strategies, the molecular details of their assembly within TJs are still unclear. Two different structural models have been recently introduced, in which Cldn5 dimers belonging to opposite cells join to generate paracellular pores. However, a comparison of these models in terms of ionic transport features is still lacking. In this work, we used molecular dynamics simulations and free energy (FE) calculations to assess the two Cldn5 pore models and investigate the thermodynamic properties of water and physiological ions permeating through them. Despite different FE profiles, both structures present single/multiple FE barriers to ionic permeation, while being permissive to water flux. These results reveal that both models are compatible with the physiological role of Cldn5 TJ strands. By identifying the protein-protein surface at the core of TJ Cldn5 assemblies, our computational investigation provides a basis for the rational design of synthetic peptides and other molecules capable of opening paracellular pores in the BBB.
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Affiliation(s)
- Alessandro Berselli
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy,Department
of Experimental Medicine, Università
Degli Studi di Genova, Viale Benedetto XV, 3, Genova 16132, Italy
| | - Giulio Alberini
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy,IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, Genova 16132, Italy
| | - Fabio Benfenati
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy,IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, Genova 16132, Italy,
| | - Luca Maragliano
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy,Department
of Life and Environmental Sciences, Polytechnic
University of Marche, Via Brecce Bianche, Ancona 60131, Italy,
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8
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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9
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Mentor S, Fisher D. The Ism between Endothelial Cilia and Endothelial Nanotubules Is an Evolving Concept in the Genesis of the BBB. Int J Mol Sci 2022; 23:ijms23052457. [PMID: 35269595 PMCID: PMC8910322 DOI: 10.3390/ijms23052457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 02/06/2023] Open
Abstract
The blood–brain barrier (BBB) is fundamental in maintaining central nervous system (CNS) homeostasis by regulating the chemical environment of the underlying brain parenchyma. Brain endothelial cells (BECs) constitute the anatomical and functional basis of the BBB. Communication between adjacent BECs is critical for establishing BBB integrity, and knowledge of its nanoscopic landscape will contribute to our understanding of how juxtaposed zones of tight-junction protein interactions between BECs are aligned. The review discusses and critiques types of nanostructures contributing to the process of BBB genesis. We further critically evaluate earlier findings in light of novel high-resolution electron microscopy descriptions of nanoscopic tubules. One such phenotypic structure is BEC cytoplasmic projections, which, early in the literature, is postulated as brain capillary endothelial cilia, and is evaluated and compared to the recently discovered nanotubules (NTs) formed in the paracellular spaces between BECs during barrier-genesis. The review attempts to elucidate a myriad of unique topographical ultrastructures that have been reported to be associated with the development of the BBB, viz., structures ranging from cilia to BEC tunneling nanotubules (TUNTs) and BEC tethering nanotubules (TENTs).
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Affiliation(s)
- Shireen Mentor
- Neurobiology Research Group, Department of Medical Biosciences, University of the Western Cape, Bellville, Cape Town 7535, South Africa;
| | - David Fisher
- Neurobiology Research Group, Department of Medical Biosciences, University of the Western Cape, Bellville, Cape Town 7535, South Africa;
- School of Health Professions, University of Missouri, Columbia, MO 65211, USA
- Correspondence:
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10
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Khedri M, Maleki R, Dahri M, Sadeghi MM, Rezvantalab S, Santos HA, Shahbazi MA. Engineering of 2D nanomaterials to trap and kill SARS-CoV-2: a new insight from multi-microsecond atomistic simulations. Drug Deliv Transl Res 2021; 12:1408-1422. [PMID: 34476766 PMCID: PMC8413075 DOI: 10.1007/s13346-021-01054-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
In late 2019, coronavirus disease 2019 (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Spike protein is one of the surface proteins of SARS-CoV-2 that is essential for its infectious function. Therefore, it received lots of attention for the preparation of antiviral drugs, vaccines, and diagnostic tools. In the current study, we use computational methods of chemistry and biology to study the interaction between spike protein and its receptor in the body, angiotensin-I-converting enzyme-2 (ACE2). Additionally, the possible interaction of two-dimensional (2D) nanomaterials, including graphene, bismuthene, phosphorene, p-doped graphene, and functionalized p-doped graphene, with spike protein is investigated. The functionalized p-doped graphene nanomaterials were found to interfere with spike protein better than the other tested nanomaterials. In addition, the interaction of the proposed nanomaterials with the main protease (Mpro) of SARS-CoV-2 was studied. Functionalized p-doped graphene nanomaterials showed more capacity to prevent the activity of Mpro. These 2D nanomaterials efficiently reduce the transmissibility and infectivity of SARS-CoV-2 by both the deformation of the spike protein and inhibiting the Mpro. The results suggest the potential use of 2D nanomaterials in a variety of prophylactic approaches, such as masks or surface coatings, and would deserve further studies in the coming years.
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Affiliation(s)
- Mohammad Khedri
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland.,Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mohammad Dahri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Moein Sadeghi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sima Rezvantalab
- Renewable Energies Department, Faculty of Chemical Engineering, Urmia University of Technology, 57166-419, Urmia, Iran.
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland. .,Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014, Helsinki, Finland.
| | - Mohammad-Ali Shahbazi
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland. .,Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC), Zanjan University of Medical Sciences, 45139-56184, Zanjan, Iran.
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11
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Itaya H, Kasahara K, Xie Q, Yano Y, Matsuzaki K, Takahashi T. All-Atom Molecular Dynamics Elucidating Molecular Mechanisms of Single-Transmembrane Model Peptide Dimerization in a Lipid Bilayer. ACS OMEGA 2021; 6:11458-11465. [PMID: 34056301 PMCID: PMC8153988 DOI: 10.1021/acsomega.1c00482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Protein-protein interactions between transmembrane helices are essential elements for membrane protein structures and functions. To understand the effects of peptide sequences and lipid compositions on these interactions, single-molecule experiments using model systems comprising artificial peptides and membranes have been extensively performed. However, their dynamic behavior at the atomic level remains largely unclear. In this study, we applied the all-atom molecular dynamics (MD) method to simulate the interactions of single-transmembrane helical peptide dimers in membrane environments, which has previously been analyzed by single-molecule experiments. The simulations were performed with two peptides (Ala- and Leu-based artificially designed peptides, termed "host peptide", and the host peptide added with the GXXXG motif, termed "GXXXG peptide"), two membranes (pure-POPC and POPC mixed with 30% cholesterols), and two dimer directions (parallel and antiparallel), consistent with those in the previous experiment. As a result, the MD simulations with parallel dimers reproduced the experimentally observed tendency that introducing cholesterols weakened the interactions in the GXXXG dimer and facilitated those in the host dimer. Our simulation suggested that the host dimer formed hydrogen bonds but the GXXXG dimer did not. However, some discrepancies were also observed between the experiments and simulations. Limitations in the space and time scales of simulations restrict the large-scale undulation and peristaltic motions of the membranes, resulting in differences in lateral pressure profiles. This effect could cause a discrepancy in the rotation angles of helices against the membrane normal.
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Affiliation(s)
- Hayato Itaya
- Graduate
School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Kota Kasahara
- College
of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Qilin Xie
- College
of Pharmaceutical Sciences, Ritsumeikan
University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Yoshiaki Yano
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate
School of Pharmaceutical Sciences, Kyoto
University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Takahashi
- College
of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
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12
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Roterman I, Stapor K, Fabian P, Konieczny L, Banach M. Model of Environmental Membrane Field for Transmembrane Proteins. Int J Mol Sci 2021; 22:ijms22073619. [PMID: 33807215 PMCID: PMC8036355 DOI: 10.3390/ijms22073619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/20/2021] [Accepted: 03/27/2021] [Indexed: 11/16/2022] Open
Abstract
The water environment determines the activity of biological processes. The role of such an environment interpreted in the form of an external field expressed by the 3D Gaussian distribution in the fuzzy oil drop model directs the folding process towards the generation of a centrally located hydrophobic core with the simultaneous exposure of polar residues on the surface. In addition to proteins soluble in the water environment, there is a significant group of membrane proteins that act as receptors or channels, including ion channels in particular. The change of the polar (water) environment into a highly hydrophobic (membrane) environment is quite radical, resulting in a different hydrophobicity distribution within the membrane protein. Modification of the notation of the force field expressing the presence of the hydrophobic environment has been proposed in this work. A modified fuzzy oil drop model with its adaptation to membrane proteins was used to interpret the structure of membrane proteins–mechanosensitive channel. The modified model was also used to describe the so-called negative cases—i.e., for water-soluble proteins with a clear distribution consistent with the fuzzy oil drop model.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, 30-688 Kraków, Poland;
- Correspondence:
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University—Medical College, 31-034 Kraków, Poland;
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, 30-688 Kraków, Poland;
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13
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Piontek J, Krug SM, Protze J, Krause G, Fromm M. Molecular architecture and assembly of the tight junction backbone. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183279. [PMID: 32224152 DOI: 10.1016/j.bbamem.2020.183279] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/18/2022]
Abstract
The functional and structural concept of tight junctions has developed after discovery of claudin and TAMP proteins. Many of these proteins contribute to epi- and endothelial barrier but some, in contrast, form paracellular channels. Claudins form the backbone of tight junction (TJ) strands whereas other proteins regulate TJ dynamics. The current joined double-row model of TJ strands and channels is crucially based on the linear alignment of claudin-15 in the crystal. Molecular dynamics simulations, protein docking, mutagenesis, cellular TJ reconstitution, and electron microscopy studies largely support stability and functionality of the model. Here, we summarize in silico and in vitro data about TJ strand assembly including comparison of claudin crystal structures and alternative models. Sequence comparisons, experimental and structural data substantiate differentiation of classic and non-classic claudins differing in motifs related to strand assembly. Classic claudins seem to share a similar mechanism of strand formation. Interface variations likely contribute to TJ strand flexibility. Combined in vitro/in silico studies are expected to elucidate mechanistic keys determining TJ regulation.
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Affiliation(s)
- Jörg Piontek
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology, Rheumatology, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Susanne M Krug
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology, Rheumatology, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Jonas Protze
- Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Michael Fromm
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology, Rheumatology, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany.
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Rajagopal N, Irudayanathan FJ, Nangia S. Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface. Int J Mol Sci 2019; 20:E5583. [PMID: 31717316 PMCID: PMC6888702 DOI: 10.3390/ijms20225583] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.
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Affiliation(s)
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
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