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Pshetitsky Y, Buck M, Meirovitch E. Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: 2. The Role of Symmetry in GTPase Binding and Dimer Formation. J Phys Chem B 2024; 128:1573-1585. [PMID: 38350435 DOI: 10.1021/acs.jpcb.3c06745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The Rho GTPase binding domain of Plexin-B1 (RBD) prevails in solution as dimer. Under appropriate circumstances, it binds the small GTPase Rac1 to yield the complex RBD-Rac1. Here, we study RBD dimerization and complex formation from a symmetry-based perspective using data derived from 1 μs long MD simulations. The quantities investigated are the local potentials, u(MD), prevailing at the N-H sites of the protein. These potentials are statistical in character providing an empirical description of the local structure. To establish more methodical description, a method for approximating them by explicit functions, u(simulated), was developed in the preceding article in this journal issue. These functions are combinations of analytical Wigner functions, DL,K, belonging to the D2h point group. The D2h subgroups Ag and B2u are found to dominate u(simulated); the B1u subgroup contributes in some cases. The Ag (B2u) functions have axial or rhombic symmetry. For the first time, local potentials in proteins can be quantitatively characterized in terms of their strength (rhombicity) evaluated by axial Ag (rhombic Ag and B2u) contributions. Until now, the chain-segment [β3-L3-β4] and to some extent the α2-helix have been associated with GTPase binding. Here, we find that this process causes an increase (decrease) in the potential strength of β3 and β4 (the preceding L2 loop and the remote chain-segment [(α2-helix)-(α2/β5-turn)-(β5-strand)]), suggesting effects of counterbalancing and allostery. There is evidence for the L2 loop being associated with RBD-GTPase binding. Until now only the L4 loop has been associated with RBD dimerization. The latter process is found to cause an increase (decrease) in the potential strength and rhombicity of the L4 loop (the adjacent chain-segment [(α2-helix)-(α2/β5-turn)-(β5-strand)]), suggesting counterbalancing activity. On average, the RBD dimer features stronger local potentials than RBD-Rac1. The novel information inherent in these findings is mesoscopic in character. Prospects of interest include exploring relation to atomistic force-field parameters.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Pshetitsky Y, Mendelman N, Buck M, Meirovitch E. Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: A Symmetry-Based Perspective. J Phys Chem B 2024; 128:1557-1572. [PMID: 38350034 DOI: 10.1021/acs.jpcb.3c06741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
We report on a new method for the characterization of local structures in proteins based on extensive molecular dynamics (MD) simulations, here, 1 μs in length. The N-H bond of the Rho GTPase binding domain of plexin-B1 (RBD) serves as a probe and the potential, u(MD), which restricts its internal motion, as a qualifier of the local dynamic structure. u(MD) is derived from the MD trajectory as a function of the polar angles, (θ, φ), which specify the N-H orientation in the protein. u(MD) is statistical in character yielding empirical descriptions. To establish more insightful methodical descriptions, we develop a comprehensive method which approximates u(MD) by combinations of analytical Wigner functions that belong to the D2h point group. These combinations, called u(simulated), make it possible to gain a new perspective of local dynamic structures in proteins based on explicit potentials/free energy surfaces and associated probability densities, entropy, and ordering. A simpler method was developed previously using 100 ns MD simulations. In that case, the traditional "perpendicular N-H ordering" setting centered at Cα-Cα with (θ, φ) = (90, 90) and generally, featuring positive φ, prevailed. u(MD) derived from 1 μs MD simulations is considerably more complex requiring substantial model enhancement. The enhanced method applies to the well-structured sections of the RBD. It only applies partly to its loops where u(MD) extends into the negative-φ region where we detect nonperpendicular N-H ordering. This arrangement requires devising new reference structures and making substantial algorithmic changes, to be performed in future work. Here, we focus on developing the comprehensive method and using it to investigate perpendicular ordering settings. We find that secondary structures (loops) exhibit varying (virtually invariant) potentials with Ag, B2u, and B1u (Ag and B2u) D2h symmetry. Application to RBD dimerization and RBD binding to the GTPase Rac1 is described in the subsequent article. Applications to other probes, proteins, and biological functions, based on explicit local potentials, probability densities, entropy, and ordering, are possible.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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3
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Shi X, Lingerak R, Herting CJ, Ge Y, Kim S, Toth P, Wang W, Brown BP, Meiler J, Sossey-Alaoui K, Buck M, Himanen J, Hambardzumyan D, Nikolov DB, Smith AW, Wang B. Time-resolved live-cell spectroscopy reveals EphA2 multimeric assembly. Science 2023; 382:1042-1050. [PMID: 37972196 DOI: 10.1126/science.adg5314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Ephrin type-A receptor 2 (EphA2) is a receptor tyrosine kinase that initiates both ligand-dependent tumor-suppressive and ligand-independent oncogenic signaling. We used time-resolved, live-cell fluorescence spectroscopy to show that the ligand-free EphA2 assembles into multimers driven by two types of intermolecular interactions in the ectodomain. The first type entails extended symmetric interactions required for ligand-induced receptor clustering and tumor-suppressive signaling that inhibits activity of the oncogenic extracellular signal-regulated kinase (ERK) and protein kinase B (AKT) protein kinases and suppresses cell migration. The second type is an asymmetric interaction between the amino terminus and the membrane proximal domain of the neighboring receptors, which supports oncogenic signaling and promotes migration in vitro and tumor invasiveness in vivo. Our results identify the molecular interactions that drive the formation of the EphA2 multimeric signaling clusters and reveal the pivotal role of EphA2 assembly in dictating its opposing functions in oncogenesis.
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Affiliation(s)
- Xiaojun Shi
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ryan Lingerak
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cameron J Herting
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA 30322, USA
| | - Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Soyeon Kim
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Paul Toth
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Wei Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Benjamin P Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Khalid Sossey-Alaoui
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Juha Himanen
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dolores Hambardzumyan
- Departments Oncological Sciences and Neurosurgery, Tisch Cancer Institute, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Dimitar B Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
| | - Bingcheng Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Cleveland, OH 44109, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
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Matsuyama M, Ortega JT, Fedorov Y, Scott-McKean J, Muller-Greven J, Buck M, Adams D, Jastrzebska B, Greenlee W, Matsuyama S. Development of novel cytoprotective small compounds inhibiting mitochondria-dependent cell death. iScience 2023; 26:107916. [PMID: 37841588 PMCID: PMC10568349 DOI: 10.1016/j.isci.2023.107916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/27/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
We identified cytoprotective small molecules (CSMs) by a cell-based high-throughput screening of Bax inhibitors. Through a medicinal chemistry program, M109S was developed, which is orally bioactive and penetrates the blood-brain/retina barriers. M109S protected retinal cells in ocular disease mouse models. M109S directly interacted with Bax and inhibited the conformational change and mitochondrial translocation of Bax. M109S inhibited ABT-737-induced apoptosis both in Bax-only and Bak-only mouse embryonic fibroblasts. M109S also inhibited apoptosis induced by staurosporine, etoposide, and obatoclax. M109S decreased maximal mitochondrial oxygen consumption rate and reactive oxygen species production, whereas it increased glycolysis. These effects on cellular metabolism may contribute to the cytoprotective activity of M109S. M109S is a novel small molecule protecting cells from mitochondria-dependent apoptosis both in vitro and in vivo. M109S has the potential to become a research tool for studying cell death mechanisms and to develop therapeutics targeting mitochondria-dependent cell death pathway.
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Affiliation(s)
- Mieko Matsuyama
- Department of Ophthalmology and Visual Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph T. Ortega
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yuri Fedorov
- Department of Genetics and Genome Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jonah Scott-McKean
- Department of Ophthalmology and Visual Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Macromolecular Science and Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jeannie Muller-Greven
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Drew Adams
- Department of Genetics and Genome Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Beata Jastrzebska
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Shigemi Matsuyama
- Department of Ophthalmology and Visual Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
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Rybak JA, Sahoo AR, Kim S, Pyron RJ, Pitts SB, Guleryuz S, Smith AW, Buck M, Barrera FN. Allosteric inhibition of the epidermal growth factor receptor through disruption of transmembrane interactions. J Biol Chem 2023:104914. [PMID: 37315787 PMCID: PMC10362150 DOI: 10.1016/j.jbc.2023.104914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase (RTK) commonly targeted for inhibition by anti-cancer therapeutics. Current therapeutics target EGFR's kinase domain or extracellular region. However, these types of inhibitors are not specific for tumors over healthy tissue and therefore cause undesirable side effects. Our lab has recently developed a new strategy to regulate RTK activity by designing a peptide that specifically binds to the transmembrane (TM) region of the RTK to allosterically modify kinase activity. These peptides are acidity-responsive, allowing them to preferentially target acidic environments like tumors. We have applied this strategy to EGFR and created the PET1 peptide. We observed that PET1 behaves as a pH-responsive peptide that modulates the configuration of the EGFR TM through a direct interaction. Our data indicated that PET1 inhibits EGFR-mediated cell migration. Finally, we investigated the mechanism of inhibition through molecular dynamics simulations, which showed that PET1 sits between the two EGFR TM helices; this molecular mechanism was additionally supported by AlphaFold-Multimer predictions. We propose that the PET1-induced disruption of native TM interactions disturbs the conformation of the kinase domain in such a way that it inhibits EGFR's ability to send migratory cell signals. This study is a proof-of-concept that acidity-responsive membrane peptide ligands can be generally applied to RTKs. In addition, PET1 constitutes a viable approach to therapeutically target the TM of EGFR.
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Affiliation(s)
- Jennifer A Rybak
- Department of Genome Sciences and Technology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Soyeon Kim
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, USA
| | - Robert J Pyron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Savannah B Pitts
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Saffet Guleryuz
- Department of Medicine, University of Tennessee Graduate School of Medicine, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, USA; Department of Chemistry and Biochemistry, Texas Tech University, 2500 Broadway St, Lubbock, TX 79409
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA.
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Sahoo AR, Souza PCT, Meng Z, Buck M. Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer. Structure 2023; 31:735-745.e2. [PMID: 37075749 PMCID: PMC10833135 DOI: 10.1016/j.str.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Structures and dynamics of transmembrane (TM) receptor regions are key to understanding their signaling mechanism across membranes. Here we examine configurations of TM region dimers, assembled using the recent Martini 3 force field for coarse-grain (CG) molecular dynamics simulations. At first glance, our results show only a reasonable agreement with ab initio predictions using PREDDIMER and AlphaFold2 Multimer and with nuclear magnetic resonance (NMR)-derived structures. 5 of 11 CG TM structures are similar to the NMR structures (within <3.5 Å root-mean-square deviation [RMSD]) compared with 10 and 9 using PREDDIMER and AlphaFold2, respectively (with 8 structures of the later within 1.5 Å). Surprisingly, AlphaFold2 predictions are closer to NMR structures when the 2001 instead of 2020 database is used for training. The CG simulations reveal that alternative configurations of TM dimers readily interconvert with a predominant population. The implications for transmembrane signaling are discussed, including for the development of peptide-based pharmaceuticals.
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Affiliation(s)
- Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Zhiyuan Meng
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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Jamal B, Quan R, Iannucci M, Li Z, Prasanna C, Sahoo AR, Buck M. Biophysical characterization of Raf RBD-CRD-KD interactions in the autoinhibited state. Biophys J 2023; 122:328a. [PMID: 36783656 DOI: 10.1016/j.bpj.2022.11.1834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Baasit Jamal
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Ruihan Quan
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Maria Iannucci
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Zhenlu Li
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Chinmayi Prasanna
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
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Rybak JA, Sahoo AR, Kim S, Pyron RJ, Pitts SB, Smith AW, Buck M, Barrera FN. Inhibition of EGFR via an acidity-responsive transmembrane peptide ligand. Biophys J 2023; 122:369a-370a. [PMID: 36783874 DOI: 10.1016/j.bpj.2022.11.2036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Jennifer A Rybak
- Genome Science & Technology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Savannah B Pitts
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Adam W Smith
- Department of Chemistry, The University of Akron, Akron, OH, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, USA
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9
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Li ZL, Buck M. A proteome-scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics. Proteins 2023; 91:3-15. [PMID: 36053994 PMCID: PMC10087973 DOI: 10.1002/prot.26404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 07/06/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence. Here, we present a simple way to analyze the difference in amino acid occurrence by comparing highly homologous proteins on a subproteome level between several vertebrate model organisms. Specifically, we use this method to identify a pattern of amino acid conservation as well as a shift in amino acid occurrence between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, this general analysis and a specific example further establish a broad correlation, if not likely connection between the thermal adaptation of protein sequences and two of their physical features: on average a change in their protein dynamics and, even more strongly, in their solvation. For poikilotherms, such as frog and fish, the lower body temperature is expected to increase the protein-protein interaction due to a decrease in protein internal dynamics. In order to counteract the tendency for enhanced binding caused by low temperatures, poikilotherms enhance the solvation of their proteins by favoring polar amino acids. This feature appears to dominate over possible changes in dynamics for some proteins. The results suggest that a general trend for amino acid choice is part of the mechanism for thermoadaptation of vertebrate organisms at the molecular level.
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Affiliation(s)
- Zhen-Lu Li
- School of Life Science, Tianjin University, Tianjin, China.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Departments of Pharmacology and of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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Li ZL, Buck M. Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity. Comput Struct Biotechnol J 2022; 20:6078-6086. [PMID: 36373151 PMCID: PMC9638846 DOI: 10.1016/j.csbj.2022.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
SARS-CoV-2 variants often include surface mutations in the Spike protein that are important for viruses to recognize host receptors and evade antibody neutralization. The Spike protein also has mutations in the interior of the protein likely to affect the Spike protein S1 – S2 subunit’s separation propensity, the most important of which is the D614G mutation. Remarkably, the Omicron variant contains a large number of internal mutations at the S2: S1 interface, which have not been investigated yet. In this study, we examined the effects of such interfacial mutations on the S2: S1 and subunit domain interactions and on the subunit’s dissociation process. We found that the interaction with S2 is mainly contributed by the three encapsulation domains, named INT, ED1 and ED2 of S1, which are sandwiched between the S1 RBD and N-terminal NTD domain. We found that D614 is the strongest contributor for the S2: S1 interaction which is greatly weakened by the D614G mutation. Surprisingly, we found that, mutations T547K, H655Y, N764K, N856K, N969K, L981F in the Omicron variant largely enhance the S2: ED1 interaction, partially compensating the loss of S2: ED2 interaction due to the D614G mutation. Lastly, these results, together with biological considerations, allow us to suggest that in addition to the binding strength of between the RBD and ACE2, the stability of the Spike protein and the propensity of Spike protein S2: S1 separation are critical factors which likely exist in a balance for a particular infectivity and pathogenicity of the virus.
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11
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Pshetitsky Y, Mendelman N, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: N-H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry. J Phys Chem B 2022; 126:6396-6407. [PMID: 35980340 DOI: 10.1021/acs.jpcb.2c03431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Amide-bond equilibrium probability density, Peq = exp(-u) (u, local potential), and associated conformational entropy, Sk = -∫Peq (ln Peq) dΩ ─ln ∫dΩ, are derived for the Rho GTPase binding domain of Plexin-B1 (RBD) as monomer and dimer from 1 μs MD simulations. The objective is to elucidate the effect of dimerization on the dynamic structure of the RBD. Dispersed (peaked) Peq functions indicate "flexibility" ("rigidity"; the respective concepts are used below in this context). The L1 and L3 loops are throughout highly flexible, the L2 loop and the secondary structure elements are generally rigid, and the L4 loop is flexible in the monomer and rigid in the dimer. Overall, many residues are more flexible in the dimer. These features, and their implications, are discussed. Unexpectedly, we find that monomer unit 1 of the dimer (in short, d1) is unusually flexible, whereas monomer unit 2 (in short, d2) is as rigid as the RBD monomer. This is revealed due to their engagement in slow-to-intermediate conformational exchange detected previously by 15N relaxation experiments. Such motions occur with rates on the order of 103-104 s-1; hence, they cannot be completely sampled over the course of 1 μs simulation. However, the extent to which rigid d2 is affected is small enough to enable physically relevant analysis. The entropy difference between d2 and the monomer yields an entropic contribution of -7 ± 0.7 kJ/mol to the free energy of RBD dimerization. In previous work aimed at similar objectives we used 50-100 ns MD simulations. Those results and the present result differ considerably. In summary, bond-vector Peq functions derived directly from long MD simulations are useful descriptors of protein structural dynamics and provide accurate conformational entropy. Within the scope of slow conformational exchange, they can be useful, even in the presence of incomplete sampling.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhenlu Li
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Mendelman N, Pshetitsky Y, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in Ligand-Free, Rac1-Bound, and Dimer RBD. J Phys Chem B 2022; 126:6408-6418. [PMID: 35976064 DOI: 10.1021/acs.jpcb.2c03435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orientational probability densities, Peq = exp(-u) (u, local potential), of bond-vectors in proteins provide information on structural flexibility. The related conformational entropy, Sk = -∫Peq(ln Peq)dΩ - ln ∫dΩ, provides the entropic contribution to the free energy of the physical/biological process studied. We have developed a new method for deriving Peq and Sk from MD simulations, using the N-H bond as probe. Recently we used it to study the dimerization of the Rho GTPase binding domain of Plexin-B1 (RBD). Here we use it to study RBD binding to the small GTPase Rac1. In both cases 1 μs MD simulations have been employed. The RBD has the ubiquitin fold with four mostly long loops. L3 is associated with GTPase binding, L4 with RBD dimerization, L2 participates in interdomain interactions, and L1 has not been associated with function. We find that RBD-Rac1 binding renders L1, L3, and L4 more rigid and the turns β2/α1 and α2/β5 more flexible. By comparison, RBD dimerization renders L4 more rigid, and the α-helices, the β-strands, and L2 more flexible. The rigidity of L1 in RBDRAC is consistent with L1-L3 contacts seen in previous MD simulations. The analysis of the L3-loop reveals two states of distinct flexibility which we associate with involvement in slow conformational exchange processes differing in their rates. Overall, the N-H bonds make an unfavorable entropic contribution of (5.9 ± 0.9) kJ/mol to the free energy of RBD-Rac1 binding; they were found to make a favorably contribution of (-7.0 ± 0.7) kJ/mol to the free energy of RBD dimerization. In summary, the present study provides a new perspective on the impact of Rac1 binding and dimerization on the flexibility characteristics of the RBD. Further studies are stimulated by the results of this work.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhenlu Li
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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13
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Basavarajappa SC, Liu AR, Bruchez A, Li Z, Suzart VG, Liu Z, Chen Y, Xiao TS, Buck M, Ramakrishnan P. Trimeric Receptor Binding Domain of SARS-CoV-2 Acts as a Potent Inhibitor of ACE2 Receptor-Mediated Viral Entry. iScience 2022; 25:104716. [PMID: 35813876 PMCID: PMC9251894 DOI: 10.1016/j.isci.2022.104716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022] Open
Abstract
The COVID-19 pandemic has caused over four million deaths and effective methods to control CoV-2 infection, in addition to vaccines, are needed. The CoV-2 binds to the ACE2 on human cells through the receptor-binding domain (RBD) of the trimeric spike protein. Our modeling studies show that a modified trimeric RBD (tRBD) can interact with three ACE2 receptors, unlike the native spike protein, which binds to only one ACE2. We found that tRBD binds to the ACE2 with 58-fold higher affinity than monomeric RBD (mRBD) and blocks spike-dependent pseudoviral infection over 4-fold more effectively compared to the mRBD. Although mRBD failed to block CoV-2 USA-WA1/2020 infection, tRBD efficiently blocked the true virus infection in plaque assays. We show that tRBD is a potent inhibitor of CoV-2 through both competitive binding to the ACE2 and steric hindrance, and has the potential to emerge as a first-line therapeutic method to control COVID-19. tRBD binds multiple ACE2 receptors, while mRBD and spike bind one ACE2 receptor tRBD shows 4-fold higher inhibition of CoV-2 pseudovirus infection than mRBD tRBD, yet not mRBD, prevents CoV-2 USA-WA1/2020 from infecting Vero cells Use of tRBD is a potential therapeutic method to block CoV-2 infection
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14
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Buck M, Sahoo A. Understanding the Structural Basis of Epha1 and Epha2 Homo‐Dimerization, Membrane Proximal Domain Interactions and its Implications for Cancer. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l8133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matthias Buck
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
| | - Amita Sahoo
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
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15
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Li ZL, Mattos C, Buck M. Computational studies of the principle of dynamic-change-driven protein interactions. Structure 2022; 30:909-916.e2. [DOI: 10.1016/j.str.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/08/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
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16
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Zhang L, Ghosh SK, Basavarajappa SC, Chen Y, Shrestha P, Penfield J, Brewer A, Ramakrishnan P, Buck M, Weinberg A. HBD-2 binds SARS-CoV-2 RBD and blocks viral entry: Strategy to combat COVID-19. iScience 2022; 25:103856. [PMID: 35128350 PMCID: PMC8808565 DOI: 10.1016/j.isci.2022.103856] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/14/2021] [Accepted: 01/28/2022] [Indexed: 12/26/2022] Open
Abstract
New approaches to complement vaccination are needed to combat the spread of SARS-CoV-2 and stop COVID-19-related deaths and medical complications. Human beta defensin 2 (hBD-2) is a naturally occurring epithelial cell-derived host defense peptide that has anti-viral properties. Our comprehensive in-silico studies demonstrate that hBD-2 binds the site on the CoV-2-RBD that docks with the ACE2 receptor. Biophysical measurements confirm that hBD-2 indeed binds to the CoV-2-receptor-binding domain (RBD) (KD ∼ 2μM by surface plasmon resonance), preventing it from binding to ACE2-expressing cells. Importantly, hBD-2 shows specificity by blocking CoV-2/spike pseudoviral infection, but not VSVG-mediated infection, of ACE2-expressing human cells with an IC50 of 2.8 ± 0.4 μM. These promising findings offer opportunities to develop hBD-2 and/or its derivatives and mimetics to safely and effectively use as agents to prevent SARS-CoV-2 infection. HBD-2 binds spike-RBD at the ACE2 interaction site in silico Biophysical and biological assays confirm hBD-2 binding to spike-RBD HBD-2 blocks spike-RBD:ACE2 binding HBD-2 prevents CoV-2/spike pseudovirions from infecting ACE2-expressing human cells
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Affiliation(s)
- Liqun Zhang
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505, USA
| | - Santosh K. Ghosh
- Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Yinghua Chen
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Pravesh Shrestha
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jackson Penfield
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505, USA
| | - Ann Brewer
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505, USA
| | - Parameswaran Ramakrishnan
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Corresponding author
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Corresponding author
| | - Aaron Weinberg
- Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Corresponding author
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17
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Sahoo AR, Souza PCT, Meng Z, Buck M. How transmembrane helices of type 1 receptors transmit information: prediction of dimers with the Martini 3 coarse grained model. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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18
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Di Mauro GM, Iannucci M, Whitehouse C, Smyers J, Buck M. Analysis of the interaction of Plexin-a family with collapsin response mediator protein-2. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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19
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Hartmann L, Hecker J, Rothenberg-Thurley M, Rivière J, Ksienzyk B, Buck M, Van Der Garde M, Fischer L, Winter S, Rauner M, Tsourdi E, Sockel K, Schneider M, Kubasch A, Nolde M, Hausmann D, Lützner J, Roth A, Bassermann F, Spiekermann K, Hofbauer L, Platzbecker U, Götze K, Metzeler K. Topic: AS04-MDS Biology and Pathogenesis/AS04b-Clonal diversity & evolution. Leuk Res 2021. [DOI: 10.1016/j.leukres.2021.106681.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci 2021; 22:ijms22168593. [PMID: 34445298 PMCID: PMC8395321 DOI: 10.3390/ijms22168593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022] Open
Abstract
Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.
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Affiliation(s)
- Amita R. Sahoo
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
- Department of Neurosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence:
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21
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Buck M. Letting go: Deep computational modeling insights into pH-dependent calcium affinity. J Biol Chem 2021; 297:100974. [PMID: 34280436 PMCID: PMC8350533 DOI: 10.1016/j.jbc.2021.100974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Calcium and other cofactors can feature as key additions to a molecular interface, to the extent that the cofactor is completely buried in the bound state. How can such an interaction be regulated then? The answer: By facilitating a switch through an allosteric network. Although a number of unbinding mechanisms are being characterized, an extensive computational study by Joswig et al. reveals a detailed model for the pattern recognition receptor langerin.
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Affiliation(s)
- Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, USA.
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22
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Mahajan M, Bharambe N, Shang Y, Lu B, Mandal A, Madan Mohan P, Wang R, Boatz JC, Manuel Martinez Galvez J, Shnyrova AV, Qi X, Buck M, van der Wel PCA, Ramachandran R. NMR identification of a conserved Drp1 cardiolipin-binding motif essential for stress-induced mitochondrial fission. Proc Natl Acad Sci U S A 2021; 118:e2023079118. [PMID: 34261790 PMCID: PMC8307854 DOI: 10.1073/pnas.2023079118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondria form tubular networks that undergo coordinated cycles of fission and fusion. Emerging evidence suggests that a direct yet unresolved interaction of the mechanoenzymatic GTPase dynamin-related protein 1 (Drp1) with mitochondrial outer membrane-localized cardiolipin (CL), externalized under stress conditions including mitophagy, catalyzes essential mitochondrial hyperfragmentation. Here, using a comprehensive set of structural, biophysical, and cell biological tools, we have uncovered a CL-binding motif (CBM) conserved between the Drp1 variable domain (VD) and the unrelated ADP/ATP carrier (AAC/ANT) that intercalates into the membrane core to effect specific CL interactions. CBM mutations that weaken VD-CL interactions manifestly impair Drp1-dependent fission under stress conditions and induce "donut" mitochondria formation. Importantly, VD membrane insertion and GTP-dependent conformational rearrangements mediate only transient CL nonbilayer topological forays and high local membrane constriction, indicating that Drp1-CL interactions alone are insufficient for fission. Our studies establish the structural and mechanistic bases of Drp1-CL interactions in stress-induced mitochondrial fission.
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Affiliation(s)
- Mukesh Mahajan
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Nikhil Bharambe
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Yutong Shang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Bin Lu
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Rihua Wang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Juan Manuel Martinez Galvez
- Instituto Biofisika and Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Anna V Shnyrova
- Instituto Biofisika and Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Zernike Institute for Advanced Materials, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106;
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106
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23
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Li ZL, Buck M. Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2. Biophys J 2021; 120:2828-2837. [PMID: 34087218 PMCID: PMC8169233 DOI: 10.1016/j.bpj.2021.05.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/30/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1-685) and the S2 (res. 686-1273) domains by furin protease. Nrp1 predominantly binds to the C-terminal RRAR amino acid motif (res. 682-685) of the S1 domain. In this study, we firstly modeled the association of an Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640-685) and thereby assists the detachment of S2 N-terminal region (res. 686-700). Without Nrp1 bound, S1 tends to become stretched, whereas the bound Nrp1 stimulates an earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes; thus, Nrp1 likely increases virus infectivity by facilitating the S1 and S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and angiotensin-converting enzyme 2 (ACE2). Understanding of such an Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1-ACE2 targeted combination therapy.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, School of Medicine, Cleveland, Ohio
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Cleveland, Ohio; Department of Pharmacology, School of Medicine, Cleveland, Ohio; Department of Neurosciences, School of Medicine, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, Ohio.
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24
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Christie SM, Hao J, Tracy E, Buck M, Yu JS, Smith AW. Interactions between semaphorins and plexin-neuropilin receptor complexes in the membranes of live cells. J Biol Chem 2021; 297:100965. [PMID: 34270956 PMCID: PMC8350011 DOI: 10.1016/j.jbc.2021.100965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 11/27/2022] Open
Abstract
Signaling of semaphorin ligands via their plexin–neuropilin receptors is involved in tissue patterning in the developing embryo. These proteins play roles in cell migration and adhesion but are also important in disease etiology, including in cancer angiogenesis and metastasis. While some structures of the soluble domains of these receptors have been determined, the conformations of the full-length receptor complexes are just beginning to be elucidated, especially within the context of the plasma membrane. Pulsed-interleaved excitation fluorescence cross-correlation spectroscopy allows direct insight into the formation of protein–protein interactions in the membranes of live cells. Here, we investigated the homodimerization of neuropilin-1 (Nrp1), plexin A2, plexin A4, and plexin D1 using pulsed-interleaved excitation fluorescence cross-correlation spectroscopy. Consistent with previous studies, we found that Nrp1, plexin A2, and plexin A4 are present as dimers in the absence of exogenous ligand. Plexin D1, on the other hand, was monomeric under similar conditions, which had not been previously reported. We also found that plexin A2 and A4 assemble into a heteromeric complex. Stimulation with semaphorin 3A or semaphorin 3C neither disrupts nor enhances the dimerization of the receptors when expressed alone, suggesting that activation involves a conformational change rather than a shift in the monomer–dimer equilibrium. However, upon stimulation with semaphorin 3C, plexin D1 and Nrp1 form a heteromeric complex. This analysis of interactions provides a complementary approach to the existing structural and biochemical data that will aid in the development of new therapeutic strategies to target these receptors in cancer.
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Affiliation(s)
| | - Jing Hao
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Erin Tracy
- Department of Chemistry, University of Akron, Akron, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer S Yu
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA; Department of Radiation Oncology, Cleveland Clinic, Cleveland, Ohio, USA; Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, Ohio, USA.
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25
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Westerfield JM, Sahoo AR, Alves DS, Grau B, Cameron A, Maxwell M, Schuster JA, Souza PCT, Mingarro I, Buck M, Barrera FN. Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. J Mol Biol 2021; 433:167144. [PMID: 34229012 DOI: 10.1016/j.jmb.2021.167144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Brayan Grau
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Mikayla Maxwell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Jennifer A Schuster
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, F-69367 Lyon, France
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA.
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26
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Sahoo A, Shrestha P, Buck M. Understanding the Structural Basis of Epha2‐dimerization, ‐membrane Interactions and Its Implications in Cancer Progression. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.03851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Amita Sahoo
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
| | - Pravesh Shrestha
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
| | - Matthias Buck
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
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27
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Shrestha P, Li Z, Sahoo A, Shi X, Javier F, Bowman D, Mueller‐Greven J, Willard B, Wang B, Smith A, Buck M. Structural and Functional Studies of the Effects of Phosphorylation on Ephrin Receptor Tyrosine Kinase, Epha2, and the Relationship With Its SAM Domain as an Autoinhibitor. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.02967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Zhen‐Lu Li
- Case Western Reserve UniversityClevelandOH
| | | | - Xiaojun Shi
- Department of MedicineMetroHealthClevelandOH
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Packer M, Parker J, Chung J, Li Z, Lee Y, Cookis T, Guterres H, Alvarez S, Hossain MD, Donnelly D, Agar J, Makowski L, Buck M, Groves J, Mattos C. Raf promotes dimerization of the Ras G‐domain with increased allosteric connections. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.03183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Morgan Packer
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Jillian Parker
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Jean Chung
- ChemistryUniversity of California BerkeleyBerkeleyCA
| | - Zhenlu Li
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
| | - Young Lee
- ChemistryUniversity of California BerkeleyBerkeleyCA
| | - Trinity Cookis
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Hugo Guterres
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Steven Alvarez
- ChemistryUniversity of California BerkeleyBerkeleyCA
- Materials Science and EngineeringUniversity of California BerkeleyBerkeleyCA
| | - MD Hossain
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Daniel Donnelly
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
| | - Jeffrey Agar
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
- Pharmaceutical SciencesNortheastern UniversityBostonMA
| | | | - Matthias Buck
- Physiology and BiophysicsCase Western Reserve UniversityClevelandOH
| | - Jay Groves
- ChemistryUniversity of California BerkeleyBerkeleyCA
| | - Carla Mattos
- Chemistry and Chemical BiologyNortheastern UniversityBostonMA
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Li ZL, Buck M. Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank. Protein Sci 2021; 30:745-760. [PMID: 33550681 DOI: 10.1002/pro.4038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Of the roughly 20,000 canonical human protein sequences, as of January 20, 2021, 7,077 proteins have had their full or partial, medium- to high-resolution structures determined by x-ray crystallography or other methods. Which of these proteins dominate the protein data bank (the PDB) and why? In this paper, we list the 273 top human protein structures based on the number of their PDB entries. This set of proteins accounts for more than 40% of all available human PDB entries and represent past trends as well as current status for protein structural biology. We briefly discuss the relationship which some of the prominent protein structures have with protein research as a whole and mention their relevance to human diseases. The top-10 soluble and membrane proteins are all well-known (most of their first structures being deposited more than 30 years ago). Overall, there is no dramatic change in recent trends in the PDB. Remarkably, the number of structure depositions has grown nearly exponentially over the last 10 or more years (with a doubling time of 7 years for proteins, obtained from any organism). Growth in human protein structures is slightly faster (at 5.9 years). The information in this paper may be informative to senior scientists but also inspire researchers who are new to protein science, providing the year 2021 snap-shot for the state of protein structural biology.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA.,Department of Pharmacology; Department of Neurosciences and Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
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30
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Shrestha P, Li ZL, Rani Sahoo A, Shi X, Razelle Javier F, Bowman D, Mueller-Greven J, Willard B, Wang BC, Smith AW, Buck M. Structural and Functional Studies of the Effects of Phosphorylation on Ephrin Receptor Tyrosine Kinase, EphA2, and the Relationship with its Sam Domain as an Autoinhibitor. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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31
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Li Z, Buck M. Proteome-Scale Analysis of Vertebrate Protein Thermoadaptation Modulated by Dynamic Allostery and Protein Solvation. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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32
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Abstract
The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR amino acid sequence of the S1 domain. In this study, we model the association of a Nrp1 (a2-b1-b2) protein with the Spike protein computationally and analyze the topological constraints in the SARS-CoV-2 Spike protein for binding with Nrp1 and ACE2. Importantly, we study the exit mechanism of S2 from the S1 domain with the assistance of ACE2 as well as Nrp1 by molecular dynamics pulling simulations. In the presence of Nrp1, by binding the S1 more strongly to the host membrane, there is a high probability of S2 being pulled out, rather than S1 being stretched. Thus, Nrp1 binding could stimulate the exit of S2 from the S1 domain, which will likely increase virus infectivity as the liberated S2 domain mediates the fusion of virus and host membranes. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future combination therapy.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
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33
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Zhang L, Ghosh SK, Basavarajappa SC, Muller-Greven J, Penfield J, Brewer A, Ramakrishnan P, Buck M, Weinberg A. Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells. bioRxiv 2021:2021.01.07.425621. [PMID: 33442698 PMCID: PMC7805467 DOI: 10.1101/2021.01.07.425621] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
New approaches to complement vaccination are needed to combat the spread of SARS-CoV-2 and stop COVID-19 related deaths and long-term medical complications. Human beta defensin 2 (hBD-2) is a naturally occurring epithelial cell derived host defense peptide that has antiviral properties. Our comprehensive in-silico studies demonstrate that hBD-2 binds the site on the CoV-2-RBD that docks with the ACE2 receptor. Biophysical and biochemical assays confirm that hBD-2 indeed binds to the CoV-2-receptor binding domain (RBD) (KD ~ 300 nM), preventing it from binding to ACE2 expressing cells. Importantly, hBD-2 shows specificity by blocking CoV-2/spike pseudoviral infection, but not VSV-G mediated infection, of ACE2 expressing human cells with an IC50 of 2.4± 0.1 μM. These promising findings offer opportunities to develop hBD-2 and/or its derivatives and mimetics to safely and effectively use as novel agents to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Liqun Zhang
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505
- contributed equally
| | - Santosh K. Ghosh
- Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44124
- contributed equally
| | - Shrikanth C. Basavarajappa
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44124
- contributed equally
| | - Jeannine Muller-Greven
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44124
| | - Jackson Penfield
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505
| | - Ann Brewer
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505
| | | | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44124
| | - Aaron Weinberg
- Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44124
- Lead contact
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34
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Madhavan SM, Buck M. The Relationship between APOL1 Structure and Function: Clinical Implications. Kidney360 2020; 2:134-140. [PMID: 35368828 PMCID: PMC8785724 DOI: 10.34067/kid.0002482020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/04/2020] [Indexed: 02/04/2023]
Abstract
Common variants in the APOL1 gene are associated with an increased risk of nondiabetic kidney disease in individuals of African ancestry. Mechanisms by which APOL1 variants mediate kidney disease pathogenesis are not well understood. Amino acid changes resulting from the kidney disease-associated APOL1 variants alter the three-dimensional structure and conformational dynamics of the C-terminal α-helical domain of the protein, which can rationalize the functional consequences. Understanding the three-dimensional structure of the protein, with and without the risk variants, can provide insights into the pathogenesis of kidney diseases mediated by APOL1 variants.
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Affiliation(s)
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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35
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Mendelman N, Zerbetto M, Buck M, Meirovitch E. Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR Relaxation Theory and Molecular Dynamics Simulation Approaches. J Phys Chem B 2020; 124:9323-9334. [PMID: 32981310 DOI: 10.1021/acs.jpcb.0c05846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method for determining conformational entropy in proteins is reported. Proteins prevail as conformational ensembles, p ∝ exp(-u). By selecting a bond vector (e.g., N-H) as a conformation representative, molecular dynamics simulations can provide (relative to a reference structure) p as approximate Boltzmann probability density and u as N-H potential of mean force (POMF). The latter is as accurate as implied by the force field but statistical in character; this limits the insights it can provide and its utilization. Conformational entropy is given exclusively by u. Deriving it from POMFs renders it accurate but statistical in character. Previously, we devised explicit (i.e., analytical but not exact) potentials made of Wigner functions, D0KL, with L ≤ 4, which closely resemble the corresponding POMFs in form; hence, they also approach the latter in accuracy. Such potentials can be beneficially characterized/compared in terms of composition, symmetry, and associated order parameters. In this study, we develop a method for deriving conformational entropy from them, which also features the benefits specified above. The method developed is applied to the dimerization of the Rho GTPase-binding domain of plexin-B1. Insights into local ordering, entropy compensation, and features of allostery are gained. In previous work, we developed the slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation from restricted bond vector motion in proteins. SRLS comprises explicit (restricting) potentials of the kind developed here. It also comprises diffusion tensors describing the local motion and related features of local geometry. The complete model fits experimental data. In future work, the explicit potentials developed here will be inserted unchanged in SRLS-based data fitting, thereby improving the picture of structural dynamics. Given that SRLS is unique in featuring potentials that can closely approach the corresponding POMFs in accuracy, the present study is an important step toward generally improving protein dynamics by NMR relaxation.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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36
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Li ZL, Müller-Greven J, Kim S, Tamagnone L, Buck M. Plexin-Bs enhance their GAP activity with a novel activation switch loop generating a cooperative enzyme. Cell Mol Life Sci 2020; 78:1101-1112. [PMID: 32601713 DOI: 10.1007/s00018-020-03571-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/24/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023]
Abstract
Plexins receive guidance cues from semaphorin ligands and transmit their signal through the plasma membrane. This family of proteins is unique amongst single-pass transmembrane receptors as their intracellular regions interact directly with several small GTPases, which regulate cytoskeletal dynamics and cell adhesion. Here, we characterize the GTPase Activating Protein (GAP) function of Plexin-B1 and find that a cooperative GAP activity towards the substrate GTPase, Rap1b, is associated with the N-terminal Juxtamembrane region of Plexin-B1. Importantly, we unveil an activation mechanism of Plexin-B1 by identifying a novel functional loop which partially blocks Rap1b entry into the plexin GAP domain. Consistent with the concept of allokairy developed for other systems, Plexin-B activity is increased by an apparent substrate-mediated cooperative effect. Simulations and mutagenesis suggest the repositioned JM conformation is stabilized by the new activation switch loop when the active site is occupied, giving rise to faster enzymatic turnover and cooperative behavior. The biological implications, essentially those of a threshold behavior for cell migration, are discussed.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Jeannine Müller-Greven
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - SoonJeung Kim
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Luca Tamagnone
- School of Medicine, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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37
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Bernard J, Lumley LM, Buck M, Cobb TP. A new species of rake-legged mite, Caeculus cassiopeiae (Prostigmata, Caeculidae), from Canada and a systematic analysis of its genus. Zookeys 2020; 926:1-23. [PMID: 32336917 PMCID: PMC7170984 DOI: 10.3897/zookeys.926.48741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/02/2020] [Indexed: 12/01/2022] Open
Abstract
The genus Caeculus Dufour (Prostigmata, Caeculidae) contains 19 previously described species, most of which are found in North America, and for which no comprehensive phylogenetic treatment exists. Here, one new species from Alberta, Canada, is described: Caeculuscassiopeiae Bernard & Lumley, sp. nov., and another caeculid known to be present in Canada is documented. The new species is characterized within the genus with a character state matrix, from which an updated key is produced. A systematic analysis of all 20 species based on morphological and geographical distribution traits obtained from literature represents the first phylogenetic review of the genus.
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Affiliation(s)
- Jared Bernard
- Invertebrate Zoology, Royal Alberta Museum, 9810 103A Avenue NW, Edmonton, Alberta T5J 0G2, Canada Royal Alberta Museum Edmonton Canada.,Plant & Environmental Protection Sciences, University of Hawaii-Mānoa, 3050 Maile Way, Honolulu, HI 96822, USA University of Hawaii-Mānoa Honolulu United States of America
| | - Lisa M Lumley
- Invertebrate Zoology, Royal Alberta Museum, 9810 103A Avenue NW, Edmonton, Alberta T5J 0G2, Canada Royal Alberta Museum Edmonton Canada
| | - Matthias Buck
- Invertebrate Zoology, Royal Alberta Museum, 9810 103A Avenue NW, Edmonton, Alberta T5J 0G2, Canada Royal Alberta Museum Edmonton Canada
| | - Tyler P Cobb
- Invertebrate Zoology, Royal Alberta Museum, 9810 103A Avenue NW, Edmonton, Alberta T5J 0G2, Canada Royal Alberta Museum Edmonton Canada
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38
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Packer MR, Parker JA, Chung JK, Li ZL, Lee YK, Guterres H, Cookis T, Hossain A, Donnelly DP, Agar JN, Makowski L, Buck M, Groves JT, Mattos C. Raf promotes dimerization of the Ras G‐domain. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Buck M, Gerken T. Two Hands Grip Better Than One for Tight Binding and Specificity: How a Phage Endolysin Fits into the Cell Wall of Its Host. Structure 2020; 27:1350-1352. [PMID: 31484048 DOI: 10.1016/j.str.2019.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Endolysin enzymes of bacteriophages that cut up cell walls have a potential use in combating bacterial antibiotic resistance. In this issue of Structure, Lee et al. (2019) present tandem SH3b domains as the structural basis of an endolysin against Bacillus cereus that selectively recognize opposing glycan strands of the bacterial cell wall peptidoglycan.
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Affiliation(s)
- Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106, USA; Department of Neurosciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106, USA.
| | - Thomas Gerken
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106, USA.
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40
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Li Z, Buck M. Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface. J Chem Inf Model 2019; 60:306-315. [DOI: 10.1021/acs.jcim.9b00690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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41
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Abstract
AbstractThe Fukushima accident reveals the need for additional safety systems for nuclear power plants. One promising option is the supercritical carbon-dioxide (sCO2) heat removal system, which consists of a simple Brayton cycle. This study provides an overview of the extensions and validation of the thermal-hydraulic system code ATHLET for the simulation of sCO2 power cycles, especially with regard to the sCO2 heat removal system. The properties of CO2, heat transfer and pressure drop correlations, as well as compact heat exchanger and turbomachinery modelling are considered.
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Affiliation(s)
- M. Hofer
- 1University of Stuttgart, Institute of Nuclear Technology and Energy Systems, E-mail: , Tel.: 004971168560855
| | - M. Buck
- 2University of Stuttgart, Institute of Nuclear Technology and Energy Systems, E-mail:
| | - J. Starflinger
- 3University of Stuttgart, Institute of Nuclear Technology and Energy Systems, E-mail:
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42
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Mendelman N, Zerbetto M, Buck M, Meirovitch E. Local Ordering at the N-H Sites of the Rho GTPase Binding Domain of Plexin-B1: Impact of Dimerization. J Phys Chem B 2019; 123:8019-8033. [PMID: 31469564 DOI: 10.1021/acs.jpcb.9b05905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new molecular dynamics (MD) based method for describing analytically local potentials at mobile N-H sites in proteins. Here we apply it to the monomer and dimer of the Rho GTPase binding domain (RBD) of the transmembrane receptor plexin-B1 to gain insight into dimerization, which can compete with Rho GTPase binding. In our method, the local potential is given by linear combinations, u(DL,K), of the real combinations of the Wigner rotation matrix elements, DL,K, with L = 1-4 and appropriate symmetry. The combination that "fits best" the corresponding MD potential of mean force, u(MD), is the potential we are seeking, u(DL,K - BEST). For practical reasons the fitting process involves probability distributions, Peq ∝ exp(-u), instead of potentials, u. The symmetry of the potential, u(DL,K), may be related to the irreducible representations of the D2h point group. The monomer (dimer) potentials have mostly Ag and B2u (B1u and B2u) symmetry. For the monomer, the associated probability distributions are generally dispersed in space, shallow, and centered at the "reference N-H orientation" (defined in section 3.1. below); for the dimer many are more concentrated, deep and centered away from the "reference N-H orientation". The u(DL,K) functions provide a consistent description of the potential energy landscape at protein N-H sites. The L1-loop of the plexin-B1 RBD is not seen in the crystal structure, and many resonances of the L4 loop are missing in the NMR 15N-1H HSQC spectrum of the dimer; we suggest reasons for these features. An allosteric signal transmission pathway was reported previously for the monomer. We find that it has shallow N-H potentials at its ends, which become deeper as one proceeds toward the middle, complementing structurally the previously derived dynamic picture. Prospects of this study include correlating u(DL,K - BEST) with MD force-fields, and using them without further adjustment in NMR relaxation analysis schemes.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences , University of Padova , Padova 35131 , Italy
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University , Cleveland Ohio 44106 , United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 52900 , Israel
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43
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Freiría López M, Buck M, Starflinger J. Neutronic modeling of debris beds for a criticality evaluation. ANN NUCL ENERGY 2019. [DOI: 10.1016/j.anucene.2019.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Li ZL, Buck M. Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein-Protein Interactions. J Chem Theory Comput 2019; 15:4318-4331. [PMID: 31241940 DOI: 10.1021/acs.jctc.9b00195] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water interaction in the CHARMM36 force field, in order to better fit the solvation free energy of amino acids side-chain analogues. We find that the molecular dynamics simulation with the scaled force field, CHARMM36s, as well as a recently released version, CHARMM36m, effectively improve on the overly sticky association of proteins, such as ubiquitin. We investigate the formation of a heterodimer protein complex between the SAM domains of the EphA2 receptor and the SHIP2 enzyme by performing a combined total of 48 μs simulations with the different potential functions. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% with CHARMM36s, and to 18.3% with CHARMM36m. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a preorientation guided by Coulomb interactions, consistent with an electrostatic steering mechanism. In 12 cases, the complex could directly transform to the native protein interaction surfaces with only small adjustments in domain orientation. In the other 13 cases, orientational and/or translational adjustments are needed to reach the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a dissociation followed by a reassociation to the correct complex structure is still rare. Instead, the remaining non-native complexes undergo configurational changes/surface searching, which, however, rarely leads to native structures on a time scale of 250 ns. These observations provide a rich picture of the mechanisms of protein-protein complex formation and suggest that computational predictions of native complex PPIs could be improved further.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States.,Departments of Pharmacology and Neurosciences, and Case Comprehensive Cancer Center , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
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45
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Cao S, Chung S, Kim S, Li Z, Manor D, Buck M. K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function. J Biol Chem 2019; 294:7068-7084. [PMID: 30792310 DOI: 10.1074/jbc.ra118.004021] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Ras genes potently drive human cancers, with mutated proto-oncogene GTPase KRAS4B (K-Ras4B) being the most abundant isoform. Targeted inhibition of oncogenic gene products is considered the "holy grail" of present-day cancer therapy, and recent discoveries of small-molecule KRas4B inhibitors were made thanks to a deeper understanding of the structure and dynamics of this GTPase. Because interactions with biological membranes are key for Ras function, Ras-lipid interactions have become a major focus, especially because such interactions evidently involve both the Ras C terminus for lipid anchoring and its G-protein domain. Here, using NMR spectroscopy and molecular dynamics simulations complemented by biophysical- and cell-biology assays, we investigated the interaction between K-Ras4B with the signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2). We discovered that the β2 and β3 strands as well as helices 4 and 5 of the GTPase G-domain bind to PIP2 and identified the specific residues in these structural elements employed in these interactions, likely occurring in two K-Ras4B orientation states relative to the membrane. Importantly, we found that some of these residues known to be oncogenic when mutated (D47K, D92N, K104M, and D126N) are critical for K-Ras-mediated transformation of fibroblast cells, but do not substantially affect basal and assisted nucleotide hydrolysis and exchange. Moreover, the K104M substitution abolished localization of K-Ras to the plasma membrane. The findings suggest that specific G-domain residues can critically regulate Ras function by mediating interactions with membrane-associated PIP2 lipids; these insights that may inform the future design of therapeutic reagents targeting Ras activity.
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Affiliation(s)
- Shufen Cao
- From the Departments of Physiology and Biophysics
| | | | | | - Zhenlu Li
- From the Departments of Physiology and Biophysics
| | - Danny Manor
- Nutrition, .,Pharmacology, and.,the Case Comprehensive Cancer Center and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, .,the Case Comprehensive Cancer Center and.,Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106 and.,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
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46
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Li Z, Buck M. Unveiling a New Regulation Mechanism of Small Gtpases on the Activity of Plexin-B1 Membrane Receptor. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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47
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Razelle Javier F, Shi X, Li Z, Mueller-Greven J, Bowman D, Willard B, Wang BC, Smith AW, Buck M. Structural and Functional Studies of the Effects of Phosphorylation on Ephrin Receptor Tyrosine Kinase, EphA2, Receptor Intracellular Domains and the Relationship with its Sam Domain as an Autoinhibitor. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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48
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Yeasmin R, Buck M, Weinberg A, Zhang L. Translocation of Human β Defensin Type 3 through a Neutrally Charged Lipid Membrane: A Free Energy Study. J Phys Chem B 2018; 122:11883-11894. [DOI: 10.1021/acs.jpcb.8b08285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Rabeta Yeasmin
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, Tennessee 38505, United States
| | | | | | - Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, Tennessee 38505, United States
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49
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Babinchak WM, Li Z, Buck M. Keys to Amyloid City: Computation and NMR Reveal Potential TDP-43 ALS Intermediates. Biophys J 2018; 115:1625-1627. [PMID: 30290957 PMCID: PMC6225042 DOI: 10.1016/j.bpj.2018.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 11/26/2022] Open
Affiliation(s)
- W Michael Babinchak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Zhenlu Li
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio.
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50
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Zhang X, Cao S, Barila G, Edreira MM, Hong K, Wankhede M, Naim N, Buck M, Altschuler DL. Correction: Cyclase-associated protein 1 (CAP1) is a prenyl-binding partner of Rap1 GTPase. J Biol Chem 2018; 293:13849. [PMID: 30194256 DOI: 10.1074/jbc.aac118.005290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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