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Moosavi-Movahedi Z, Salehi N, Habibi-Rezaei M, Qassemi F, Karimi-Jafari MH. Intermediate-aided allostery mechanism for α-glucosidase by Xanthene-11v as an inhibitor using residue interaction network analysis. J Mol Graph Model 2023; 122:108495. [PMID: 37116337 DOI: 10.1016/j.jmgm.2023.108495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
Exploring allosteric inhibition and the discovery of new inhibitor binding sites are important studies in protein regulation mechanisms and drug discovery. Structural and network-based analyses of trajectories resulting from molecular dynamics (MD) simulations have been developed to discover protein dynamics, landscape, functions, and allosteric regions. Here, an experimentally suggested non-competitive inhibitor, xanthene-11v, was considered to explore its allosteric inhibition mechanism in α-glucosidase MAL12. Comparative structural and network analyses were applied to eight 250 ns independent MD simulations, four of which were performed in the free state and four of which were performed in ligand-bound forms. Projected two-dimensional free energy landscapes (FEL) were constructed from the probabilistic distribution of conformations along the first two principal components. The post-simulation analyses of the coordinates, side-chain torsion angles, non-covalent interaction networks, network communities, and their centralities were performed on α-glucosidase conformations and the intermediate sub-states. Important communities of residues have been found that connect the allosteric site to the active site. Some of these residues like Thr307, Arg312, TYR344, ILE345, Phe357, Asp406, Val407, Asp408, and Leu436 are the key messengers in the transition pathway between allosteric and active sites. Evaluating the probability distribution of distances between gate residues including Val407 in one community and Phe158, and Pro65 in another community depicted the closure of this gate due to the inhibitor binding. Six macro states of protein were deduced from the topology of FEL and analysis of conformational preference of free and ligand-bound systems to these macro states shows a combination of lock-and-key, conformational selection, and induced fit mechanisms are effective in ligand binding. All these results reveal structural states, allosteric mechanisms, and key players in the inhibition pathway of α-glucosidase by xanthene-11v.
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Affiliation(s)
- Zahra Moosavi-Movahedi
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Najmeh Salehi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | | | | | - Mohammad Hossein Karimi-Jafari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
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2
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George A, Kim DN, Moser T, Gildea IT, Evans JE, Cheung MS. Graph identification of proteins in tomograms (GRIP-Tomo). Protein Sci 2023; 32:e4538. [PMID: 36482866 PMCID: PMC9798246 DOI: 10.1002/pro.4538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three-dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo-multimeric complexes from 10 topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single-domain protein native topologies as well as distinct single-domain proteins from multimeric complexes within noisy volumes.
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Affiliation(s)
- August George
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
- Department of Biomedical EngineeringOregon Health & Science UniversityPortlandOregonUSA
| | - Doo Nam Kim
- Biological Science DivisionPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Trevor Moser
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Ian T. Gildea
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - James E. Evans
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Margaret S. Cheung
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
- Department of PhysicsUniversity of WashingtonSeattleWashingtonUSA
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3
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Design, construction and in vivo functional assessment of a hinge truncated sFLT01. Gene Ther 2022; 30:347-361. [PMID: 36114375 DOI: 10.1038/s41434-022-00362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 11/08/2022]
Abstract
Gene therapy for the treatment of ocular neovascularization has reached clinical trial phases. The AAV2-sFLT01 construct was already evaluated in a phase 1 open-label trial administered intravitreally to patients with advanced neovascular age-related macular degeneration. SFLT01 protein functions by binding to VEGF and PlGF molecules and inhibiting their activities simultaneously. It consists of human VEGFR1/Flt-1 (hVEGFR1), a polyglycine linker, and the Fc region of human IgG1. The IgG1 upper hinge region of the sFLT01 molecule makes it vulnerable to radical attacks and prone to causing immune reactions. This study pursued two goals: (i) minimizing the immunogenicity and vulnerability of the molecule by designing a truncated molecule called htsFLT01 (hinge truncated sFLT01) that lacked the IgG1 upper hinge and lacked 2 amino acids from the core hinge region; and (ii) investigating the structural and functional properties of the aforesaid chimeric molecule at different levels (in silico, in vitro, and in vivo). Molecular dynamics simulations and molecular mechanics energies combined with Poisson-Boltzmann and surface area continuum solvation calculations revealed comparable free energy of binding and binding affinity for sFLT01 and htsFLT01 to their cognate ligands. Conditioned media from human retinal pigment epithelial (hRPE) cells that expressed htsFLT01 significantly reduced tube formation in HUVECs. The AAV2-htsFLT01 virus suppressed vascular development in the eyes of newborn mice. The htsFLT01 gene construct is a novel anti-angiogenic tool with promising improvements compared to existing treatments.
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Chinigò G, Grolez GP, Audero M, Bokhobza A, Bernardini M, Cicero J, Toillon RA, Bailleul Q, Visentin L, Ruffinatti FA, Brysbaert G, Lensink MF, De Ruyck J, Cantelmo AR, Fiorio Pla A, Gkika D. TRPM8-Rap1A Interaction Sites as Critical Determinants for Adhesion and Migration of Prostate and Other Epithelial Cancer Cells. Cancers (Basel) 2022; 14:2261. [PMID: 35565390 PMCID: PMC9102551 DOI: 10.3390/cancers14092261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Emerging evidence indicates that the TRPM8 channel plays an important role in prostate cancer (PCa) progression, by impairing the motility of these cancer cells. Here, we reveal a novel facet of PCa motility control via direct protein-protein interaction (PPI) of the channel with the small GTPase Rap1A. The functional interaction of the two proteins was assessed by active Rap1 pull-down assays and live-cell imaging experiments. Molecular modeling analysis allowed the identification of four putative residues involved in TRPM8-Rap1A interaction. Point mutations of these sites impaired PPI as shown by GST-pull-down, co-immunoprecipitation, and PLA experiments and revealed their key functional role in the adhesion and migration of PC3 prostate cancer cells. More precisely, TRPM8 inhibits cell migration and adhesion by trapping Rap1A in its GDP-bound inactive form, thus preventing its activation at the plasma membrane. In particular, residues E207 and Y240 in the sequence of TRPM8 and Y32 in that of Rap1A are critical for the interaction between the two proteins not only in PC3 cells but also in cervical (HeLa) and breast (MCF-7) cancer cells. This study deepens our knowledge of the mechanism through which TRPM8 would exert a protective role in cancer progression and provides new insights into the possible use of TRPM8 as a new therapeutic target in cancer treatment.
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Affiliation(s)
- Giorgia Chinigò
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Guillaume P. Grolez
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Madelaine Audero
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Alexandre Bokhobza
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Michela Bernardini
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
| | - Julien Cicero
- CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020-UMR 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France; (J.C.); (R.-A.T.)
- UR 2465—Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University of Artois, F-62300 Lens, France
| | - Robert-Alain Toillon
- CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020-UMR 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France; (J.C.); (R.-A.T.)
| | - Quentin Bailleul
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Luca Visentin
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
| | - Federico Alessandro Ruffinatti
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
| | - Guillaume Brysbaert
- CNRS UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, 59000 Lille, France; (G.B.); (M.F.L.); (J.D.R.)
| | - Marc F. Lensink
- CNRS UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, 59000 Lille, France; (G.B.); (M.F.L.); (J.D.R.)
| | - Jerome De Ruyck
- CNRS UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, 59000 Lille, France; (G.B.); (M.F.L.); (J.D.R.)
| | - Anna Rita Cantelmo
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Alessandra Fiorio Pla
- Department of Life Sciences and Systems Biology, University of Torino, 10123 Torino, Italy; (G.C.); (M.A.); (M.B.); (L.V.); (F.A.R.); (A.F.P.)
- INSERM, U1003—PHYCEL—Physiologie Cellulaire, University of Lille, F-59000 Lille, France; (G.P.G.); (A.B.); (Q.B.); (A.R.C.)
| | - Dimitra Gkika
- CNRS, INSERM, CHU Lille, Centre Oscar Lambret, UMR 9020-UMR 1277-Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, F-59000 Lille, France; (J.C.); (R.-A.T.)
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Institut Universitaire de France (IUF), 75231 Paris, France
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Trouvilliez S, Cicero J, Lévêque R, Aubert L, Corbet C, Van Outryve A, Streule K, Angrand PO, Völkel P, Magnez R, Brysbaert G, Mysiorek C, Gosselet F, Bourette R, Adriaenssens E, Thuru X, Lagadec C, de Ruyck J, Orian-Rousseau V, Le Bourhis X, Toillon RA. Direct interaction of TrkA/CD44v3 is essential for NGF-promoted aggressiveness of breast cancer cells. J Exp Clin Cancer Res 2022; 41:110. [PMID: 35346305 PMCID: PMC8962522 DOI: 10.1186/s13046-022-02314-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/03/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND CD44 is a multifunctional membrane glycoprotein. Through its heparan sulfate chain, CD44 presents growth factors to their receptors. We have shown that CD44 and Tropomyosin kinase A (TrkA) form a complex following nerve growth factor (NGF) induction. Our study aimed to understand how CD44 and TrkA interact and the consequences of inhibiting this interaction regarding the pro-tumoral effect of NGF in breast cancer. METHODS After determining which CD44 isoforms (variants) are involved in forming the TrkA/CD44 complex using proximity ligation assays, we investigated the molecular determinants of this interaction. By molecular modeling, we isolated the amino acids involved and confirmed their involvement using mutations. A CD44v3 mimetic peptide was then synthesized to block the TrkA/CD44v3 interaction. The effects of this peptide on the growth, migration and invasion of xenografted triple-negative breast cancer cells were assessed. Finally, we investigated the correlations between the expression of the TrkA/CD44v3 complex in tumors and histo-pronostic parameters. RESULTS We demonstrated that isoform v3 (CD44v3), but not v6, binds to TrkA in response to NGF stimulation. The final 10 amino acids of exon v3 and the TrkA H112 residue are necessary for the association of CD44v3 with TrkA. Functionally, the CD44v3 mimetic peptide impairs not only NGF-induced RhoA activation, clonogenicity, and migration/invasion of breast cancer cells in vitro but also tumor growth and metastasis in a xenograft mouse model. We also detected TrkA/CD44v3 only in cancerous cells, not in normal adjacent tissues. CONCLUSION Collectively, our results suggest that blocking the CD44v3/TrkA interaction can be a new therapeutic option for triple-negative breast cancers.
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Affiliation(s)
- Sarah Trouvilliez
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Julien Cicero
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- University Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300, Lens, France
| | - Romain Lévêque
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Léo Aubert
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Cyril Corbet
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Alexandre Van Outryve
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Karolin Streule
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pierre-Olivier Angrand
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Pamela Völkel
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Romain Magnez
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Guillaume Brysbaert
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Caroline Mysiorek
- University Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300, Lens, France
| | - Fabien Gosselet
- University Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300, Lens, France
| | - Roland Bourette
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Eric Adriaenssens
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Xavier Thuru
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Chann Lagadec
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Jérôme de Ruyck
- University Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Véronique Orian-Rousseau
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, 76344, Eggenstein-Leopoldshafen, Germany
| | - Xuefen Le Bourhis
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Robert-Alain Toillon
- University Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France.
- Université de Lille, Faculté des Sciences et Technologies, UMR CNRS 9020- INSERM U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Bâtiment SN3, 3ème étage, Cité scientifique, 59655, Villeneuve d'Ascq, France.
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Brysbaert G, Lensink MF. Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding. FRONTIERS IN BIOINFORMATICS 2021; 1:684970. [PMID: 36303777 PMCID: PMC9581030 DOI: 10.3389/fbinf.2021.684970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022] Open
Abstract
Residue interaction networks (RINs) describe a protein structure as a network of interacting residues. Central nodes in these networks, identified by centrality analyses, highlight those residues that play a role in the structure and function of the protein. However, little is known about the capability of such analyses to identify residues involved in the formation of macromolecular complexes. Here, we performed six different centrality measures on the RINs generated from the complexes of the SKEMPI 2 database of changes in protein–protein binding upon mutation in order to evaluate the capability of each of these measures to identify major binding residues. The analyses were performed with and without the crystallographic water molecules, in addition to the protein residues. We also investigated the use of a weight factor based on the inter-residue distances to improve the detection of these residues. We show that for the identification of major binding residues, closeness, degree, and PageRank result in good precision, whereas betweenness, eigenvector, and residue centrality analyses give a higher sensitivity. Including water in the analysis improves the sensitivity of all measures without losing precision. Applying weights only slightly raises the sensitivity of eigenvector centrality analysis. We finally show that a combination of multiple centrality analyses is the optimal approach to identify residues that play a role in protein–protein interaction.
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Foutch D, Pham B, Shen T. Protein conformational switch discerned via network centrality properties. Comput Struct Biotechnol J 2021; 19:3599-3608. [PMID: 34257839 PMCID: PMC8246261 DOI: 10.1016/j.csbj.2021.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensemble-informed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.
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Affiliation(s)
- David Foutch
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.,UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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8
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Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies. Int J Mol Sci 2021; 22:ijms22115989. [PMID: 34206009 PMCID: PMC8198660 DOI: 10.3390/ijms22115989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/29/2021] [Indexed: 01/16/2023] Open
Abstract
Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the mechanism of action into the progression of immune responses. Multiple strategies, including phage display and hybridoma technologies, have been used to enhance the affinity of antibodies for their respective epitopes. Here, we investigate the TLR4 antibody-binding epitope by computational-driven approach. We demonstrate that three important residues, i.e., Y328, N329, and K349 of TLR4 antibody binding epitope identified upon in silico mutagenesis, affect not only the interaction and binding affinity of antibody but also influence the structural integrity of TLR4. Furthermore, we predict a novel epitope at the TLR4-MD2 interface which can be targeted and explored for therapeutic antibodies and small molecules. This technique provides an in-depth insight into antibody-antigen interactions at the resolution and will be beneficial for the development of new monoclonal antibodies. Computational techniques, if coupled with experimental methods, will shorten the duration of rational design and development of antibody therapeutics.
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Newaz K, Wright G, Piland J, Li J, Clark PL, Emrich SJ, Milenković T. Network analysis of synonymous codon usage. Bioinformatics 2020; 36:4876-4884. [PMID: 32609328 DOI: 10.1093/bioinformatics/btaa603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 05/05/2020] [Accepted: 06/22/2020] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Most amino acids are encoded by multiple synonymous codons, some of which are used more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionarily conserved. Analyses of their positions in protein 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. RESULTS We model protein structures as networks and use network centrality to measure the structural position of an amino acid. We first validate that amino acids buried within the structural core are network-central, and those on the surface are not. Then, we study potential differences between network centralities and thus structural positions of amino acids encoded by conserved rare, non-conserved rare and commonly used codons. We find that in 84% of proteins, the three codon categories occupy significantly different structural positions. We examine protein groups showing different codon centrality trends, i.e. different relationships between structural positions of the three codon categories. We see several cases of all proteins from our data with some structural or functional property being in the same group. Also, we see a case of all proteins in some group having the same property. Our work shows that codon usage is linked to the final protein structure and thus possibly to co-translational protein folding. AVAILABILITY AND IMPLEMENTATION https://nd.edu/∼cone/CodonUsage/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Khalique Newaz
- Department of Computer Science and Engineering.,Center for Network and Data Science.,Eck institute for Global Health
| | - Gabriel Wright
- Department of Computer Science and Engineering.,Eck institute for Global Health
| | - Jacob Piland
- Department of Computer Science and Engineering.,Center for Network and Data Science.,Eck institute for Global Health
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics
| | - Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Tijana Milenković
- Department of Computer Science and Engineering.,Center for Network and Data Science.,Eck institute for Global Health
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10
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Wako H, Endo S. Dynamic properties of oligomers that characterize low-frequency normal modes. Biophys Physicobiol 2019; 16:220-231. [PMID: 31984175 PMCID: PMC6976002 DOI: 10.2142/biophysico.16.0_220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/09/2019] [Indexed: 01/09/2023] Open
Abstract
Dynamics of oligomeric proteins (one trimer, two tetramers, and one hexamer) were studied by elastic network model-based normal mode analysis to characterize their large-scale concerted motions. First, the oligomer motions were simplified by considering rigid-body motions of individual subunits. The subunit motions were resolved into three components in a cylindrical coordinate system: radial, tangential, and axial ones. Single component is dominant in certain normal modes. However, more than one component is mixed in others. The subunits move symmetrically in certain normal modes and as a standing wave with several wave nodes in others. Secondly, special attention was paid to atoms on inter-subunit interfaces. Their displacement vectors were decomposed into intra-subunit deformative (internal) and rigid-body (external) motions in individual subunits. The fact that most of the cosines of the internal and external motion vectors were negative for the atoms on the inter-subunit interfaces, indicated their opposing movements. Finally, a structural network of residues defined for each normal mode was investigated; the network was constructed by connecting two residues in contact and moving coherently. The centrality measure “betweenness” of each residue was calculated for the networks. Several residues with significantly high betweenness were observed on the inter-subunit interfaces. The results indicate that these residues are responsible for oligomer dynamics. It was also observed that amino acid residues with significantly high betweenness were more conservative. This supports that the betweenness is an effective characteristic for identifying an important residue in protein dynamics.
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Affiliation(s)
- Hiroshi Wako
- School of Social Sciences, Waseda University, Shinjuku-ku, Tokyo 169-8050, Japan
| | - Shigeru Endo
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
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11
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Aydınkal RM, Serçinoğlu O, Ozbek P. ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. Nucleic Acids Res 2019; 47:W471-W476. [PMID: 31114881 PMCID: PMC6602423 DOI: 10.1093/nar/gkz390] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/17/2019] [Accepted: 05/09/2019] [Indexed: 01/14/2023] Open
Abstract
ProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx constructs a PSN by adding nodes to represent residues and edges between these nodes using user-specified interaction distance cutoffs for either carbon-alpha, carbon-beta or atom-pair contact networks. Different types of weighted networks can also be constructed by using either (i) the residue-residue interaction energies in the format returned by gRINN, resulting in a Protein Energy Network (PEN); (ii) the dynamical cross correlations from a coarse-grained Normal Mode Analysis (NMA) of the protein structure; (iii) interaction strength. Upon construction of the network, common network metrics (such as node centralities) as well as shortest paths between nodes and k-cliques are calculated. Moreover, additional features of each residue in the form of conservation scores and mutation/natural variant information are included in the analysis. By this way, tool offers an enhanced and direct comparison of network-based residue metrics with other types of biological information. ProSNEx is free and open to all users without login requirement at http://prosnex-tool.com.
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Affiliation(s)
- Rasim Murat Aydınkal
- Department of Bioengineering, Faculty of Engineering, Marmara University, Kadikoy, Istanbul 34722, Turkey
- Ali Nihat Gokyigit Foundation, Etiler, Istanbul 34340, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Kadikoy, Istanbul 34722, Turkey
- Department of Bioengineering, Faculty of Engineering, Recep Tayyip Erdoğan University, Rize 53100, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Kadikoy, Istanbul 34722, Turkey
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12
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Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair. Genes (Basel) 2019; 10:genes10030206. [PMID: 30857266 PMCID: PMC6470857 DOI: 10.3390/genes10030206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/03/2022] Open
Abstract
The transcription factor Ets-1 (ETS proto-oncogene 1) shows low expression levels except in specific biological processes like haematopoiesis or angiogenesis. Elevated levels of expression are observed in tumor progression, resulting in Ets-1 being named an oncoprotein. It has recently been shown that Ets-1 interacts with two DNA repair enzymes, PARP-1 (poly(ADP-ribose) polymerase 1) and DNA-PK (DNA-dependent protein kinase), through two different domains and that these interactions play a role in cancer. Considering that Ets-1 can bind to distinctly different domains of two DNA repair enzymes, we hypothesized that the interaction can be transposed onto homologs of the respective domains. We have searched for sequence and structure homologs of the interacting ETS(Ets-1), BRCT(PARP-1) and SAP(DNA-PK) domains, and have identified several candidate binding pairs that are currently not annotated as such. Many of the Ets-1 partners are associated to DNA repair mechanisms. We have applied protein-protein docking to establish putative interaction poses and investigated these using centrality analyses at the protein residue level. Most of the identified poses are virtually similar to our recently established interaction model for Ets-1/PARP-1 and Ets-1/DNA-PK. Our work illustrates the potentially high number of interactors of Ets-1, in particular involved in DNA repair mechanisms, which shows the oncoprotein as a potential important regulator of the mechanism.
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