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Shi XX, Wang ZZ, Wang YL, Huang GY, Yang JF, Wang F, Hao GF, Yang GF. PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics. Brief Bioinform 2021; 23:6394992. [PMID: 34643234 DOI: 10.1093/bib/bbab424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/19/2021] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 11/14/2022] Open
Abstract
Protein post-translational modifications (PTM) play vital roles in cellular regulation, modulating functions by driving changes in protein structure and dynamics. Exploring comprehensively the influence of PTM on conformational dynamics can facilitate the understanding of the related biological function and molecular mechanism. Currently, a series of excellent computation tools have been designed to analyze the time-dependent structural properties of proteins. However, the protocol aimed to explore conformational dynamics of post-translational modified protein is still a blank. To fill this gap, we present PTMdyna to visually predict the conformational dynamics differences between unmodified and modified proteins, thus indicating the influence of specific PTM. PTMdyna exhibits an AUC of 0.884 tested on 220 protein-protein complex structures. The case of heterochromatin protein 1α complexed with lysine 9-methylated histone H3, which is critical for genomic stability and cell differentiation, was used to demonstrate its applicability. PTMdyna provides a reliable platform to predict the influence of PTM on protein dynamics, making it easier to interpret PTM functionality at the structure level. The web server is freely available at http://ccbportal.com/PTMdyna.
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Affiliation(s)
- Xing-Xing Shi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Zhi-Zheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Yu-Liang Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Guang-Yi Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China.,State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China.,International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei, P. R. China
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Lechuga GC, Souza-Silva F, Sacramento CQ, Trugilho MRO, Valente RH, Napoleão-Pêgo P, Dias SSG, Fintelman-Rodrigues N, Temerozo JR, Carels N, Alves CR, Pereira MCS, Provance DW, Souza TML, De-Simone SG. SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites. Int J Mol Sci 2021; 22:9035. [PMID: 34445741 PMCID: PMC8396565 DOI: 10.3390/ijms22169035] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 01/19/2023] Open
Abstract
(1) Background: coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been linked to hematological dysfunctions, but there are little experimental data that explain this. Spike (S) and Nucleoprotein (N) proteins have been putatively associated with these dysfunctions. In this work, we analyzed the recruitment of hemoglobin (Hb) and other metabolites (hemin and protoporphyrin IX-PpIX) by SARS-Cov2 proteins using different approaches. (2) Methods: shotgun proteomics (LC-MS/MS) after affinity column adsorption identified hemin-binding SARS-CoV-2 proteins. The parallel synthesis of the peptides technique was used to study the interaction of the receptor bind domain (RBD) and N-terminal domain (NTD) of the S protein with Hb and in silico analysis to identify the binding motifs of the N protein. The plaque assay was used to investigate the inhibitory effect of Hb and the metabolites hemin and PpIX on virus adsorption and replication in Vero cells. (3) Results: the proteomic analysis by LC-MS/MS identified the S, N, M, Nsp3, and Nsp7 as putative hemin-binding proteins. Six short sequences in the RBD and 11 in the NTD of the spike were identified by microarray of peptides to interact with Hb and tree motifs in the N protein by in silico analysis to bind with heme. An inhibitory effect in vitro of Hb, hemin, and PpIX at different levels was observed. Strikingly, free Hb at 1mM suppressed viral replication (99%), and its interaction with SARS-CoV-2 was localized into the RBD region of the spike protein. (4) Conclusions: in this study, we identified that (at least) five proteins (S, N, M, Nsp3, and Nsp7) of SARS-CoV-2 recruit Hb/metabolites. The motifs of the RDB of SARS-CoV-2 spike, which binds Hb, and the sites of the heme bind-N protein were disclosed. In addition, these compounds and PpIX block the virus's adsorption and replication. Furthermore, we also identified heme-binding motifs and interaction with hemin in N protein and other structural (S and M) and non-structural (Nsp3 and Nsp7) proteins.
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Affiliation(s)
- Guilherme C. Lechuga
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Celular Ultrastructure, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Franklin Souza-Silva
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Biology and Heath Science Faculty, Iguaçu University, Nova Iguaçu 26260-045, RJ, Brazil
| | - Carolina Q. Sacramento
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Monique R. O. Trugilho
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Toxinology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Richard H. Valente
- Laboratory of Toxinology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Paloma Napoleão-Pêgo
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
| | - Suelen S. G. Dias
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Natalia Fintelman-Rodrigues
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Jairo R. Temerozo
- Laboratory of Thymus Research, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
- FIOCRUZ, National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Rio de Janeiro 21040-900, RJ, Brazil
| | - Nicolas Carels
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Biology and Heath Science Faculty, Iguaçu University, Nova Iguaçu 26260-045, RJ, Brazil
| | - Carlos R. Alves
- Laboratory of Molecular Biology and Endemic Diseases, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Mirian C. S. Pereira
- Laboratory of Celular Ultrastructure, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - David W. Provance
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
| | - Thiago M. L. Souza
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Salvatore G. De-Simone
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, RJ, Brazil
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Pahari S, Li G, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. Int J Mol Sci 2020; 21:E2563. [PMID: 32272725 PMCID: PMC7177817 DOI: 10.3390/ijms21072563] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/26/2022] Open
Abstract
Maintaining wild type protein-protein interactions is essential for the normal function of cell and any mutation that alter their characteristics can cause disease. Therefore, the ability to correctly and quickly predict the effect of amino acid mutations is crucial for understanding disease effects and to be able to carry out genome-wide studies. Here, we report a new development of the SAAMBE method, SAAMBE-3D, which is a machine learning-based approach, resulting in accurate predictions and is extremely fast. It achieves the Pearson correlation coefficient ranging from 0.78 to 0.82 depending on the training protocol in benchmarking five-fold validation test against the SKEMPI v2.0 database and outperforms currently existing algorithms on various blind-tests. Furthermore, optimized and tested via five-fold cross-validation on the Cornell University dataset, the SAAMBE-3D achieves AUC of 1.0 and 0.96 on a homo and hereto-dimer test datasets. Another important feature of SAAMBE-3D is that it is very fast, it takes less than a fraction of a second to complete a prediction. SAAMBE-3D is available as a web server and as well as a stand-alone code, the last one being another important feature allowing other researchers to directly download the code and run it on their local computer. Combined all together, SAAMBE-3D is an accurate and fast software applicable for genome-wide studies to assess the effect of amino acid mutations on protein-protein interactions. The webserver and the stand-alone codes (SAAMBE-3D for predicting the change of binding free energy and SAAMBE-3D-DN for predicting if the mutation is disruptive or non-disruptive) are available.
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Affiliation(s)
- Swagata Pahari
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
| | - Gen Li
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
| | - Adithya Krishna Murthy
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA; (S.L.); (R.F.); (H.Y.)
| | - Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA; (S.L.); (R.F.); (H.Y.)
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA; (S.L.); (R.F.); (H.Y.)
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
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