Assuncao-Miranda I, Amaral FA, Bozza FA, Fagundes CT, Sousa LP et al (2010) Contribution of macrophage migration inhibitory factor to the pathogenesis of dengue virus infection. FASEB J 24:218–228
Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81(8):3684–3690. https://doi.org/10.1063/1.448118
Byk LA, Gamarnik AV (2016) Properties and functions of the dengue virus capsid protein. Annu Rev Virol 3(1):263–281. https://doi.org/10.1146/annurev-virology-110615-042334
Article CAS PubMed PubMed Central Google Scholar
Cermelli S, Guo Y, Gross SP, Welte MA (2006) The lipid-droplet proteome reveals that droplets are a protein-storage depot. Curr Biol 16:1783–1795
Article CAS PubMed Google Scholar
Chaturvedi UC, Shrivastava R (2004) Dengue haemorrhagic fever: a global challenge. Indian J Med Microbiol 22(1):5–6
Article CAS PubMed Google Scholar
Chatzigoulas A, Cournia Z (2022a) DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design. Bioinformatics 38(24):5449–5451. https://doi.org/10.1093/bioinformatics/btac680
Article CAS PubMed PubMed Central Google Scholar
Chatzigoulas A, Cournia Z (2022) Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning. Brief Bioinform 23(2):bbab518. https://doi.org/10.1093/bib/bbab518
Article CAS PubMed PubMed Central Google Scholar
Davidchack RL, Handel R, Tretyakov MV (2009) Langevin thermostat for rigid body dynamics. J Chem Phys 130(23):234101. https://doi.org/10.1063/1.3149788
Article CAS PubMed Google Scholar
Dobson L, Reményi I, Tusnády GE (2015) CCTOP: a consensus constrained TOPology prediction web server. Nucleic Acids Res 43(W1):W408–W412. https://doi.org/10.1093/nar/gkv451
Article CAS PubMed PubMed Central Google Scholar
ECDC (2021) Geographical distribution of dengue cases reported worldwide, 2021. Retrieved from https://www.ecdc.europa.eu/en/publications-data/geographical-distribution-dengue-cases-reported-worldwide-2021
Farelo MA, Korrou-Karava D, Brooks KF, Russell TA, Maringer K, Mayerhofer PU (2022) Dengue and Zika virus capsid proteins contain a common PEX19-binding motif. Viruses 14(2):253. https://doi.org/10.3390/v14020253
Article CAS PubMed PubMed Central Google Scholar
Faustino AF, Martins AS, Karguth N, Artilheiro V, Enguita FJ, Ricardo JC, Santos NC, Martins IC (2019) Structural and functional properties of the capsid protein of dengue and related Flavivirus. Int J Mol Sci 20(16):3870. https://doi.org/10.3390/ijms20163870
Article CAS PubMed PubMed Central Google Scholar
Figueira-Mansur J, Aguilera EA, Stoque RM, Ventura GT, Mohana-Borges R (2019) Mutations in the dimer interfaces of the dengue virus capsid protein affect structural stability and impair RNA-capsid interaction. Sci Rep 9(1):2829. https://doi.org/10.1038/s41598-019-39185-3
Article CAS PubMed PubMed Central Google Scholar
Freites JA, Tobias DJ, von Heijne G, White SH (2005) Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci USA 102:15059–15064
Article CAS PubMed PubMed Central Google Scholar
Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita JM, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J (2014) MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics 30(10):1478–1480. https://doi.org/10.1093/bioinformatics/btu037
Article CAS PubMed Google Scholar
Herker E (2024) Lipid droplets in virus replication. FEBS Lett. https://doi.org/10.1002/1873-3468.14819
Hsia JZ, Liu D, Haynes L, Cruz-Cosme R, Tang Q (2024) Lipid droplets: formation, degradation, and their role in cellular responses to flavivirus infections. Microorganisms 12(4):647. https://doi.org/10.3390/microorganisms12040647
Article CAS PubMed PubMed Central Google Scholar
Huang J, MacKerell AD Jr (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34(25):2135–2145. https://doi.org/10.1002/jcc.23354
Article CAS PubMed PubMed Central Google Scholar
Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD Jr, Klauda JB, Qi Y, Im W (2017) CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 38(15):1114–1124. https://doi.org/10.1002/jcc.24660
Article CAS PubMed Google Scholar
Johansson ACV, Lindahl E (2006) Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations. Biophys J 91:4450–4463
Article CAS PubMed PubMed Central Google Scholar
Jones CT, Ma L, Burgner JW, Groesch TD, Post CB, Kuhn RJ (2003) Flavivirus capsid is a dimeric α-helical protein. J Virol 77:7143–7149
Article CAS PubMed PubMed Central Google Scholar
Kang K, Wang L, Song C (2023) ProtRAP: predicting lipid accessibility together with solvent accessibility of proteins in one run. J Chem Inf Model 63(3):1058–1065. https://doi.org/10.1021/acs.jcim.2c01235
Article CAS PubMed Google Scholar
Knapp B, Ospina L, Deane CM (2018) Avoiding false positive conclusions in molecular simulation: the importance of replicas. J Chem Theory Comput 14(12):6127–6138. https://doi.org/10.1021/acs.jctc.8b00391
Article CAS PubMed Google Scholar
Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580. https://doi.org/10.1006/jmbi.2000.4315
Article CAS PubMed Google Scholar
Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M (2014) Discovery of novel membrane binding structures and functions. Biochem Cell Biol 92(6):555–563. https://doi.org/10.1139/bcb-2014-0074
Article CAS PubMed PubMed Central Google Scholar
Kuhn RJ, Zhang W, Rossmann MG, Pletnev SV, Corver J, Lenches E, Jones CT, Mukhopadhyay S, Chipman PR, Strauss EG, Baker TS, Strauss JH (2002) Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell 108(5):717–725. https://doi.org/10.1016/s0092-8674(02)00660-8
Article CAS PubMed PubMed Central Google Scholar
Kumari R, Kumar R, Open Source Drug Discovery Consortium, Lynn A (2014) g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54(7):1951–62. https://doi.org/10.1021/ci500020m
Kumari P, Kaur S, Sharma S, Kashyap HK (2018) Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: insights from atomistic simulations. J Chem Phys 148(16):165102. https://doi.org/10.1063/1.5021310
Comments (0)