Mapping the APOE structurally on missense variants in elderly Brazilians

References

• Abdul Samad, F., Suliman, B. A., Basha, S. H., Manivasagam, T., & Essa, M. M. (2016). A comprehensive in silico analysis on the structural and functional impact of SNPs in the congenital heart defects associated with NKX2-5 gene—A molecular dynamic simulation approach. PLoS One, 11(5), e0153999. https://doi.org/10.1371/journal.pone.0153999
   PubMed Web of Science ®Google Scholar
• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Anderson, R. J., Weng, Z., Campbell, R. K., & Jiang, X. (2005). Main-chain conformational tendencies of amino acids. Proteins, 60(4), 679–689. https://doi.org/10.1002/prot.20530
   PubMed Web of Science ®Google Scholar
• Banks, E., Joshy, G., Abhayaratna, W. P., Kritharides, L., Macdonald, P. S., Korda, R. J., & Chalmers, J. P. (2013). Erectile dysfunction severity as a risk marker for cardiovascular disease hospitalisation and all-cause mortality: A prospective cohort study. PLoS Medicine, 10(1), e1001372. https://doi.org/10.1371/journal.pmed.1001372
   PubMed Web of Science ®Google Scholar
• Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., Felts, A. K., Halgren, T. A., Mainz, D. T., Maple, J. R., Murphy, R., Philipp, D. M., Repasky, M. P., Zhang, L. Y., Berne, B. J., Friesner, R. A., Gallicchio, E., & Levy, R. M. (2005). Integrated modeling program, applied chemical theory (IMPACT). Journal of Computational Chemistry, 26(16), 1752–1780. https://doi.org/10.1002/JCC.20292
   PubMed Web of Science ®Google Scholar
• Bas, D. C., Rogers, D. M., & Jensen, J. H. (2008). Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins, 73, 765–783. https://doi.org/10.1002/prot.22102
   Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662
   PubMed Web of Science ®Google Scholar
• Blokhina, A. V., Ershova, A. I., Kiseleva, A. V., Sotnikova, E. A., Zharikova, A. A., Zaicenoka, M., Vyatkin, Y. V., Ramensky, V. E., Kutsenko, V. A., Shalnova, S. A., Meshkov, A. N., & Drapkina, O. M. (2023). Applicability of diagnostic criteria and high prevalence of familial dysbetalipoproteinemia in Russia: A pilot study. International Journal of Molecular Sciences, 24(17), 13159. https://doi.org/10.3390/ijms241713159
   PubMed Web of Science ®Google Scholar
• Borges, J. B., Oliveira, V. F. D., Ferreira, G. M., Los, B., Barbosa, T. K. A. A., Marçal, E. D S. R., Dagli-Hernandez, C., de Freitas, R. C. C., Bortolin, R. H., Mori, A. A., Hirata, T. D. C., Nakaya, H. T. I., Bastos, G. M., Thurow, H. S., Gonçalves, R. M., Araujo, D. B. D., Zatz, H. P., Bertolami, A., Faludi, A. A., … Hirata, M. H. (2021). Genomics, epigenomics and pharmacogenomics of familial hypercholesterolemia (FHBGEP): A study protocol. Research in Social & Administrative Pharmacy, 17(7), 1347–1355. https://doi.org/10.1016/j.sapharm.2020.10.007
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Sacerdoti, F. D., Salmon, J. K., Shan, Y., Shaw, D. E., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., & Moraes, M. A. (2006). Molecular dynamics—Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing - SC ’06, 84. https://doi.org/10.1145/1188455.1188544
   Google Scholar
• Chetty, P. S., Mayne, L., Lund-Katz, S., Englander, S. W., & Phillips, M. C. (2017). Helical structure, stability, and dynamics in human apolipoprotein E3 and E4 by hydrogen exchange and mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America, 114(5), 968–973. https://doi.org/10.1073/pnas.1617523114
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N ⋅log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J., Richardson, J. S., & Richardson, D. C. (2007). MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research, 35, W375–383. https://doi.org/10.1093/nar/gkm216
   PubMed Web of Science ®Google Scholar
• Dong, J., Peters-Libeu, C. A., Weisgraber, K. H., Segelke, B. W., Rupp, B., Capila, I., Hernáiz, M. J., LeBrun, L. A., & Linhardt, R. J. (2001). Interaction of the N-terminal domain of apolipoprotein E4 with heparin. Biochemistry, 40, 2826–2834. https://doi.org/10.1021/bi002417n
   Google Scholar
• Frieden, C., Wang, H., & Ho, C. M. W. (2017). A mechanism for lipid binding to apoE and the role of intrinsically disordered regions coupled to domain–domain interactions. Proceedings of the National Academy of Sciences of the United States of America, 114(24), 6292–6297. https://doi.org/10.1073/pnas.1705080114
   PubMed Web of Science ®Google Scholar
• Giulini, D., & Großardt, A. (2014). Centre-of-mass motion in multi-particle Schrödinger–Newton dynamics. New Journal of Physics, 16(7), 075005. https://doi.org/10.1088/1367-2630/16/7/075005
   Google Scholar
• Huang, Y., & Mahley, R. W. (2014). Apolipoprotein E: Structure and function in lipid metabolism, neurobiology, and Alzheimer’s diseases. Neurobiology of Disease, 72 Pt A, 3–12. https://doi.org/10.1016/j.nbd.2014.08.025
   PubMed Web of Science ®Google Scholar
• Husain, M. A., Laurent, B., & Plourde, M. (2021). APOE and Alzheimer’s disease: From lipid transport to physiopathology and therapeutics. Frontiers in Neuroscience, 15, 630502. https://doi.org/10.3389/fnins.2021.630502
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Leren, T. P., Strøm, T. B., & Berge, K. E. (2016). Variable phenotypic expression of nonsense mutation p.Thr5* in the APOE gene. Molecular Genetics and Metabolism Reports, 9, 67–70. https://doi.org/10.1016/j.ymgmr.2016.10.007
   PubMed Web of Science ®Google Scholar
• Lewkowicz, E., Nakamura, M. N., Rynkiewicz, M. J., & Gursky, O. (2023). Molecular modeling of apoE in complexes with Alzheimer’s amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids. bioRxiv: The Preprint Server for Biology, 2023.08.04.551703. https://doi.org/10.1101/2023.08.04.551703
   Google Scholar
• Liao, F., Yoon, H., & Kim, J. (2017). Apolipoprotein e metabolism and functions in brain and its role in Alzheimer’s disease. Current Opinion in Lipidology, 28(1), 60–67. https://doi.org/10.1097/MOL.0000000000000383
   PubMed Web of Science ®Google Scholar
• Mahley, R. W., Weisgraber, K. H., & Huang, Y. (2009). Apolipoprotein e: Structure determines function, from atherosclerosis to Alzheimer’s disease to AIDS. Journal of Lipid Research, 50, S183–S188. https://doi.org/10.1194/jlr.R800069-JLR200
   PubMed Web of Science ®Google Scholar
• Masoodi, T. A., Al Shammari, S. A., Al-Muammar, M. N., & Alhamdan, A. A. (2012). Screening and evaluation of deleterious SNPs in APOE gene of Alzheimer’s disease. Neurology Research International, 2012, 480609. https://doi.org/10.1155/2012/480609
   PubMedGoogle Scholar
• Medway, C. W., Abdul-Hay, S., Mims, T., Ma, L., Bisceglio, G., Zou, F., Pankratz, S., Sando, S. B., Aasly, J. O., Barcikowska, M., Siuda, J., Wszolek, Z. K., Ross, O. A., Carrasquillo, M., Dickson, D. W., Graff-Radford, N., Petersen, R. C., Ertekin-Taner, N., Morgan, K., Bu, G., & Younkin, S. G. (2014). ApoE variant p.V236E is associated with markedly reduced risk of Alzheimer’s disease. Molecular Neurodegeneration, 9(1), 11. https://doi.org/10.1186/1750-1326-9-11
   PubMedGoogle Scholar
• Minta, K., Brinkmalm, G., Janelidze, S., Sjödin, S., Portelius, E., Stomrud, E., Zetterberg, H., Blennow, K., Hansson, O., & Andreasson, U. (2020). Quantification of total apolipoprotein E and its isoforms in cerebrospinal fluid from patients with neurodegenerative diseases. Alzheimer’s Research & Therapy, 12(1), 19. https://doi.org/10.1186/s13195-020-00585-7
   PubMed Web of Science ®Google Scholar
• Naslavsky, M. S., Yamamoto, G. L., de Almeida, T. F., Ezquina, S. A. M., Sunaga, D. Y., Pho, N., Bozoklian, D., Sandberg, T. O. M., Brito, L. A., Lazar, M., Bernardo, D. V., Amaro, E., Jr, Duarte, Y. A. O., Lebrão, M. L., Passos-Bueno, M. R., & Zatz, M. (2017). Exomic variants of an elderly cohort of Brazilians in the ABraOM database. Human Mutation, 38(7), 751–763. https://doi.org/10.1002/humu.23220
   PubMed Web of Science ®Google Scholar
• Pirim, D., Radwan, Z. H., Wang, X., Niemsiri, V., Hokanson, J. E., Hamman, R. F., Feingold, E., Bunker, C. H., Demirci, F. Y., & Kamboh, M. I. (2019). Apolipoprotein E-C1-C4-C2 gene cluster region and inter-individual variation in plasma lipoprotein levels: A comprehensive genetic association study in two ethnic groups. PLoS One, 14(3), e0214060. https://doi.org/10.1371/journal.pone.0214060
   PubMed Web of Science ®Google Scholar
• Radwan, Z. H., Wang, X., Waqar, F., Pirim, D., Niemsiri, V., Hokanson, J. E., Hamman, R. F., Bunker, C. H., Barmada, M. M., Demirci, F. Y., & Kamboh, M. I. (2014). Comprehensive evaluation of the association of APOE genetic variation with plasma lipoprotein traits in US whites and African blacks. PLoS One, 9(12), e114618. https://doi.org/10.1371/journal.pone.0114618
   PubMed Web of Science ®Google Scholar
• Rasmussen, K. L., Tybjaerg-Hansen, A., Nordestgaard, B. G., & Frikke-Schmidt, R. (2020). APOE and dementia—Resequencing and genotyping in 105,597 individuals. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association, 16(12), 1624–1637. https://doi.org/10.1002/alz.12165
   PubMed Web of Science ®Google Scholar
• Raulin, A. C., Doss, S. V., Trottier, Z. A., Ikezu, T. C., Bu, G., & Liu, C. C. (2022). ApoE in Alzheimer’s disease: Pathophysiology and therapeutic strategies. Molecular Neurodegeneration, 17(1), 72. https://doi.org/10.1186/s13024-022-00574-4
   PubMed Web of Science ®Google Scholar
• Ray, A., Ahalawat, N., & Mondal, J. (2017). Atomistic insights into structural differences between E3 and E4 isoforms of apolipoprotein E. Biophysical Journal, 113(12), 2682–2694. https://doi.org/10.1016/j.bpj.2017.10.006
   PubMed Web of Science ®Google Scholar
• Wang, C., Ji, X., Tang, Z., Zhang, Z., Gu, X., & Fang, X. (2022). Combined homocysteine and apoE rs429358 and rs7412 polymorphism in association with serum lipid levels and cognition in Chinese community-dwelling older adults. BMC Psychiatry, 22(1), 223. https://doi.org/10.1186/s12888-022-03877-4
   PubMed Web of Science ®Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54(1), 5.6.1–5.6.37. https://doi.org/10.1002/cpbi.3
   PubMedGoogle Scholar
• Wilsie, L. C., & Orlando, R. A. (2003). The low density lipoprotein receptor-related protein complexes with cell surface heparan sulfate proteoglycans to regulate proteoglycan-mediated lipoprotein catabolism*. The Journal of Biological Chemistry, 278(18), 15758–15764. https://doi.org/10.1074/jbc.M208786200
   PubMed Web of Science ®Google Scholar
• Wu, L., Zhang, X., & Zhao, L. (2018). Human ApoE isoforms differentially modulate brain glucose and Ketone body metabolism: Implications for Alzheimer’s disease risk reduction and early intervention. The Journal of Neuroscience, 38(30), 6665–6681. https://doi.org/10.1523/JNEUROSCI.2262-17.2018
   PubMed Web of Science ®Google Scholar
• Ye, Z., Tan, D., Luo, T., Gou, R., Cai, J., Wei, Y., He, K., Xiao, S., Mai, T., Tang, X., Liu, Q., Mo, X., Lin, Y., Huang, S., Li, Y., Qin, J., & Zhang, Z. (2023). ApoE gene polymorphisms and metals and their interactions with cognitive function. BMC Medical Genomics, 16(1), 206. https://doi.org/10.1186/s12920-023-01632-6
   PubMed Web of Science ®Google Scholar
• Zhen, J., Huang, X., Van Halm-Lutterodt, N., Dong, S., Ma, W., Xiao, R., & Yuan, L. (2017). ApoE rs429358 and rs7412 polymorphism and gender differences of serum lipid profile and cognition in aging Chinese population. Frontiers in Aging Neuroscience, 9, 248. https://doi.org/10.3389/fnagi.2017.00248
   PubMed Web of Science ®Google Scholar