The point mutation of the cholesterol trafficking membrane protein NPC1 may affect its proper function in more than a single step: Molecular dynamics simulation study

Computational Biology and Chemistry - Tập 99 - Trang 107725 - 2022
Hye-Jin Yoon1, Jian Jeong2, Guun Kim3, Hyung Ho Lee1, Soonmin Jang2
1Department of Chemistry, Seoul National University, Seoul, the Republic of Korea
2Department of Chemistry, Sejong University, Seoul, the Republic of Korea
3Department of Physics, Sejong University, Seoul, the Republic of Korea

Tài liệu tham khảo

Costafreda, 2020, Exosome mimicry by a HAVCR1–NPC1 pathway of endosomal fusion mediates hepatitis A virus infection, Nat. Microbiol., 5, 1096, 10.1038/s41564-020-0740-y Davies, 2000, Evidence for a Niemann–Pick C (NPC) gene family: identification and characterization of NPC1L1, Genomics, 65, 137, 10.1006/geno.2000.6151 Deffieu, 2011, Niemann–Pick type C 1 function requires lumenal domain residues that mediate cholesterol-dependent NPC2 binding, Proc. Natl. Acad. Sci. USA, 108, 18932, 10.1073/pnas.1110439108 Du, 2015, Akt activation increases cellular cholesterol by promoting the proteasomal degradation of Niemann–Pick C1, Biochem. J., 471, 243, 10.1042/BJ20150602 Dubey, 2020, Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain, PLoS Comput. Biol., 16, 10.1371/journal.pcbi.1007554 Elghobashi-Meinhardt, 2019, Computational tools unravel putative sterol binding sites in the lysosomal NPC1 protein, J. Chem. Inf. Model., 59, 2432, 10.1021/acs.jcim.9b00186 Elghobashi-Meinhardt, 2020, Cholesterol transport in wild-type NPC1 and P691S: molecular dynamics simulations reveal changes in dynamical behavior, Int. J. Mol. Sci., 21, 2962, 10.3390/ijms21082962 Feenstra, 1999, Improving efficiency of large time‐scale molecular dynamics simulations of hydrogen‐rich systems, J. Comput. Chem., 20, 786, 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B Gong, 2016, Structural insights into the Niemann-Pick C1 (NPC1)-mediated cholesterol transfer and Ebola infection, Cell, 165, 1467, 10.1016/j.cell.2016.05.022 Huang, 2017, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat. Methods, 14, 71, 10.1038/nmeth.4067 Kastritis, 2011, A structure‐based benchmark for protein–protein binding affinity, Protein Sci., 20, 482, 10.1002/pro.580 Li, 2005, Very fast empirical prediction and rationalization of protein pKa values. proteins: structure, Proteins Struct. Funct. Bioinform., 61, 704, 10.1002/prot.20660 Li, 2017, 3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport, Proc. Natl. Acad. Sci. USA, 114, 9116, 10.1073/pnas.1711716114 Li, 2016, Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2, Proc. Natl. Acad. Sci. USA, 113, 10079, 10.1073/pnas.1611956113 Li, 2016, Structure of human Niemann–Pick C1 protein, Proc. Natl. Acad. Sci. USA, 113, 8212, 10.1073/pnas.1607795113 Loftus, 1997, Murine model of Niemann-Pick C disease: mutation in a cholesterol homeostasis gene, Science, 277, 232, 10.1126/science.277.5323.232 Long, 2020, Structural basis for itraconazole-mediated NPC1 inhibition, Nat. Commun., 11, 1, 10.1038/s41467-019-13917-5 Marchi, 1999, Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular systems, J. Chem. Phys., 110, 3697, 10.1063/1.478259 Martínez-Archundia, 2019, Molecular dynamics simulations reveal structural differences among wild-type NPC1 protein and its mutant forms, J. Biomol. Struct. Dyn., 1 Millat, 2001, Niemann-Pick C1 disease: correlations between NPC1 mutations, levels of NPC1 protein, and phenotypes emphasize the functional significance of the putative sterol-sensing domain and of the cysteine-rich luminal loop, Am. J. Hum. Genet., 68, 1373, 10.1086/320606 Miller, 2012, Ebola virus entry requires the host‐programmed recognition of an intracellular receptor, EMBO J., 31, 1947, 10.1038/emboj.2012.53 Park, 2003, Identification of 58 novel mutations in Niemann‐Pick disease type C: Correlation with biochemical phenotype and importance of PTC1–like domains in NPC1, Hum. Mutat., 22, 313, 10.1002/humu.10255 Qi, 2019, Structural basis of sterol recognition by human hedgehog receptor PTCH1, Sci. Adv., 5, eaaw6490, 10.1126/sciadv.aaw6490 Qian, 2020, Structural basis of low-pH-dependent lysosomal cholesterol egress by NPC1 and NPC2, Cell, 182, 98, 10.1016/j.cell.2020.05.020 Saha, 2020, Inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins, Elife, 9, 10.7554/eLife.57089 Salsbury, 2010, Molecular dynamics simulations of protein dynamics and their relevance to drug discovery, Curr. Opin. Pharmacol., 10, 738, 10.1016/j.coph.2010.09.016 Schrodinger, L.L.C., 2015. The PyMOL Molecular Graphics System, Version 1.8. In: Secondary. Schuchman, 2015, Types A and B niemann-pick disease, Best. Pract. Res. Clin. Endocrinol. Metab., 29, 237, 10.1016/j.beem.2014.10.002 Sofos, 2021, Nanoscale slip length prediction with machine learning tools, Sci. Rep., 11, 1, 10.1038/s41598-021-91885-x Sofos, 2013, Fluid flow at the nanoscale: how fluid properties deviate from the bulk, Nanosci. Nanotechnol. Lett., 5, 457, 10.1166/nnl.2013.1555 Sturley, S., Márka, Z., Márka, S., Hammond, N., Rajakumar, T. , Munkacsi, A. , 2020, Insights Into the COVID-19 Pandemic From a rAre Neurodegenerative Disease. Tribello, 2014, PLUMED 2: new feathers for an old bird, Comput. Phys. Commun., 185, 604, 10.1016/j.cpc.2013.09.018 Van Der Spoel, 2005, GROMACS: fast, flexible, and free, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291 Vanharanta, 2020, High‐content imaging and structure‐based predictions reveal functional differences between Niemann‐Pick C1 variants, Traffic, 21, 386, 10.1111/tra.12727 Vanier, J. , Tomescu, C. 2015, The Quantum Physics of Atomic Frequency Standards: Recent Developments. Vanier, 1991, Type C Niemann-Pick disease: spectrum of phenotypic variation in disruption of intracellular LDL-derived cholesterol processing, Biochim. Biophys. Acta (BBA) Mol. Basis Dis., 1096, 328, 10.1016/0925-4439(91)90069-L Vanier, 1998, Recent advances in elucidating Niemann‐Pick C disease, Brain Pathol., 8, 163, 10.1111/j.1750-3639.1998.tb00143.x Wang, 2010, Identification of surface residues on Niemann-Pick C2 essential for hydrophobic handoff of cholesterol to NPC1 in lysosomes, Cell Metab., 12, 166, 10.1016/j.cmet.2010.05.016 Wijers, 2015, The life cycle of the low-density lipoprotein receptor: insights from cellular and in-vivo studies, Curr. Opin. Lipidol., 26, 82, 10.1097/MOL.0000000000000157 Winkler, 2019, Structural insight into eukaryotic sterol transport through Niemann-Pick type C proteins, Cell, 179, 485, 10.1016/j.cell.2019.08.038 Winkler, M.B., Nel, L., Frain, K.M., Dedic, E., Olesen, E. , Pedersen, B.P. 2021. Sterol uptake by the NPC system in eukaryotes: a Saccharomyces cerevisiae perspective. FEBS Lett. Xu, 2020, Cholesterol metabolism: new functions and therapeutic approaches in cancer, Biochim.Biophys. Acta (BBA) Rev. Cancer, 10.1016/j.bbcan.2020.188394 Xu, 2019, The characteristics and biological significance of NPC2: mutation and disease, Mutat. Res. Rev. Mutat. Res., 782, 10.1016/j.mrrev.2019.108284 Yamamoto, 1999, NPC1 gene mutations in Japanese patients with Niemann-Pick disease typeáC, Hum. Genet., 105, 10 Yang, 2017, In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level, Nucleic Acids Res., 45, 12648, 10.1093/nar/gkx1079 Yoon, 2021, Molecular dynamics study with mutation shows that N‐terminal domain structural re‐orientation in Niemann‐Pick type C1 is required for proper alignment of cholesterol transport, J. Neurochem., 156, 967, 10.1111/jnc.15150