Abstract
Intrinsically disordered proteins represent a class of proteins that lack fixed and well-defined three-dimensional structures in solution. HIV-1 Nef is an intrinsically disordered peripheral membrane protein involved in the replication and pathogenesis of HIV-1 infection. Nef controls expression levels of cell surface CD4 molecules that are essential for adaptive immunity. Despite the lack of fixed and stable structures, Nef physically interacts with the host cellular proteins (AP-1/MHC-I) and modulates intracellular trafficking pathways. Therefore, it is essential to understand how this dynamic conformational flexibility affects Nef structures and function. In this study, we combined all-atom molecular dynamics (MD) simulations and dynamic network approaches to better understand the structure and dynamics of Nef in two different forms, the free unbound and the bound state. Using the MD simulation approach, we show that the intrinsically disordered Nef exhibit a large dynamic field with more atomic fluctuations and lesser thermodynamic stability in the unbound conditions. The conformations of Nef change over time, and this protein remains more compact, folded, and stable in the bound form. The dynamic network analysis revealed regions of the protein capable of modulating the conformational behavior of the disordered Nef. The average betweenness centrality (BC) unveiled residues that are critical for mediating protein–protein interactions. The average shortest path length (L) and the perturbation response scanning exposed residues that are likely to be important in steering protein conformational changes. Overall, the study demonstrates how all-atom MD simulations combined with the dynamic network approach can be used to gain further insights into the structure and dynamics-function relationship of intrinsically disordered HIV-1 Nef.
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References
Abdizadeh H, Guven G, Atilgan AR, Atilgan C (2015) Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability. J Enzyme Inhib Med Chem 30:867–873. https://doi.org/10.3109/14756366.2014.979345
Abraham MJ, Murtola T, Schulz R et al (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
Amadei A, Linssen ABM, Berendsen HJC (1993) Essential dynamics of proteins. Proteins Struct Funct Bioinform 17:412–425. https://doi.org/10.1002/prot.340170408
Amala A, Emerson IA (2018) Understanding contact patterns of protein structures from protein contact map and investigation of unique patterns in the globin-like folded domains. J Cell Biochem 120:9877–9886
Atilgan C, Atilgan AR (2009) Perturbation-response scanning reveals ligand entry–exit mechanisms of ferric binding protein. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1000544
Atilgan AR, Akan P, Baysal C (2004) Small-world communication of residues and significance for protein dynamics. Biophys J 86:85–91. https://doi.org/10.1016/S0006-3495(04)74086-2
Babu MM, van der Lee R, de Groot NS, Gsponer J (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21:432–440
Best RB (2017) Computational and theoretical advances in studies of intrinsically disordered proteins. Curr Opin Struct Biol 42:147–154. https://doi.org/10.1016/j.sbi.2017.01.006
Best RB, Hummer G (2009) Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B. https://doi.org/10.1021/jp901540t
Boehr DD, Schnell JR, McElheny D et al (2013) A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase. Biochemistry 52:4605–4619. https://doi.org/10.1021/bi400563c
Bornot A, Etchebest C, De Brevern AG (2011) Predicting protein flexibility through the prediction of local structures. Proteins Struct Funct Bioinform. https://doi.org/10.1002/prot.22922
Brandes U (2001) A faster algorithm for betweenness centrality. J Math Sociol. https://doi.org/10.1080/0022250X.2001.9990249
Brown DK, Penkler DL, Amamuddy OS et al (2017) MD-TASK: a software suite for analyzing molecular dynamics trajectories. Bioinformatics 33:2768–2771. https://doi.org/10.1093/bioinformatics/btx349
Chaudhuri R, Lindwasser OW, Smith WJ et al (2007) Downregulation of CD4 by human immunodeficiency virus type 1 Nef Is dependent on clathrin and involves direct interaction of Nef with the AP2 clathrin adaptor. J Virol. https://doi.org/10.1128/jvi.02725-06
Collins KL, Chen BK, Kalams SA et al (1998) HIV-1 Nef protein protects infected primary cells against killing by cytotoxic T lymphocytes. Nature 391:397–401. https://doi.org/10.1038/34929
Cullen BR (1994) The role of Nef in the replication cycle of the human and simian immunodeficiency viruses. Virology 205:1–6. https://doi.org/10.1006/viro.1994.1613
del Sol A, Fujihashi H, O’Meara P (2005) Topology of small-world networks of protein-protein complex structures. Bioinformatics. https://doi.org/10.1093/bioinformatics/bti167
Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol cell Biol 6:197–208
Greenberg ME, Bronson S, Lock M et al (1997) Co-localization of HIV-1 Nef with the AP-2 adaptor protein complex correlates with Nef-induced CD4 down-regulation. EMBO J. https://doi.org/10.1093/emboj/16.23.6964
Grzesiek S, Bax AD, Hu JS et al (1997) Refined solution structure and backbone dynamics of HIV-1 Nef. Protein Sci 6:1248–1263. https://doi.org/10.1002/pro.5560060613
Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. https://doi.org/10.1002/elps.1150181505
Habchi J, Tompa P, Longhi S, Uversky VN (2014) Introducing protein intrinsic disorder. Chem Rev 114:6561–6588
Haider S, Parkinson GN, Neidle S (2008) Molecular dynamics and principal components analysis of human telomeric quadruplex multimers. Biophys J. https://doi.org/10.1529/biophysj.107.120501
Hanwell MD, Curtis DE, Lonie DC et al (2012) Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. J Cheminform. https://doi.org/10.1186/1758-2946-4-17
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12%3c1463::AID-JCC4%3e3.0.CO;2-H
Hornak V, Abel R, Okur A et al (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins Struct Funct Genet 65:712–725
Hub JS, De Groot BL (2009) Detection of functional modes in protein dynamics. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1000480
Ichiye T, Karplus M (1991) Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins Struct Funct Bioinform 11:205–217. https://doi.org/10.1002/prot.340110305
Ithuralde RE, Roitberg AE, Turjanski AG (2016) Structured and unstructured binding of an intrinsically disordered protein as revealed by atomistic simulations. J Am Chem Soc 138:8742–8751. https://doi.org/10.1021/jacs.6b02016
Jensen MR, Zweckstetter M, Huang JR, Blackledge M (2014) Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 114:6632–6660. https://doi.org/10.1021/cr400688u
Jia X, Singh R, Homann S et al (2012) Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef. Nat Struct Mol Biol. https://doi.org/10.1038/nsmb.2328
Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935. https://doi.org/10.1038/189771a0
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9:646–652
Kasahara K, Fukuda I, Nakamura H (2014) A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex. PLoS ONE. https://doi.org/10.1371/journal.pone.0112419
Kirchhoff F, Schindler M, Specht A et al (2008) Role of Nef in primate lentiviral immunopathogenesis. Cell Mol Life Sci 65:2621–2636
Li Y, Li G, Wen Z et al (2011) Novel feature for catalytic protein residues reflecting interactions with other residues. PLoS ONE. https://doi.org/10.1371/journal.pone.0016932
Liu H, Song D, Zhang Y et al (2019) Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Phys Chem Chem Phys. https://doi.org/10.1039/c9cp03434j
Lobanov MY, Bogatyreva NS, Galzitskaya OV (2008) Radius of gyration as an indicator of protein structure compactness. Mol Biol. https://doi.org/10.1134/S0026893308040195
Lyle N, Das RK, Pappu RV (2013) A quantitative measure for protein conformational heterogeneity. J Chem Phys doi 10(1063/1):4812791
Mao G, Zhang N (2013) Analysis of average shortest-path length of scale-free network. J Appl Math 2013:1–5. https://doi.org/10.1155/2013/865643
Penkler DL, Atilgan C, Tastan Bishop O (2018) Allosteric modulation of human Hsp90α conformational dynamics. J Chem Inf Model 58:383–404. https://doi.org/10.1021/acs.jcim.7b00630
Piovesan D, Tabaro F, Micetic I et al (2017) DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res 45:D219–D227. https://doi.org/10.1093/nar/gkw1056
Satoshi O, Fuchigami S, Mitsunori I, Kidera A (2009) Linear response theory in dihedral angle space for protein structural change upon ligand binding. J Comput Chem 30:2602–2608. https://doi.org/10.1002/jcc.21269
Schwartz O, Marechal V, Le Gall S et al (1996) Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nat Med 2:338–342. https://doi.org/10.1038/nm0396-338
Stanley N, Esteban-Martan S, De Fabritiis G (2015) Progress in studying intrinsically disordered proteins with atomistic simulations. Prog Biophys Mol Biol 119:47–52
Taylor NR (2013) Small world network strategies for studying protein structures and binding. Comput Struct Biotechnol J 5:e201302006
Turner P (2005) XMGRACE, Version 5.1. 19. Cent Coast Land-Margin Res Oregon Grad Inst Sci Technol Beavert. https://doi.org/10.1163/_q3_SIM_00374
Vendruscolo M, Paci E, Dobson CM, Karplus M (2001) Three key residues form a critical contact network in a protein folding transition state. Nature 409:641–645. https://doi.org/10.1038/35054591
Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr Protoc Bioinform. https://doi.org/10.1002/cpbi.3
Wright PE, Dyson HJ (2015) Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol cell Biol 16:18
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Bhattarai, A., Emerson, I.A. Exploring the conformational dynamics and flexibility of intrinsically disordered HIV-1 Nef protein using molecular dynamic network approaches. 3 Biotech 11, 156 (2021). https://doi.org/10.1007/s13205-021-02698-8
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DOI: https://doi.org/10.1007/s13205-021-02698-8