[1]WRIGHT P E, DYSON H J. Intrinsically disordered proteins in cellular signalling and regulation[J]. Nature Reviews Molecular Cell Biology, 2015, 16(1): 18-29.
[2] SORANNO A, KOENIG I, BORGIA M B, et al. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(13): 4874-4879.
[3] KONIG I, SORANNO A, NETTELS D, et al. Impact of in-cell and in-vitro crowding on the conformations and dynamics of an intrinsically disordered protein[J].Angewandte Chemie International Edition in English, 2021, 60(19): 10724-10729.
[4] CINO E A, KARTTUNEN M, CHOY W Y. Effects of molecular crowding on the dynamics of intrinsically disordered proteins[J]. Public Library of Science, 2012,7(11): e49876.
[5] SASAHARA K, MCPHIE P, MINTON A P. Effect of dextran on protein stability and conformation attributed to macromolecular crowding[J]. Journal of Molecular Biology, 2003, 326(4): 1227-1237.
[6] DHAR A, SAMIOTAKIS A, EBBINGHAUS S, et al. Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding[J].Proceedings of the National Academy of Sciences of the United States of America,2010, 107(41): 17586-17591.
[7] STAGG L, ZHANG S-Q, CHEUNG M S, et al. Molecular crowding enhances native structure and stability of α/β protein flavodoxin[J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(48): 18976-18981.
[8] MCGUFFEE S R, ELCOCK A H. Diffusion, crowding & protein stability in a dynamicmolecular model of the bacterial cytoplasm[J]. Public Library of Science Computational Biology, 2010, 6(3): e1000694.
[9] YAQIANG W, CONGGANG L, J P G. Effects of proteins on protein diffusion[J].Journal of Chemical Physics, 2010, 132(27): 9392-9397.
[10] LEDUC C, PADBERG-GEHLE K, VARGA V, et al. Molecular crowding creates traffic jams of kinesin motors on microtubules[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(16): 6100-6105.
[11] ZHOU Z, YAN X, PAN K, et al. Fibril formation of the rabbit/human/bovine prion proteins[J]. Biophysical Journal, 2011, 101(6): 1483-1492.
[12] JOHANSEN D, JEFFRIES C M, HAMMOUDA B, et al. Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching[J]. Biophysical Journal, 2011, 100(4): 1120-1128.
[13] FONIN A V, DARLING A L, KUZNETSOVA I M, et al. Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo[J]. Cellular and Molecular Life Sciences, 2018, 75(21): 3907-3929.
[14] MAXIMOVA K, WOJTCZAK J, TRYLSKA J. Enzyme kinetics in crowded solutions from isothermal titration calorimetry[J]. Analytical Biochemistry, 2019, 567: 96-105.
[15] FEIG M, YU I, WANG P H, et al. Crowding in cellular environments at an atomistic level from computer simulations[J]. Journal of Physical Chemistry B, 2017, 121(34):8009-8025.
[16] CHEN A, ZHAO N. Comparative study of the crowding-induced collapse effect in hard-sphere, flexible polymer and rod-like polymer systems[J]. Physical Chemistry Chemical Physics, 2019, 21(23): 12335-12345.
[17] ZEGARRA F C, HOMOUZ D, GASIC A G, et al. Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico[J]. Journal of Chemical Physics, 2019, 123(17): 3607-3617.
[18] WANG X, BOWMAN J, TU S, et al. Polyethylene Glycol Crowder's Effect on Enzyme Aggregation, Thermal Stability, and Residual Catalytic Activity[J]. Langmuir, 2021,37(28): 8474-8485.
[19] QIN S, ZHOU H X. Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability[J]. Journal of Chemical Physics, 2009, 97(1): 12-19.
[20] QIN S, ZHOU H X. Effects of macromolecular crowding on the conformational ensembles of disordered proteins[J]. Journal of Chemical Physics, 2013, 4(20):3429-3434.
[21] 白佳. 不同环境下α-突触核蛋白系综结构的核磁共振研究 [D]. 武汉: 中国科学院物理与数学研究所, 2016.
[22] VLACHAKIS D, BENCUROVA E, PAPANGELOPOULOS N, et al. Current state-ofthe-art molecular dynamics methods and applications[J]. Advances in Protein Chemistry and Structural Biology, 2014, 94: 269-313.
[23] STERNBERG U, WITTER R. Molecular dynamics simulations on PGLa using NMR orientational constraints[J]. Journal of Biomolecular NMR, 2015, 63(3): 265-274.
[24] MARTIN K. Molecular dynamics simulations of biomolecules[J]. Accounts of chemical research, 2002, 35(6): 321-323.
[25] MULHOLLAND A J. Introduction biomolecular simulation[J]. Journal of the Royal Society Interface, 2008, 5: 169-172.
[26] VAN DER KAMP M W, SHAW K E, WOODS C J, et al. Biomolecular simulation and modelling: status, progress and prospects[J]. Journal of the Royal Society Interface,2008, 5: 173-190.
[27] M K, J K. Molecular dynamics and protein function[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(19): 6679-6685.
[28] Lü S, LONG M. Molecular dynamics simulation and molecular biomechanics[J]. Acta Biophysica Sinica, 2012, 28(1): 6-14.
[29] VERLET L. Computer "Experiments" on classical fluids. ii. equilibrium correlation functions[J]. Physical Review, 1968, 165(1): 201-214.
[30] DUAN Y, KOLLMAN P A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution[J]. Science, 1998, 282(5389): 740-744.
[31] FRENKEL D, SMIT B, RATNER M A. Understanding molecular simulation: from algorithms to applications[J]. Physics Today, 2008, 50(7).
[32] GALINDO-MURILLO R, ROE D R, CHEATHAM T E. Convergence and repro ducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)[J]. BBA - General Subjects, 2015, 1850(5): 1041-1058.
[33] SHAW D E, MARAGAKIS P, LINDORFF-LARSEN K, et al. Atomic-Level characterization of the structural dynamics of proteins[J]. Science, 2010, 330(6002): 341-346.
[34] SHAW D E, DROR R O, SALMON J K, et al. Millisecond-scale molecular dynamics simulations on anton[J]. High Performance Computing Networking, Storage and Analysis, 2009: 341-346.
[35] RAVAL A, PIANA S, EASTWOOD M P, et al. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations[J]. Proteins,2012, 80(8): 2071-2079.
[36] V L, J-M T, B R. Classical force field for hydrofluorocarbon molecular simulations application to the study of gas solubility in poly(vinylidene fluoride)[J]. Journal of Chemical Physics, 2015, 119(1): 140-151.
[37] HARDT S. Free-molecule heat transfer in a conservative force field between parallel surfaces[J]. Physical Review E, 2016, 93(5): 052139.
[38] BORN M, OPPENHEIMER R. Zur quantentheorie der molekeln[J]. Annalen der Physik, 1927, 389(20): 216-217.
[39] DICKSON C J, MADEJ B D, SKJEVIK A A, et al. Lipid14: The Amber lipid force field[J]. Journal of Chemical Physics, 2014, 10(2): 865-879.
[40] RODRIGO G-M, C R J, MARIE Z, et al. Assessing the current state of Amber force field modifications for DNA[J]. Journal of Chemical Physics, 2016, 12(8): 4114-4127.
[41] LIU H, TAN Q, HAN L, et al. Observations on AMBER Force Field Performance under the Conditions of Low pH and High Salt Concentrations[J]. Journal of Chemical Physics, 2017, 121(42): 9838-9847.
[42] BATISTA M L, PEREZ-SANCHEZ G, GOMES J R, et al. Evaluation of the GROMOS56ACARBO force field for the calculation of structural, Volumetric, and dynamic properties of aqueous glucose systems[J]. Journal of Chemical Physics, 2015, 119(49):15310-15319.
[43] HORTA B A, MERZ P T, FUCHS P F, et al. A GROMOS-Compatible force field for small organic molecules in the condensed phase[J]. Journal of Chemical Physics, 2016,12(8): 3825-3850.
[44] RAMOS SASSELLI I, ULIJN R V, TUTTLE T. CHARMM force field paramet erization protocol for self-assembling peptide amphiphiles: the Fmoc moiety[J].Journal of Chemical Physics, 2016, 18(6): 4659-4667.
[45] ADAM S, KNAPP-MOHAMMADY M, YI J, et al. Revised CHARMM force field parameters for iron-containing cofactors of photosystem II[J]. Journal of Chemical Physics, 2018, 39(1): 7-20.
[46] MACIEJEWSKI A, PASENKIEWICZ-GIERULA M, CRAMARIUC O, et al. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration[J]. Journal of Chemical Physics, 118(17): 4571-4581.
[47] SMITH M D, RAO J S, SEGELKEN E, et al. Force-Field induced bias in the structure of Abeta21-30: A comparison of OPLS, AMBER, CHARMM, and GROMOS force fields[J]. Journal of Chemical Information and Modeling, 2015, 55(12): 2587-2595.
[48] WANG B, ZHANG H, HUAI J, et al. Condensation of SEUSS promotes hyperosmotic stress tolerance in Arabidopsis[J]. Nature Chemical Biology, 2022, 18(12): 1361-1369.
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