Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
Tóm tắt
Từ khóa
Tài liệu tham khảo
AJ Pratt, 2009, The RNA-induced Silencing Complex: A Versatile Gene-silencing Machine, J Biol Chem, 284, 17897, 10.1074/jbc.R900012200
DJ Obbard, 2009, The evolution of RNAi as a defence against viruses and transposable elements, Philos Trans R Soc, 364, 99, 10.1098/rstb.2008.0168
DG Sashital, 2010, Structural insights into RNA interference, Curr Opin Struct Biol, 20, 90, 10.1016/j.sbi.2009.12.001
RC Wilson, 2013, Molecular Mechanisms of RNA Interference, Annu Rev Biophys, 42, 217, 10.1146/annurev-biophys-083012-130404
FV Rivas, 2005, Purified Argonaute2 and an siRNA form recombinant human RISC, Nat Struct Mol Biol, 12, 340, 10.1038/nsmb918
L Joshua-Tor, 2011, Ancestral Roles of Small RNAs: An Ago-Centric Perspective, Cold Spring Harbor Perspect Biol, 3, a003772, 10.1101/cshperspect.a003772
HM Sasaki, 2012, The true core of RNA silencing revealed, Nat Struct Mol Biol, 19, 657, 10.1038/nsmb.2302
G Meister, 2013, Argonaute proteins: functional insights and emerging roles, Nat Rev Genet, 14, 447, 10.1038/nrg3462
YL Wang, 2008, Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex, Nature, 456, 921, 10.1038/nature07666
YL Wang, 2009, Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes, Nature, 461, 754, 10.1038/nature08434
YL Wang, 2008, Structure of the guide-strand-containing argonaute silencing complex, Nature, 456, 209, 10.1038/nature07315
BP Lewis, 2005, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120, 15, 10.1016/j.cell.2004.12.035
A Azuma-Mukai, 2008, Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing, Proc Natl Acad Sci U S A, 105, 7964, 10.1073/pnas.0800334105
A Turchinovich, 2012, Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma, RNA Biol, 9, 1066, 10.4161/rna.21083
A Dueck, 2012, microRNAs associated with the different human Argonaute proteins, Nucleic Acids Res, 40, 9850, 10.1093/nar/gks705
A Esquela-Kerscher, 2008, The let-7 microRNA reduces tumor growth in mouse models of lung cancer, Cell Cycle, 7, 759, 10.4161/cc.7.6.5834
P Trang, 2009, Regression of murine lung tumors by the let-7 microRNA, J Thorac Oncol, 29, 1580
GG Hammes, 2009, Conformational selection or induced fit: A flux description of reaction mechanism, Proc Natl Acad Sci U S A, 106, 13737, 10.1073/pnas.0907195106
P Csermely, 2010, Induced fit, conformational selection and independent dynamic segments: an extended view of binding events, Trends Biochem Sci, 35, 539, 10.1016/j.tibs.2010.04.009
H Frauenfelder, 1991, The Energy Landscapes and Motions of Proteins, Science, 254, 1598, 10.1126/science.1749933
CJ Tsai, 1999, Folding funnels, binding funnels, and protein function, Protein Sci, 8, 1181, 10.1110/ps.8.6.1181
DE Koshland, 1958, Application of a Theory of Enzyme Specificity to Protein Synthesis, Proc Natl Acad Sci U S A, 44, 98, 10.1073/pnas.44.2.98
CD Mackereth, 2011, Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF, Nature, 475, 408, 10.1038/nature10171
JP DiNitto, 2003, Mutual induced fit binding of Xenopus ribosomal protein L5 to 5 S rRNA, J Mol Biol, 330, 979, 10.1016/S0022-2836(03)00685-5
DD Boehr, 2009, The role of dynamic conformational ensembles in biomolecular recognition, Nat Chem Biol, 5, 789, 10.1038/nchembio.232
HX Zhou, 2010, From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions, Biophys J, 98, L15, 10.1016/j.bpj.2009.11.029
N Greives, 2014, Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit, Proc Natl Acad Sci U S A, 111, 10197, 10.1073/pnas.1407545111
K Nakanishi, 2012, Structure of yeast Argonaute with guide RNA, Nature, 486, 368, 10.1038/nature11211
E Elkayam, 2012, The Structure of Human Argonaute-2 in Complex with miR-20a, Cell, 150, 233, 10.1016/j.cell.2012.06.021
CR Faehnle, 2013, The Making of a Slicer: Activation of Human Argonaute-1, Cell Rep, 3, 1901, 10.1016/j.celrep.2013.05.033
K Nakanishi, 2013, Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity, Cell Rep, 3, 1893, 10.1016/j.celrep.2013.06.010
A Deerberg, 2013, Minimal mechanistic model of siRNA-dependent target RNA slicing by recombinant human Argonaute 2 protein, Proc Natl Acad Sci U S A, 110, 17850, 10.1073/pnas.1217838110
YH Wang, 2010, Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis, PLoS Comput Biol, 6, e1000866, 10.1371/journal.pcbi.1000866
Z Xia, 2012, Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets, Sci Rep, 2, 569, 10.1038/srep00569
Z Xia, 2013, Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process, Plos One, 8, e54620, 10.1371/journal.pone.0054620
F Noe, 2008, Transition networks for modeling the kinetics of conformational change in macromolecules, Curr Opin Struct Biol, 18, 154, 10.1016/j.sbi.2008.01.008
JD Chodera, 2007, Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics, J Chem Phys, 126, 155101, 10.1063/1.2714538
F Morcos, 2010, Modeling conformational ensembles of slow functional motions in Pin1-WW, PLoS Comput Biol, 6, e1001015, 10.1371/journal.pcbi.1001015
NV Buchete, 2008, Coarse master equations for peptide folding dynamics, J Phys Chem B, 112, 6057, 10.1021/jp0761665
W Zheng, 2007, Simulating replica exchange simulations of protein folding with a kinetic network model, Proc Natl Acad Sci U S A, 104, 15340, 10.1073/pnas.0704418104
AC Pan, 2008, Building Markov state models along pathways to determine free energies and rates of transitions, J Chem Phys, 129, 064107, 10.1063/1.2959573
JH Prinz, 2011, Markov models of molecular kinetics: Generation and validation, J Chem Phys, 134, 174105, 10.1063/1.3565032
Schütte C, Huisinga W (2000) Biomolecular Conformations as Metastable Sets of Markov Chains. Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing. pp. 1106–1115.
D Gfeller, 2007, Complex network analysis of free-energy landscapes, Proc Natl Acad Sci U S A, 104, 1817, 10.1073/pnas.0608099104
G Perez-Hernandez, 2013, Identification of slow molecular order parameters for Markov model construction, J Chem Phys, 139, 015102, 10.1063/1.4811489
A Jain, 2012, Identifying Metastable States of Folding Proteins, J Chem Theory Comput, 8, 3810, 10.1021/ct300077q
GR Bowman, 2009, Using generalized ensemble simulations and Markov state models to identify conformational states, Methods, 49, 197, 10.1016/j.ymeth.2009.04.013
Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, et al. (2010) Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms. Pac Symp Biocomput: 228–239.
X Huang, 2009, Rapid equilibrium sampling initiated from nonequilibrium data, Proc Natl Acad Sci U S A, 106, 19765, 10.1073/pnas.0909088106
LT Da, 2012, Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II, J Am Chem Soc, 134, 2399, 10.1021/ja210656k
F Noe, 2009, Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations, Proc Natl Acad Sci U S A, 106, 19011, 10.1073/pnas.0905466106
GR Bowman, 2011, Taming the complexity of protein folding, Curr Opin Struct Biol, 21, 4, 10.1016/j.sbi.2010.10.006
JD Chodera, 2014, Markov state models of biomolecular conformational dynamics, Curr Opin Struct Biol, 25, 135, 10.1016/j.sbi.2014.04.002
AM Razavi, 2014, Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models, J Chem Inf Model, 54, 1425, 10.1021/ci500102y
W Zhuang, 2011, Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach, J Phys Chem B, 115, 5415, 10.1021/jp109592b
VA Voelz, 2010, Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1–39), J Am Chem Soc, 132, 1526, 10.1021/ja9090353
I Buch, 2011, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, Proc Natl Acad Sci U S A, 108, 10184, 10.1073/pnas.1103547108
S Doerr, 2014, On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations, J Chem Theory Comput, 10, 2064, 10.1021/ct400919u
C Dominguez, 2003, HADDOCK: a protein-protein docking approach based on biochemical or biophysical information, J Am Chem Soc, 125, 1731, 10.1021/ja026939x
SJ de Vries, 2007, HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets, Proteins: Struct, Funct, Bioinf, 69, 726, 10.1002/prot.21723
SJ Fleishman, 2011, Community-wide assessment of protein-interface modeling suggests improvements to design methodology, J Mol Biol, 414, 289, 10.1016/j.jmb.2011.09.031
FK Sheong, 2015, Automatic state Partitioning for Multi-body systems (APM): An Efficient Algorithm for Constructing Markov State Models to Elucidate Conformational Dynamics of Multi-body Systems, J Chem Theory Comput, 11, 17, 10.1021/ct5007168
T Wlodarski, 2009, Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin, Proc Natl Acad Sci U S A, 106, 19346, 10.1073/pnas.0906966106
DA Silva, 2011, A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein, PLoS Comput Biol, 7, e1002054, 10.1371/journal.pcbi.1002054
S Rudel, 2011, Phosphorylation of human Argonaute proteins affects small RNA binding, Nucleic Acids Res, 39, 2330, 10.1093/nar/gkq1032
A Mazumder, 2013, A transient reversal of miRNA-mediated repression controls macrophage activation, EMBO Rep, 14, 1008, 10.1038/embor.2013.149
A Sali, 1993, Comparative Protein Modeling by Satisfaction of Spatial Restraints, J Mol Biol, 234, 779, 10.1006/jmbi.1993.1626
MA Marti-Renom, 2000, Comparative protein structure modeling of genes and genomes, Annu Rev Biophys Biomol Struct, 29, 291, 10.1146/annurev.biophys.29.1.291
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Chapter 5: Unit 5.6.
H Berendsen, 1981, Intermolecular Forces, 331
B Hess, 2008, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J Chem Theory Comput, 4, 435, 10.1021/ct700301q
K Lindorff-Larsen, 2010, Improved side-chain torsion potentials for the Amber ff99SB protein force field, Proteins: Struct, Funct, Bioinf, 78, 1950, 10.1002/prot.22711
T Darden, 1993, Particle Mesh Ewald—an N.Log(N) Method for Ewald Sums in Large Systems, J Chem Phys, 98, 10089, 10.1063/1.464397
B Hess, 1997, LINCS: A linear constraint solver for molecular simulations, J Comput Chem, 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
G Bussi, 2007, Canonical sampling through velocity rescaling, J Chem Phys, 126, 014101, 10.1063/1.2408420
M Parrinello, 1981, Polymorphic Transitions in Single-Crystals—a New Molecular-Dynamics Method, J Appl Phys, 52, 7182, 10.1063/1.328693
TF Gonzalez, 1985, Clustering to Minimize the Maximum Intercluster Distance, Theor Comput Sci, 38, 293, 10.1016/0304-3975(85)90224-5
AY Ng, 2002, On spectral clustering: Analysis and an algorithm, Adv Neural Inf Process Syst, 14, 849
K Rother, 2011, RNA and protein 3D structure modeling: similarities and differences, J Mol Model, 17, 2325, 10.1007/s00894-010-0951-x
AT Brunger, 1998, Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr, Sect D: Biol Crystallogr, 54, 905, 10.1107/S0907444998003254
AT Brunger, 2007, Version 1.2 of the Crystallography and NMR system, Nat Protoc, 2, 2728, 10.1038/nprot.2007.406
JP Linge, 1999, Influence of non-bonded parameters on the quality of NMR structures: A new force field for NMR structure calculation, J Biomol NMR, 13, 51, 10.1023/A:1008365802830
JP Linge, 2003, Refinement of protein structures in explicit solvent, Proteins: Struct, Funct, Bioinf, 50, 496, 10.1002/prot.10299
WL Jorgensen, 1988, The Opls Potential Functions for Proteins—Energy Minimizations for Crystals of Cyclic-Peptides and Crambin, J Am Chem Soc, 110, 1657, 10.1021/ja00214a001