-
1
-
-
0034610814
-
The language of covalent histone modifications
-
Strahl BD, Allis CD, (2000) The language of covalent histone modifications. Nature 403: 41-45.
-
(2000)
Nature
, vol.403
, pp. 41-45
-
-
Strahl, B.D.1
Allis, C.D.2
-
2
-
-
0037309997
-
Structure of SET domain proteins: a new twist on histone methylation
-
Marmorstein R, (2003) Structure of SET domain proteins: a new twist on histone methylation. Trends Biochem Sci 28: 59-62.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 59-62
-
-
Marmorstein, R.1
-
3
-
-
33745632390
-
The epigenetic magic of histone lysine methylation
-
Jenuwein T, (2006) The epigenetic magic of histone lysine methylation. FEBS J 273: 3121-3135.
-
(2006)
FEBS J
, vol.273
, pp. 3121-3135
-
-
Jenuwein, T.1
-
4
-
-
27644589675
-
The diverse functions of histone lysine methylation
-
Martin C, Zhang Y, (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6: 838-849.
-
(2005)
Nat Rev Mol Cell Biol
, vol.6
, pp. 838-849
-
-
Martin, C.1
Zhang, Y.2
-
5
-
-
35848961668
-
How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers
-
Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ, (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struc Mol Biol 14: 1025-1040.
-
(2007)
Nat Struc Mol Biol
, vol.14
, pp. 1025-1040
-
-
Taverna, S.D.1
Li, H.2
Ruthenburg, A.J.3
Allis, C.D.4
Patel, D.J.5
-
6
-
-
35848946372
-
Primers on chromatin
-
Lall S, (2007) Primers on chromatin. Nat Struc Mol Biol 14: 1110-1115.
-
(2007)
Nat Struc Mol Biol
, vol.14
, pp. 1110-1115
-
-
Lall, S.1
-
7
-
-
15044358494
-
Reading signals on the nucleosome with a new nomenclature for modified histones
-
Turner BM, (2005) Reading signals on the nucleosome with a new nomenclature for modified histones. Nat Struc Mol Biol 12: 110-112.
-
(2005)
Nat Struc Mol Biol
, vol.12
, pp. 110-112
-
-
Turner, B.M.1
-
8
-
-
0037020217
-
Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase
-
Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, et al. (2002) Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell 111: 117-127.
-
(2002)
Cell
, vol.111
, pp. 117-127
-
-
Zhang, X.1
Tamaru, H.2
Khan, S.I.3
Horton, J.R.4
Keefe, L.J.5
-
9
-
-
0042164227
-
Structural basis for the product specificity of histone lysine methyltransferases
-
Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, et al. (2003) Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell 12: 177-185.
-
(2003)
Mol Cell
, vol.12
, pp. 177-185
-
-
Zhang, X.1
Yang, Z.2
Khan, S.I.3
Horton, J.R.4
Tamaru, H.5
-
10
-
-
22344454519
-
Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase
-
Couture JF, Collazo E, Brunzelle JS, Trievel RC, (2005) Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Genes Dev 19: 1455-1465.
-
(2005)
Genes Dev
, vol.19
, pp. 1455-1465
-
-
Couture, J.F.1
Collazo, E.2
Brunzelle, J.S.3
Trievel, R.C.4
-
11
-
-
22344455665
-
Specificity and mechanism of the histone methyltransferase Pr-Set7
-
Xiao B, Jing C, Kelly G, Walker PA, Muskett FW, et al. (2005) Specificity and mechanism of the histone methyltransferase Pr-Set7. Genes Dev 19: 1444-1454.
-
(2005)
Genes Dev
, vol.19
, pp. 1444-1454
-
-
Xiao, B.1
Jing, C.2
Kelly, G.3
Walker, P.A.4
Muskett, F.W.5
-
12
-
-
0037421847
-
Structure and catalytic mechanism of the human histone methyltransferase SET7/9
-
Xiao B, Jing C, Wilson JR, Walker PA, Vasisht N, et al. (2003) Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 421: 652-656.
-
(2003)
Nature
, vol.421
, pp. 652-656
-
-
Xiao, B.1
Jing, C.2
Wilson, J.R.3
Walker, P.A.4
Vasisht, N.5
-
13
-
-
58549112187
-
Structural origins for the product specificity of SET domain protein methyltransferases
-
Couture JF, Dirk LMA, Brunzelle JS, Houtz RL, Trievel RC, (2008) Structural origins for the product specificity of SET domain protein methyltransferases. Proc Natl Acad Sci USA 105: 20659-20664.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 20659-20664
-
-
Couture, J.F.1
Dirk, L.M.A.2
Brunzelle, J.S.3
Houtz, R.L.4
Trievel, R.C.5
-
14
-
-
14044256546
-
In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases
-
Collins RE, Tachibana M, Tamaru H, Smith KM, Jia D, et al. (2005) In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem 280: 5563-5570.
-
(2005)
J Biol Chem
, vol.280
, pp. 5563-5570
-
-
Collins, R.E.1
Tachibana, M.2
Tamaru, H.3
Smith, K.M.4
Jia, D.5
-
15
-
-
77952488976
-
Structural Biology of Human H3K9 Methyltransferases
-
Wu H, Min JR, Lunin VV, Antoshenko T, Dombrovski L, et al. (2010) Structural Biology of Human H3K9 Methyltransferases. Plos One 5: e8570.
-
(2010)
Plos One
, vol.5
-
-
Wu, H.1
Min, J.R.2
Lunin, V.V.3
Antoshenko, T.4
Dombrovski, L.5
-
16
-
-
79961241001
-
Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding
-
Xu ST, Wu J, Sun BF, Zhong C, Ding JP, (2011) Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding. Nucleic Acids Res 39: 4438-4449.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 4438-4449
-
-
Xu, S.T.1
Wu, J.2
Sun, B.F.3
Zhong, C.4
Ding, J.P.5
-
17
-
-
77957770113
-
SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation
-
Del Rizzo PA, Couture JF, Dirk LMA, Strunk BS, Roiko MS, et al. (2010) SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation. J Bio Chem 285: 31849-31858.
-
(2010)
J Bio Chem
, vol.285
, pp. 31849-31858
-
-
Del Rizzo, P.A.1
Couture, J.F.2
Dirk, L.M.A.3
Strunk, B.S.4
Roiko, M.S.5
-
18
-
-
71549139127
-
Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free-Energy Simulations of Protein Lysine Methyltransferases
-
Xu Q, Chu YZ, Guo HB, Smith JC, Guo H, (2009) Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free-Energy Simulations of Protein Lysine Methyltransferases. Chem Eur J 15: 12596-12599.
-
(2009)
Chem Eur J
, vol.15
, pp. 12596-12599
-
-
Xu, Q.1
Chu, Y.Z.2
Guo, H.B.3
Smith, J.C.4
Guo, H.5
-
19
-
-
77951116407
-
Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations: What Causes the Stop of Methyl Addition during Histone Lysine Methylation?
-
Chu YZ, Xu Q, Guo H, (2008) Understanding Energetic Origins of Product Specificity of SET8 from QM/MM Free Energy Simulations: What Causes the Stop of Methyl Addition during Histone Lysine Methylation? J Chem Theory Comput 6: 1380-1389.
-
(2008)
J Chem Theory Comput
, vol.6
, pp. 1380-1389
-
-
Chu, Y.Z.1
Xu, Q.2
Guo, H.3
-
20
-
-
34547433238
-
Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity
-
Guo HB, Guo H, (2007) Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity. Proc Natl Acad Sci USA 104: 8797-8802.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8797-8802
-
-
Guo, H.B.1
Guo, H.2
-
21
-
-
45749140396
-
Product specificity and mechanism of protein lysine methyltransferases: Insights from the histone lysine methyltransferase SET8
-
Zhang XD, Bruice TC, (2008) Product specificity and mechanism of protein lysine methyltransferases: Insights from the histone lysine methyltransferase SET8. Biochemistry 47: 6671-6677.
-
(2008)
Biochemistry
, vol.47
, pp. 6671-6677
-
-
Zhang, X.D.1
Bruice, T.C.2
-
22
-
-
79956279966
-
Modeling a New Water Channel That Allows SET9 to Dimethylate p53
-
Bai QF, Shen YL, Yao XJ, Wang F, Du YP, et al. (2011) Modeling a New Water Channel That Allows SET9 to Dimethylate p53. Plos One 6: e19856.
-
(2011)
Plos One
, vol.6
-
-
Bai, Q.F.1
Shen, Y.L.2
Yao, X.J.3
Wang, F.4
Du, Y.P.5
-
23
-
-
41149125431
-
How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by ab initio QM/MM molecular dynamics simulations
-
Hu P, Wang S, Zhang Y, (2008) How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by ab initio QM/MM molecular dynamics simulations. J Am Chem Soc 130: 3806-3813.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 3806-3813
-
-
Hu, P.1
Wang, S.2
Zhang, Y.3
-
24
-
-
34248219463
-
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9
-
Wang SL, Hu P, Zhang YK, (2007) Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9. J Phys Chem B 111: 3758-3764.
-
(2007)
J Phys Chem B
, vol.111
, pp. 3758-3764
-
-
Wang, S.L.1
Hu, P.2
Zhang, Y.K.3
-
25
-
-
31944437048
-
Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: An ab initio QM/MM-FE study with multiple initial structures
-
Hu P, Zhang YK, (2006) Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: An ab initio QM/MM-FE study with multiple initial structures. J Am Chem Soc 128: 1272-1278.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 1272-1278
-
-
Hu, P.1
Zhang, Y.K.2
-
26
-
-
44449162039
-
Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases
-
Zhang X, Bruice TC, (2008) Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases. Proc Natl Acad Sci USA 105: 5728-5732.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 5728-5732
-
-
Zhang, X.1
Bruice, T.C.2
-
27
-
-
84986513644
-
A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
-
Field MJ, Bash PA, Karplus M, (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J Comput Chem 11: 700-733.
-
(1990)
J Comput Chem
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
28
-
-
84986512474
-
CHARMM - a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4: 187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
-
29
-
-
0004016501
-
Comparision of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML, (1983) Comparision of simple potential functions for simulating liquid water. J Chem Phys 79: 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
30
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria E, Fischer S, Karplus M, (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105: 1902-1921.
-
(1996)
J Chem Phys
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
31
-
-
0022068152
-
Active-site dynamics in protein molecules - a stochastic boundary molecular-dynamics approach
-
Brooks CL, Brunger A, Karplus M, (1985) Active-site dynamics in protein molecules - a stochastic boundary molecular-dynamics approach. Biopolymers 24: 843-865.
-
(1985)
Biopolymers
, vol.24
, pp. 843-865
-
-
Brooks, C.L.1
Brunger, A.2
Karplus, M.3
-
32
-
-
0035138648
-
A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
-
Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M, (2001) A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J Phys Chem B 105: 569-585.
-
(2001)
J Phys Chem B
, vol.105
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
33
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
-
34
-
-
16444385400
-
Monte-carlo free-energy estimates using non-boltzmann sampling - application to subcritical lennard -jones fluid
-
Torrie GM, Valleau JP, (1974) Monte-carlo free-energy estimates using non-boltzmann sampling - application to subcritical lennard-jones fluid. Chem Phys Lett 28: 578-581.
-
(1974)
Chem Phys Lett
, vol.28
, pp. 578-581
-
-
Torrie, G.M.1
Valleau, J.P.2
-
35
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM, (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. J Comput Chem 13: 1011-1021.
-
(1992)
J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
36
-
-
73349135352
-
Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems
-
Glowacki DR, Paci E, Shalashilin DV, (2009) Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems. Journal of Physical Chemistry B 113: 16603-16611.
-
(2009)
Journal of Physical Chemistry B
, vol.113
, pp. 16603-16611
-
-
Glowacki, D.R.1
Paci, E.2
Shalashilin, D.V.3
-
37
-
-
80051906268
-
Communication: Conformation state diagram of polypeptides: A chain length induced alpha-beta transition
-
Ricchiuto P, Brukhno AV, Paci E, Auer S, (2011) Communication: Conformation state diagram of polypeptides: A chain length induced alpha-beta transition. Journal of Chemical Physics 135.
-
(2011)
Journal of Chemical Physics
, vol.135
-
-
Ricchiuto, P.1
Brukhno, A.V.2
Paci, E.3
Auer, S.4
|