-
1
-
-
79953779607
-
Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins
-
Rizk, S.S. et al. Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins. Nat. Struct. Mol. Biol. (2011).
-
(2011)
Nat. Struct. Mol. Biol.
-
-
Rizk, S.S.1
-
2
-
-
62549093913
-
Two-state selection of conformation-specific antibodies
-
Gao, J., Sidhu, S.S. & Wells, J.A. Two-state selection of conformation-specific antibodies. Proc. Natl. Acad. Sci. USA 106, 3071-3076 (2009).
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3071-3076
-
-
Gao, J.1
Sidhu, S.S.2
Wells, J.A.3
-
3
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange, O.F. et al. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320, 1471-1475 (2008).
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
-
4
-
-
78650100616
-
Ubiquitin: Same molecule, different degradation pathways
-
Clague, M.J. & Urbé, S. Ubiquitin: same molecule, different degradation pathways. Cell 143, 682-685 (2010).
-
(2010)
Cell
, vol.143
, pp. 682-685
-
-
Clague, M.J.1
Urbé, S.2
-
5
-
-
0034915764
-
Mechanisms underlying ubiquitination
-
Pickart, C.M. Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 70, 503-533 (2001).
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 503-533
-
-
Pickart, C.M.1
-
6
-
-
8844237615
-
Polyubiquitin chains: Polymeric protein signals
-
Pickart, C.M. & Fushman, D. Polyubiquitin chains: polymeric protein signals. Curr. Opin. Chem. Biol. 8, 610-616 (2004).
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 610-616
-
-
Pickart, C.M.1
Fushman, D.2
-
7
-
-
34548383489
-
Design of multi-specificity in protein interfaces
-
Humphris, E.L. & Kortemme, T. Design of multi-specificity in protein interfaces. PLoS Comput. Biol. 3, e164 (2007).
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Humphris, E.L.1
Kortemme, T.2
-
8
-
-
67049155677
-
A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
-
Friedland, G.D., Lakomek, N.-A., Griesinger, C., Meiler, J. & Kortemme, T. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput. Biol. 5, e1000393 (2009).
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Friedland, G.D.1
Lakomek, N.-A.2
Griesinger, C.3
Meiler, J.4
Kortemme, T.5
-
9
-
-
68049084674
-
Breaking the chains: Structure and function of the deubiquitinases
-
Komander, D., Clague, M.J. & Urbé, S. Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10, 550-563 (2009).
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 550-563
-
-
Komander, D.1
Clague, M.J.2
Urbé, S.3
-
10
-
-
79955938866
-
The multifaceted roles of USP7: New therapeutic opportunities
-
Nicholson, B. & Suresh Kumar, K.G. The multifaceted roles of USP7: new therapeutic opportunities. Cell Biochem. Biophys. 60, 61-68 (2011).
-
(2011)
Cell Biochem. Biophys.
, vol.60
, pp. 61-68
-
-
Nicholson, B.1
Suresh Kumar, K.G.2
-
11
-
-
66749083491
-
DUBs and cancer: The role of deubiquitinating enzymes as oncogenes, non-oncogenes and tumor suppressors
-
Hussain, S., Zhang, Y. & Galardy, P.J. DUBs and cancer: the role of deubiquitinating enzymes as oncogenes, non-oncogenes and tumor suppressors. Cell Cycle 8, 1688-1697 (2009).
-
(2009)
Cell Cycle
, vol.8
, pp. 1688-1697
-
-
Hussain, S.1
Zhang, Y.2
Galardy, P.J.3
-
12
-
-
1842421376
-
A dynamic role of HAUSP in the p53-Mdm2 pathway
-
Li, M., Brooks, C.L., Kon, N. & Gu, W. A dynamic role of HAUSP in the p53-Mdm2 pathway. Mol. Cell 13, 879-886 (2004).
-
(2004)
Mol. Cell
, vol.13
, pp. 879-886
-
-
Li, M.1
Brooks, C.L.2
Kon, N.3
Gu, W.4
-
13
-
-
0037061508
-
Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization
-
Li, M. et al. Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416, 648-653 (2002).
-
(2002)
Nature
, vol.416
, pp. 648-653
-
-
Li, M.1
-
14
-
-
80053594090
-
Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase
-
Faesen, A.C. et al. Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase. Mol. Cell 44, 147-159 (2011).
-
(2011)
Mol. Cell
, vol.44
, pp. 147-159
-
-
Faesen, A.C.1
-
15
-
-
34547799647
-
Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization
-
Fernández-Montalván, A. et al. Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization. FEBS J. 274, 4256-4270 (2007).
-
(2007)
FEBS J.
, vol.274
, pp. 4256-4270
-
-
Fernández-Montalván, A.1
-
16
-
-
0027136111
-
Affinity maturation of human growth hormone by monovalent phage display
-
Lowman, H.B. & Wells, J.A. Affinity maturation of human growth hormone by monovalent phage display. J. Mol. Biol. 234, 564-578 (1993).
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 564-578
-
-
Lowman, H.B.1
Wells, J.A.2
-
17
-
-
84862776988
-
Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'
-
Levin, A.M. et al. Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'. Nature 484, 529-533 (2012).
-
(2012)
Nature
, vol.484
, pp. 529-533
-
-
Levin, A.M.1
-
18
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay, A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545-574 (2011).
-
(2011)
Methods Enzymol.
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
-
19
-
-
0037184947
-
Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde
-
Hu, M. et al. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell 111, 1041-1054 (2002).
-
(2002)
Cell
, vol.111
, pp. 1041-1054
-
-
Hu, M.1
-
20
-
-
75749132016
-
USP10 regulates p53 localization and stability by deubiquitinating p53
-
Yuan, J., Luo, K., Zhang, L., Cheville, J.C. & Lou, Z. USP10 regulates p53 localization and stability by deubiquitinating p53. Cell 140, 384-396 (2010).
-
(2010)
Cell
, vol.140
, pp. 384-396
-
-
Yuan, J.1
Luo, K.2
Zhang, L.3
Cheville, J.C.4
Lou, Z.5
-
21
-
-
84856708042
-
Phosphorylation-dependent activity of the deubiquitinase DUBA
-
Huang, O.W. et al. Phosphorylation-dependent activity of the deubiquitinase DUBA. Nat. Struct. Mol. Biol. 19, 171-175 (2012).
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 171-175
-
-
Huang, O.W.1
-
22
-
-
33646066025
-
The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin
-
Reyes-Turcu, F.E. et al. The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell 124, 1197-1208 (2006).
-
(2006)
Cell
, vol.124
, pp. 1197-1208
-
-
Reyes-Turcu, F.E.1
-
23
-
-
33746827805
-
Structural basis of ubiquitin recognition by the deubiquitinating protease USP2
-
Renatus, M. et al. Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure 14, 1293-1302 (2006).
-
(2006)
Structure
, vol.14
, pp. 1293-1302
-
-
Renatus, M.1
-
24
-
-
71049189254
-
Unraveling the allosteric mechanism of serine protease inhibition by an antibody
-
Ganesan, R. et al. Unraveling the allosteric mechanism of serine protease inhibition by an antibody. Structure 17, 1614-1624 (2009).
-
(2009)
Structure
, vol.17
, pp. 1614-1624
-
-
Ganesan, R.1
-
25
-
-
0028217202
-
The crystal structure of affinity-matured human growth hormone at 2-Å resolution
-
Ultsch, M.H., Somers, W., Kossiakoff, A.A. & de Vos, A.M. The crystal structure of affinity-matured human growth hormone at 2-Å resolution. J. Mol. Biol. 236, 286-299 (1994).
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 286-299
-
-
Ultsch, M.H.1
Somers, W.2
Kossiakoff, A.A.3
De Vos, A.M.4
-
26
-
-
0033458847
-
Rotamer strain as a determinant of protein structural specificity
-
Lazar, G.A., Johnson, E.C., Desjarlais, J.R. & Handel, T.M. Rotamer strain as a determinant of protein structural specificity. Protein Sci. 8, 2598-2610 (1999).
-
(1999)
Protein Sci.
, vol.8
, pp. 2598-2610
-
-
Lazar, G.A.1
Johnson, E.C.2
Desjarlais, J.R.3
Handel, T.M.4
-
28
-
-
0028808005
-
Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities
-
Giebel, L.B. et al. Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities. Biochemistry 34, 15430-15435 (1995).
-
(1995)
Biochemistry
, vol.34
, pp. 15430-15435
-
-
Giebel, L.B.1
-
29
-
-
0026437442
-
Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library
-
O'Neil, K.T. et al. Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library. Proteins 14, 509-515 (1992).
-
(1992)
Proteins
, vol.14
, pp. 509-515
-
-
O'Neil, K.T.1
-
30
-
-
70450191983
-
Dynamic activation of an allosteric regulatory protein
-
Tzeng, S.-R. & Kalodimos, C.G. Dynamic activation of an allosteric regulatory protein. Nature 462, 368-372 (2009).
-
(2009)
Nature
, vol.462
, pp. 368-372
-
-
Tzeng, S.-R.1
Kalodimos, C.G.2
-
31
-
-
84864651001
-
Protein activity regulation by conformational entropy
-
Tzeng, S.-R. & Kalodimos, C.G. Protein activity regulation by conformational entropy. Nature 488, 236-240 (2012).
-
(2012)
Nature
, vol.488
, pp. 236-240
-
-
Tzeng, S.-R.1
Kalodimos, C.G.2
-
32
-
-
82455219011
-
Flexibility diversity, and cooperativity: Pillars of enzyme catalysis
-
Hammes, G.G., Benkovic, S.J. & Hammes-Schiffer, S. Flexibility, diversity, and cooperativity: pillars of enzyme catalysis. Biochemistry 50, 10422-10430 (2011).
-
(2011)
Biochemistry
, vol.50
, pp. 10422-10430
-
-
Hammes, G.G.1
Benkovic, S.J.2
Hammes-Schiffer, S.3
-
33
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay, A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545-574 (2011).
-
(2011)
Methods Enzymol.
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
-
34
-
-
80051514401
-
Preparation of distinct ubiquitin chain reagents of high purity and yield
-
Dong, K.C. et al. Preparation of distinct ubiquitin chain reagents of high purity and yield. Structure 19, 1053-1063 (2011).
-
(2011)
Structure
, vol.19
, pp. 1053-1063
-
-
Dong, K.C.1
-
35
-
-
34250748507
-
Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries
-
Tonikian, R., Zhang, Y., Boone, C. & Sidhu, S.S. Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat. Protoc. 2, 1368-1386 (2007).
-
(2007)
Nat. Protoc.
, vol.2
, pp. 1368-1386
-
-
Tonikian, R.1
Zhang, Y.2
Boone, C.3
Sidhu, S.S.4
-
36
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
37
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
-
38
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435-447 (2008).
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
39
-
-
77955135754
-
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data
-
Lange, O.F., van der Spoel, D. & de Groot, B.L. Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys. J. 99, 647-655 (2010).
-
(2010)
Biophys. J.
, vol.99
, pp. 647-655
-
-
Lange, O.F.1
Van Der Spoel, D.2
De Groot, B.L.3
-
40
-
-
0031627465
-
An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli
-
Cai, M. et al. An efficient and cost-effective isotope labeling protocol for proteins expressed in Escherichia coli. J. Biomol. NMR 11, 97-102 (1998).
-
(1998)
J. Biomol. NMR
, vol.11
, pp. 97-102
-
-
Cai, M.1
-
41
-
-
35048898436
-
An exchange-free measure of 15N transverse relaxation: An NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange
-
Hansen, D.F. et al. An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange. J. Am. Chem. Soc. 129, 11468-11479 (2007).
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 11468-11479
-
-
Hansen, D.F.1
-
42
-
-
63549111769
-
Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy
-
Bahrami, A., Assadi, A.H., Markley, J.L. & Eghbalnia, H.R. Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput. Biol. 5, e1000307 (2009).
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Bahrami, A.1
Assadi, A.H.2
Markley, J.L.3
Eghbalnia, H.R.4
-
43
-
-
33846626899
-
A 1H-NMR thermometer suitable for cryoprobes
-
Findeisen, M., Brand, T. & Berger, S. A 1H-NMR thermometer suitable for cryoprobes. Magn. Reson. Chem. 45, 175-178 (2007).
-
(2007)
Magn. Reson. Chem.
, vol.45
, pp. 175-178
-
-
Findeisen, M.1
Brand, T.2
Berger, S.3
-
44
-
-
0027787894
-
The importance of not saturating water in protein NMR. Application to sensitivity enhancement and NOE measurements
-
Grzesiek, S. & Bax, A. The importance of not saturating water in protein NMR. Application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115, 12593-12594 (1993).
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 12593-12594
-
-
Grzesiek, S.1
Bax, A.2
-
45
-
-
70450184385
-
Selective characterization of microsecond motions in proteins by NMR relaxation
-
Hansen, D.F., Feng, H., Zhou, Z., Bai, Y. & Kay, L.E. Selective characterization of microsecond motions in proteins by NMR relaxation. J. Am. Chem. Soc. 131, 16257-16265 (2009).
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 16257-16265
-
-
Hansen, D.F.1
Feng, H.2
Zhou, Z.3
Bai, Y.4
Kay, L.E.5
-
46
-
-
0029400480
-
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
-
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).
-
(1995)
J. Biomol. NMR
, vol.6
, pp. 277-293
-
-
Delaglio, F.1
-
47
-
-
0035930026
-
Slow dynamics in folded and unfolded states of an SH3 domain
-
Tollinger, M., Skrynnikov, N.R., Mulder, F.A., Forman-Kay, J.D. & Kay, L.E. Slow dynamics in folded and unfolded states of an SH3 domain. J. Am. Chem. Soc. 123, 11341-11352 (2001).
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 11341-11352
-
-
Tollinger, M.1
Skrynnikov, N.R.2
Mulder, F.A.3
Forman-Kay, J.D.4
Kay, L.E.5
-
48
-
-
0035819455
-
Measurement of slow (μs-ms) time scale dynamics in protein side chains by 15N relaxation dispersion NMR spectroscopy: Application to Asn and Gln residues in a cavity mutant of T4 lysozyme
-
Mulder, F.A.A., Skrynnikov, N.R., Hon, B., Dahlquist, F.W. & Kay, L.E. Measurement of slow (μs-ms) time scale dynamics in protein side chains by 15N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 123, 967-975 (2001).
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 967-975
-
-
Mulder, F.A.A.1
Skrynnikov, N.R.2
Hon, B.3
Dahlquist, F.W.4
Kay, L.E.5
-
49
-
-
3943054838
-
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling
-
Wertz, I.E. et al. De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling. Nature 430, 694-699 (2004).
-
(2004)
Nature
, vol.430
, pp. 694-699
-
-
Wertz, I.E.1
-
50
-
-
84858208097
-
Using linkage-specific monoclonal antibodies to analyze cellular ubiquitylation
-
Newton, K. et al. Using linkage-specific monoclonal antibodies to analyze cellular ubiquitylation. Methods Mol. Biol. 832, 185-196 (2012).
-
(2012)
Methods Mol. Biol.
, vol.832
, pp. 185-196
-
-
Newton, K.1
-
51
-
-
84859265771
-
Engineering and structural characterization of a linear polyubiquitin-specific antibody
-
10.1016/j.jmb.2011.12.053
-
Matsumoto, M.L. et al. Engineering and structural characterization of a linear polyubiquitin-specific antibody. J. Mol. Biol. 10.1016/j.jmb.2011.12.053 (2011).
-
(2011)
J. Mol. Biol.
-
-
Matsumoto, M.L.1
-
52
-
-
77955516435
-
K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody
-
Matsumoto, M.L. et al. K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody. Mol. Cell 39, 477-484 (2010).
-
(2010)
Mol. Cell
, vol.39
, pp. 477-484
-
-
Matsumoto, M.L.1
-
53
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999).
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
|