메뉴 건너뛰기




Volumn 528, Issue 7583, 2015, Pages 585-588

Rational design of α-helical tandem repeat proteins with closed architectures

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; TANDEM REPEAT PROTEIN; UNCLASSIFIED DRUG;

EID: 84951325903     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature16191     Document Type: Article
Times cited : (106)

References (46)
  • 2
    • 84865174088 scopus 로고    scopus 로고
    • Tandem repeats in proteins: From sequence to structure
    • Kajava, A. V. Tandem repeats in proteins: from sequence to structure. J. Struct. Biol. 179, 279-288 (2012).
    • (2012) J. Struct. Biol. , vol.179 , pp. 279-288
    • Kajava, A.V.1
  • 3
    • 0035783061 scopus 로고    scopus 로고
    • Protein repeats: Structures, functions, and evolution
    • Andrade, M. A., Perez-Iratxeta, C. & Ponting, C. P. Protein repeats: structures, functions, and evolution. J. Struct. Biol. 134, 117-131 (2001).
    • (2001) J. Struct. Biol. , vol.134 , pp. 117-131
    • Andrade, M.A.1    Perez-Iratxeta, C.2    Ponting, C.P.3
  • 5
    • 0037162703 scopus 로고    scopus 로고
    • Modular recognition of RNA by a human pumilio-homology domain
    • Wang, X., McLachlan, J., Zamore, P. D. & Hall, T. M. Modular recognition of RNA by a human pumilio-homology domain. Cell 110, 501-512 (2002).
    • (2002) Cell , vol.110 , pp. 501-512
    • Wang, X.1    McLachlan, J.2    Zamore, P.D.3    Hall, T.M.4
  • 6
    • 84857029597 scopus 로고    scopus 로고
    • The crystal structure of TAL effector PthXo1 bound to its DNA target
    • Mak, A. N., Bradley, P., Cernadas, R. A., Bogdanove, A. J. & Stoddard, B. L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 335, 716-719 (2012).
    • (2012) Science , vol.335 , pp. 716-719
    • Mak, A.N.1    Bradley, P.2    Cernadas, R.A.3    Bogdanove, A.J.4    Stoddard, B.L.5
  • 7
    • 84857032466 scopus 로고    scopus 로고
    • Structural basis for sequence-specific recognition of DNA by TAL effectors
    • Deng, D. et al. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science 335, 720-723 (2012).
    • (2012) Science , vol.335 , pp. 720-723
    • Deng, D.1
  • 8
    • 84866145891 scopus 로고    scopus 로고
    • A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins
    • Barkan, A. et al. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet. 8, e1002910 (2012).
    • (2012) PLoS Genet. , vol.8
    • Barkan, A.1
  • 9
    • 84895035916 scopus 로고    scopus 로고
    • Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins
    • Reichen, C., Hansen, S. & Plückthun, A. Modular peptide binding: from a comparison of natural binders to designed armadillo repeat proteins. J. Struct. Biol. 185, 147-162 (2014).
    • (2014) J. Struct. Biol. , vol.185 , pp. 147-162
    • Reichen, C.1    Hansen, S.2    Plückthun, A.3
  • 10
    • 0035896377 scopus 로고    scopus 로고
    • The TIM-barrel fold: A versatile framework for efficient enzymes
    • Wierenga, R. K. The TIM-barrel fold: a versatile framework for efficient enzymes. FEBS Lett. 492, 193-198 (2001).
    • (2001) FEBS Lett. , vol.492 , pp. 193-198
    • Wierenga, R.K.1
  • 11
    • 0034306119 scopus 로고    scopus 로고
    • When protein folding is simplified to protein coiling: The continuum of solenoid protein structures
    • Kobe, B. & Kajava, A. V. When protein folding is simplified to protein coiling: the continuum of solenoid protein structures. Trends Biochem. Sci. 25, 509-515 (2000).
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 509-515
    • Kobe, B.1    Kajava, A.V.2
  • 12
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable alpha-helical arrays from an idealized TPR motif
    • Main, E. R., Xiong, Y., Cocco, M. J., D'Andrea, L. & Regan, L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 11, 497-508 (2003).
    • (2003) Structure , vol.11 , pp. 497-508
    • Main, E.R.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5
  • 13
    • 2342624119 scopus 로고    scopus 로고
    • High-affinity binders selected from designed ankyrin repeat protein libraries
    • Binz, H. K. et al. High-affinity binders selected from designed ankyrin repeat protein libraries. Nature Biotechnol. 22, 575-582 (2004).
    • (2004) Nature Biotechnol. , vol.22 , pp. 575-582
    • Binz, H.K.1
  • 14
    • 39149098445 scopus 로고    scopus 로고
    • Designed armadillo repeat proteins as general peptide-binding scaffolds: Consensus design and computational optimization of the hydrophobic core
    • Parmeggiani, F. et al. Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. J. Mol. Biol. 376, 1282-1304 (2008).
    • (2008) J. Mol. Biol. , vol.376 , pp. 1282-1304
    • Parmeggiani, F.1
  • 15
    • 78349304669 scopus 로고    scopus 로고
    • Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats
    • Urvoas, A. et al. Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats. J. Mol. Biol. 404, 307-327 (2010).
    • (2010) J. Mol. Biol. , vol.404 , pp. 307-327
    • Urvoas, A.1
  • 16
    • 80054856259 scopus 로고    scopus 로고
    • DARPins and other repeat protein scaffolds: Advances in engineering and applications
    • Boersma, Y. L. & Plückthun, A. DARPins and other repeat protein scaffolds: advances in engineering and applications. Curr. Opin. Biotechnol. 22, 849-857 (2011).
    • (2011) Curr. Opin. Biotechnol. , vol.22 , pp. 849-857
    • Boersma, Y.L.1    Plückthun, A.2
  • 17
    • 84918555133 scopus 로고    scopus 로고
    • Computational design of a leucine-rich repeat protein with a predefined geometry
    • Rämisch, S., Weininger, U., Martinsson, J., Akke, M. & André, I. Computational design of a leucine-rich repeat protein with a predefined geometry. Proc. Natl Acad. Sci. USA 111, 17875-17880 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 17875-17880
    • Rämisch, S.1    Weininger, U.2    Martinsson, J.3    Akke, M.4    André, I.5
  • 18
    • 84908072118 scopus 로고    scopus 로고
    • Computational design of a self-assembling symmetrical β-propeller protein
    • Voet, A. R. et al. Computational design of a self-assembling symmetrical β-propeller protein. Proc. Natl Acad. Sci. USA 111, 15102-15107 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 15102-15107
    • Voet, A.R.1
  • 19
    • 84926289262 scopus 로고    scopus 로고
    • Control of repeat-protein curvature by computational protein design
    • Park, K. et al. Control of repeat-protein curvature by computational protein design. Nature Struct. Mol. Biol. 22, 167-174 (2015).
    • (2015) Nature Struct. Mol. Biol. , vol.22 , pp. 167-174
    • Park, K.1
  • 20
    • 84920768290 scopus 로고    scopus 로고
    • A general computational approach for repeat protein design
    • Parmeggiani, F. et al. A general computational approach for repeat protein design. J. Mol. Biol. 427, 563-575 (2015).
    • (2015) J. Mol. Biol. , vol.427 , pp. 563-575
    • Parmeggiani, F.1
  • 21
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 22
    • 78650905964 scopus 로고    scopus 로고
    • 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
  • 23
    • 84868611622 scopus 로고    scopus 로고
    • Principles for designing ideal protein structures
    • Koga, N. et al. Principles for designing ideal protein structures. Nature 491, 222-227 (2012).
    • (2012) Nature , vol.491 , pp. 222-227
    • Koga, N.1
  • 24
    • 34250796909 scopus 로고    scopus 로고
    • Structure and stability of designed TPR protein superhelices: Unusual crystal packing and implications for natural TPR proteins
    • Kajander, T., Cortajarena, A. L., Mochrie, S. & Regan, L. Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins. Acta Crystallogr. D 63, 800-811 (2007).
    • (2007) Acta Crystallogr. D , vol.63 , pp. 800-811
    • Kajander, T.1    Cortajarena, A.L.2    Mochrie, S.3    Regan, L.4
  • 25
    • 77954385327 scopus 로고    scopus 로고
    • Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat
    • Jiménez-Menéndez, N. et al. Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat. Nature Struct. Mol. Biol. 17, 891-893 (2010).
    • (2010) Nature Struct. Mol. Biol. , vol.17 , pp. 891-893
    • Jiménez-Menéndez, N.1
  • 27
    • 0029863769 scopus 로고    scopus 로고
    • Automatic classification and analysis of alpha alpha-turn motifs in proteins
    • Wintjens, R. T., Rooman, M. J. & Wodak, S. J. Automatic classification and analysis of alpha alpha-turn motifs in proteins. J. Mol. Biol. 255, 235-253 (1996).
    • (1996) J. Mol. Biol. , vol.255 , pp. 235-253
    • Wintjens, R.T.1    Rooman, M.J.2    Wodak, S.J.3
  • 28
    • 84877274659 scopus 로고    scopus 로고
    • Nanostructured functional films from engineered repeat proteins
    • Grove, T. Z., Regan, L. & Cortajarena, A. L. Nanostructured functional films from engineered repeat proteins. J. R. Soc. Interface 10, http://dx.doi.org/10.1098/rsif.2013.0051 (2013).
    • (2013) J. R. Soc. Interface , vol.10
    • Grove, T.Z.1    Regan, L.2    Cortajarena, A.L.3
  • 29
    • 84860799377 scopus 로고    scopus 로고
    • Computational design of a protein crystal
    • Lanci, C. J. et al. Computational design of a protein crystal. Proc. Natl Acad. Sci. USA 109, 7304-7309 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 7304-7309
    • Lanci, C.J.1
  • 30
    • 84923875797 scopus 로고    scopus 로고
    • Design of protein crystals in the development of solid biomaterials
    • Abe, S. & Ueno, T. Design of protein crystals in the development of solid biomaterials. RSC Adv. 5, 21366-21375 (2015).
    • (2015) RSC Adv. , vol.5 , pp. 21366-21375
    • Abe, S.1    Ueno, T.2
  • 31
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268, 209-225 (1997).
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 32
    • 33846603216 scopus 로고    scopus 로고
    • High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design
    • Dantas, G. et al. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J. Mol. Biol. 366, 1209-1221 (2007).
    • (2007) J. Mol. Biol. , vol.366 , pp. 1209-1221
    • Dantas, G.1
  • 33
    • 0028871926 scopus 로고
    • Dali: A network tool for protein structure comparison
    • Holm, L. & Sander, C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20, 478-480 (1995).
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 34
    • 84941039390 scopus 로고    scopus 로고
    • CATH: Comprehensive structural and functional annotations for genome sequences
    • Sillitoe, I. et al. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res. 43, D376-D381 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D376-D381
    • Sillitoe, I.1
  • 35
    • 84891811692 scopus 로고    scopus 로고
    • SCOPe: Structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures
    • Fox, N. K., Brenner, S. E. & Chandonia, J. M. SCOPe: Structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 42, D304-D309 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D304-D309
    • Fox, N.K.1    Brenner, S.E.2    Chandonia, J.M.3
  • 36
    • 84919623580 scopus 로고    scopus 로고
    • ECOD: An evolutionary classification of protein domains
    • Cheng, H. et al. ECOD: an evolutionary classification of protein domains. PLOS Comput. Biol. 10, e1003926 (2014).
    • (2014) PLOS Comput. Biol. , vol.10
    • Cheng, H.1
  • 37
    • 77957803837 scopus 로고    scopus 로고
    • Folding, DNA recognition, and function of GIY-YIG endonucleases: Crystal structures of R.Eco29kI
    • Mak, A. N., Lambert, A. R. & Stoddard, B. L. Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI. Structure 18, 1321-1331 (2010).
    • (2010) Structure , vol.18 , pp. 1321-1331
    • Mak, A.N.1    Lambert, A.R.2    Stoddard, B.L.3
  • 38
    • 77950821956 scopus 로고    scopus 로고
    • Selenium incorporation using recombinant techniques
    • Walden, H. Selenium incorporation using recombinant techniques. Acta Crystallogr. D 66, 352-357 (2010).
    • (2010) Acta Crystallogr. D , vol.66 , pp. 352-357
    • Walden, H.1
  • 39
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 40
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
    • (2007) J. Appl. Crystallogr. , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 41
    • 79953737180 scopus 로고    scopus 로고
    • Overview of the CCP4 suite and current developments
    • Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235-242 (2011).
    • (2011) Acta Crystallogr. D , vol.67 , pp. 235-242
    • Winn, M.D.1
  • 43
    • 13844301139 scopus 로고    scopus 로고
    • Direct incorporation of experimental phase information in model refinement
    • Skubák, P., Murshudov, G. N. & Pannu, N. S. Direct incorporation of experimental phase information in model refinement. Acta Crystallogr. D 60, 2196-2201 (2004).
    • (2004) Acta Crystallogr. D , vol.60 , pp. 2196-2201
    • Skubák, P.1    Murshudov, G.N.2    Pannu, N.S.3
  • 44
    • 76449098262 scopus 로고    scopus 로고
    • 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 66, 213-221 (2010).
    • (2010) Acta Crystallogr. D , vol.66 , pp. 213-221
    • Adams, P.D.1
  • 45
    • 84860273177 scopus 로고    scopus 로고
    • Towards automated crystallographic structure refinement with phenix.refine
    • Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352-367 (2012).
    • (2012) Acta Crystallogr. D , vol.68 , pp. 352-367
    • Afonine, P.V.1
  • 46
    • 84857935771 scopus 로고    scopus 로고
    • The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings
    • He, J. et al. The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings. Structure 20, 513-521 (2012).
    • (2012) Structure , vol.20 , pp. 513-521
    • He, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.