What has de novo protein design taught us about protein folding and biophysics?

被引：120

作者：

Baker, David ^{[1
]}

机构：

[1] Univ Washington, Dept Biochem, Box 357350,1705 NE Pacific St, Seattle, WA 98195 USA

来源：

PROTEIN SCIENCE | 2019年 / 28卷 / 04期

关键词：

protein design; protein folding; computational modeling; COMPUTATIONAL DESIGN; PRINCIPLES; SEQUENCES;

D O I：

10.1002/pro.3588

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Recent progress in de novo protein design has led to an explosion of new protein structures, functions and assemblies. In this essay, I consider how the successes and failures in this new area inform our understanding of the proteins in nature and, more generally, the predictive computational modeling of biological systems.

引用

页码：678 / 683

页数：6

共 18 条

[1] A surprising simplicity to protein folding [J].

Baker, D .

NATURE, 2000, 405 (6782) :39-42

[2] A PROTEIN-FOLDING REACTION UNDER KINETIC CONTROL [J].

BAKER, D ;

SOHL, JL ;

AGARD, DA .

NATURE, 1992, 356 (6366) :263-265

[3] Accurate design of megadalton-scale two-component icosahedral protein complexes [J].

Bale, Jacob B. ;

Gonen, Shane ;

Liu, Yuxi ;

Sheffler, William ;

Ellis, Daniel ;

Thomas, Chantz ;

Cascio, Duilio ;

Yeates, Todd O. ;

Gonen, Tamir ;

King, Neil P. ;

Baker, David .

SCIENCE, 2016, 353 (6297) :389-394

[4] De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity [J].

Boyken, Scott E. ;

Chen, Zibo ;

Groves, Benjamin ;

Langan, Robert A. ;

Oberdorfer, Gustav ;

Ford, Alex ;

Gilmore, Jason M. ;

Xu, Chunfu ;

DiMaio, Frank ;

Pereira, Jose Henrique ;

Sankaran, Banumathi ;

Seelig, Georg ;

Zwart, Peter H. ;

Baker, David .

SCIENCE, 2016, 352 (6286) :680-687

[5] Exploring the repeat protein universe through computational protein design [J].

Brunette, T. J. ;

Parmeggiani, Fabio ;

Huang, Po-Ssu ;

Bhabha, Gira ;

Ekiert, Damian C. ;

Tsutakawa, Susan E. ;

Hura, Greg L. ;

Tainer, John A. ;

Baker, David .

NATURE, 2015, 528 (7583) :580-+

[6] Programmable design of orthogonal protein heterodimers [J].

Chen, Zibo ;

Boyken, Scott E. ;

Jia, Mengxuan ;

Busch, Florian ;

Flores-Solis, David ;

Bick, Matthew J. ;

Lu, Peilong ;

VanAernum, Zachary L. ;

Sahasrabuddhe, Aniruddha ;

Langan, Robert A. ;

Bermeo, Sherry ;

Brunette, T. J. ;

Mulligan, Vikram Khipple ;

Carter, Lauren P. ;

DiMaio, Frank ;

Sgourakis, Nikolaos G. ;

Wysocki, Vicki H. ;

Baker, David .

NATURE, 2019, 565 (7737) :106-+

[7] De novo design of a fluorescence-activating β-barrel [J].

Dou, Jiayi ;

Vorobieva, Anastassia A. ;

Sheffler, William ;

Doyle, Lindsey A. ;

Park, Hahnbeom ;

Bick, Matthew J. ;

Mao, Binchen ;

Foight, Glenna W. ;

Lee, Min Yen ;

Gagnon, Lauren A. ;

Carter, Lauren ;

Sankaran, Banumathi ;

Ovchinnikov, Sergey ;

Marcos, Enrique ;

Huang, Po-Ssu ;

Vaughan, Joshua C. ;

Stoddard, Barry L. ;

Baker, David .

NATURE, 2018, 561 (7724) :485-+

[8] Comprehensive computational design of ordered peptide macrocycles [J].

Hosseinzadeh, Parisa ;

Bhardwaj, Gaurav ;

Mulligan, Vikram Khipple ;

Shortridge, Matthew D. ;

Craven, Timothy W. ;

Pardo-Avila, Fatima ;

Retti, Stephen A. ;

Kim, David E. ;

Silva, Daniel-Adriano ;

Ibrahim, Yehia M. ;

Webb, Ian K. ;

Cort, John R. ;

Adkins, Joshua N. ;

Varani, Gabriele ;

Baker, David .

SCIENCE, 2017, 358 (6369) :1461-1466

[9] The coming of age of de novo protein design [J].

Huang, Po-Ssu ;

Boyken, Scott E. ;

Baker, David .

NATURE, 2016, 537 (7620) :320-327

[10] The sequences of small proteins are not extensively optimized for rapid folding by natural selection [J].

Kim, DE ;

Gu, HD ;

Baker, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (09) :4982-4986

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