The coming of age of de novo protein design

被引:1019
作者
Huang, Po-Ssu [1 ,2 ,3 ,4 ]
Boyken, Scott E. [1 ,2 ,3 ]
Baker, David [1 ,2 ,3 ]
机构
[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA
[2] Univ Washington, Inst Prot Design, Seattle, WA 98195 USA
[3] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA
[4] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA
关键词
COMPUTATIONAL DESIGN; REPEAT-PROTEIN; ACCURATE DESIGN; SEQUENCE; DNA; OLIGOMERS; EVOLUTION; ENZYMES; PACKING; MODEL;
D O I
10.1038/nature19946
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
There are 20(200) possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range of structures can be designed from scratch with atomic-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnology.
引用
收藏
页码:320 / 327
页数:8
相关论文
共 85 条
[51]   Principles for designing ideal protein structures [J].
Koga, Nobuyasu ;
Tatsumi-Koga, Rie ;
Liu, Gaohua ;
Xiao, Rong ;
Acton, Thomas B. ;
Montelione, Gaetano T. ;
Baker, David .
NATURE, 2012, 491 (7423) :222-227
[52]   De novo enzymes by computational design [J].
Kries, Hajo ;
Blomberg, Rebecca ;
Hilvert, Donald .
CURRENT OPINION IN CHEMICAL BIOLOGY, 2013, 17 (02) :221-228
[53]   Native protein sequences are close to optimal for their structures [J].
Kuhlman, B ;
Baker, D .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (19) :10383-10388
[54]   Design of a novel globular protein fold with atomic-level accuracy [J].
Kuhlman, B ;
Dantas, G ;
Ireton, GC ;
Varani, G ;
Stoddard, BL ;
Baker, D .
SCIENCE, 2003, 302 (5649) :1364-1368
[55]  
Leaver-Fay A, 2011, METHOD ENZYMOL, P545, DOI [10.1016/S0076-6879(11)87019-9, 10.1016/B978-0-12-381270-4.00019-6]
[56]   Control over overall shape and size in de novo designed proteins [J].
Lin, Yu-Ru ;
Koga, Nobuyasu ;
Tatsumi-Koga, Rie ;
Liu, Gaohua ;
Clouser, Amanda F. ;
Montelione, Gaetano T. ;
Baker, David .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (40) :E5478-E5485
[57]   The enabled state of DNA nanotechnology [J].
Linko, Veikko ;
Dietz, Hendrik .
CURRENT OPINION IN BIOTECHNOLOGY, 2013, 24 (04) :555-561
[58]   An accurate binding interaction model in de novo computational protein design of interactions: If you build it, they will bind [J].
London, Nir ;
Ambroggio, Xavier .
JOURNAL OF STRUCTURAL BIOLOGY, 2014, 185 (02) :136-146
[59]   Computational design and experimental verification of a symmetric protein homodimer [J].
Mou, Yun ;
Huang, Po-Ssu ;
Hsu, Fang-Ciao ;
Huang, Shing-Jong ;
Mayo, Stephen L. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (34) :10714-10719
[60]   De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic [J].
Murphy, Grant S. ;
Greisman, Jack B. ;
Hecht, Michael H. .
JOURNAL OF MOLECULAR BIOLOGY, 2016, 428 (02) :399-411