Literature DB >> 30746840

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

David Baker1.   

Abstract

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.
© 2019 The Protein Society.

Keywords:  computational modeling; protein design; protein folding

Year:  2019        PMID： 30746840      PMCID： PMC6423711          DOI： 10.1002/pro.3588

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  18 in total

1.  A protein-folding reaction under kinetic control.

Authors:  D Baker; J L Sohl; D A Agard
Journal:  Nature       Date:  1992-03-19       Impact factor: 49.962

2.  Programmable design of orthogonal protein heterodimers.

Authors:  Zibo Chen; Scott E Boyken; Mengxuan Jia; Florian Busch; David Flores-Solis; Matthew J Bick; Peilong Lu; Zachary L VanAernum; Aniruddha Sahasrabuddhe; Robert A Langan; Sherry Bermeo; T J Brunette; Vikram Khipple Mulligan; Lauren P Carter; Frank DiMaio; Nikolaos G Sgourakis; Vicki H Wysocki; David Baker
Journal:  Nature       Date:  2018-12-19       Impact factor: 49.962

3.  Functional rapidly folding proteins from simplified amino acid sequences.

Authors:  D S Riddle; J V Santiago; S T Bray-Hall; N Doshi; V P Grantcharova; Q Yi; D Baker
Journal:  Nat Struct Biol       Date:  1997-10

Review 4.  The coming of age of de novo protein design.

Authors:  Po-Ssu Huang; Scott E Boyken; David Baker
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

5.  Comprehensive computational design of ordered peptide macrocycles.

Authors:  Parisa Hosseinzadeh; Gaurav Bhardwaj; Vikram Khipple Mulligan; Matthew D Shortridge; Timothy W Craven; Fátima Pardo-Avila; Stephen A Rettie; David E Kim; Daniel-Adriano Silva; Yehia M Ibrahim; Ian K Webb; John R Cort; Joshua N Adkins; Gabriele Varani; David Baker
Journal:  Science       Date:  2017-12-15       Impact factor: 47.728

6.  Protein structure determination using metagenome sequence data.

Authors:  Sergey Ovchinnikov; Hahnbeom Park; Neha Varghese; Po-Ssu Huang; Georgios A Pavlopoulos; David E Kim; Hetunandan Kamisetty; Nikos C Kyrpides; David Baker
Journal:  Science       Date:  2017-01-20       Impact factor: 47.728

7.  Principles for designing proteins with cavities formed by curved β sheets.

Authors:  Enrique Marcos; Benjamin Basanta; Tamuka M Chidyausiku; Yuefeng Tang; Gustav Oberdorfer; Gaohua Liu; G V T Swapna; Rongjin Guan; Daniel-Adriano Silva; Jiayi Dou; Jose Henrique Pereira; Rong Xiao; Banumathi Sankaran; Peter H Zwart; Gaetano T Montelione; David Baker
Journal:  Science       Date:  2017-01-13       Impact factor: 47.728

8.  Accurate design of megadalton-scale two-component icosahedral protein complexes.

Authors:  Jacob B Bale; Shane Gonen; Yuxi Liu; William Sheffler; Daniel Ellis; Chantz Thomas; Duilio Cascio; Todd O Yeates; Tamir Gonen; Neil P King; David Baker
Journal:  Science       Date:  2016-07-22       Impact factor: 47.728

9.  Exploring the repeat protein universe through computational protein design.

Authors:  T J Brunette; Fabio Parmeggiani; Po-Ssu Huang; Gira Bhabha; Damian C Ekiert; Susan E Tsutakawa; Greg L Hura; John A Tainer; David Baker
Journal:  Nature       Date:  2015-12-16       Impact factor: 49.962

10.  De novo design of a fluorescence-activating β-barrel.

Authors:  Jiayi Dou; Anastassia A Vorobieva; William Sheffler; Lindsey A Doyle; Hahnbeom Park; Matthew J Bick; Binchen Mao; Glenna W Foight; Min Yen Lee; Lauren A Gagnon; Lauren Carter; Banumathi Sankaran; Sergey Ovchinnikov; Enrique Marcos; Po-Ssu Huang; Joshua C Vaughan; Barry L Stoddard; David Baker
Journal:  Nature       Date:  2018-09-12       Impact factor: 49.962
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  35 in total

1.  Toward the computational design of protein crystals with improved resolution.

Authors:  Jeliazko R Jeliazkov; Aaron C Robinson; Bertrand García-Moreno E; James M Berger; Jeffrey J Gray
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-11-01       Impact factor: 7.652

Review 2.  Protein Engineering for Improving and Diversifying Natural Product Biosynthesis.

Authors:  Chenyi Li; Ruihua Zhang; Jian Wang; Lauren Marie Wilson; Yajun Yan
Journal:  Trends Biotechnol       Date:  2020-01-15       Impact factor: 19.536

Review 3.  Building machines with DNA molecules.

Authors:  Hamid Ramezani; Hendrik Dietz
Journal:  Nat Rev Genet       Date:  2019-10-21       Impact factor: 53.242

4.  Computationally Designed Cyclic Peptides Derived from an Antibody Loop Increase Breadth of Binding for Influenza Variants.

Authors:  Alexander M Sevy; Iuliia M Gilchuk; Benjamin P Brown; Nina G Bozhanova; Rachel Nargi; Mattie Jensen; Jens Meiler; James E Crowe
Journal:  Structure       Date:  2020-06-30       Impact factor: 5.006

Review 5.  Bioprospecting of microbial enzymes: current trends in industry and healthcare.

Authors:  Eswar Rao Tatta; Madangchanok Imchen; Jamseel Moopantakath; Ranjith Kumavath
Journal:  Appl Microbiol Biotechnol       Date:  2022-03-07       Impact factor: 4.813

Review 6.  Engineering spatiotemporal organization and dynamics in synthetic cells.

Authors:  Alessandro Groaz; Hossein Moghimianavval; Franco Tavella; Tobias W Giessen; Anthony G Vecchiarelli; Qiong Yang; Allen P Liu
Journal:  Wiley Interdiscip Rev Nanomed Nanobiotechnol       Date:  2020-11-21

7.  Expanding the space of protein geometries by computational design of de novo fold families.

Authors:  Xingjie Pan; Michael C Thompson; Yang Zhang; Lin Liu; James S Fraser; Mark J S Kelly; Tanja Kortemme
Journal:  Science       Date:  2020-08-28       Impact factor: 47.728

8.  The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics.

Authors:  Anthony T Bogetti; Maria F Presti; Stewart N Loh; Lillian T Chong
Journal:  J Phys Chem B       Date:  2021-07-29       Impact factor: 2.991

9.  De novo design of modular and tunable protein biosensors.

Authors:  Alfredo Quijano-Rubio; Hsien-Wei Yeh; Jooyoung Park; Hansol Lee; Robert A Langan; Scott E Boyken; Marc J Lajoie; Longxing Cao; Cameron M Chow; Marcos C Miranda; Jimin Wi; Hyo Jeong Hong; Lance Stewart; Byung-Ha Oh; David Baker
Journal:  Nature       Date:  2021-01-27       Impact factor: 49.962

10.  Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning.

Authors:  Elizabeth K Unger; Jacob P Keller; Michael Altermatt; Ruqiang Liang; Aya Matsui; Chunyang Dong; Olivia J Hon; Zi Yao; Junqing Sun; Samba Banala; Meghan E Flanigan; David A Jaffe; Samantha Hartanto; Jane Carlen; Grace O Mizuno; Phillip M Borden; Amol V Shivange; Lindsay P Cameron; Steffen Sinning; Suzanne M Underhill; David E Olson; Susan G Amara; Duncan Temple Lang; Gary Rudnick; Jonathan S Marvin; Luke D Lavis; Henry A Lester; Veronica A Alvarez; Andrew J Fisher; Jennifer A Prescher; Thomas L Kash; Vladimir Yarov-Yarovoy; Viviana Gradinaru; Loren L Looger; Lin Tian
Journal:  Cell       Date:  2020-12-16       Impact factor: 41.582
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