Literature DB >> 27629638

The coming of age of de novo protein design.

Po-Ssu Huang1,2,3, Scott E Boyken1,2,4, David Baker1,2,4.   

Abstract

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.

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Year:  2016        PMID: 27629638     DOI: 10.1038/nature19946

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  83 in total

1.  Native protein sequences are close to optimal for their structures.

Authors:  B Kuhlman; D Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2000-09-12       Impact factor: 11.205

Review 2.  Protein binding specificity versus promiscuity.

Authors:  Gideon Schreiber; Amy E Keating
Journal:  Curr Opin Struct Biol       Date:  2010-11-09       Impact factor: 6.809

3.  Learning generative models for protein fold families.

Authors:  Sivaraman Balakrishnan; Hetunandan Kamisetty; Jaime G Carbonell; Su-In Lee; Christopher James Langmead
Journal:  Proteins       Date:  2011-01-25

4.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.

Authors:  J W Ponder; F M Richards
Journal:  J Mol Biol       Date:  1987-02-20       Impact factor: 5.469

5.  Computational design of ligand-binding proteins with high affinity and selectivity.

Authors:  Christine E Tinberg; Sagar D Khare; Jiayi Dou; Lindsey Doyle; Jorgen W Nelson; Alberto Schena; Wojciech Jankowski; Charalampos G Kalodimos; Kai Johnsson; Barry L Stoddard; David Baker
Journal:  Nature       Date:  2013-09-04       Impact factor: 49.962

Review 6.  The structure and function of G-protein-coupled receptors.

Authors:  Daniel M Rosenbaum; Søren G F Rasmussen; Brian K Kobilka
Journal:  Nature       Date:  2009-05-21       Impact factor: 49.962

7.  Self-assembling cages from coiled-coil peptide modules.

Authors:  Jordan M Fletcher; Robert L Harniman; Frederick R H Barnes; Aimee L Boyle; Andrew Collins; Judith Mantell; Thomas H Sharp; Massimo Antognozzi; Paula J Booth; Noah Linden; Mervyn J Miles; Richard B Sessions; Paul Verkade; Derek N Woolfson
Journal:  Science       Date:  2013-04-11       Impact factor: 47.728

8.  CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.

Authors:  Christopher W Wood; Marc Bruning; Amaurys Á Ibarra; Gail J Bartlett; Andrew R Thomson; Richard B Sessions; R Leo Brady; Derek N Woolfson
Journal:  Bioinformatics       Date:  2014-07-26       Impact factor: 6.937

9.  Design of a hyperstable 60-subunit protein dodecahedron. [corrected].

Authors:  Yang Hsia; Jacob B Bale; Shane Gonen; Dan Shi; William Sheffler; Kimberly K Fong; Una Nattermann; Chunfu Xu; Po-Ssu Huang; Rashmi Ravichandran; Sue Yi; Trisha N Davis; Tamir Gonen; Neil P King; David Baker
Journal:  Nature       Date:  2016-06-15       Impact factor: 49.962

10.  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

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  259 in total

1.  Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.

Authors:  Abigail R Lambert; Jazmine P Hallinan; Rachel Werther; Dawid Głów; Barry L Stoddard
Journal:  Structure       Date:  2020-04-30       Impact factor: 5.006

2.  Simple yet functional phosphate-loop proteins.

Authors:  Maria Luisa Romero Romero; Fan Yang; Yu-Ru Lin; Agnes Toth-Petroczy; Igor N Berezovsky; Alexander Goncearenco; Wen Yang; Alon Wellner; Fanindra Kumar-Deshmukh; Michal Sharon; David Baker; Gabriele Varani; Dan S Tawfik
Journal:  Proc Natl Acad Sci U S A       Date:  2018-11-30       Impact factor: 11.205

3.  Noncoded Amino Acids in de Novo Metalloprotein Design: Controlling Coordination Number and Catalysis.

Authors:  Karl J Koebke; Vincent L Pecoraro
Journal:  Acc Chem Res       Date:  2019-04-01       Impact factor: 22.384

4.  Multi-scale structural analysis of proteins by deep semantic segmentation.

Authors:  Raphael R Eguchi; Po-Ssu Huang
Journal:  Bioinformatics       Date:  2020-03-01       Impact factor: 6.937

Review 5.  Lectin engineering: the possible and the actual.

Authors:  Jun Hirabayashi; Ryoichi Arai
Journal:  Interface Focus       Date:  2019-02-15       Impact factor: 3.906

Review 6.  What has de novo protein design taught us about protein folding and biophysics?

Authors:  David Baker
Journal:  Protein Sci       Date:  2019-04       Impact factor: 6.725

Review 7.  The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins.

Authors:  Rajeswari Appadurai; Vladimir N Uversky; Anand Srivastava
Journal:  J Membr Biol       Date:  2019-05-28       Impact factor: 1.843

8.  Computational explorations in the space of one-component crystals.

Authors:  Jonathan P K Doye; Eva G Noya
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-08       Impact factor: 11.205

9.  Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers.

Authors:  Cangjie Yang; Kevin B Wu; Yu Deng; Jingsong Yuan; Jia Niu
Journal:  ACS Macro Lett       Date:  2021-01-20       Impact factor: 6.903

Review 10.  Biomolecular Assemblies: Moving from Observation to Predictive Design.

Authors:  Corey J Wilson; Andreas S Bommarius; Julie A Champion; Yury O Chernoff; David G Lynn; Anant K Paravastu; Chen Liang; Ming-Chien Hsieh; Jennifer M Heemstra
Journal:  Chem Rev       Date:  2018-10-03       Impact factor: 60.622

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