Literature DB >> 29243094

Hierarchical design of artificial proteins and complexes toward synthetic structural biology.

Ryoichi Arai1,2,3,4.   

Abstract

In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.

Entities:  

Keywords:  Artificial protein and complex; Combinatorial library; Computational design; Directed evolution; Hierarchical design; Protein engineering

Year:  2017        PMID: 29243094      PMCID: PMC5899735          DOI: 10.1007/s12551-017-0376-1

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  167 in total

1.  Domain-swapped dimeric structure of a stable and functional de novo four-helix bundle protein, WA20.

Authors:  Ryoichi Arai; Naoya Kobayashi; Akiho Kimura; Takaaki Sato; Kyoko Matsuo; Anna F Wang; Jesse M Platt; Luke H Bradley; Michael H Hecht
Journal:  J Phys Chem B       Date:  2012-04-10       Impact factor: 2.991

Review 2.  Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems.

Authors:  Christopher J Hipolito; Hiroaki Suga
Journal:  Curr Opin Chem Biol       Date:  2012-03-06       Impact factor: 8.822

3.  Directed evolution of the peroxidase activity of a de novo-designed protein.

Authors:  Shona C Patel; Michael H Hecht
Journal:  Protein Eng Des Sel       Date:  2012-06-03       Impact factor: 1.650

Review 4.  Macromolecular modeling with rosetta.

Authors:  Rhiju Das; David Baker
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

5.  Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning.

Authors:  Yasuhiro Fujino; Risako Fujita; Kouichi Wada; Kotomi Fujishige; Takashi Kanamori; Lindsey Hunt; Yoshihiro Shimizu; Takuya Ueda
Journal:  Biochem Biophys Res Commun       Date:  2012-10-26       Impact factor: 3.575

Review 6.  Designer three-dimensional DNA architectures.

Authors:  Yonggang Ke
Journal:  Curr Opin Struct Biol       Date:  2014-08-11       Impact factor: 6.809

7.  Principles of assembly reveal a periodic table of protein complexes.

Authors:  Sebastian E Ahnert; Joseph A Marsh; Helena Hernández; Carol V Robinson; Sarah A Teichmann
Journal:  Science       Date:  2015-12-11       Impact factor: 47.728

Review 8.  Deep sequencing methods for protein engineering and design.

Authors:  Emily E Wrenbeck; Matthew S Faber; Timothy A Whitehead
Journal:  Curr Opin Struct Biol       Date:  2016-11-22       Impact factor: 6.809

9.  Rational design of heterodimeric protein using domain swapping for myoglobin.

Authors:  Ying-Wu Lin; Satoshi Nagao; Mohan Zhang; Yasuhito Shomura; Yoshiki Higuchi; Shun Hirota
Journal:  Angew Chem Int Ed Engl       Date:  2014-11-04       Impact factor: 15.336

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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  8 in total

Review 1.  Lectin engineering: the possible and the actual.

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

2.  Employing 25-Residue Docking Motifs from Modular Polyketide Synthases as Orthogonal Protein Connectors.

Authors:  Jessica L Meinke; Anna J Simon; Drew T Wagner; Barrett R Morrow; Shaochen You; Andrew D Ellington; Adrian T Keatinge-Clay
Journal:  ACS Synth Biol       Date:  2019-09-12       Impact factor: 5.110

3.  Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday.

Authors:  Damien Hall; Junichi Takagi; Haruki Nakamura
Journal:  Biophys Rev       Date:  2018-03-02

Review 4.  Biological Nanopores: Engineering on Demand.

Authors:  Ana Crnković; Marija Srnko; Gregor Anderluh
Journal:  Life (Basel)       Date:  2021-01-05

5.  Rational thermostabilisation of four-helix bundle dimeric de novo proteins.

Authors:  Shin Irumagawa; Kaito Kobayashi; Yutaka Saito; Takeshi Miyata; Mitsuo Umetsu; Tomoshi Kameda; Ryoichi Arai
Journal:  Sci Rep       Date:  2021-04-06       Impact factor: 4.379

Review 6.  Yeast-Based Biosensors: Current Applications and New Developments.

Authors:  Helene Martin-Yken
Journal:  Biosensors (Basel)       Date:  2020-05-13

7.  Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages.

Authors:  James F Ross; Gemma C Wildsmith; Michael Johnson; Daniel L Hurdiss; Kristian Hollingsworth; Rebecca F Thompson; Majid Mosayebi; Chi H Trinh; Emanuele Paci; Arwen R Pearson; Michael E Webb; W Bruce Turnbull
Journal:  J Am Chem Soc       Date:  2019-03-21       Impact factor: 15.419

8.  Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans.

Authors:  Shin Irumagawa; Keiko Hiemori; Sayoko Saito; Hiroaki Tateno; Ryoichi Arai
Journal:  Int J Mol Sci       Date:  2022-01-08       Impact factor: 5.923

  8 in total

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