Literature DB >> 17691729

De novo design of a single-chain diphenylporphyrin metalloprotein.

Gretchen M Bender1, Andreas Lehmann, Hongling Zou, Hong Cheng, H Christopher Fry, Don Engel, Michael J Therien, J Kent Blasie, Heinrich Roder, Jeffrey G Saven, William F DeGrado.   

Abstract

We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes.

Entities:  

Mesh:

Substances:

Year:  2007        PMID: 17691729      PMCID: PMC2542652          DOI: 10.1021/ja071199j

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  25 in total

1.  Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

Authors:  H Kono; J G Saven
Journal:  J Mol Biol       Date:  2001-02-23       Impact factor: 5.469

2.  X-ray structure of a maquette scaffold.

Authors:  Steve S Huang; Brian R Gibney; Steven E Stayrook; P Leslie Dutton; Mitchell Lewis
Journal:  J Mol Biol       Date:  2003-02-28       Impact factor: 5.469

Review 3.  Hydrophilic to amphiphilic design in redox protein maquettes.

Authors:  Bohdana M Discher; Ronald L Koder; Christopher C Moser; P Leslie Dutton
Journal:  Curr Opin Chem Biol       Date:  2003-12       Impact factor: 8.822

4.  Amino acid propensities are position-dependent throughout the length of alpha-helices.

Authors:  Donald E Engel; William F DeGrado
Journal:  J Mol Biol       Date:  2004-04-09       Impact factor: 5.469

Review 5.  Expanding the genetic code.

Authors:  Lei Wang; Jianming Xie; Peter G Schultz
Journal:  Annu Rev Biophys Biomol Struct       Date:  2006

6.  Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations.

Authors:  Hongling Zou; Joseph Strzalka; Ting Xu; Andrey Tronin; J Kent Blasie
Journal:  J Phys Chem B       Date:  2007-01-27       Impact factor: 2.991

7.  Incorporation of designed extended chromophores into amphiphilic 4-helix bundle peptides for nonlinear optical biomolecular materials.

Authors:  Ting Xu; Sophia P Wu; Ivan Miloradovic; Michael J Therien; J Kent Blasie
Journal:  Nano Lett       Date:  2006-11       Impact factor: 11.189

8.  Heme redox potential control in de novo designed four-alpha-helix bundle proteins.

Authors:  J M Shifman; B R Gibney; R E Sharp; P L Dutton
Journal:  Biochemistry       Date:  2000-12-05       Impact factor: 3.162

9.  De novo design of a redox-active minimal rubredoxin mimic.

Authors:  Vikas Nanda; Michael M Rosenblatt; Artur Osyczka; Hidetoshi Kono; Zelleka Getahun; P Leslie Dutton; Jeffery G Saven; William F Degrado
Journal:  J Am Chem Soc       Date:  2005-04-27       Impact factor: 15.419

10.  De novo designed cyclic-peptide heme complexes.

Authors:  Michael M Rosenblatt; Jiangyun Wang; Kenneth S Suslick
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-31       Impact factor: 11.205

View more
  43 in total

1.  DNA targeting and cleavage by an engineered metalloprotein dimer.

Authors:  Siu Wah Wong-Deyrup; Charulata Prasannan; Cynthia M Dupureur; Sonya J Franklin
Journal:  J Biol Inorg Chem       Date:  2011-11-25       Impact factor: 3.358

2.  Computational design of a protein crystal.

Authors:  Christopher J Lanci; Christopher M MacDermaid; Seung-gu Kang; Rudresh Acharya; Benjamin North; Xi Yang; X Jade Qiu; William F DeGrado; Jeffery G Saven
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-25       Impact factor: 11.205

3.  Improving computational protein design by using structure-derived sequence profile.

Authors:  Liang Dai; Yuedong Yang; Hyung Rae Kim; Yaoqi Zhou
Journal:  Proteins       Date:  2010-08-01

4.  Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein.

Authors:  Lei Zhang; J L Ross Anderson; Ismail Ahmed; Jessica A Norman; Christopher Negron; Andrew C Mutter; P Leslie Dutton; Ronald L Koder
Journal:  Biochemistry       Date:  2011-11-08       Impact factor: 3.162

Review 5.  Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins.

Authors:  Jeffery G Saven
Journal:  Curr Opin Chem Biol       Date:  2011-04-12       Impact factor: 8.822

6.  Alteration of enzyme specificity by computational loop remodeling and design.

Authors:  Paul M Murphy; Jill M Bolduc; Jasmine L Gallaher; Barry L Stoddard; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-21       Impact factor: 11.205

7.  Elementary tetrahelical protein design for diverse oxidoreductase functions.

Authors:  Tammer A Farid; Goutham Kodali; Lee A Solomon; Bruce R Lichtenstein; Molly M Sheehan; Bryan A Fry; Chris Bialas; Nathan M Ennist; Jessica A Siedlecki; Zhenyu Zhao; Matthew A Stetz; Kathleen G Valentine; J L Ross Anderson; A Joshua Wand; Bohdana M Discher; Christopher C Moser; P Leslie Dutton
Journal:  Nat Chem Biol       Date:  2013-10-13       Impact factor: 15.040

Review 8.  Energy functions in de novo protein design: current challenges and future prospects.

Authors:  Zhixiu Li; Yuedong Yang; Jian Zhan; Liang Dai; Yaoqi Zhou
Journal:  Annu Rev Biophys       Date:  2013-02-28       Impact factor: 12.981

9.  Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein.

Authors:  Lei Zhang; Eskil M E Andersen; Abdelahad Khajo; Richard S Magliozzo; Ronald L Koder
Journal:  Biochemistry       Date:  2013-01-10       Impact factor: 3.162

10.  Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.

Authors:  Chu Wang; Robert Vernon; Oliver Lange; Michael Tyka; David Baker
Journal:  Protein Sci       Date:  2010-03       Impact factor: 6.725

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.