Literature DB >> 18710226

Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays.

Karen A McAllister1, Hongling Zou, Frank V Cochran, Gretchen M Bender, Alessandro Senes, H Christopher Fry, Vikas Nanda, Patricia A Keenan, James D Lear, Jeffery G Saven, Michael J Therien, J Kent Blasie, William F DeGrado.   

Abstract

We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors.

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Year:  2008        PMID: 18710226      PMCID: PMC3663296          DOI: 10.1021/ja800697g

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


  9 in total

1.  Determination of the sedimentation coefficient distribution by least-squares boundary modeling.

Authors:  P Schuck; P Rossmanith
Journal:  Biopolymers       Date:  2000-10-15       Impact factor: 2.505

Review 2.  De novo design and structural characterization of proteins and metalloproteins.

Authors:  W F DeGrado; C M Summa; V Pavone; F Nastri; A Lombardi
Journal:  Annu Rev Biochem       Date:  1999       Impact factor: 23.643

Review 3.  Engineering novel metalloproteins: design of metal-binding sites into native protein scaffolds.

Authors:  Y Lu; S M Berry; T D Pfister
Journal:  Chem Rev       Date:  2001-10       Impact factor: 60.622

4.  D(n)-symmetrical tertiary templates for the design of tubular proteins.

Authors:  B North; C M Summa; G Ghirlanda; W F DeGrado
Journal:  J Mol Biol       Date:  2001-08-31       Impact factor: 5.469

Review 5.  Models of the bis-histidine-ligated electron-transferring cytochromes. Comparative geometric and electronic structure of low-spin ferro- and ferrihemes.

Authors:  F Ann Walker
Journal:  Chem Rev       Date:  2004-02       Impact factor: 60.622

6.  Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra.

Authors:  E A Berry; B L Trumpower
Journal:  Anal Biochem       Date:  1987-02-15       Impact factor: 3.365

7.  Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor.

Authors:  Frank V Cochran; Sophia P Wu; Wei Wang; Vikas Nanda; Jeffery G Saven; Michael J Therien; William F DeGrado
Journal:  J Am Chem Soc       Date:  2005-02-09       Impact factor: 15.419

8.  Theoretical analysis of the porphyrin-porphyrin exciton interaction in circular dichroism spectra of dimeric tetraarylporphyrins.

Authors:  Gennaro Pescitelli; Sven Gabriel; Yuekui Wang; Jörg Fleischhauer; Robert W Woody; Nina Berova
Journal:  J Am Chem Soc       Date:  2003-06-25       Impact factor: 15.419

9.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

  9 in total
  21 in total

Review 1.  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

2.  A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering.

Authors:  Aaron W Reinke; Robert A Grant; Amy E Keating
Journal:  J Am Chem Soc       Date:  2010-05-05       Impact factor: 15.419

3.  Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides.

Authors:  Douglas H Pike; Vikas Nanda
Journal:  Biopolymers       Date:  2015-07       Impact factor: 2.505

Review 4.  Computational design of membrane proteins.

Authors:  Jose Manuel Perez-Aguilar; Jeffery G Saven
Journal:  Structure       Date:  2012-01-11       Impact factor: 5.006

5.  Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides.

Authors:  Olga Iranzo; Saumen Chakraborty; Lars Hemmingsen; Vincent L Pecoraro
Journal:  J Am Chem Soc       Date:  2010-12-16       Impact factor: 15.419

6.  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

7.  Heterotrimeric coiled coils with core residue urea side chains.

Authors:  Maria L Diss; Alan J Kennan
Journal:  J Org Chem       Date:  2008-12-19       Impact factor: 4.354

Review 8.  Strategies to control the binding mode of de novo designed protein interactions.

Authors:  Bryan S Der; Brian Kuhlman
Journal:  Curr Opin Struct Biol       Date:  2013-05-31       Impact factor: 6.809

9.  Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore.

Authors:  H Christopher Fry; Andreas Lehmann; Louise E Sinks; Inge Asselberghs; Andrey Tronin; Venkata Krishnan; J Kent Blasie; Koen Clays; William F DeGrado; Jeffery G Saven; Michael J Therien
Journal:  J Am Chem Soc       Date:  2013-09-05       Impact factor: 15.419

Review 10.  Structural principles for computational and de novo design of 4Fe-4S metalloproteins.

Authors:  Vikas Nanda; Stefan Senn; Douglas H Pike; Agustina Rodriguez-Granillo; Will A Hansen; Sagar D Khare; Dror Noy
Journal:  Biochim Biophys Acta       Date:  2015-10-09
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