Literature DB >> 21544231

Computational protein design: Advances in the design and redesign of biomolecular nanostructures.

Jeffery G Saven1.   

Abstract

Computational protein design facilitates the continued development of methods for the design of biomolecular structure, sequence and function. Recent applications include the design of novel protein sequences and structures, proteins incorporating nonbiological components, protein assemblies, soluble variants of membrane proteins, and proteins that modulate membrane function.

Entities:  

Year:  2010        PMID： 21544231      PMCID： PMC3085470          DOI： 10.1016/j.cocis.2009.06.002

Source DB:  PubMed          Journal:  Curr Opin Colloid Interface Sci        ISSN： 1359-0294            Impact factor:   6.448


  29 in total

1.  Artificial diiron proteins: from structure to function.

Authors:  Jennifer R Calhoun; Flavia Nastri; Ornella Maglio; Vincenzo Pavone; Angela Lombardi; William F DeGrado
Journal:  Biopolymers       Date:  2005       Impact factor: 2.505

2.  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

Review 3.  Full-sequence computational design and solution structure of a thermostable protein variant.

Authors:  Premal S Shah; Geoffrey K Hom; Scott A Ross; Jonathan Kyle Lassila; Karin A Crowhurst; Stephen L Mayo
Journal:  J Mol Biol       Date:  2007-06-16       Impact factor: 5.469

4.  Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops.

Authors:  Ornella Maglio; Flavia Nastri; Jennifer R Calhoun; Stephen Lahr; Herschel Wade; Vincenzo Pavone; William F DeGrado; Angela Lombardi
Journal:  J Biol Inorg Chem       Date:  2005-09-23       Impact factor: 3.358

5.  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

6.  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

7.  Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications.

Authors:  Eun Jung Choi; Jessica Mao; Stephen L Mayo
Journal:  Protein Sci       Date:  2007-04       Impact factor: 6.725

8.  Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

Authors:  Jennifer R Calhoun; Weixia Liu; Katrin Spiegel; Matteo Dal Peraro; Michael L Klein; Kathleen G Valentine; A Joshua Wand; William F DeGrado
Journal:  Structure       Date:  2008-02       Impact factor: 5.006

9.  Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework.

Authors:  Martin S Taylor; Ho K Fung; Rohit Rajgaria; Marta Filizola; Harel Weinstein; Christodoulos A Floudas
Journal:  Biophys J       Date:  2008-01-04       Impact factor: 4.033

10.  Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.

Authors:  Xiaozhen Hu; Huanchen Wang; Hengming Ke; Brian Kuhlman
Journal:  Structure       Date:  2008-12-10       Impact factor: 5.006
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  5 in total

1.  Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure.

Authors:  Marco Chino; Ornella Maglio; Flavia Nastri; Vincenzo Pavone; William F DeGrado; Angela Lombardi
Journal:  Eur J Inorg Chem       Date:  2015-07-06       Impact factor: 2.524

2.  Computational Design of PDZ-Peptide Binding.

Authors:  Nicolas Panel; Francesco Villa; Vaitea Opuu; David Mignon; Thomas Simonson
Journal:  Methods Mol Biol       Date:  2021

3.  Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

Authors:  Diana Fusco; Timothy J Barnum; Andrew E Bruno; Joseph R Luft; Edward H Snell; Sayan Mukherjee; Patrick Charbonneau
Journal:  PLoS One       Date:  2014-07-02       Impact factor: 3.240

4.  Molecular origin of drug release by water boiling inside carbon nanotubes from reactive molecular dynamics simulation and DFT perspectives.

Authors:  M Darvish Ganji; Sh Mirzaei; Z Dalirandeh
Journal:  Sci Rep       Date:  2017-07-05       Impact factor: 4.379

5.  De novo design and experimental characterization of ultrashort self-associating peptides.

Authors:  James Smadbeck; Kiat Hwa Chan; George A Khoury; Bo Xue; Robert C Robinson; Charlotte A E Hauser; Christodoulos A Floudas
Journal:  PLoS Comput Biol       Date:  2014-07-10       Impact factor: 4.475
  5 in total

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