Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2

by: Ho K Fung, Christodoulos A Floudas, Martin S Taylor, Li Zhang, Dimitrios Morikis

Biophys. J., Vol. 94, No. 2. (15 January 2008), pp. 584-599.

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In this article, we introduce and apply our de novo protein design framework, which observes true backbone flexibility, to the redesign of human -defensin-2, a 41-residue cationic antimicrobial peptide of the innate immune system. The flexible design templates are generated using molecular dynamics simulations with both Generalized Born implicit solvation and explicit water molecules. These backbone templates were employed in addition to the x-ray crystal structure for designing human -defensin-2. The computational efficiency of our framework was demonstrated with the full-sequence design of the peptide with flexible backbone templates, corresponding to the mutation of all positions except the native cysteines. 10.1529/biophysj.107.110627

@article{Fung2008, abstract = {In this article, we introduce and apply our de novo protein design framework, which observes true backbone flexibility, to the redesign of human -defensin-2, a 41-residue cationic antimicrobial peptide of the innate immune system. The flexible design templates are generated using molecular dynamics simulations with both Generalized Born implicit solvation and explicit water molecules. These backbone templates were employed in addition to the x-ray crystal structure for designing human -defensin-2. The computational efficiency of our framework was demonstrated with the full-sequence design of the peptide with flexible backbone templates, corresponding to the mutation of all positions except the native cysteines. 10.1529/biophysj.107.110627}, author = {Fung, Ho K. and Floudas, Christodoulos A. and Taylor, Martin S. and Zhang, Li and Morikis, Dimitrios }, citeulike-article-id = {2972080}, doi = {http://dx.doi.org/10.1529/biophysj.107.110627}, journal = {Biophys. J.}, keywords = {protein\_design}, month = {January}, number = {2}, pages = {584--599}, posted-at = {2008-07-08 10:54:40}, priority = {2}, title = {Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2}, url = {http://dx.doi.org/10.1529/biophysj.107.110627}, volume = {94}, year = {2008} }

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TY - JOUR ID - Fung2008 L3 - citeulike-article-id:2972080 TI - Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2 JF - Biophys. J. VL - 94 IS - 2 SP - 584 EP - 599 N2 - In this article, we introduce and apply our de novo protein design framework, which observes true backbone flexibility, to the redesign of human -defensin-2, a 41-residue cationic antimicrobial peptide of the innate immune system. The flexible design templates are generated using molecular dynamics simulations with both Generalized Born implicit solvation and explicit water molecules. These backbone templates were employed in addition to the x-ray crystal structure for designing human -defensin-2. The computational efficiency of our framework was demonstrated with the full-sequence design of the peptide with flexible backbone templates, corresponding to the mutation of all positions except the native cysteines. 10.1529/biophysj.107.110627 KW - protein_design AU - Fung, Ho AU - Floudas, Christodoulos AU - Taylor, Martin AU - Zhang, Li AU - Morikis, Dimitrios PY - 2008/01/15/ UR - http://dx.doi.org/10.1529/biophysj.107.110627 ER -

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