Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field
The utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were u...
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| Format: | Article |
| Language: | English |
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Wiley
2010-01-01
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| Series: | Bioinorganic Chemistry and Applications |
| Online Access: | http://dx.doi.org/10.1155/2010/724210 |
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| author | Faina Ryvkin Frederick T. Greenaway |
| author_facet | Faina Ryvkin Frederick T. Greenaway |
| author_sort | Faina Ryvkin |
| collection | DOAJ |
| description | The utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were used to constrain all combinations of three histidine ligands to be within bonding distance of the copper and the best results were utilized as starting structures for the ESFF computations. All likely copper geometries were modeled, but the results showed only a small dependence on the geometrical model in that all resulted in a distorted square pyramidal geometry about the copper, some of the imidazole rings were poorly oriented for ligation to the Cu(II), and the copper-nitrogen bond distances were too long. The results suggest that ESFF should be used with caution for Cu(II) complexes where the copper-ligand bonds have significant covalency and when the ligands are not geometrically constrained to be planar. |
| format | Article |
| id | doaj-art-611a6a6168dd40be95835eaedcf58ce4 |
| institution | Kabale University |
| issn | 1565-3633 1687-479X |
| language | English |
| publishDate | 2010-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Bioinorganic Chemistry and Applications |
| spelling | doaj-art-611a6a6168dd40be95835eaedcf58ce42025-02-03T05:44:10ZengWileyBioinorganic Chemistry and Applications1565-36331687-479X2010-01-01201010.1155/2010/724210724210Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force FieldFaina Ryvkin0Frederick T. Greenaway1Department of Chemistry, Emmanuel College, Boston, MA 02115, USACarlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USAThe utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were used to constrain all combinations of three histidine ligands to be within bonding distance of the copper and the best results were utilized as starting structures for the ESFF computations. All likely copper geometries were modeled, but the results showed only a small dependence on the geometrical model in that all resulted in a distorted square pyramidal geometry about the copper, some of the imidazole rings were poorly oriented for ligation to the Cu(II), and the copper-nitrogen bond distances were too long. The results suggest that ESFF should be used with caution for Cu(II) complexes where the copper-ligand bonds have significant covalency and when the ligands are not geometrically constrained to be planar.http://dx.doi.org/10.1155/2010/724210 |
| spellingShingle | Faina Ryvkin Frederick T. Greenaway Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field Bioinorganic Chemistry and Applications |
| title | Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field |
| title_full | Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field |
| title_fullStr | Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field |
| title_full_unstemmed | Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field |
| title_short | Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field |
| title_sort | modeling cu ii binding to peptides using the extensible systematic force field |
| url | http://dx.doi.org/10.1155/2010/724210 |
| work_keys_str_mv | AT fainaryvkin modelingcuiibindingtopeptidesusingtheextensiblesystematicforcefield AT fredericktgreenaway modelingcuiibindingtopeptidesusingtheextensiblesystematicforcefield |