Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations
Abstract
Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. Additionally, for conformations along transition regions-$$\phi$$ from -60 to 60°-a very good agreement with representative high-resolution experimental X-ray (≤1.5 Å) protein structures is obtained for both backbone C-1 -N-Cα angle and the nonbonded O-1 …C distance, while "standard geometry" leads to the "clashing" of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high-energy or unusual regions.
- Authors:
-
[1];
[2]
- Shanghai Univ. (China)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1735533
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proteins
- Additional Journal Information:
- Journal Volume: 86; Journal Issue: 3; Journal ID: ISSN 0887-3585
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; backbone; B3LYP-D3; DFT; local structure; poly-peptides; protein; unusual arrangements
Citation Formats
Jiang, Zhongming, Biczysko, Malgorzata, and Moriarty, Nigel W. Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations. United States: N. p., 2018.
Web. doi:10.1002/prot.25451.
Jiang, Zhongming, Biczysko, Malgorzata, & Moriarty, Nigel W. Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations. United States. https://doi.org/10.1002/prot.25451
Jiang, Zhongming, Biczysko, Malgorzata, and Moriarty, Nigel W. Fri .
"Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations". United States. https://doi.org/10.1002/prot.25451. https://www.osti.gov/servlets/purl/1735533.
@article{osti_1735533,
title = {Accurate geometries for “Mountain pass” regions of the Ramachandran plot using quantum chemical calculations},
author = {Jiang, Zhongming and Biczysko, Malgorzata and Moriarty, Nigel W.},
abstractNote = {Unusual local arrangements of protein in Ramachandran space are not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. In contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. Additionally, for conformations along transition regions-$\phi$ from -60 to 60°-a very good agreement with representative high-resolution experimental X-ray (≤1.5 Å) protein structures is obtained for both backbone C-1 -N-Cα angle and the nonbonded O-1 …C distance, while "standard geometry" leads to the "clashing" of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high-energy or unusual regions.},
doi = {10.1002/prot.25451},
journal = {Proteins},
number = 3,
volume = 86,
place = {United States},
year = {Fri Jan 12 00:00:00 EST 2018},
month = {Fri Jan 12 00:00:00 EST 2018}
}
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Data from: Accurate geometries for “mountain pass” regions of the Ramachandran plot using quantum chemical calculations
dataset, January 2019
- Jiang, Zhongming; Biczysko, Malgorzata; Moriarty, Nigel W.
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Data from: Accurate geometries for “mountain pass” regions of the Ramachandran plot using quantum chemical calculations
dataset, January 2019
- Jiang, Zhongming; Biczysko, Malgorzata; Moriarty, Nigel W.
- Dryad
Works referencing / citing this record:
Data from: Accurate geometries for “mountain pass” regions of the Ramachandran plot using quantum chemical calculations
dataset, January 2019
- Jiang, Zhongming; Biczysko, Malgorzata; Moriarty, Nigel W.
- Dryad
Data from: Accurate geometries for “mountain pass” regions of the Ramachandran plot using quantum chemical calculations
dataset, January 2019
- Jiang, Zhongming; Biczysko, Malgorzata; Moriarty, Nigel W.
- Dryad
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