Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids

2021 ◽  
Author(s):  
John P. Stoppelman ◽  
Tracey T. Ng ◽  
Paul S. Nerenberg ◽  
Lee-Ping Wang
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Force Field Parameters ◽  
Development And Validation

scholarly journals Development and Validation of the QUBE Protein Force Field

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations ◽  
Complete Protein ◽  
Development And Validation

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the QUantum mechanical BEspoke (QUBE) force field by deriving non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

Development and Validation of the QUBE Protein Force Field

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations ◽  
Complete Protein ◽  
Development And Validation

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the QUantum mechanical BEspoke (QUBE) force field by deriving non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

Validation of molecular force field parameters for peptides including isomerized amino acids

Chirality ◽  
2018 ◽  
Vol 30 (4) ◽  
pp. 332-341 ◽  
Author(s):  
Akifumi Oda ◽  
Tomoki Nakayoshi ◽  
Shuichi Fukuyoshi ◽  
Eiji Kurimoto ◽  
Noriyuki Yamaotsu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Molecular Force ◽  
Force Field Parameters ◽  
Molecular Force Field

Development and Validation of the QUBE Protein Force Field

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations ◽  
Complete Protein ◽  
Development And Validation

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the QUantum mechanical BEspoke (QUBE) force field by deriving non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

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