Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes

2017 ◽  
Vol 13 (5) ◽  
pp. 2098-2111 ◽  
Author(s):  
Cui Liu ◽  
Yue Li ◽  
Bing-Yu Han ◽  
Li-Dong Gong ◽  
Li-Nan Lu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Force Field ◽  
Amino Acid Residue ◽  
Base Pairs ◽  
Polarization Force

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

scholarly journals Kinetic characterization of yeast alcohol dehydrogenases. Amino acid residue 294 and substrate specificity.

1987 ◽  
Vol 262 (8) ◽  
pp. 3754-3761
Author(s):  
A.J. Ganzhorn ◽  
D.W. Green ◽  
A.D. Hershey ◽  
R.M. Gould ◽  
B.V. Plapp
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Amino Acid Residue ◽  
Kinetic Characterization ◽  
Alcohol Dehydrogenases

scholarly journals Amino Acid Residue at the 165th Position Tunes Eyfp Chromophore Maturation. A Structure-Based Design

2021 ◽  
Author(s):  
Nadya V. Pletneva ◽  
Eugene G. Maksimov ◽  
Elena A. Protasova ◽  
Anastasia V. Mamontova ◽  
Tatiana R. Simonyan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue
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