scholarly journals Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

2014 ◽  
Vol 10 (5) ◽  
pp. 2194-2203 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Andrei Niadzvedtski ◽  
Harold A. Scheraga ◽  
Adam Liwo
Keyword(s):  
Amino Acid ◽  
Force Field ◽  
Bond Angle ◽  
Coarse Grained ◽  
Amino Acid Residues

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 New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations

Plural Origins of Molecular Homochirality in Our Biota Part II. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides

1997 ◽  
Vol 52 (1-2) ◽  
pp. 89-96 ◽  
Author(s):  
Thereza Amélia Soares ◽  
Roberto Dias Lins ◽  
Ricardo Longo ◽  
Richard Garratt ◽  
Ricardo Ferreira
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Mechanics ◽  
Computer Simulations ◽  
The Other ◽  
Amino Acid Residues ◽  
Relative Stabilities ◽  
Amber Force Field ◽  
Cross Inhibition

Abstract By computer simulations -molecular mechanics and molecular dynamics with the amber force field (Weiner et al., (1986), J. Comp. Chem. 7, 2 30-252) -we have determined the stabilities of oligoribotide strands built with ᴅ -and ʟ-riboses, and of peptide chains with ᴅ -and ʟ-amino acid residues. In particular, complementary double-chains of oligoribotides were studied, since they are an important feature of the growing mechanism of modern nucleic acids. Peptide chains on the other hand, grow without need of a template. We found that mixed oligoribotides are less stable than homochiral ones, and that this chiral effect is less noticeable in peptide chains. The results support the interpretation that ʟ-riboses act as terminators to the template-assisted growth of oligo-r-Gᴅ (enantiomeric cross-inhibition; Joyce et al., (1987), Proc. Natl. Acad. Sci. USA 84, 4398-4402). Based on this effect, a chemical pathway is proposed which could, under assumed prebiotic conditions, bypass the hindrance of homochiral growth.

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

2017 ◽  
Vol 116 (5-6) ◽  
pp. 649-657 ◽  
Author(s):  
Kazutomo Kawaguchi ◽  
Satoshi Nakagawa ◽  
Isman Kurniawan ◽  
Koichi Kodama ◽  
Muhammad Saleh Arwansyah ◽  
...  
Keyword(s):  
Amino Acid ◽  
Effective Interaction ◽  
Coarse Grained ◽  
Amino Acid Residues ◽  
Coarse Grained Model

scholarly journals Evaluating Inositol phospholipid interactions with Inward Rectifier Potassium Channels and characterising their role in Disease

2020 ◽  
Author(s):  
Tanadet Pipatpolkai ◽  
Robin A. Corey ◽  
Peter Proks ◽  
Frances M. Ashcroft ◽  
Phillip J. Stansfeld
Keyword(s):  
Amino Acid ◽  
Neonatal Diabetes ◽  
Specific Protein ◽  
Coarse Grained ◽  
Congenital Hyperinsulinism ◽  
Amino Acid Residues ◽  
Inward Rectifier Potassium Channels ◽  
Lipid Species ◽  
Energy Perturbation ◽  
Good Agreement

AbstractMembrane proteins are frequently modulated by specific protein-lipid interactions. The activation of human inward rectifying potassium (hKir) channels by phosphoinositides (PI) has been well characterised. Here, we apply a coarse-grained molecular dynamics free-energy perturbation (CG-FEP) protocol to capture the energetics of binding of PI lipids to hKir channels. By using either a single- or multi-step approach, we establish a consistent value for the binding of PIP2 to hKir channels, relative to the binding of the bulk phosphatidylcholine phospholipid. Furthermore, by perturbing amino acid side chains on hKir6.2, we show that the neonatal diabetes mutation E179K increases PIP2 affinity, while the congenital hyperinsulinism mutation K67N results in a reduced affinity. We show good agreement with electrophysiological data where E179K exhibits a reduction in neomycin sensitivity, implying that PIP2 binds more tightly E179K channels. This illustrates the application of CG-FEP to compare affinities between lipid species, and for annotating amino acid residues.

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 Evaluating inositol phospholipid interactions with inward rectifier potassium channels and characterising their role in disease

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Tanadet Pipatpolkai ◽  
Robin A. Corey ◽  
Peter Proks ◽  
Frances M. Ashcroft ◽  
Phillip J. Stansfeld
Keyword(s):  
Amino Acid ◽  
Neonatal Diabetes ◽  
Specific Protein ◽  
Coarse Grained ◽  
Congenital Hyperinsulinism ◽  
Amino Acid Residues ◽  
Inward Rectifier Potassium Channels ◽  
Lipid Species ◽  
Energy Perturbation ◽  
Good Agreement

Abstract Membrane proteins are frequently modulated by specific protein-lipid interactions. The activation of human inward rectifying potassium (hKir) channels by phosphoinositides (PI) has been well characterised. Here, we apply a coarse-grained molecular dynamics free-energy perturbation (CG-FEP) protocol to capture the energetics of binding of PI lipids to hKir channels. By using either a single- or multi-step approach, we establish a consistent value for the binding of PIP2 to hKir channels, relative to the binding of the bulk phosphatidylcholine phospholipid. Furthermore, by perturbing amino acid side chains on hKir6.2, we show that the neonatal diabetes mutation E179K increases PIP2 affinity, while the congenital hyperinsulinism mutation K67N results in a reduced affinity. We show good agreement with electrophysiological data where E179K exhibits a reduction in neomycin sensitivity, implying that PIP2 binds more tightly E179K channels. This illustrates the application of CG-FEP to compare affinities between lipid species, and for annotating amino acid residues.

Do Molecular Dynamics Force Fields Accurately Model Ramachandran Distributions of Amino Acid Residues in Water?

2022 ◽  
Author(s):  
Brian Andrews ◽  
Jose Guerra ◽  
Reinhard Schweitzer-Stenner ◽  
Brigita Urbanc
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Intrinsically Disordered Proteins ◽  
Force Fields ◽  
Disordered Proteins ◽  
Amino Acid Residues ◽  
Intrinsically Disordered

Molecular dynamics (MD) is a powerful tool for studying intrinsically disordered proteins, however, its reliability depends on the accuracy of the force field. We here assess Amber ff14SB, Amber ff14SB,...

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