scholarly journals Development and Validation of Fluorinated Amino Acid Parameters for use with the AMBER ff15ipq Protein Force Field

2022 ◽  
Author(s):  
Darian Yang ◽  
Angela Gronenborn ◽  
Lillian Chong
Keyword(s):  
Force Field ◽  
Aromatic Amino Acids ◽  
Md Simulations ◽  
Water Molecules ◽  
Relaxation Rates ◽  
Structure And Dynamics ◽  
Experimental Values ◽  
Development And Validation ◽  
Explicit Water ◽  
Good Agreement

We developed force field parameters for fluorinated aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs-timescale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling structure and dynamics of fluorine containing proteins at the atomic level.

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

Force field development and simulations of senior dialkyl sulfoxides

2016 ◽  
Vol 18 (15) ◽  
pp. 10507-10515 ◽  
Author(s):  
Vitaly V. Chaban
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Md Simulations ◽  
Field Development ◽  
Force Field Development ◽  
Structure And Dynamics ◽  
Ethyl Methyl ◽  
Methyl Sulfoxide ◽  
Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

scholarly journals Structural and dynamical heterogeneity of water trapped inside Na+-pumping KR2 rhodopsin in the dark state

2020 ◽  
Author(s):  
Mantu Santra ◽  
Aniruddha Seal ◽  
Kankana Bhattacharjee ◽  
Suman Chakrabarty
Keyword(s):  
Md Simulations ◽  
Active Role ◽  
Water Molecules ◽  
Dark State ◽  
Dynamical Heterogeneity ◽  
Structure And Dynamics ◽  
Channel Opening ◽  
Conserved Water Molecules ◽  
Ion Proton ◽  
Ion Pumping

AbstractPhotoisomerisation in retinal leads to a channel opening in the rhodopsins that triggers translocation of an ion/proton. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this work, we investigate the localisation, local structure and dynamics of water molecules along the channel for the resting/dark state of KR2 rhodopsin. Employing 1.5 μs long atomistic molecular dynamics (MD) simulations of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by the protein side-chains. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities. The exchange time-scale of these buried water with bulk ranges from tens of nanoseconds to > 1.5 μs. The translational and rotational dynamics of buried water are found to be strongly dependent on protein cavity size and local interactions with possible functional significance.

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2020 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

Development and Validation of Subject-Specific Finite Element Models for Blunt Trauma Study

2008 ◽  
Vol 130 (2) ◽  
Author(s):  
Weixin Shen ◽  
Yuqing Niu ◽  
Robert F. Mattrey ◽  
Adam Fournier ◽  
Jackie Corbeil ◽  
...  
Keyword(s):  
Finite Element ◽  
Ct Images ◽  
Fe Model ◽  
Rib Cage ◽  
Abdominal Organs ◽  
Subject Specific ◽  
Experimental Values ◽  
Thoracic And Abdominal ◽  
Development And Validation ◽  
Good Agreement

This study developed and validated finite element (FE) models of swine and human thoraxes and abdomens that had subject-specific anatomies and could accurately and efficiently predict body responses to blunt impacts. Anatomies of the rib cage, torso walls, thoracic, and abdominal organs were reconstructed from X-ray computed tomography (CT) images and extracted into geometries to build FE meshes. The rib cage was modeled as an inhomogeneous beam structure with geometry and bone material parameters determined directly from CT images. Meshes of soft components were generated by mapping structured mesh templates representative of organ topologies onto the geometries. The swine models were developed from and validated by 30 animal tests in which blunt insults were applied to swine subjects and CT images, chest wall motions, lung pressures, and pathological data were acquired. A comparison of the FE calculations of animal responses and experimental measurements showed a good agreement. The errors in calculated response time traces were within 10% for most tests. Calculated peak responses showed strong correlations with the experimental values. The stress concentration inside the ribs, lungs, and livers produced by FE simulations also compared favorably to the injury locations. A human FE model was developed from CT images from the Visible Human project and was scaled to simulate historical frontal and side post mortem human subject (PMHS) impact tests. The calculated chest deformation also showed a good agreement with the measurements. The models developed in this study can be of great value for studying blunt thoracic and abdominal trauma and for designing injury prevention techniques, equipments, and devices.

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