Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

2014 ◽  
Vol 13 (04) ◽  
pp. 1450026 ◽  
Author(s):  
Lirong Mou ◽  
Xiangyu Jia ◽  
Ya Gao ◽  
Yongxiu Li ◽  
John Z. H. Zhang ◽  
...  
Keyword(s):  
Force Field ◽  
Main Chain ◽  
Md Simulations ◽  
Replica Exchange ◽  
Hydrophobic Core ◽  
Native Structure ◽  
Folding Simulation ◽  
Torsion Potential ◽  
Folding Simulations ◽  
Α Helix

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cvis only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032Dis an accurate force field that can be used for protein folding simulations.

scholarly journals Accelerating molecular simulations of proteins using Bayesian inference on weak information

2015 ◽  
Vol 112 (38) ◽  
pp. 11846-11851 ◽  
Author(s):  
Alberto Perez ◽  
Justin L. MacCallum ◽  
Ken A. Dill
Keyword(s):  
Molecular Dynamics ◽  
Detailed Balance ◽  
Protein Structures ◽  
Md Simulations ◽  
Amino Acid Sequences ◽  
Hydrophobic Core ◽  
Physical Knowledge ◽  
Small Proteins ◽  
Physical Insight ◽  
Folding Simulations

Atomistic molecular dynamics (MD) simulations of protein molecules are too computationally expensive to predict most native structures from amino acid sequences. Here, we integrate “weak” external knowledge into folding simulations to predict protein structures, given their sequence. For example, we instruct the computer “to form a hydrophobic core,” “to form good secondary structures,” or “to seek a compact state.” This kind of information has been too combinatoric, nonspecific, and vague to help guide MD simulations before. Within atomistic replica-exchange molecular dynamics (REMD), we develop a statistical mechanical framework, modeling using limited data with coarse physical insight(s) (MELD + CPI), for harnessing weak information. As a test, we apply MELD + CPI to predict the native structures of 20 small proteins. MELD + CPI samples to within less than 3.2 Å from native for all 20 and correctly chooses the native structures (<4 Å) for 15 of them, including ubiquitin, a millisecond folder. MELD + CPI is up to five orders of magnitude faster than brute-force MD, satisfies detailed balance, and should scale well to larger proteins. MELD + CPI may be useful where physics-based simulations are needed to study protein mechanisms and populations and where we have some heuristic or coarse physical knowledge about states of interest.

scholarly journals Effects of Force Fields on the Conformational and Dynamic Properties of Amyloid β(1-40) Dimer Explored by Replica Exchange Molecular Dynamics Simulations

2017 ◽  
Author(s):  
Charles R. Watts ◽  
Andrew Gregory ◽  
Cole Frisbie ◽  
Sándor Lovas
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Dynamic Properties ◽  
Amyloid Β ◽  
Md Simulations ◽  
Conformational Space ◽  
Random Coil ◽  
Replica Exchange ◽  
Β Sheet

AbstractAlzheimer’s disease is histologically marked by fibrils of Amyloid beta (Aβ) peptide within the extracellular matrix. Fibrils themselves are benign compared to the cytotoxicity of the oligomers and pre-fibrillary aggregates. The conformational space and structural ensembles of Aβ peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1–40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8±6.4%) and CHARMM36 (2.7±4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3±5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3±12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.

scholarly journals Folding of the Transmembrane 25-Residues Influenza A M2 and Ala-25 Peptides

2020 ◽  
Author(s):  
Ioannis Stylianakis ◽  
Steve Scheiner ◽  
Isaiah Arkin ◽  
Nikolas Glykos ◽  
Antonios Kolocouris
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Influenza A ◽  
Single Point ◽  
Cumulative Effect ◽  
Md Simulations ◽  
Helical Structures ◽  
Hydrogen Bonding Interactions ◽  
Peptide Hydrogen ◽  
Α Helix

<p>The correct balance between hydrophobic London dispersion (LD) and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors we sought a comparison of the influenza A transmembrane M2 protein (M2TM) 25-residues monomer and the 25-Ala (Ala<sub>25</sub>) peptide, used as reference since alanine is the only amino acid forming a standard peptide helix which is stabilized by the backbone peptide hydrogen bonding interactions. Folding molecular dynamics (MD) simulations were performed ing the AMBER99SB-STAR-ILDN force field in trifluoroethanol (TFE) as a membrane mimetic, to study the α-helical stability of M2TM and Ala<sub>25</sub> peptides. It was shown that M2TM peptide did not form a single stable α-helix compared to Ala<sub>25</sub>. Instead appears to be dynamic in nature and quickly inter-converts between an ensemble of various folded helical structures having the highest thermal stability to the N-terminal compared to Ala<sub>25</sub>. Circular dichroism (CD) experiments confirm the stability of the α-helical M2TM. DFT calculations results revealed an extra stabilization for the folding of M2TM from b-strand to the α-helix compared to Ala<sub>25</sub>, due to forces that can't be described from a force field. On a technical level, calculations using D95(d,p) single point at a ONIOM (6-31G,3-21G) minimized geometry, in which the backbone is calculated with 6-31G and alkyl side chains with 3-21G, produced an energy differential for M2TM comparable with full D95(d,p). Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) calculations were applied to investigate the relative contribution of N-H∙∙∙O as compared to C-H∙∙∙O hydrogen bonding interactions in the M2TM which included 17 lipophilic residues; 26 CH∙∙∙O interactions were identified, as compared to 22 NH∙∙∙O H-bonds. The calculations suggested that CH∙∙∙O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total interaction energy when compared to NH∙∙∙O to the stabilization of the folded α-helix in M2TM compared to Ala<sub>25</sub>.</p>

scholarly journals Folding of the Transmembrane 25-Residues Influenza A M2 and Ala-25 Peptides

2020 ◽  
Author(s):  
Ioannis Stylianakis ◽  
Steve Scheiner ◽  
Isaiah Arkin ◽  
Nikolas Glykos ◽  
Antonios Kolocouris
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Influenza A ◽  
Single Point ◽  
Cumulative Effect ◽  
Md Simulations ◽  
Helical Structures ◽  
Hydrogen Bonding Interactions ◽  
Peptide Hydrogen ◽  
Α Helix

<p>The correct balance between hydrophobic London dispersion (LD) and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors we sought a comparison of the influenza A transmembrane M2 protein (M2TM) 25-residues monomer and the 25-Ala (Ala<sub>25</sub>) peptide, used as reference since alanine is the only amino acid forming a standard peptide helix which is stabilized by the backbone peptide hydrogen bonding interactions. Folding molecular dynamics (MD) simulations were performed ing the AMBER99SB-STAR-ILDN force field in trifluoroethanol (TFE) as a membrane mimetic, to study the α-helical stability of M2TM and Ala<sub>25</sub> peptides. It was shown that M2TM peptide did not form a single stable α-helix compared to Ala<sub>25</sub>. Instead appears to be dynamic in nature and quickly inter-converts between an ensemble of various folded helical structures having the highest thermal stability to the N-terminal compared to Ala<sub>25</sub>. Circular dichroism (CD) experiments confirm the stability of the α-helical M2TM. DFT calculations results revealed an extra stabilization for the folding of M2TM from b-strand to the α-helix compared to Ala<sub>25</sub>, due to forces that can't be described from a force field. On a technical level, calculations using D95(d,p) single point at a ONIOM (6-31G,3-21G) minimized geometry, in which the backbone is calculated with 6-31G and alkyl side chains with 3-21G, produced an energy differential for M2TM comparable with full D95(d,p). Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) calculations were applied to investigate the relative contribution of N-H∙∙∙O as compared to C-H∙∙∙O hydrogen bonding interactions in the M2TM which included 17 lipophilic residues; 26 CH∙∙∙O interactions were identified, as compared to 22 NH∙∙∙O H-bonds. The calculations suggested that CH∙∙∙O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total interaction energy when compared to NH∙∙∙O to the stabilization of the folded α-helix in M2TM compared to Ala<sub>25</sub>.</p>

scholarly journals Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

2021 ◽  
Vol 22 (6) ◽  
pp. 3244
Author(s):  
Charuvaka Muvva ◽  
Natarajan Arul Murugan ◽  
Venkatesan Subramanian
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Amyloid Β ◽  
Density Functional Theory Calculations ◽  
Tau Proteins ◽  
Functional Theory ◽  
Energy Profiles ◽  
Α Helix ◽  
Semi Empirical ◽  
Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

Citrate chelation as a potential mechanism against aluminum toxicity in cells: the role of calmodulin

1985 ◽  
Vol 63 (11) ◽  
pp. 1167-1175 ◽  
Author(s):  
Charles G. Suhayda ◽  
Alfred Haug
Keyword(s):  
Circular Dichroism ◽  
Conceptual Understanding ◽  
Aluminum Toxicity ◽  
Hydrophobic Surface ◽  
Native Structure ◽  
Calcium Calmodulin Dependent ◽  
Α Helix ◽  
Kinetics Of ◽  
Circular Dichroïsm

At a molar excess of [citrate]/[aluminum], this organic acid can protect calmodulin from aluminum binding if the metal is presented to the protein in stoichiometric micromolar quantities, as judged by fluorescence and circular dichroism spectroscopy. Similar citrate concentrations are also capable of fully restoring calmodulin's hydrophobic surface exposure to that of the native protein when calmodulin was initially damaged by aluminum binding. Fluoride anions are equally effective in restoring calmodulin's native structure as determined by fluorescence spectroscopy. Measurements of the kinetics of citrate-mediated aluminum removal also indicated that the metal ions are completely removed from calmodulin, consistent with results derived from atomic absorption experiments. On the other hand, results from circular dichroism studies indicated that citrate-mediated aluminum removal from calmodulin can only partially restore the α-helix content to that originally present in apocalmodulin or in calcium–calmodulin, dependent upon the absence or presence of calcium ions. The results that chelators like citrate can protect calmodulin from aluminum injury may provide a conceptual understanding of physiological observations regarding aluminum-tolerant plant species which are generally rich in certain organic acids.

scholarly journals A hierarchical Bayesian framework for force field selection in molecular dynamics simulations

2016 ◽  
Vol 374 (2060) ◽  
pp. 20150032 ◽  
Author(s):  
S. Wu ◽  
P. Angelikopoulos ◽  
C. Papadimitriou ◽  
R. Moser ◽  
P. Koumoutsakos
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Force Field ◽  
Computational Cost ◽  
Md Simulations ◽  
Bayesian Framework ◽  
Underlying Structure ◽  
Hierarchical Bayesian ◽  
Wide Range ◽  
Selection Of

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

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