Conformational Space of a Polyphilic Molecule with a Fluorophilic Side Chain Integrated in a DPPC Bilayer

2017 ◽  
Vol 38 (9) ◽  
pp. 576-583 ◽  
Author(s):  
Guido F. von Rudorff ◽  
Tobias Watermann ◽  
Xiang-Yang Guo ◽  
Daniel Sebastiani
Keyword(s):  
Conformational Space ◽  
Side Chain ◽  
Dppc Bilayer

scholarly journals Glycine in Water Favors the Polyproline II State

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1121 ◽  
Author(s):  
Brian Andrews ◽  
Shuting Zhang ◽  
Reinhard Schweitzer-Stenner ◽  
Brigita Urbanc
Keyword(s):  
Amino Acid ◽  
Spectroscopic Data ◽  
Heavy Atom ◽  
Conformational Space ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Glycine Residue ◽  
Polyproline Ii ◽  
Conformational Preferences ◽  
Central Residue

Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.

scholarly journals Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Genetic Algorithm ◽  
Energy Surface ◽  
Energy Analysis ◽  
Theoretical Study ◽  
Molecular Structures ◽  
Conformational Space ◽  
Side Chain ◽  
Am1 Method ◽  
The Subject ◽  
Semi Empirical

The generation of molecular structures constituting the conformational space of trans-N-For-L-Cys-NH2 was accomplished using the genetic algorithm MNC coupled to the semi-empirical AM1 method, AM1/GA-MNC. The structural and energy analysis of the obtained conformational space E=E(,ψ) locates 7 regions or minima ɣL, ɣD, L, D, L, ɛD and ɛL. The combination of these folds to structuring modes adopted by the side chain CH2-SH has allowed us to identify 27 stable geometric structures. The regions corresponding to helical folds αD and αL are not favorable for the system that is the subject of current study.

scholarly journals Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation

2017 ◽  
Author(s):  
Kyle A. Barlow ◽  
Shane O Conchúir ◽  
Samuel Thompson ◽  
Pooja Suresh ◽  
James E. Lucas ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Energy Function ◽  
Large Scale ◽  
Additive Model ◽  
Conformational Space ◽  
Side Chain ◽  
Free Energies ◽  
Protein Protein Interactions ◽  
Conformational Plasticity ◽  
Macromolecular Modeling

AbstractComputationally modeling changes in binding free energies upon mutation (interface ΔΔG) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticity should be able to achieve higher prediction accuracy over methods that do not. To test this hypothesis, we developed a method within the Rosetta macromolecular modeling suite (flex ddG) that samples conformational diversity using “backrub” to generate an ensemble of models, then applying torsion minimization, side chain repacking and averaging across this ensemble to estimate interface ΔΔG values. We tested our method on a curated benchmark set of 1240 mutants, and found the method outperformed existing methods that sampled conformational space to a lesser degree. We observed considerable improvements with flex ddG over existing methods on the subset of small side chain to large side chain mutations, as well as for multiple simultaneous non-alanine mutations, stabilizing mutations, and mutations in antibody-antigen interfaces. Finally, we applied a generalized additive model (GAM) approach to the Rosetta energy function; the resulting non-linear reweighting model improved agreement with experimentally determined interface DDG values, but also highlights the necessity of future energy function improvements.

scholarly journals Theoretical study of the potential energy surface of N-formyl-L-cysteine-amide by using a genetic algorithm multi niche crowding

2019 ◽  
Author(s):  
Chem Int ◽  
Malika Bourjila
Keyword(s):  
Genetic Algorithm ◽  
Energy Surface ◽  
Energy Analysis ◽  
Theoretical Study ◽  
Molecular Structures ◽  
Conformational Space ◽  
Side Chain ◽  
Am1 Method ◽  
The Subject ◽  
Semi Empirical

The generation of molecular structures constituting the conformational space of trans-N-For-L-Cys-NH2 was accomplished using the genetic algorithm MNC coupled to the semi-empirical AM1 method, AM1/GA-MNC. The structural and energy analysis of the obtained conformational space E=E(,ψ) locates 7 regions or minima ɣL, ɣD, L, D, L, ɛD and ɛL. The combination of these folds to structuring modes adopted by the side chain CH2-SH has allowed us to identify 27 stable geometric structures. The regions corresponding to helical folds αD and αL are not favorable for the system that is the subject of current study.

scholarly journals Linearised loop kinematics to study pathways between conformations

2021 ◽  
Author(s):  
Antonius G.L. Hoevenaars ◽  
Ingemar Andre
Keyword(s):  
Molecular Dynamics ◽  
Energy Function ◽  
Inverse Kinematics ◽  
Degrees Of Freedom ◽  
Conformational Space ◽  
Side Chain ◽  
Single Point Mutation ◽  
Cartesian Coordinates ◽  
Chain Conformations

Conformational changes are central to the function of many proteins. Characterization of these changes using molecular simulation requires methods to effectively sample pathways between protein conformational states. In this paper we present an iterative algorithm that samples conformational transitions in protein loops, referred to as the Jacobian-based Loop Transition (JaLT) algorithm. The method uses internal coordinates to minimise the sampling space, while Cartesian coordinates are used to maintain loop closure. Information from the two representations is combined to push sampling towards a desired target conformation. The innovation that enables the simultaneous use of Cartesian coordinates and internal coordinate is the linearisation of the inverse kinematics of a protein backbone. The algorithm uses the Rosetta all-atom energy function to steer sampling through low-energy regions and uses Rosetta's side-chain energy minimiser to update side-chain conformations along the way. Because the JaLT algorithm combines a detailed energy function with a low-dimensional conformational space, it is positioned in between molecular dynamics (MD) and elastic network model (ENM) methods. As a proof of principle, we apply the JaLT algorithm to study the conformational transition between the open and occluded state in the MET20 loop of the Escherichia coli dihydrofolate reductase enzyme. Our results show that the algorithm generates semi-continuous pathways between the two states with realistic energy profiles. These pathways can be used to identify energy barriers along the transition. The effect of a single point mutation of the MET20 loop was also investigated and the predicted increase in energy barrier is consistent with the experimentally observed reduction in catalytic rate of the enzyme. Additionally, it is demonstrated how the JaLT algorithm can be used to identify dominant degrees of freedom during a transition. This can be valuable input for a more extensive characterization of the free energy pathway along a transition using molecular dynamics, which is often performed with a reduced set of degrees of freedom. This study has thereby provided the first examples of how linearisation of inverse kinematics can be applied to the analysis of proteins.

Electroluminescent properties of side-chain naphthalimide-derivated polymers

1998 ◽  
Vol 95 (6) ◽  
pp. 1351-1354 ◽  
Author(s):  
C.-M. Bouché ◽  
P. Le Barny ◽  
H. Facoetti ◽  
F. Soyer ◽  
P. Robin
Keyword(s):  
Side Chain
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