| 1. |
- Akke, Mikael, et al.
(författare)
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NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins
- 2023
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 127:3, s. 591-599
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Forskningsöversikt (refereegranskat)abstract
- Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale “breathing” motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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| 2. |
- Al-Tikriti, Yassir, et al.
(författare)
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Drug-Eluting Polyacrylate Microgels : Loading and Release of Amitriptyline
- 2020
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Ingår i: Journal of Physical Chemistry B. - : AMER CHEMICAL SOC. - 1520-6106 .- 1520-5207. ; 124:11, s. 2289-2304
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the loading of an amphiphilic drug, amitriptyline hydrochloride (AMT), onto sodium polyacrylate hydrogels at low ionic strength and its release at high ionic strength. The purpose was to show how the self-assembling properties of the drug and the swelling of the gel network influenced the loading/release mechanisms and kinetics, important for the development of improved controlled-release systems for parenteral administration of amphiphilic drugs. Equilibrium studies showed that single microgels (similar to 100 mu m) in a large solution volume underwent a discrete transition between swollen and dense states at a critical drug concentration in the solution. For single macrogels in a small solution volume, the transition progressed gradually with increasing amount of added drug, with swollen and dense phases coexisting in the same gel; in a suspension of microgels, swollen and collapsed particles coexisted. Time-resolved micropipette-assisted microscopy studies showed that drug self-assemblies accumulated in a dense shell enclosing the swollen core during loading and that a dense core was surrounded by a swollen shell during release. The time evolution of the radius of single microgels was determined as functions of liquid flow rate, network size, and AMT concentration in the solution. Mass transport of AMT in the surrounding liquid, and in the dense shell, influenced the deswelling rate during loading. Mass transport in the swollen shell controlled the swelling rate during release. A steady-state kinetic model taking into account drug self-assembly, core-shell phase separation, and microgel volume changes was developed and found to be in semiquantitative agreement with the experimental loading and release data.
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| 3. |
- Andersson, C. David, 1978-, et al.
(författare)
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Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu
- 2020
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:30, s. 6529-6539
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Tidskriftsartikel (refereegranskat)abstract
- Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.
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| 4. |
- Andreev, Georgy, et al.
(författare)
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Colabind : A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes
- 2024
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 128:13, s. 3211-3219
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Tidskriftsartikel (refereegranskat)abstract
- Binding site prediction is a crucial step in understanding protein-ligand and protein-protein interactions (PPIs) with broad implications in drug discovery and bioinformatics. This study introduces Colabind, a robust, versatile, and user-friendly cloud-based approach that employs coarse-grained molecular dynamics simulations in the presence of molecular probes, mimicking fragments of drug-like compounds. Our method has demonstrated high effectiveness when validated across a diverse range of biological targets spanning various protein classes, successfully identifying orthosteric binding sites, as well as known druggable allosteric or PPI sites, in both experimentally determined and AI-predicted protein structures, consistently placing them among the top-ranked sites. Furthermore, we suggest that careful inspection of the identified regions with a high affinity for specific probes can provide valuable insights for the development of pharmacophore hypotheses. The approach is available at https://github.com/porekhov/CG_probeMD
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| 5. |
- Antonsson, Jakob, et al.
(författare)
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Modeling Colloidal Particle Aggregation Using Cluster Aggregation with Multiple Particle Interactions
- 2024
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 128:18, s. 4513-4524
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigate the aggregation dynamics of colloidal silica by generating simulated structures and comparing them to experimental data gathered through scanning transmission electron microscopy (STEM). More specifically, diffusion-limited cluster aggregation and reaction-limited cluster aggregation models with different functions for the probability of particles sticking upon contact were used. Aside from using a constant sticking probability, the sticking probability was allowed to depend on the masses of the colliding clusters and on the number of particles close to the collision between clusters. The different models of the sticking probability were evaluated based on the goodness-of-fit of spatial summary statistics. Furthermore, the models were compared to the experimental data by calculating the structures’ fractal dimension and mass transport properties from simulations of flow and diffusion. The sticking probability, depending on the interaction with multiple particles close to the collision site, led to structures most similar to the STEM data.
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| 6. |
- Atri, Ria S., et al.
(författare)
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Morphology Modulation of Ionic Surfactant Micelles in Ternary Deep Eutectic Solvents
- 2020
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:28, s. 6004-6014
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Tidskriftsartikel (refereegranskat)abstract
- Deep eutectic solvents (DES) are potentially greener solvents obtained through the complexation of simple precursors which, among other applications, have been investigated in recent years for their ability to support the self-assembly of amphiphilic molecules. It is crucial to understand the factors which influence surfactant solubility and self-assembly with respect to the interaction of the surfactant molecule with the DES components. In this work, small-angle neutron scattering (SANS) has been used to investigate the micellization of cationic (CnTAB) and anionic (SDS) surfactants in a ternary DES comprising choline chloride, urea, and glycerol, where the hydrogen bond donors are mixed in varying molar ratios. The results show that in each case either globular or rodlike micelles are formed with the degree of elongation being directly dependent on the composition of the DES. It is hypothesized that this composition dependence arises largely from the poor solubility of the counterions in the DES, especially at low glycerol content, leading to a tighter binding of the counterion to the micelle surface and giving rise to micelles with a high aspect ratio. This potential for accurate control over micelle morphology presents unique opportunities for rheology control or to develop templated syntheses of porous materials in DES, utilizing the solvent composition to tailor micelle shape and size, and hence the pore structure of the resulting material.
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| 7. |
- Baronio, Cesare M., et al.
(författare)
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The Amide I Spectrum of Proteins—Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations
- 2020
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:9, s. 1703-1714
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Tidskriftsartikel (refereegranskat)abstract
- The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.
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| 8. |
- Barroso da Silva, Fernando L., et al.
(författare)
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Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule
- 2022
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:36, s. 6835-6852
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Tidskriftsartikel (refereegranskat)abstract
- Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein–protein systems under different physical–chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This “RBD charge rule” should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
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| 9. |
- Beck, Christian, et al.
(författare)
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Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture.
- 2022
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 126:38, s. 7400-7408
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Tidskriftsartikel (refereegranskat)abstract
- The crowded environment of biological systems such as the interior of living cells is occupied by macromolecules with a broad size distribution. This situation of polydispersity might influence the dependence of the diffusive dynamics of a given tracer macromolecule in a monodisperse solution on its hydrodynamic size and on the volume fraction. The resulting size dependence of diffusive transport crucially influences the function of a living cell. Here, we investigate a simplified model system consisting of two constituents in aqueous solution, namely, of the proteins bovine serum albumin (BSA) and bovine polyclonal gamma-globulin (Ig), systematically depending on the total volume fraction and ratio of these constituents. From high-resolution quasi-elastic neutron spectroscopy, the separate apparent short-time diffusion coefficients for BSA and Ig in the mixture are extracted, which show substantial deviations from the diffusion coefficients measured in monodisperse solutions at the same total volume fraction. These deviations can be modeled quantitatively using results from the short-time rotational and translational diffusion in a two-component hard sphere system with two distinct, effective hydrodynamic radii. Thus, we find that a simple colloid picture well describes short-time diffusion in binary mixtures as a function of the mixing ratio and the total volume fraction. Notably, the self-diffusion of the smaller protein BSA in the mixture is faster than the diffusion in a pure BSA solution, whereas the self-diffusion of Ig in the mixture is slower than in the pure Ig solution.
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| 10. |
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