| 1521. |
- Nabu, Sunanta, et al.
(författare)
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Proteochemometric model for predicting the inhibition of penicillin-binding proteins
- 2015
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Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 29:2, s. 127-141
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Tidskriftsartikel (refereegranskat)abstract
- Neisseria gonorrhoeae infection threatens to become an untreatable sexually transmitted disease in the near future owing to the increasing emergence of N. gonorrhoeae strains with reduced susceptibility and resistance to the extended-spectrum cephalosporins (ESCs), i.e. ceftriaxone and cefixime, which are the last remaining option for first-line treatment of gonorrhea. Alteration of the penA gene, encoding penicillin-binding protein 2 (PBP2), is the main mechanism conferring penicillin resistance including reduced susceptibility and resistance to ESCs. To predict and investigate putative amino acid mutations causing beta-lactam resistance particularly for ESCs, we applied proteochemometric modeling to generalize N. gonorrhoeae susceptibility data for predicting the interaction of PBP2 with therapeutic beta-lactam antibiotics. This was afforded by correlating publicly available data on antimicrobial susceptibility of wild-type and mutant N. gonorrhoeae strains for penicillin-G, cefixime and ceftriaxone with 50 PBP2 protein sequence data using partial least-squares projections to latent structures. The generated model revealed excellent predictability (R (2) = 0.91, Q (2) = 0.77, Q (Ext) (2) = 0.78). Moreover, our model identified amino acid mutations in PBP2 with the highest impact on antimicrobial susceptibility and provided information on physicochemical properties of amino acid mutations affecting antimicrobial susceptibility. Our model thus provided insight into the physicochemical basis for resistance development in PBP2 suggesting its use for predicting and monitoring novel PBP2 mutations that may emerge in the future.
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| 1522. |
- Ng, Janice S.W., et al.
(författare)
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Using Tetracysteine-Tagged TDP-43 with a Biarsenical Dye to Monitor Real-Time Trafficking in a Cell Model of Amyotrophic Lateral Sclerosis
- 2019
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 58:39, s. 4086-4095
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Tidskriftsartikel (refereegranskat)abstract
- TAR DNA-binding protein 43 (TDP-43) has been identified as the major constituent of the proteinaceous inclusions that are characteristic of most forms of amyotrophic lateral sclerosis (ALS) and ubiquitin positive frontotemporal lobar degeneration (FTLD). Wild type TDP-43 inclusions are a pathological hallmark of >95% of patients with sporadic ALS and of the majority of familial ALS cases, and they are also found in a significant proportion of FTLD cases. ALS is the most common form of motor neuron disease, characterized by progressive weakness and muscular wasting, and typically leads to death within a few years of diagnosis. To determine how the translocation and misfolding of TDP-43 contribute to ALS pathogenicity, it is crucial to define the dynamic behavior of this protein within the cellular environment. It is therefore necessary to develop cell models that allow the location of the protein to be defined. We report the use of TDP-43 with a tetracysteine tag for visualization using fluorogenic biarsenical compounds and show that this model displays features of ALS observed in other cell models. We also demonstrate that this labeling procedure enables live-cell imaging of the translocation of the protein from the nucleus into the cytosol.
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| 1523. |
- Nguyen, Trung Hai, et al.
(författare)
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Interfacial water molecules at biological membranes : Structural features and role for lateral proton diffusion
- 2018
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 13:2
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Tidskriftsartikel (refereegranskat)abstract
- Proton transport at water/membrane interfaces plays a fundamental role for a myriad of bioenergetic processes. Here we have performed ab initio molecular dynamics simulations of proton transfer along two phosphatidylcholine bilayers. As found in previous theoretical studies, the excess proton is preferably located at the water/membrane interface. Further, our simulations indicate that it interacts not only with phosphate head groups, but also with water molecules at the interfaces. Interfacial water molecules turn out to be oriented relative to the lipid bilayers, consistently with experimental evidence. Hence, the specific water-proton interaction may help explain the proton mobility experimentally observed at the membrane interface.
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| 1524. |
- Nilsson, Michelle, et al.
(författare)
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An epilepsy-associated KV1.2 charge-transfer-center mutation impairs KV1.2 and KV1.4 trafficking
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:17
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Tidskriftsartikel (refereegranskat)abstract
- Significance: A child with epilepsy has a previously unreported, heterozygous mutation in KCNA2, the gene encoding KV1.2 proteins. Four KV1.2 assemble into a potassium-selective channel, a protein complex at the neuronal cell surface regulating electrical signaling. KV1.2 subunits assemble with other KV1-family members to form heterotetrameric channels, contributing to neuronal potassium-channel diversity. The most striking consequence of this mutation is preventing KV1.2-subunit trafficking, i.e., their ability to reach the cell surface. Moreover, the mutation is dominant negative, as mutant subunits can assemble with wild-type KV1.2 and KV1.4, trapping them into nontrafficking heterotetramers and decreasing their functional expression. Thus, KV1-family genes’ ability to form heterotetrameric channels is a double-edged sword, rendering KV1-family members vulnerable to dominant-negative mutations in a single member gene.Abstract: We report on a heterozygous KCNA2 variant in a child with epilepsy. KCNA2 encodes KV1.2 subunits, which form homotetrameric potassium channels and participate in heterotetrameric channel complexes with other KV1-family subunits, regulating neuronal excitability. The mutation causes substitution F233S at the KV1.2 charge transfer center of the voltage-sensing domain. Immunocytochemical trafficking assays showed that KV1.2(F233S) subunits are trafficking deficient and reduce the surface expression of wild-type KV1.2 and KV1.4: a dominant-negative phenotype extending beyond KCNA2, likely profoundly perturbing electrical signaling. Yet some KV1.2(F233S) trafficking was rescued by wild-type KV1.2 and KV1.4 subunits, likely in permissible heterotetrameric stoichiometries: electrophysiological studies utilizing applied transcriptomics and concatemer constructs support that up to one or two KV1.2(F233S) subunits can participate in trafficking-capable heterotetramers with wild-type KV1.2 or KV1.4, respectively, and that both early and late events along the biosynthesis and secretion pathway impair trafficking. These studies suggested that F233S causes a depolarizing shift of ∼48 mV on KV1.2 voltage dependence. Optical tracking of the KV1.2(F233S) voltage-sensing domain (rescued by wild-type KV1.2 or KV1.4) revealed that it operates with modestly perturbed voltage dependence and retains pore coupling, evidenced by off-charge immobilization. The equivalent mutation in the Shaker K+ channel (F290S) was reported to modestly affect trafficking and strongly affect function: an ∼80-mV depolarizing shift, disrupted voltage sensor activation and pore coupling. Our work exposes the multigenic, molecular etiology of a variant associated with epilepsy and reveals that charge-transfer-center disruption has different effects in KV1.2 and Shaker, the archetypes for potassium channel structure and function.
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| 1525. |
- Nilsson, Martin, et al.
(författare)
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Channel current fluctuations conclusively explain neuronal encoding of internal potential into spike trains
- 2021
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Ingår i: Physical review. E. - : American Physical Society. - 2470-0045 .- 2470-0053. ; 103:2
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Tidskriftsartikel (refereegranskat)abstract
- Hodgkin and Huxley's seminal neuron model describes the propagation of voltage spikes in axons, but it cannot explain certain full-neuron features crucial for understanding the neural code. We consider channel current fluctuations in a trisection of the Hodgkin-Huxley model, allowing an analytic-mechanistic explanation of these features and yielding consistently excellent matches with in vivo recordings of cerebellar Purkinje neurons, which we use as model systems. This shows that the neuronal encoding is described conclusively by a soft-thresholding function having just three parameters. © 2021 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.
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| 1526. |
- Norling, Karin, 1988
(författare)
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Liposomes for mucosal vaccine delivery: physicochemical characterization and biological application
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Liposomes are attractive vaccine carriers due to their potential to act as adjuvants, and to the fact that their composition and characteristics are virtually endlessly customizable. However, the precise physicochemical profile of an ideal carrier liposome for mucosal vaccines is still widely unknown, and how different properties affect key steps in the acquisition of protective immunity remains to be elucidated. Additionally, there is no consensus in the field regarding characterization of vaccine formulations, often with incomplete reporting of properties as a result. The focus of this work is therefore twofold: i) to contribute to a better understanding of how the physicochemical profile of vaccine carrier liposomes impacts the development of protective immunity using models at different levels of complexity, and ii) to improve and simplify the physicochemical characterization of liposomes through development and use of new analytical methods. The work in the first area consists of, firstly, an in vivo characterization of the biological response to vaccine liposomes carrying a vaccine protein and characterized by varying surface hydrophilicity (PEGylation). This study showed that non-PEGylated vaccine liposomes more efficiently induced local cell- and antibody-mediated immune responses, as well as better protection against a lethal virus challenge than both PEGylated liposomes and free vaccine protein. Secondly, in vitro studies focused on how liposome stiffness influences dendritic cells, investigating effects on uptake, antigen presentation and cellular activation. These investigations demonstrated that stiff, gel phase liposomes were able to more efficiently activate dendritic cells and induce significantly higher levels of antigen presentation and co-stimulatory signaling compared to both soft, fluid phase liposomes, and free vaccine protein. The work in the second part comprises two studies: a surface plasmon resonance-based method to characterize the influence on liposome deformation from specific multivalent interactions with supported cell membrane mimics, and a waveguide microscopy technique for characterization of optical properties of individual liposomes. While the latter method might become valuable in the context of quantifying the efficiency of dye labelling of liposomes, the surface plasmon resonance study offered information on how liposome deformation depends on membrane stiffness and ligand-receptor pair density. Taken together, the work presented in this thesis demonstrate the value of multidisciplinary approaches to complex biological and medical challenges.
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| 1527. |
- Odelli, Davide, et al.
(författare)
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Interaction between Fish Skin Gelatin and Pea Protein at Air-Water Interface after Ultrasound Treatment
- 2022
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Ingår i: Foods. - : MDPI AG. - 2304-8158. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between fish skin gelatin (FG) and pea protein isolate (PPI) was investigated at the air-water interface (A-W) before and after a high intensity (275 W, 5 min) ultrasound treatment (US). We analyzed the properties of the single protein suspensions as well as an equal ratio of FG:PPI (MIX), in terms of ζ-potential, particle size, molecular weight, bulk viscosity and interfacial tension. The foaming properties were then evaluated by visual analysis and by Turbiscan Tower. Confocal laser scanning microscopy (CLSM) was employed to explore the role of the proteins on the microstructure of foams. The results showed that the ultrasound treatment slightly influenced physicochemical properties of the proteins, while in general, did not significantly affect their behavior both in bulk and at the air-water interface. In particular, PPI aggregate size was reduced (−48 nm) while their negative charges were increased (−1 mV) after the treatment. However, when the proteins were combined, higher molecular weight of aggregates, higher foam stability values (+14%) and lower interfacial tension (IFT) values (47.2 ± 0.2 mN/m) were obtained, leading us to assume that a weak interaction was developed between them.
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| 1528. |
- Ojeda-May, Pedro, Application Expert
(författare)
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Exploring the dynamics of shikimate kinase through molecular mechanics
- 2022
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Ingår i: Biophysica. - : MDPI. - 2673-4125. ; 2:3, s. 194-202
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Tidskriftsartikel (refereegranskat)abstract
- Shikimate kinase (SK) enzyme is a suitable target for antimicrobial drugs as it is present in pathogenic microorganisms and absent in mammals. A complete understanding of the functioning of this enzyme can unveil novel methods to inactivate it. To do this, a clear understanding of SK performance is needed. Previously, the chemical step of SK was studied in detail, but a study of longer-term scale simulations is still missing. In the present work, we performed molecular dynamics (MD) simulations in the µs time scale that allowed us to explore further regions of the SK energy landscape than previously. Simulations were conducted on the wild-type (WT) enzyme and the R116A and R116K mutants. We analyzed the dynamics of the enzymes through standard MD tools, and we found that the global motions in the mutants were perturbed. These motions can be linked to the observed undetectable binding affinity of the WT enzyme and the R116A and R116K mutants.
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| 1529. |
- Ollila, O H Samuli, et al.
(författare)
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3D pressure field in lipid membranes and membrane-protein complexes
- 2009
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 102:7, s. 078101-
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Tidskriftsartikel (refereegranskat)abstract
- We calculate full 3D pressure fields for inhomogeneous nanoscale systems using molecular dynamics simulation data. The fields represent systems with increasing level of complexity, ranging from semivesicles and vesicles to membranes characterized by coexistence of two phases, including also a protein-membrane complex. We show that the 3D pressure field is distinctly different for curved and planar bilayers, the pressure field depends strongly on the phase of the membrane, and that an integral protein modulates the tension and elastic properties of the membrane.
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| 1530. |
- Olsson, Martin A., et al.
(författare)
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Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level
- 2016
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:17, s. 1589-1600
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Tidskriftsartikel (refereegranskat)abstract
- In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions.
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