| 1. |
- Hersleth, Hans-Petter, et al.
(författare)
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The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection
- 2008
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Ingår i: Biochemical Journal. - 0264-6021. ; 412, s. 257-264
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Tidskriftsartikel (refereegranskat)abstract
- Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallograpic data collection. We have generated and solved the 1.30 angstrom (1 angstrom= 0.1 nin) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe-O distance of 1.8 angstrom and O-O bond of 1.3 angstrom in accordance with a Fe-II-O-O- (or Fe-III-O-O2-) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metal loproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O-O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.
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| 2. |
- Hersleth, Hans-Petter, et al.
(författare)
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The Influence of X-Rays on the Structural Studies of Peroxide-Derived Myoglobin Intermediates
- 2008
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Ingår i: Chemistry and Biodiversity. - 1612-1872. ; 5:10, s. 2067-2089
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Forskningsöversikt (refereegranskat)abstract
- In recent years, the awareness of potential radiation damage of metal centers in protein crystals during crystallographic data collection has received increasing attention. The radiation damage can lead to radiation-induced changes and reduction of the metal sites. One of the research fields where these concerns have been comprehensively addressed is the study of the reaction intermediates of the heme peroxidase and oxygenase reaction cycles. For both the resting states and the high-valent intermediates, the X-rays used in the structure determination have given undesired side effects through radiation-induced changes to the trapped intermediates. However, X-rays have been used to generate and trap the peroxy/hydroperoxy state in crystals. In this review, the structural work and the influence of X-rays on these intermediates in myoglobin are summarized and viewed in light of analogous studies on similar intermediates in peroxidases and oxygenases.
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| 3. |
- Hsiao, Ya-Wen, et al.
(författare)
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A Pragmatic Approach Using First-Principle Methods to Address Site of Metabolism with Implications for Reactive Metabolite Formation
- 2012
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Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 52:3, s. 686-695
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Tidskriftsartikel (refereegranskat)abstract
- A majority of xenobiotics are metabolized by cytochrome P450 (CYP) enzymes. The discovery of drug candidates with low propensity to form reactive metabolites and low clearance can be facilitated by understanding CYP-mediated xenobiotic metabolism. Being able to predict the sites where reactive metabolites form is beneficial in drug design to produce drug candidates free of reactive metabolite issues. Herein, we report a pragmatic protocol using first-principle density functional theory (DFT) calculations for predicting sites of epoxidation and hydroxylation of aromatic substrates mediated by CYP. The method is based on the relative stabilities of the CYP-substrate intermediates or the substrate epoxides. Consequently, it concerns mainly the electronic reactivity of the substrates. Comparing to the experimental findings, the presented protocol gave excellent first-ranked epoxidation site predictions of 83%, and when the test was extended to CYP-mediated sites of aromatic hydroxylation, satisfactory results were also obtained (73%). This indicates that our assumptions are valid and also implies that the intrinsic reactivities of the substrates are in general more important than their binding poses in proteins, although the protocol may benefit from the addition of docking information.
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| 4. |
- Hsiao, Ya-Wen, et al.
(författare)
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EXAFS structure refinement supplemented by computational chemistry
- 2006
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 74:21
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Tidskriftsartikel (refereegranskat)abstract
- We present a method that combines structure determination using extended x-ray absorption fine structure (EXAFS) measurements and computational chemistry (CC) calculations, EXAFS/CC. Using such an approach, it is possible to obtain a full structure of model complexes or protein metal active sites, although the EXAFS data primarily give radial distance information about the metal ion's nearest neighbors. In essence, CC provides a formalism within which chemical knowledge can be introduced to EXAFS modeling. In this sense, the method is analogous to the use of molecular mechanics in standard crystallographic or NMR structure refinement. In addition, the method provides structures that are a compromise between EXAFS data and the CC calculations. Therefore, they can be used directly to obtain energies or study reaction mechanisms. The method is implemented for both density functional theory and molecular mechanics calculations. It is applied to five Ni(II) (both low- and high-spin) and Cu(I/II) complexes with known crystal structures and it is shown to perform well. We also show that the method can be successfully combined with the calculation of ab initio Debye-Waller factors for all paths using the equation-of-motion method and force constants obtained from the CC calculations.
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| 5. |
- Hsiao, Ya-Wen, et al.
(författare)
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Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
- 2006
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Ingår i: Inorganica Chimica Acta. - : Elsevier BV. - 0020-1693. ; 359:4, s. 1081-1092
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Tidskriftsartikel (refereegranskat)abstract
- The metallation of tetrapyrroles is believed to proceed via a sitting-atop (SAT) complex, in which some of the pyrrole nitrogen atoms are protonated and the metal ion resides above the ring plane. No crystal structure of such a complex has been presented, but NMR and EXAFS (extended X-ray absorption fine structure) data has been reported for Cu2+ in acetonitrile, which have been interpreted as the observation of a SAT complex. However, this interpretation has been challenged and other investigations have shown that there are many possible SAT structures. We have recently developed a method to combine quantum mechanical (QM) calculations and EXAFS fits (EXAFS/QM), which in principle is a standard EXAFS fit that employs all multiple-scattering information in an optimum and self-consistent way and uses the QM calculations to ensure that the obtained structures are chemically reasonable. By this approach, we show that out of the 15 putative SAT complexes, structures with the copper ion coordinating to two cis pyrrolenine nitrogen atoms and two or three acetonitrile molecules fit the experimental EXAFS spectrum best. However, an equally good fit can be obtained also by a mixture of the reactant and product complexes. (c) 2005 Elsevier B.V. All rights reserved.
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| 6. |
- Hsiao, Ya-Wen, et al.
(författare)
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Molecular Dynamics Simulations of NaCl Permeation in Bihydrated Montmorillonite Inter layer Nanopores
- 2015
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:30, s. 17352-17361
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Tidskriftsartikel (refereegranskat)abstract
- We investigated NaCl diffusion between external bulk solution atid bihydrated rhontmorilIonite interlayers using atomistic molecular dynamics (MD) simulations. Two different bulk concentrations, 0.55 and 1.67 M, were tested. In both cases, the simulations showed that excess salt entered the niterlayers. Barriers for Cl- entering the interlayer were calculated from the potential of mean force using adaptive biasing forces, and full consistocy with the MD results was found. In part the barrier stems from hydration free energy cost for the ions moving from bulk water to clay interlayers. This cost was calculated using free-energy perturbation. We compared the equilibrium interlayer anion concentrations to ion-equilibrium thermodynamics, the general Dorman theory that includes excess tree energy contributions in addition to the electrostatic Donnan potential. Numerically consistent predictions of the interlayer Cl- concentration were obtained between MD and Donnan equation When the hydration energy cost was incorporated as the excess free energy. This demonstrates the validity of using the approximation of a Dofinan potential for the interlayer electrostatics. The MD density profiles show that cations and anions in the clay interlayers share the same physical space in the center of the two water layers.
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| 7. |
- Hsiao, Ya-Wen, et al.
(författare)
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NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S
- 2005
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Ingår i: Journal of Biomolecular NMR. - : Springer Science and Business Media LLC. - 1573-5001 .- 0925-2738. ; 31:2, s. 97-114
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Tidskriftsartikel (refereegranskat)abstract
- We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular dynamics simulations restrained to experimental NMR data. In the first, we replace the molecular mechanics force field ( employed in standard refinement to supplement experimental data) for a site of interest by quantum chemical calculations. This way, we obtain an accurate description of the site, even if a molecular mechanics force field does not exist for this site, or if there is little experimental information about the site. Moreover, the site may change its bonding during the refinement, which often is the case for metal sites. The second method is to extract a molecular mechanics potential for the site of interest from a quantum chemical geometry optimisation and frequency calculation. We apply both methods to the two Ca2+ sites in the epidermal growth factor-like domains 3 and 4 in the vitamin K-dependent protein S and compare them to various methods to treat these sites in standard refinement. We show that both methods perform well and have their advantages and disadvantages. We also show that the glutamate Ca2+ ligand is unlikely to bind in a bidentate mode, in contrast to the crystal structure of an EGF domain of factor IX.
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| 8. |
- Hsiao, Ya-Wen, et al.
(författare)
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Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics
- 2014
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Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 1573-4951 .- 0920-654X. ; 28:4, s. 443-454
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Tidskriftsartikel (refereegranskat)abstract
- Accurately predicting binding affinities between ligands and macromolecules has been a much sought-after goal. A tremendous amount of resources can be saved in the pharmaceutical industry through accurate binding-affinity prediction and hence correct decision-making for the drug discovery processes. Owing to the structural complexity of macromolecules, one of the issues in binding affinity prediction using molecular dynamics is the adequate sampling of the conformational space. Recently, the funnel metadynamics method (Limongelli et al. in Proc Natl Acad Sci USA 110: 6358, 2013) was developed to enhance the sampling of the ligand at the binding site as well as in the solvated state, and offer the possibility to predict the absolute binding free energy. We apply funnel metadynamics to predict host-guest binding affinities for the cucurbit[7]uril host as part of the SAMPL4 blind challenge. Using total simulation times of 300-400 ns per ligand, we show that the errors due to inadequate sampling are below 1 kcal/mol. However, despite the large investment in terms of computational time, the results compared to experiment are not better than a random guess. As we obtain differences of up to 11 kcal/mol when switching between two commonly used force fields (with automatically generated parameters), we strongly believe that in the pursuit of accurate binding free energies a more careful force-field parametrization is needed to address this type of system.
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| 9. |
- Ryde, Ulf, et al.
(författare)
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Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements
- 2007
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 129:4, s. 726-727
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a computational method that combines extended X-ray absorption fine structure (EXAFS) refinements with the integrated quantum mechanical and molecular mechanics (QM/MM) method. This method allows us to obtain a structure of a metal site inside a protein that is compatible with both EXAFS data and QM calculations (i.e., that is chemically reasonable). Thereby, the QM/MM calculations play the same role as MM in nearly all NMR and crystallographic refinements-EXAFS ensures that the metal-ligand distances are accurate and QM/MM fills in all the other structural data. We have used this method to show that a structure with a peroxide ion in the center of the trinuclear cluster fits experimental EXAFS data better than a structure with the peroxide ion on the side of the cluster for the peroxide adduct of multicopper oxidases.
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| 10. |
- Tesei, Giulio, et al.
(författare)
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Lipid shape and packing are key for optimal design of pH-sensitive mRNA lipid nanoparticles
- 2024
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424. ; 121:2
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Tidskriftsartikel (refereegranskat)abstract
- The ionizable-lipid component of RNA-containing nanoparticles controls the pH-dependent behavior necessary for an efficient delivery of the cargo - the so-called endosomal escape. However, it is still an empirical exercise to identify optimally performing lipids. Here, we study two well-known ionizable lipids, DLin-MC3-DMA and DLin-DMA using a combination of experiments, multiscale computer simulations, and electrostatic theory. All-atom molecular dynamics simulations, and experimentally measured polar headgroup pKavalues, are used to develop a coarse-grained representation of the lipids, which enables the investigation of the pH-dependent behavior of lipid nanoparticles (LNPs) through Monte Carlo simulations, in the absence and presence of RNA molecules. Our results show that the charge state of the lipids is determined by the interplay between lipid shape and headgroup chemistry, providing an explanation for the similar pH-dependent ionization state observed for lipids with headgroup pKa values about one-pH-unit apart. The pH dependence of lipid ionization is significantly influenced by the presence of RNA, whereby charge neutrality is achieved by imparting a finite and constant charge per lipid at intermediate pH values. The simulation results are experimentally supported by measurements of α-carbon 13C-NMR chemical shifts for eGFP mRNA LNPs of both DLin-MC3-DMA and DLin-DMA at various pH conditions. Further, we evaluate the applicability of a mean-field Poisson-Boltzmann theory to capture these phenomena.
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