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Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta.
Combs SA, Mueller BK, Meiler J
(2018) J Chem Inf Model 58: 1021-1036
MeSH Terms: Crystallography, X-Ray, Databases, Protein, Electrons, Hydrogen Bonding, Models, Molecular, Protein Conformation, Proteins, Rotation
Show Abstract · Added March 21, 2020
Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the relative orientation of electron deficient hydrogen atoms and electron-rich lone pair or π orbitals are evaluated. We demonstrate that nativelike geometries of hydrogen bonds, salt bridges, cation-π, and π-π interactions are recapitulated during minimization of protein conformation. The packing density of tested protein structures increased from the standard score function from 0.62 to 0.64, closer to the native value of 0.70. Overall, rotamer recovery improved when using the PCI score function (75%) as compared to the standard Rosetta score function (74%). The PCI score function represents an improvement over the standard Rosetta score function for protein model scoring; in addition, it provides a platform for future directions in the analysis of small molecule to protein interactions, which depend on partial covalent interactions.
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Scalp-sparing total skin electron therapy in mycosis fungoides: Case report featuring a technique without lead.
Patel CG, Ding G, Kirschner A
(2017) Pract Radiat Oncol 7: 400-402
MeSH Terms: Electrons, Humans, Male, Middle Aged, Mycosis Fungoides, Scalp, Skin Neoplasms, Treatment Outcome
Added April 2, 2019
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Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory.
Norman P, Parello J, Polavarapu PL, Linares M
(2015) Phys Chem Chem Phys 17: 21866-79
MeSH Terms: Base Pairing, Circular Dichroism, DNA, B-Form, Electrons, Models, Molecular, Nucleosides, Nucleosomes, Quantum Theory, Spectrophotometry, Ultraviolet, Thermodynamics
Show Abstract · Added April 10, 2018
It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles. At the DFT/B3LYP level of theory, the ECD signal response is reduced by a factor of 6.7 in going from the B-DNA to the N-DNA form, and it is illustrated how more than 90% of the individual base-pair dimers contribute to this strong hypochromic effect. Of the several inter-base pair parameters, an increase in twist angles is identified as to strongly contribute to a reduced ellipticity. The present work provides first evidence that first-principles calculations can elucidate changes in DNA dichroism due to the supramolecular organization of the nucleoprotein particle and associates these changes with the local structural features of nucleosomal DNA.
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The signaling phospholipid PIP3 creates a new interaction surface on the nuclear receptor SF-1.
Blind RD, Sablin EP, Kuchenbecker KM, Chiu HJ, Deacon AM, Das D, Fletterick RJ, Ingraham HA
(2014) Proc Natl Acad Sci U S A 111: 15054-9
MeSH Terms: Amino Acids, Animals, Biological Transport, Cell Nucleus, Chromatography, Computer Simulation, Crystallography, X-Ray, Electrons, Humans, Ligands, Lipids, Mice, Models, Molecular, Molecular Conformation, Mutation, Mutation, Missense, Peptides, Phosphatidylinositols, Signal Transduction, Solvents, Steroidogenic Factor 1, Surface Plasmon Resonance, Surface Properties, Temperature, Water
Show Abstract · Added August 18, 2015
The signaling phosphatidylinositol lipids PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) ligand binding domain (LBD) bound to PIP2 and PIP3 show the lipid hydrophobic tails sequestered in the hormone pocket, as predicted. However, unlike classic nuclear receptor hormones, the phosphoinositide head groups are fully solvent-exposed and complete the LBD fold by organizing the receptor architecture at the hormone pocket entrance. The highest affinity phosphoinositide ligand PIP3 stabilizes the coactivator binding groove and increases coactivator peptide recruitment. This receptor-ligand topology defines a previously unidentified regulatory protein-lipid surface on SF-1 with the phosphoinositide head group at its nexus and poised to interact with other proteins. This surface on SF-1 coincides with the predicted binding site of the corepressor DAX-1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region on chromosome X), and importantly harbors missense mutations associated with human endocrine disorders. Our data provide the structural basis for this poorly understood cluster of human SF-1 mutations and demonstrates how signaling phosphoinositides function as regulatory ligands for NR5As.
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25 MeSH Terms
Alkylation damage by lipid electrophiles targets functional protein systems.
Codreanu SG, Ullery JC, Zhu J, Tallman KA, Beavers WN, Porter NA, Marnett LJ, Zhang B, Liebler DC
(2014) Mol Cell Proteomics 13: 849-59
MeSH Terms: Aldehydes, Alkylation, Cell Line, Electrons, Glutathione, Humans, Lipids, Protein Interaction Maps, Proteins, Proteome
Show Abstract · Added March 20, 2014
Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively across functional protein interaction networks, with the most highly alkylation-susceptible proteins mapping to networks involved in cytoskeletal regulation. Proteins with lower damage susceptibility mapped to networks involved in protein synthesis and turnover and were alkylated only at electrophile concentrations that caused significant toxicity. Hierarchical susceptibility of proteome systems to alkylation may allow cells to survive sublethal damage while protecting critical cell functions.
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Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme.
Islam SM, Stein RA, McHaourab HS, Roux B
(2013) J Phys Chem B 117: 4740-54
MeSH Terms: Bacteriophage T4, Crystallography, X-Ray, Cyclic N-Oxides, Electron Spin Resonance Spectroscopy, Electrons, Mesylates, Molecular Dynamics Simulation, Muramidase, Protein Structure, Tertiary, Spin Labels
Show Abstract · Added February 19, 2015
DEER (double electron-electron resonance) is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of distance histograms between pairs of nitroxide spin-labels linked to a protein in a native-like solution environment. However, exploiting the huge amount of information provided by ESR/DEER histograms to refine structural models is extremely challenging. In this study, a restrained ensemble (RE) molecular dynamics (MD) simulation methodology is developed to address this issue. In RE simulation, the spin-spin distance distribution histograms calculated from a multiple-copy MD simulation are enforced, via a global ensemble-based energy restraint, to match those obtained from ESR/DEER experiments. The RE simulation is applied to 51 ESR/DEER distance histogram data from spin-labels inserted at 37 different positions in T4 lysozyme (T4L). The rotamer population distribution along the five dihedral angles connecting the nitroxide ring to the protein backbone is determined and shown to be consistent with available information from X-ray crystallography. For the purpose of structural refinement, the concept of a simplified nitroxide dummy spin-label is designed and parametrized on the basis of these all-atom RE simulations with explicit solvent. It is demonstrated that RE simulations with the dummy nitroxide spin-labels imposing the ESR/DEER experimental distance distribution data are able to systematically correct and refine a series of distorted T4L structures, while simple harmonic distance restraints are unsuccessful. This computationally efficient approach allows experimental restraints from DEER experiments to be incorporated into RE simulations for efficient structural refinement.
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Targeted protein capture for analysis of electrophile-protein adducts.
Connor RE, Codreanu SG, Marnett LJ, Liebler DC
(2013) Methods Mol Biol 987: 163-76
MeSH Terms: Affinity Labels, Aldehydes, Benzoquinones, Blotting, Western, Cell Line, Tumor, Databases, Protein, Electrons, HSP90 Heat-Shock Proteins, Humans, Immunoprecipitation, Lactams, Macrocyclic, Mass Spectrometry, Protein Structure, Tertiary, Trypsin
Show Abstract · Added March 20, 2014
Proteomic analyses of protein-electrophile adducts generally employ affinity capture of the adduct moiety, which enables global analyses, but is poorly suited to targeted studies of specific proteins. We describe a targeted molecular probe approach to study modifications of the molecular chaperone heat-shock protein 90 (Hsp90), which regulates diverse client proteins. Noncovalent affinity capture with a biotinyl analog of the HSP90 inhibitor geldanamycin enables detection of the native protein isoforms Hsp90α and Hsp90β and their phosphorylated forms. We applied this probe to map and quantify adducts formed on Hsp90 by 4-hydroxynonenal (HNE) in RKO cells. This approach was also applied to measure the kinetics of site-specific adduction of selected Hsp90 residues. A protein-selective affinity capture approach is broadly applicable for targeted analysis of electrophile adducts and their biological effects.
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14 MeSH Terms
Conformation of receptor-bound visual arrestin.
Kim M, Vishnivetskiy SA, Van Eps N, Alexander NS, Cleghorn WM, Zhan X, Hanson SM, Morizumi T, Ernst OP, Meiler J, Gurevich VV, Hubbell WL
(2012) Proc Natl Acad Sci U S A 109: 18407-12
MeSH Terms: Arrestin, Crystallography, X-Ray, Electrons, Models, Molecular, Mutant Proteins, Phosphorylation, Protein Binding, Protein Multimerization, Protein Stability, Protein Structure, Secondary, Rhodopsin, Sequence Deletion, Solutions, Staining and Labeling, Temperature
Show Abstract · Added January 24, 2015
Arrestin-1 (visual arrestin) binds to light-activated phosphorylated rhodopsin (P-Rh*) to terminate G-protein signaling. To map conformational changes upon binding to the receptor, pairs of spin labels were introduced in arrestin-1 and double electron-electron resonance was used to monitor interspin distance changes upon P-Rh* binding. The results indicate that the relative position of the N and C domains remains largely unchanged, contrary to expectations of a "clam-shell" model. A loop implicated in P-Rh* binding that connects β-strands V and VI (the "finger loop," residues 67-79) moves toward the expected location of P-Rh* in the complex, but does not assume a fully extended conformation. A striking and unexpected movement of a loop containing residue 139 away from the adjacent finger loop is observed, which appears to facilitate P-Rh* binding. This change is accompanied by smaller movements of distal loops containing residues 157 and 344 at the tips of the N and C domains, which correspond to "plastic" regions of arrestin-1 that have distinct conformations in monomers of the crystal tetramer. Remarkably, the loops containing residues 139, 157, and 344 appear to have high flexibility in both free arrestin-1 and the P-Rh*complex.
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15 MeSH Terms
Potential of discrete Gaussian edge feathering method for improving abutment dosimetry in eMLC-delivered segmented-field electron conformal therapy.
Eley JG, Hogstrom KR, Matthews KL, Parker BC, Price MJ
(2011) Med Phys 38: 6610-22
MeSH Terms: Algorithms, Cluster Analysis, Computer-Aided Design, Electrons, Equipment Design, Equipment Failure Analysis, Feasibility Studies, Learning, Normal Distribution, Radiometry, Radiotherapy, Conformal, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 30, 2020
PURPOSE - The purpose of this work was to investigate the potential of discrete Gaussian edge feathering of the higher energy electron fields for improving abutment dosimetry in the planning volume when using an electron multileaf collimator (eMLC) to deliver segmented-field electron conformal therapy (ECT).
METHODS - A discrete (five-step) Gaussian edge spread function was used to match dose penumbras of differing beam energies (6-20 MeV) at a specified depth in a water phantom. Software was developed to define the leaf eMLC positions of an eMLC that most closely fit each electron field shape. The effect of 1D edge feathering of the higher energy field on dose homogeneity was computed and measured for segmented-field ECT treatment plans for three 2D PTVs in a water phantom, i.e., depth from the water surface to the distal PTV surface varied as a function of the x-axis (parallel to leaf motion) and remained constant along the y-axis (perpendicular to leaf motion). Additionally, the effect of 2D edge feathering was computed and measured for one radially symmetric, 3D PTV in a water phantom, i.e., depth from the water surface to the distal PTV surface varied as a function of both axes. For the 3D PTV, the feathering scheme was evaluated for 0.1-1.0-cm leaf widths. Dose calculations were performed using the pencil beam dose algorithm in the Pinnacle(3) treatment planning system. Dose verification measurements were made using a prototype eMLC (1-cm leaf width).
RESULTS - 1D discrete Gaussian edge feathering reduced the standard deviation of dose in the 2D PTVs by 34, 34, and 39%. In the 3D PTV, the broad leaf width (1 cm) of the eMLC hindered the 2D application of the feathering solution to the 3D PTV, and the standard deviation of dose increased by 10%. However, 2D discrete Gaussian edge feathering with simulated eMLC leaf widths of 0.1-0.5 cm reduced the standard deviation of dose in the 3D PTV by 33-28%, respectively.
CONCLUSIONS - A five-step discrete Gaussian edge spread function applied in 2D improves the abutment dosimetry but requires an eMLC leaf resolution better than 1 cm.
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Nanometer-resolution electron microscopy through micrometers-thick water layers.
de Jonge N, Poirier-Demers N, Demers H, Peckys DB, Drouin D
(2010) Ultramicroscopy 110: 1114-9
MeSH Terms: Animals, Electrons, Eukaryotic Cells, Gold, Humans, Microscopy, Electron, Scanning Transmission, Monte Carlo Method, Nanoparticles, Nanotechnology, Water
Show Abstract · Added May 27, 2014
Scanning transmission electron microscopy (STEM) was used to image gold nanoparticles on top of and below saline water layers of several micrometers thickness. The smallest gold nanoparticles studied had diameters of 1.4 nm and were visible for a liquid thickness of up to 3.3 microm. The imaging of gold nanoparticles below several micrometers of liquid was limited by broadening of the electron probe caused by scattering of the electron beam in the liquid. The experimental data corresponded to analytical models of the resolution and of the electron probe broadening as function of the liquid thickness. The results were also compared with Monte Carlo simulations of the STEM imaging on modeled specimens of similar geometry and composition as used for the experiments. Applications of STEM imaging in liquid can be found in cell biology, e.g., to study tagged proteins in whole eukaryotic cells in liquid and in materials science to study the interaction of solid:liquid interfaces at the nanoscale.
Published by Elsevier B.V.
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10 MeSH Terms