Browsing by Subject "Crystal structure"

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Approaching the crystal structure of the polymerase γ catalytic complex
(2011-08) Meng, Qingchao, master of arts in cell and molecular biology; Yin, Yuhui Whitney; Molineux, Ian
In this thesis, a 4.7Å crystal structure of the human mitochondria DNA polymerase γ catalytic complex is reported. Though the DNA substrate-binding site is not identifiable in the structure, two conformational changes in the enzyme architecture are described: 1) rotation of the distal monomer of the accessory subunit towards the catalytic subunit, and 2) shift of the thumb motif of the polymerase domain towards the active site. Both conformational changes suggest a structure of Pol γ in the DNA-bound state and in its active site “closed” conformation.
A Comparison of the Crystal Structures of Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions
(Public Library of Science, 2012-05-31) Lee, Jung C.; Gutell, Robin R.
While the majority of the ribosomal RNA structure is conserved in the three major domains of life – archaea, bacteria, and eukaryotes, specific regions of the rRNA structure are unique to at least one of these three primary forms of life. In particular, the comparative secondary structure for the eukaryotic SSU rRNA contains several regions that are different from the analogous regions in the bacteria. Our detailed analysis of two recently determined eukaryotic 40S ribosomal crystal structures, Tetrahymena thermophila and Saccharomyces cerevisiae, and the comparison of these results with the bacterial Thermus thermophilus 30S ribosomal crystal structure: (1) revealed that the vast majority of the comparative structure model for the eukaryotic SSU rRNA is substantiated, including the secondary structure that is similar to both bacteria and archaea as well as specific for the eukaryotes, (2) resolved the secondary structure for regions of the eukaryotic SSU rRNA that were not determined with comparative methods, (3) identified eukaryotic helices that are equivalent to the bacterial helices in several of the hypervariable regions, (4) revealed that, while the coaxially stacked compound helix in the 540 region in the central domain maintains the constant length of 10 base pairs, its two constituent helices contain 5+5 bp rather than the 6+4 bp predicted with comparative analysis of archaeal and eukaryotic SSU rRNAs.
The crystal structure of anhydrous sodium chromate
(1936) Miller, John Jaimerson; Colby, M. Y. (Malcolm Young), 1892-
The crystal structure of the aragonite group
(1933) LaCoste, Lucien Jean Batiste; Colby, M. Y. (Malcolm Young), 1892-
Elasticity across the post-stishovite transition in subducted basalt
(2022-11-18) Zhang, Yanyao; Lin, Jung-Fu; Grand, Stephen P.; Gardner, James E.; Sun, Chenguang; Zhou, Jianshi
Regional seismic studies have found many small-scale scatterers with shear wave velocity (Vₛ) anomalies near subducting slabs in the lower mantle, indicating chemical anomalies at depth. Subducting slabs transport surface hydrated mid-ocean ridge basalt (MORB) into deep Earth, which is chemically and physically distinct from the surrounding mantle. Physical properties of MORB materials are thus important to understand observed seismic Vₛ anomalies. In this dissertation, physical properties of stishovite and CaCl₂-type post-stishovite, which are abundant MORB components, have been determined at high pressure in order to study geophysical consequences across the post-stishovite transition in MORB. Specifically, I measured sound velocities using Brillouin light scattering and impulsive stimulated light scattering, Raman shifts of optic modes using Raman spectroscopy, and atomistic properties using synchrotron single-crystal X-ray diffraction in diamond anvil cells at high pressure. Sound velocity results show that the elastic modulus C₁₂ of pure-endmember stishovite converges with C₁₁ at 55 GPa where the shear wave Vₛ₁ propagating along [110] direction becomes zero and aggregate shear wave Vₛ drops by ~26%. Microscopically, this abnormal elastic property can be correlated with a crossover of the apical and equatorial Si-O bond lengths that results in the occurrence of the symmetry-breaking spontaneous strain in the post-stishovite phase. Furthermore, the Al and H incorporation into stishovite lattice structure can significantly reduce transition pressure and slightly enhance Vₛ reduction. For example, stishovite with 1.3-2.1 mol % Al undergoes the ferroelastic transition at ~16-21 GPa where Vₛ drops by ~29%. This Al,H-dependent post-stishovite transition in subducted MORB materials has been used to explain depth-dependent small-scale seismic Vₛ anomalies beneath the Tonga subduction region. The coupled H and Al substitution, together with literature element partitioning data, indicates that stishovite with 1.3 mol% Al in the upper part of the lower mantle could accommodate ~0.3 wt% H₂O.
Flanking Residues Are Central to DO11.10 T Cell Hybridoma Stimulation by Ovalbumin 323–339
(Public Library of Science, 2012-10-23) Roy, Benjamin M.; Zhukov, Dmitriy V.; Maynard, Jennifer A.
T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of N-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.
Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors
(Public Library of Science, 2012-10-04) Murail, Samuel; Howard, Rebecca J.; Broemstrup, Torben; Bertaccini, Edward J.; Harris, R. Adron; Trudell, James R.; Lindahl, Erik
Cys-loop receptors constitute a superfamily of pentameric ligand-gated ion channels (pLGICs), including receptors for acetylcholine, serotonin, glycine and γ-aminobutyric acid. Several bacterial homologues have been identified that are excellent models for understanding allosteric binding of alcohols and anesthetics in human Cys-loop receptors. Recently, we showed that a single point mutation on a prokaryotic homologue (GLIC) could transform it from a channel weakly potentiated by ethanol into a highly ethanol-sensitive channel. Here, we have employed molecular simulations to study ethanol binding to GLIC, and to elucidate the role of the ethanol-enhancing mutation in GLIC modulation. By performing 1-µs simulations with and without ethanol on wild-type and mutated GLIC, we observed spontaneous binding in both intra-subunit and inter-subunit transmembrane cavities. In contrast to the glycine receptor GlyR, in which we previously observed ethanol binding primarily in an inter-subunit cavity, ethanol primarily occupied an intra-subunit cavity in wild-type GLIC. However, the highly ethanol-sensitive GLIC mutation significantly enhanced ethanol binding in the inter-subunit cavity. These results demonstrate dramatic effects of the F(14′)A mutation on the distribution of ligands, and are consistent with a two-site model of pLGIC inhibition and potentiation.
Selective anion exchange and anion-tuned gas sorption in a phosphine coordination material
(2019-05-06) Riparetti, Ryan Douglas; Humphrey, Simon M.
Herein we report a new ligand tris(4-(pyrid-4-yl)phenyl)phosphine sulfide (tppps) as a building block for the synthesis of a zeolite-like Phosphine Coordination Material (PCM). PCM-63 was made solvothermally with tppps and AgNO₃, producing off-white prisms. The material underwent selective anion exchange with PF₆ ̄ and ClO₄ ̄ over five other anions in a competition experiment. PCM-63 could remove 36.4% and 27.0% of 1 mM ReO₄ ̄ and ClO₄ ̄ in the presence of 100 mM Cl ̄, respectively. Four single-crystal to single-crystal studies were carried out with ReO₄ ̄, PF₆ ̄, ClO₄ ̄, and BF₄ ̄, each showing numerous CH···X (X = O, F) interactions between the framework and the anion. The anion-exchanged materials exhibited a large increase in surface areas for gases. Most notably, PCM-63-BF₄ and PCM-63-PF₆ exhibited a CO₂ surface area of 463 m²g⁻¹ and 466 m²g⁻¹, respectively. This is a large increase in surface area from PCM-63, which has a CO₂ surface area of 80 m²g⁻¹, suggesting that CH···F interactions stabilize the framework
Structural Constraints Identified with Covariation Analysis in Ribosomal RNA
(Public Library of Science, 2012-06-19) Shang, Lei; Xu, Weijia; Ozer, Stuart; Gutell, Robin R.
"Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab’s new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab’s Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair.
Structural studies of Gαq signaling and regulation
(2008-12) Shankaranarayanan, Aruna; Tesmer, John; Hackert, Marvin L.
Gαq signaling is implicated in a number of physiological processes that include platelet activation, cardiovascular development and smooth muscle function. Historically, Gαq is known to function by activating its effector, phospholipase Cβ. Desensitization of Gαq signaling is mediated by G-protein coupled receptor kinases (GRK) such as GRK2 that phosphorylates the activated receptor and also sequesters activated Gαq and Gβγ subunits. Our crystal structure of Gαq-GRK2-Gβγ complex shows that Gαq forms effector-like interactions with the regulator of G-protein signaling (RGS) homology domain of GRK2 involving the classic effector-binding site of Gα subunits, raising the question if GRK2 can itself be a Gáq effector and initiate its own signaling cascade. In the structure, Gα and Gβγ subunits are completely dissociated from one another and the orientation of activated Gαq with respect to the predicted cell membrane is drastically different from its position in the inactive Gαβγ heterotrimer. Recent studies have identified a novel Gαq effector, p63RhoGEF that activates RhoA. Our crystal structure of the Gαq-p63RhoGEF-RhoA complex reveals that Gαq interacts with both the Dbl homology (DH) and pleckstrin homology (PH) domains of p63RhoGEF with its C-terminal helix and its effector-binding site, respectively. The structure predicts that Gαq relieves auto-inhibition of the catalytic DH domain by the PH domain. We show that Gαq activates p63RhoGEF-related family members, Trio and Kalirin, revealing several conduits by which RhoA is activated in response to Gq-coupled receptors. The Gαq effector-site interaction with p63RhoGEF/GRK2 does not overlap with the Gαq-binding site of RGS2/RGS4 that function as GTPase activating proteins (GAPs). This suggests that activated G proteins, effectors, RGS proteins, and activated receptors can form high-order complexes at the cell membrane. We confirmed the formation of RGS-Gαq-effector complexes and our results suggest that signaling pathways initiated by GRK2 and p63RhoGEF are regulated by RGS proteins via both allosteric and GAP mechanisms. Our structural studies of Gαq signaling provide insight into protein-protein interactions that induce profound physiological changes. Understanding such protein interfaces is a key step towards structure-based drug design that can be targeted to treat diseases concerned with impaired Gαq signaling.
Synthesis and crystal growth of complex oxides with novel physical properties
(2023-08) He, Jiaming; Zhou, Jianshi; Mangolini, Filippo; Orbach, Raymond L.; Fiete, Gregory A.
The synthesis and crystal growth of complex oxides, particularly those with perovskite structures and their derivatives, have been a subject of intense interest due to the rich diversity of their physical properties. The focus of this dissertation lies in the exploration of the interplay between the structure, magnetism, and electronic properties within these crystalline materials, with a spotlight on the rare earth orthoferrites, RFeO₃. We delve into the profound implications of the crystal and magnetic structure relationships, with an emphasis on the effects of octahedral tilting on the canted spin structure. The ensuing weak ferromagnetism in these materials sets the stage for an array of fascinating spin phenomena, extending from fundamental spin structure and spin excitations to the application-centric aspects such as the spin Hall effect, inverse spin Hall effect, and the spin Seebeck effect. This research not only strengthens our understanding of the magnetic and structural attributes of these complex oxides, but also aims to unveil potential pathways to exploit these phenomena in the realm of spintronics. A major aspect of this dissertation involves exploring the topological nature of magnon bands, which offers a fresh perspective towards the behavior of magnetic materials. The dissertation is organized into six chapters, encompassing the connection between crystal structure and magnetic structure, an overview of spintronics and magnon band topology, detailed descriptions of experimental techniques, investigation of the spin Seebeck effect, examination of the magnon Hall effect in quantum magnets, and an in-depth study of 3d and 5d perovskite oxides. This work provides significant contributions to the existing knowledge base in the field of complex oxides, and could potentially catalyze the design of future magnetic devices.