Synthesis, Crystal Structures, and Surface Photovoltage and Molecular Recognition Properties of Three Novel Metal Carboxyphosphonates with a 3D Pillared-Layered Structure

2014 ◽  
Vol 14 (4) ◽  
pp. 1580-1590 ◽  
Author(s):  
Shao-Ping Shi ◽  
Yan-Yu Zhu ◽  
Zhen-Gang Sun ◽  
Wei Zhou ◽  
Lu-Lu Dai ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Crystal Structures ◽  
Layered Structure ◽  
Surface Photovoltage

Syntheses, crystal structures and physical properties of three new chalcogenides: NaGaGe3Se8, K3Ga3Ge7S20, and K3Ga3Ge7Se20

2016 ◽  
Vol 45 (2) ◽  
pp. 532-538 ◽  
Author(s):  
Xiaoshuang Li ◽  
Chao Li ◽  
Pifu Gong ◽  
Zheshuai Lin ◽  
Jiyong Yao ◽  
...  
Keyword(s):  
Physical Properties ◽  
Crystal Structures ◽  
Layered Structure

NaGaGe3Se8 has a layered structure, while K3Ga3Ge7Q20 (Q = S, Se) are constructed by incompletely isolated quasi-2D layers, leading to large channels loosely occupied by K+ cations.

scholarly journals Molecular recognition of sugar binding in a melibiose transporter MelB by X-ray crystallography

2020 ◽  
Author(s):  
Lan Guan ◽  
Parameswaran Hariharan
Keyword(s):  
Molecular Recognition ◽  
Binding Site ◽  
Crystal Structures ◽  
Mammalian Cells ◽  
Substrate Binding ◽  
Structural Basis ◽  
Cooperative Binding ◽  
Recognition Mechanism ◽  
Substrate Binding Site ◽  
X Ray

AbstractThe symporter melibiose permease MelB is the best-studied representative from MFS_2 family and the only protein in this large family with crystal structure determined. Previous thermodynamic studies show that MelB utilizes a cooperative binding as the core mechanism for its obligatory symport. Here we present two sugar-bound X-ray crystal structures of a Salmonella typhimurium MelB D59C uniport mutant that binds and catalyzes melibiose transport uncoupled to either cation, as determined by biochemical and biophysical characterizations. The two structures with bound nitrophenyl-α-D-galactoside or dodecyl-β-D-melibioside, which were refined to a resolution of 3.05 or 3.15 Å, respectively, are virtually identical at an outward-facing conformation; each one contains a α-galactoside molecule in the middle of protein. In the substrate-binding site, the galactosyl moiety on both ligands are at an essentially same configuration, so a galactoside specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for the binding of sugar in MelB is deciphered. The data also allow to assign the conserved cation-binding pocket, which is directly connected to the sugar specificity determinant pocket. The intimate connection between the two selection sites lays the structural basis for the cooperative binding and coupled transport. This key structural finding answered the long-standing question on the substrate binding for the Na+-coupled MFS family of transporters.SignificanceMajor facilitator superfamily_2 transporters contain >10,000 members that are widely expressed from bacteria to mammalian cells, and catalyze uptake of varied nutrients from sugars to phospholipids. While several crystal structures with bound sugar for other MFS permeases have been determined, they are either uniporters or symporters coupled solely to H+. MelB catalyzes melibiose symport with either Na+, Li+, or H+, a prototype for Na+-coupled MFS transporters, but its sugar recognition has been a long-unsolved puzzle. Two high-resolution crystal structures presented here clearly reveal the molecular recognition mechanism for the binding of sugar in MelB. The substrate-binding site is characterized with a small specificity groove adjoining a large nonspecific cavity, which could offer a potential for future exploration of active transporters for drug delivery.

scholarly journals Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Thuy-Lan V Lite ◽  
Robert A Grant ◽  
Isabel Nocedal ◽  
Megan L Littlehale ◽  
Monica S Guo ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Crystal Structures ◽  
Protein Interaction ◽  
Bacterial Toxin ◽  
General Nature ◽  
Primary Sequence ◽  
Wild Type ◽  
Mutational Robustness ◽  
Protein Protein Interaction ◽  
Interface Residues

Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.

scholarly journals Species-dependent variation in the structure of the CK2α-apigenin complex

2014 ◽  
Vol 70 (a1) ◽  
pp. C819-C819
Author(s):  
Takayoshi Kinoshita ◽  
Yusuke Sekiguchi ◽  
Tetsuko Nakaniwa ◽  
Yuri Sogabe ◽  
Mai Tanaka ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Crystal Structures ◽  
Binding Mode ◽  
Species Specificity ◽  
Atp Binding ◽  
Cell Fates ◽  
Structural Conservation ◽  
Kinase Ck2 ◽  
Ck2 Inhibitors ◽  
Α Subunits

Ser/Thr kinase CK2, consisting of two catalytic α subunits and two regulatory β subunits, represents various cell fates such as proliferation and is a crucial target for cancer and glomerulonephritis therapies. To date, several planar compounds have been identified as ATP-competitive CK2-inhibitors including apigenin, a flavonoid inhibitor. We here determined the crystal structures of human CK2α complexed with apigenin and an ATP analogue (AMPPNP) at 2.3 and 2.5 Å resolution, respectively and investigated the species specificity in the molecular recognition by the structural comparisons of these complexes with each maize equivalent. The pairs of the superimposed structures reveal that apigenin binds to human and maize CK2α in the quite distinct manners. while AMPPNP binds to the both species in a similar manner. Together with the chemical calculations, we deduce that the alternation at the Leu45/Val45 position of CK2α largely contributes to the species-dependent variation in the apigenin binding mode although the discrepancy is unrelated to the structural conservation in the ATP binding mode.

scholarly journals CRYSTAL STRUCTURES OF TWO PHOSPHONATE SALTS: MONOCYCLOHEXYLAMMONIUM HYDROGEN PHOSPHONATE AND MONOCYCLOHEXYLAMMONIUM PHENYL PHOSPHONATE

2020 ◽  
Vol 26 (2) ◽  
pp. 50-56
Author(s):  
MODOU SARR ◽  
MOUHAMADOU BIRAME DIOP ◽  
MOUHAMADOU SEMBENE BOYE ◽  
AMINATA DIASSE-SARR ◽  
PHILIPPE GUIONNEAU
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Layered Structure ◽  
Hydrogen Bonding Network

Hydrogen phosphonate anions and monocyclohexylammonium cations interacting through hydrogen bonds conduct to the formation of a salt namely monocyclohexylammonium hydrogen phosphonate. In this structure, hydrogen phosphonate anions are linked by pairs through O—H···O hydrogen bonds leading to anionic dimers. Each dimer is connected to its two neighbours through cations via N—H···O hydrogen bonds leading to infinite chains which are then connected by N—H···O hydrogen bonds giving rise to a layered structure. The phenyl phosphonates form dimers that are connected through an expended hydrogen bonding network involving the cations into a layer.

Four Novel Oxomolybdenum-Organodiphosphonate Hybrids in the Presence of Cu(II)–Organonitrogen Building Blocks: Synthesis, Crystal Structures, and Surface Photovoltage Properties

2012 ◽  
Vol 13 (1) ◽  
pp. 226-238 ◽  
Author(s):  
Shou-Hui Sun ◽  
Zhen-Gang Sun ◽  
Yan-Yu Zhu ◽  
Da-Peng Dong ◽  
Cheng-Qi Jiao ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Building Blocks ◽  
Surface Photovoltage

Importance of True Satellite Reflections in the Analysis of Modulated, Composite Crystal Structures. II. The Structure of [M'2Cu2O3]7[CuO2]10, M' = Bi0.04Sr0.96

1997 ◽  
Vol 53 (1) ◽  
pp. 125-134 ◽  
Author(s):  
A. F. Jensen ◽  
V. Petříček ◽  
F. K. Larsen ◽  
E. M. McCarron
Keyword(s):  
Synchrotron Radiation ◽  
Crystal Structures ◽  
Layered Structure ◽  
Second Order ◽  
Thermal Parameters ◽  
X Ray ◽  
First Order ◽  
Composite Crystal ◽  
Zigzag Pattern ◽  
Related Compounds

The structure of the modulated, composite crystal bismuth strontium cuprate [M′2Cu2O3]7[CuO2]10, with M′ = Bi0.04Sr0.96, has been determined and refined using a model which allows modulation of the atomic positional parameters for all atoms, as well as modulation of thermal parameters for the M′ site. The structure is orthorhombic, with c being the misfit direction and a = 11.4712 (6), b = 13.3765 (13) Å. Sublattice 1, of composition (CuO2)4, has c l = 2.7509 (10) Å, while sublattice 2, of composition (M′2Cu2O3)4, has c 2 = 3.9316 (3) Å. Superspace group Amma(001 + γ)ss\overline 1; q = γc l* with γ = 0.6997 (3); λ = 0.6565 Å, μ = 25.4 mm−1. The final residual is R all = 0.0474 for all 1174 reflections, R main = 0.0451 for the 549 main reflections, R 1.sat = 0.0562 for the 442 first-order satellite reflections and R 2.sat = 0.1044 for the 183 second-order satellite reflections. The satellite reflections have been collected with X-ray synchrotron radiation. It is shown that these reflections help to unambiguously determine the superspace group. The orthorhombic compound has a layered structure, stacked along the b axis. The first sublattice consists of layers of CuO2 ribbons, with CuO4 squares sharing edges along the c axis. The second sublattice consists of CuO4 squares, which are sharing edges in a zigzag pattern. In-between these layers the disordered layers of Bi and Sr atoms are sandwiched. A comparison with structurally and chemically related compounds is made.

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