X-ray Crystal Structure and Binding Mode Analysis of HumanS-Adenosylhomocysteine Hydrolase Complexed with Novel Mechanism-Based Inhibitors, Haloneplanocin A Analogues

2011 ◽  
Vol 54 (4) ◽  
pp. 930-938 ◽  
Author(s):  
Kang Man Lee ◽  
Won Jun Choi ◽  
Yoonji Lee ◽  
Hyun Joo Lee ◽  
Long Xuan Zhao ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Mode ◽  
Mode Analysis ◽  
Adenosylhomocysteine Hydrolase ◽  
X Ray

scholarly journals Structural Studies of Overlapping Dinucleosomes in Solution

2019 ◽  
Author(s):  
A. Matsumoto ◽  
M. Sugiyama ◽  
Z. Li ◽  
A. Martel ◽  
L. Porcar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Neutron Scattering ◽  
Small Angle ◽  
Solution Structure ◽  
Scattering Data ◽  
Mode Analysis ◽  
Conformational Ensemble ◽  
Histone Tails ◽  
Nucleosome Remodeling ◽  
X Ray

AbstractAn overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In the present study, the solution structure of the OLDN was investigated through integration of small-angle X-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis, and searched for the conformations that well reproduced the SAXS and SANS scattering curves. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.Statement of SignificanceOverlapping dinucleosomes (OLDNs) are intermediate structures formed through nucleosome collision promoted by nucleosome remodeling factor(s). To study the solution structure of OLDNs, a structural library containing a wide variety of conformations was prepared though simulations, and the structures that well reproduced the small angle X-ray and neutron scattering data were selected from the library. Simultaneous evaluation of the conformational variation in the global OLDN structures and in the histone tails is difficult using conventional MD simulations. We overcame this problem by combining multiple simulation techniques, and showed the importance of the histone tails for stabilizing the structures of OLDNs in solution.

Binding mode of thiocyanate in palladium(II) complexes: x-ray crystal structure of cis-(isothiocyanato)(thiocyanato)bis(1-phenyl-3,4-dimethylphosphole)palladium(II)

1982 ◽  
Vol 21 (3) ◽  
pp. 1200-1204 ◽  
Author(s):  
John H. Nelson ◽  
J. Jeffrey. MacDougall ◽  
Nathaniel W. Alcock ◽  
Francois. Mathey
Keyword(s):  
Crystal Structure ◽  
Binding Mode ◽  
X Ray

scholarly journals Crystal structure of the formal 20 electron zirconocene pentafulvene complex Cp2Zr(η5,η1-adamantylidenepentafulvene):toluene:n-hexane = 1:0.125:0.125

2017 ◽  
Vol 73 (12) ◽  
pp. 1823-1826 ◽  
Author(s):  
Malte Fischer ◽  
Marc Schmidtmann ◽  
Rüdiger Beckhaus
Keyword(s):  
Crystal Structure ◽  
Binding Mode ◽  
X Ray Diffraction ◽  
Substitution Pattern ◽  
Complex Molecules ◽  
Coordination Environment ◽  
X Ray ◽  
Zirconocene Dichloride ◽  
Solvent Molecules ◽  
Distorted Tetrahedral Coordination

The crystal structure of a solvated zirconocene pentafulvene complex with a bulky adamantylidene substitution pattern, namely (η5,η1-adamantylidenepentafulvene)bis(η5-cyclopentadienyl)zirconium(IV)–toluene–n-hexane (8/1/1), [Zr(C15H18)(C5H5)2]·0.125C7H8·0.125C6H14, is reported. Reducing zirconocene dichloride with magnesium results in the formation of a low-valent zirconocene reagent that reacts readily with adamantylidenepentafulvene to give the aforementioned complex. Single crystal X-ray diffraction proves the dianion-like η5:η1binding mode of the fulvene ligand to the central ZrIVatom. The asymmetric unit contains four independent molecules of [η5:η1-adamantylidenepentafulvene]bis[(η5)-cyclopentadienyl]zirconium(IV), together with half a molecule of toluene disordered with half a molecule ofn-hexane (the solvent molecules have no direct influence on the complex). In each of the four complex molecules, the central ZrIVatom has a distorted tetrahedral coordination environment. The measured crystal consisted of two domains with a refined ratio of 0.77:0.23.

Divalent Europium in 1∞[Eu(Pz)2(Pz-H)2]: The First Unsubstituted Pyrazolate and Cp Analogous Pyrazole Complex of a Rare Earth Element in One

2004 ◽  
Vol 59 (5) ◽  
pp. 562-566 ◽  
Author(s):  
Catharina C. Quitmann ◽  
Klaus Müller-Buschbaum
Keyword(s):  
Crystal Structure ◽  
Rare Earth ◽  
Spectroscopic Data ◽  
Earth Element ◽  
Binding Mode ◽  
Chain Structure ◽  
X Ray ◽  
Divalent Europium ◽  
Bright Yellow ◽  
Cyclopentadienyl Anion

Abstract Bright yellow crystals of 1∞[Eu(Pz)2(Pz-H)2] were obtained by the reaction of europium metal with a melt of pyrazole. According to single crystal X-ray analysis the compound exhibits a onedimensional chain structure including both unsubstituted pyrazolate anions as well as unsubstituted neutral pyrazole molecules as ligands. The latter are isoelectronic with the cyclopentadienyl anion and link two adjacent Europium(II) centers in an η1-σ -bridging as well as Cp analogous η5-π-binding mode, whilst the pyrazolate anions are N-η1-coordinating terminal ligands. In addition to the crystal structure, MIR, FarIR, Raman and UV/vis spectroscopic data are presented.

scholarly journals Triglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme

Crystals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 444 ◽  
Author(s):  
Nam
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Main Chain ◽  
Structural Information ◽  
Substrate Recognition ◽  
Binding Mode ◽  
Recognition Site ◽  
Proteinase K ◽  
X Ray

Various peptides or non-structural amino acids are recognized by their specific target proteins, and perform a biological role in various pathways in vivo. Understanding the interactions between target protein and peptides (or non-structural amino acids) provides key information on the molecular interactions, which can be potentially translated to the development of novel drugs. However, it is experimentally challenging to determine the crystal structure of protein–peptide complexes. To obtain structural information on the substrate recognition of the peptide-recognizing enzyme, X-ray crystallographic studies were performed using triglycine (Gly-Gly-Gly) as the main-chain of the peptide. The crystal structure of Parengyodontium album Proteinase K in complex with triglcyine was determined at a 1.4 Å resolution. Two different bound conformations of triglycine were observed at the substrate recognition site. The triglycine backbone forms stable interactions with β5-α4 and α5-β6 loops of the main-chain. One of the triglycine-binding conformations was identical to the binding mode of a peptide-based inhibitor from a previously reported crystal structure of Proteinase K. Triglycine has potential application in X-ray crystallography in order to identify the substrate recognition sites in the peptide binding enzymes.

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