Chapter 3 3D Structure 1. The Structural Features of Protein-Carbohydrate Interactions Revealed by X-Ray Crystallography

1995 ◽  
pp. 29-65 ◽  
Author(s):  
Christian Cambillau
Keyword(s):  
3D Structure ◽  
Structural Features ◽  
X Ray ◽  
X Ray Crystallography

Two new zinc(II) and mercury(II) complexes based on N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide): synthesis, crystal structures and antibacterial activities

2020 ◽  
Vol 76 (5) ◽  
pp. 476-482
Author(s):  
Al-Ameen Bariz OmarAli ◽  
Ahmed Jasim M. Al-Karawi ◽  
Adil A. Awad ◽  
Necmi Dege ◽  
Sevgi Kansız ◽  
...  
Keyword(s):  
Organic Ligand ◽  
Antibacterial Activities ◽  
Structural Features ◽  
Bacterial Strains ◽  
Tetrahedral Geometry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Growth Inhibitory ◽  
The Difference

Reaction of N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide), C20H18F2N4O2, (LF ), with zinc chloride and mercury(II) chloride produced different types and shapes of neutral coordination complexes, namely, dichlorido[N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide)-κ2 N,O]zinc(II), [ZnCl2(C20H18F2N4O2)], (1), and dichlorido[N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide)-κ4 O,N,N′,O′]mercury(II), [HgCl2(C20H18F2N4O2)], (2). The organic ligand and its metal complexes are characterized using various techniques: IR, UV–Vis and nuclear magnetic resonance (NMR) spectroscopies, in addition to powder X-ray diffraction (PXRD), single-crystal X-ray crystallography and microelemental analysis. Depending upon the data from these analyses and measurements, a typical tetrahedral geometry was confirmed for zinc complex (1), in which the ZnII atom is located outside the bis(benzhydrazone) core. The HgII atom in (2) is found within the core and has a common octahedral structure. The in vitro antibacterial activities of the prepared compounds were evaluated against two different bacterial strains, i.e. gram positive Bacillus subtilis and gram negative Pseudomonas aeruginosa bacteria. The prepared compounds exhibited differentiated growth-inhibitory activities against these two bacterial strains based on the difference in their lipophilic nature and structural features.

scholarly journals Molecular mechanisms of enzyme dysfunction in human phosphoglucomutase-1 deficiency

2019 ◽  
Author(s):  
◽  
Kyle Matthew Stiers
Keyword(s):  
Molecular Mechanisms ◽  
Structural Features ◽  
Therapeutic Interventions ◽  
Structural Studies ◽  
X Ray ◽  
Missense Variants ◽  
X Ray Crystallography ◽  
Ancient Lineage ◽  
Research Opportunity

Human phosphoglucomutase-1 (PGM1) belongs to the [alpha]-D-phosphohexomutase superfamily, an ancient lineage of enzymes critical for carbohydrate metabolism. PGM1 catalyzes the interconversion of glucose-1-phosphate and glucose-6-phosphate, acting as the pivot between energy storage and utilization. Recently, PGM1 has been implicated as the monogenic cause of an inherited metabolic disease in humans, called PGM1 deficiency. The disease presents with highly variable phenotype in patients and is difficult to diagnose. Furthermore, genotype-phenotype relationships remain unclear-even in siblings with the same missense variants, no obvious correlation exists. PGM1 deficiency is a unique research opportunity due to the lack of clear rationale for varying effects of missense variants, availability of patient data, favorable in vitro behavior of recombinantly expressed PGM1, and the limited number of structural studies characterizing individual missense variants. In this work we have characterized multiple molecular mechanisms of disease through X-ray crystallography and biochemistry. Thus, this work provides a foundation for physicians to make much more accurate prognostic decisions when advising patients, identifies variants with possible therapeutic interventions, and informs us of key dynamics and structural features required for proper functioning of human PGM1.

scholarly journals Structural features and near infra-red (NIR) luminescence of isomeric Yb(iii) bipyridyl-N,N′-dioxide coordination polymers

2015 ◽  
Vol 44 (29) ◽  
pp. 13378-13383 ◽  
Author(s):  
Gail M. Sequeira ◽  
Wayne Y. Tan ◽  
Evan G. Moore
Keyword(s):  
Coordination Polymers ◽  
Structural Characterization ◽  
Lanthanide Complexes ◽  
Structural Features ◽  
X Ray ◽  
X Ray Crystallography ◽  
Infra Red ◽  
Nir Luminescence

The synthesis and structural characterization of a series of lanthanide complexes formed from YbX3 salts (X = NO3− or CF3SO3−) and the isomeric 4,4′-bipyridine-N,N′-dioxide (4,4′-bpdo) or 3,3′-bipyridine-N,N′-dioxide (3,3′-bpdo) ligands has been undertaken by X-ray crystallography.

scholarly journals Effect of the ruffled porphyrin ring on electronic structures: structure and characterization of [Fe(TalkylP)(OClO3)] and [Fe(TPrP)(THF)2]ClO4 (alkyl = Ethyl, Et and n-Propyl, Pr)

2013 ◽  
Vol 17 (01n02) ◽  
pp. 118-124 ◽  
Author(s):  
Ming Li ◽  
Allen G. Oliver ◽  
Teresa J. Neal ◽  
Charles E. Schulz ◽  
W. Robert Scheidt
Keyword(s):  
Electronic Structures ◽  
Structural Parameters ◽  
Structural Features ◽  
Magnetic Data ◽  
Porphyrin Ring ◽  
Magnetic Susceptibilities ◽  
X Ray ◽  
X Ray Crystallography ◽  
Intermediate Spin

We report the synthesis of Fe(TalkylP)(OClO3)] (alkyl = ethyl and propyl) and [Fe(TPrP)(THF)2]ClO4 , which are characterized by UV-vis, EPR, X-ray crystallography, and solid-state magnetic susceptibilities. The macrocycles of all three complexes are ruffled, all of the structural features for [Fe(TEtP(OClO3)] and [Fe(TPrP)(OClO3)] are characteristic of the nearly pure S = 3/2 state, while the structural parameters for [Fe(TPrP)(THF)2]ClO4 feature a pure intermediate-spin (S = 3/2) state, which are all consistent with EPR and magnetic data. It is clear from these studies that the ruffled conformation plays a significant role in affecting the extent of S = 3/2 character.

scholarly journals Preparation and Crystal Structure of a Rhenium Analogue of the Cationic Renal Agent, Tc-99m Diaminocyclohexane

2000 ◽  
Vol 7 (3) ◽  
pp. 141-145 ◽  
Author(s):  
Luigi G. Marzilli ◽  
Lory Hansen ◽  
Andrew Taylor ◽  
Rene Lachicotte
Keyword(s):  
Crystal Structure ◽  
Plasma Flow ◽  
Structural Parameters ◽  
Renal Plasma Flow ◽  
Chemical Study ◽  
Structural Features ◽  
Racemic Mixture ◽  
X Ray ◽  
X Ray Crystallography ◽  
Renal Agent

We report here a chemical study on a Re analogue of one of the few cationic Tc-99m tracers previously investigated as an agent for effective renal plasma flow (ERPF) measurement. Cationic Tc-99m tracers have the potential for overcoming problems associated with common anionic Tc-99m tracers in patients who have developed a uremic state. The Tc-99m-DACH tracer, prepared from 1,2-diaminocyclohexane (1,2-DACH), is the only cationic renal agent tested in humans and has seven possible isomers. The complex isolated from the reaction of the racemic mixture, (±)-trans-1,2-DACH, and ReIO2(PPh3)2 after conversion to the BPh4- salt was found by X-ray crystallography to be the meso isomer, trans-[ReO2 (trans-R,R-1,2-DACH)(trans-S,S-l,2-DACH)][BPh4]·MeOH·2H2O (1). The structural parameters for 1 are normal. The complex is highly symmetrical, suggesting that the analogous meso Tc-99m-DACH agent is also symmetrical. Studies of other Tc-99m-DACH agents that were made from cis-1,2-DACH or individual trans-1,2-DACH enantiomers show that the biodistribution is not very dependent on the starting 1,2-DACH ligand stereochemistry; these agents must be less symmetrical than the meso Tc-99m-DACH agent analogue of 1. Thus, the overall charge and lipophilicity (similar for all Tc-99m-DACH isomers) exert a greater influence on biodistribution than the specific structural features of the different Tc-99m-DACH isomers.

scholarly journals Investigation of the catalytic triad of arylamine N-acetyltransferases: essential residues required for acetyl transfer to arylamines

2005 ◽  
Vol 390 (1) ◽  
pp. 115-123 ◽  
Author(s):  
James Sandy ◽  
Adeel Mushtaq ◽  
Simon J. Holton ◽  
Pamela Schartau ◽  
Martin E. M. Noble ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Structural Model ◽  
Sequence Data ◽  
Structural Features ◽  
Catalytic Triad ◽  
Site Directed Mutagenesis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Acetyl Transfer ◽  
Insight Into

The NATs (arylamine N-acetyltransferases) are a well documented family of enzymes found in both prokaryotes and eukaryotes. NATs are responsible for the acetylation of a range of arylamine, arylhydrazine and hydrazine compounds. We present here an investigation into the catalytic triad of residues (Cys-His-Asp) and other structural features of NATs using a variety of methods, including site-directed mutagenesis, X-ray crystallography and bioinformatics analysis, in order to investigate whether each of the residues of the catalytic triad is essential for catalytic activity. The catalytic triad of residues, Cys-His-Asp, is a well defined motif present in several families of enzymes. We mutated each of the catalytic residues in turn to investigate the role they play in catalysis. We also mutated a key residue, Gly126, implicated in acetyl-CoA binding, to examine the effects on acetylation activity. In addition, we have solved the structure of a C70Q mutant of Mycobacterium smegmatis NAT to a resolution of 1.45 Å (where 1 Å=0.1 nm). This structure confirms that the mutated protein is correctly folded, and provides a structural model for an acetylated NAT intermediate. Our bioinformatics investigation analysed the extent of sequence conservation between all eukaryotic and prokaryotic NAT enzymes for which sequence data are available. This revealed several new sequences, not yet reported, of NAT paralogues. Together, these studies have provided insight into the fundamental core of NAT enzymes, and the regions where sequence differences account for the functional diversity of this family. We have confirmed that each of the three residues of the triad is essential for acetylation activity.

Magnetic Particles used in a New Approach for Designed Protein Crystallization

CrystEngComm ◽  
2021 ◽  
Author(s):  
Raquel dos Santos ◽  
Maria João Romão ◽  
Ana C A Roque ◽  
Ana Luisa Moreira Carvalho
Keyword(s):  
Structure Determination ◽  
Magnetic Particles ◽  
Protein Crystallization ◽  
Protein Structures ◽  
3D Structure ◽  
New Approach ◽  
X Ray ◽  
X Ray Crystallography ◽  
3D Structure Determination

After more than one hundred and thirty thousand protein structures determined by X-ray crystallography, the challenge of protein crystallization for 3D structure determination remains. In the quest for additives for...

scholarly journals Four-dimensional NOE-NOE spectroscopy of SARS-CoV-2 Main Protease to facilitate resonance assignment and structural analysis

2021 ◽  
Author(s):  
Angus J. Robertson ◽  
Jinfa Ying ◽  
Ad Bax
Keyword(s):  
Resonance Assignment ◽  
Structural Information ◽  
Structural Features ◽  
Structural Studies ◽  
Dipolar Relaxation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Main Protease ◽  
4D Noesy ◽  
Exchange Broadening

Abstract. Resonance assignment and structural studies of larger proteins by NMR can be challenging when exchange broadening, multiple stable conformations, and back-exchanging the fully deuterated chain pose problems. These difficulties arise for the SARS-CoV-2 Main Protease, a homodimer of 2×306 residues. We demonstrate that the combination of four-dimensional (4D) TROSY-NOESY-TROSY spectroscopy and 4D NOESY-NOESY-TROSY spectroscopy provides an effective tool for delineating the 1H-1H dipolar relaxation network. In combination with detailed structural information obtained from prior X-ray crystallography work, such data are particularly useful for extending and validating resonances assignments, as well as for probing structural features.

scholarly journals Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

2020 ◽  
Author(s):  
Haroldas Bagdonas ◽  
Daniel Ungar ◽  
Jon Agirre
Keyword(s):  
Structural Biology ◽  
Large Scale ◽  
3D Structure ◽  
Structure Validation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Glycosidic Bonds ◽  
Cryo Electron Microscopy ◽  
Structure Solution ◽  
Solution Methods

The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. Those aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: full-length glycan composition, including linkage details for the glycosidic bonds. These developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly-available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.

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