scholarly journals Structure of a protective epitope reveals the importance of acetylation ofNeisseria meningitidisserogroup A capsular polysaccharide

2020 ◽  
Vol 117 (47) ◽  
pp. 29795-29802
Author(s):  
Pedro Henriques ◽  
Lucia Dello Iacono ◽  
Ana Gimeno ◽  
Alessia Biolchi ◽  
Maria Rosaria Romano ◽  
...  
Keyword(s):  
Rational Design ◽  
Capsular Polysaccharide ◽  
Enzyme Linked Immunosorbent Assay ◽  
Mortality And Morbidity ◽  
X Ray ◽  
In Silico Docking ◽  
X Ray Crystallography ◽  
Protective Epitope ◽  
Serum Bactericidal Assay ◽  
Shed Light

Meningococcal meningitis remains a substantial cause of mortality and morbidity worldwide. Until recently, countries in the African meningitis belt were susceptible to devastating outbreaks, largely attributed to serogroup ANeisseria meningitidis(MenA). Vaccination with glycoconjugates of MenA capsular polysaccharide led to an almost complete elimination of MenA clinical cases. To understand the molecular basis of vaccine-induced protection, we generated a panel of oligosaccharide fragments of different lengths and tested them with polyclonal and monoclonal antibodies by inhibition enzyme-linked immunosorbent assay, surface plasmon resonance, and competitive human serum bactericidal assay, which is a surrogate for protection. The epitope was shown to optimize between three and six repeating units and to beO-acetylated. The molecular interactions between a protective monoclonal antibody and a MenA capsular polysaccharide fragment were further elucidated at the atomic level by saturation transfer difference NMR spectroscopy and X-ray crystallography. The epitope consists of a trisaccharide anchored to the antibody via theO- andN-acetyl moieties through either H-bonding or CH–π interactions. In silico docking showed that 3-O-acetylation of the upstream residue is essential for antibody binding, whileO-acetate could be equally accommodated at three and four positions of the other two residues. These results shed light on the mechanism of action of current MenA vaccines and provide a foundation for the rational design of improved therapies.

Examining the structure of the mature amyloid fibril

2002 ◽  
Vol 30 (4) ◽  
pp. 521-525 ◽  
Author(s):  
O. S. Makin ◽  
L. C. Serpell
Keyword(s):  
Self Assembly ◽  
Rational Design ◽  
Amyloid Fibrils ◽  
Structural Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Fibre Diffraction ◽  
Complementary Techniques ◽  
Mature Fibril

The pathogenesis of the group of diseases known collectively as the amyloidoses is characterized by the deposition of insoluble amyloid fibrils. These are straight, unbranching structures about 70–120 å (1 å = 0.1 nm) in diameter and of indeterminate length formed by the self-assembly of a diverse group of normally soluble proteins. Knowledge of the structure of these fibrils is necessary for the understanding of their abnormal assembly and deposition, possibly leading to the rational design of therapeutic agents for their prevention or disaggregation. Structural elucidation is impeded by fibril insolubility and inability to crystallize, thus preventing the use of X-ray crystallography and solution NMR. CD, Fourier-transform infrared spectroscopy and light scattering have been used in the study of the mechanism of fibril formation. This review concentrates on the structural information about the final, mature fibril and in particular the complementary techniques of cryo-electron microscopy, solid-state NMR and X-ray fibre diffraction.

scholarly journals The grease trap: uncovering the mechanism of the hydrophobic lid in Cutibacterium acnes lipase

2020 ◽  
Vol 61 (5) ◽  
pp. 722-733
Author(s):  
Hyo Jung Kim ◽  
Bong-Jin Lee ◽  
Ae-Ran Kwon
Keyword(s):  
Lipase Activity ◽  
Current Management ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cutibacterium Acnes ◽  
Open Structures ◽  
Type Ia ◽  
Future Drug ◽  
Lid Domain ◽  
Shed Light

Acne is one of the most common dermatological conditions, but the details of its pathology are unclear, and current management regimens often have adverse effects. Cutibacterium acnes is known as a major acne-associated bacterium that derives energy from lipase-mediated sebum lipid degradation. C. acnes is commensal, but lipase activity has been observed to differ among C. acnes types. For example, higher populations of the type IA strains are present in acne lesions with higher lipase activity. In the present study, we examined a conserved lipase in types IB and II that was truncated in type IA C. acnes strains. Closed, blocked, and open structures of C. acnes ATCC11828 lipases were elucidated by X-ray crystallography at 1.6–2.4 Å. The closed crystal structure, which is the most common form in aqueous solution, revealed that a hydrophobic lid domain shields the active site. By comparing closed, blocked, and open structures, we found that the lid domain-opening mechanisms of C. acnes lipases (CAlipases) involve the lid-opening residues, Phe-179 and Phe-211. To the best of our knowledge, this is the first structure-function study of CAlipases, which may help to shed light on the mechanisms involved in acne development and may aid in future drug design.

Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development

2020 ◽  
Vol 60 (1) ◽  
pp. 51-71 ◽  
Author(s):  
Javier García-Nafría ◽  
Christopher G. Tate
Keyword(s):  
Membrane Proteins ◽  
G Protein ◽  
Rational Design ◽  
Protein Complexes ◽  
Host Cells ◽  
X Ray ◽  
X Ray Crystallography ◽  
Receptor Modulation ◽  
Lipid Environment ◽  
Drug Receptors

Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein–coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR–G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR–G protein selectivity, how accessory membrane proteins alter receptor–ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.

Huprine Derivatives as Sub-Nanomolar Human Acetylcholinesterase Inhibitors: From Rational Design to Validation by X-ray Crystallography

ChemMedChem ◽  
2011 ◽  
Vol 7 (3) ◽  
pp. 400-405 ◽  
Author(s):  
Cyril Ronco ◽  
Eugénie Carletti ◽  
Jacques-Philippe Colletier ◽  
Martin Weik ◽  
Florian Nachon ◽  
...  
Keyword(s):  
Rational Design ◽  
Acetylcholinesterase Inhibitors ◽  
X Ray ◽  
X Ray Crystallography

Tuning of crystallization method and ligand conformation to give a mononuclear compound or two-dimensional SCO coordination polymer based on a new semi-rigid V-shaped bis-pyridyl bis-amide ligand

2020 ◽  
Vol 76 (5) ◽  
pp. 412-418
Author(s):  
Xiaoyun Hao ◽  
Yong Dou ◽  
Tong Cao ◽  
Lan Qin ◽  
Lu Yang ◽  
...  
Keyword(s):  
Coordination Polymer ◽  
Single Crystal ◽  
Rational Design ◽  
High Spin State ◽  
Structure Type ◽  
Two Dimensional ◽  
Thermally Induced ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ligand Conformation

With the new semi-rigid V-shaped bidentate pyridyl amide compound 5-methyl-N,N′-bis(pyridin-4-yl)benzene-1,3-dicarboxamide (L) as an auxiliary ligand and the FeII ion as the metal centre, one mononuclear complex, bis(methanol-κO)bis[5-methyl-N,N′-bis(pyridin-4-yl)benzene-1,3-dicarboxamide-κN]bis(thiocyanato-κN)iron(II), [Fe(SCN)2(C19H16N4O2)2(CH3OH)2] (1), and one two-dimensional coordination polymer, catena-poly[[[bis(thiocyanato-κN)iron(II)]-bis[μ-5-methyl-N,N′-bis(pyridin-4-yl)benzene-1,3-dicarboxamide-κ2 N:N′]] methanol disolvate dihydrate], {[Fe(SCN)2(C19H16N4O2)2]·2CH3OH·2H2O} n (2), were prepared by slow evaporation and H-tube diffusion methods, respectively, indicating the effect of the method of crystallization on the structure type of the target product. Both complexes have been structurally characterized by elemental analysis, IR spectroscopy and single-crystal X-ray crystallography. The single-crystal X-ray diffraction analysis shows that L functions as a monodentate ligand in mononuclear 1, while it coordinates in a bidentate manner to two independent Fe(SCN)2 units in complex 2, with a different conformation from that in 1 and the ligands point in two almost orthogonal directions, therefore leading to a two-dimensional grid-like network. Investigation of the magnetic properties reveals the always high-spin state of the FeII centre over the whole temperature range in 1 and a gradual thermally-induced incomplete spin crossover (SCO) behaviour below 150 K in 2, demonstrating the influence of the different coordination fields on the spin properties of the metal ions. The current results provide useful information for the rational design of functional complexes with different structure dimensionalities by employing different conformations of the ligand and different crystallization methods.

Robust Antibody–Antigen Complexes Prediction Generated by Combining Sequence Analyses, Mutagenesis, In Vitro Evolution, X-ray Crystallography and In Silico Docking

2015 ◽  
Vol 427 (16) ◽  
pp. 2647-2662 ◽  
Author(s):  
Jérémy Loyau ◽  
Gérard Didelot ◽  
Pauline Malinge ◽  
Ulla Ravn ◽  
Giovanni Magistrelli ◽  
...  
Keyword(s):  
In Silico ◽  
Sequence Analyses ◽  
In Vitro Evolution ◽  
X Ray ◽  
In Silico Docking ◽  
X Ray Crystallography

scholarly journals Synthesis of thiadiazolobenzamide via cyclization of thioxothiourea and its Ni and Pd complexes

2012 ◽  
Vol 77 (9) ◽  
pp. 1211-1222 ◽  
Author(s):  
Forogh Adhami ◽  
Nasim Nabilzadeh ◽  
Franziska Emmerling ◽  
Mina Ghiasi ◽  
Majid Heravi
Keyword(s):  
Mass Spectrometry ◽  
Hydrogen Sulfide ◽  
Membered Ring ◽  
X Ray ◽  
X Ray Crystallography ◽  
Thermal Gravimetry ◽  
Pd Complexes ◽  
Benzoyl Isothiocyanate ◽  
Shed Light

In this study, the new compound, N-(3-methyl-4- oxo[1,3,4]thiadiazolo[2,3-c][1,2,4]triazin-7-yl) benzamide, could be obtained via two different reactions: 1) reaction of 4-amino-6-Methyl-3- (Methylsulfanyl)-1,2,4-triazin-5-one with benzoyl isothiocyanate under removal of methylmercaptane, 2) reaction of 4-amino-6-Methyl-3-thioxo- 1,2,4-triazin-5-one with benzoyl isothiocyanate under elimination of hydrogen sulfide. In both reactions a new bond between sulfur and nitrogen atoms was formed and a five-membered ring was created. The oxo thiadiazolo benzamide was characterized by IR-, 1HNMR- and 13CNMR spectroscopy as well as by Mass spectrometry. X-ray crystallography was used to shed light on the structure of this new compound. Two new complexes could be generated by coordination of oxo thiadiazolo benzamide to Pd(II) and Ni(II) ions. These complexes have been analyzed by IR-, 1HNMR- and 13CNMR spectroscopy, conductometry and Thermal gravimetry (TGA). Theoretical QM Calculation GIAO has also been applied to predict the structure of the Pd complex.

scholarly journals Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

2021 ◽  
Vol 7 (21) ◽  
pp. eabg4168
Author(s):  
Jianhong Yang ◽  
Yamei Yu ◽  
Yong Li ◽  
Wei Yan ◽  
Haoyu Ye ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Stability ◽  
New Generation ◽  
Antimicrotubule Drugs ◽  
Degradation Effect ◽  
Microtubule Stabilizing Agent ◽  
Shed Light

Microtubules, composed of αβ-tubulin heterodimers, have remained popular anticancer targets for decades. Six known binding sites on tubulin dimers have been identified thus far, with five sites on β-tubulin and only one site on α-tubulin, hinting that compounds binding to α-tubulin are less well characterized. Cevipabulin, a microtubule-active antitumor clinical candidate, is widely accepted as a microtubule-stabilizing agent by binding to the vinblastine site. Our x-ray crystallography study reveals that, in addition to binding to the vinblastine site, cevipabulin also binds to a new site on α-tubulin. We find that cevipabulin at this site pushes the αT5 loop outward, making the nonexchangeable GTP exchangeable, which reduces the stability of tubulin, leading to its destabilization and degradation. Our results confirm the existence of a new agent binding site on α-tubulin and shed light on the development of tubulin degraders as a new generation of antimicrotubule drugs targeting this novel site.

scholarly journals Genetic and Serologic Evaluation of Capsule Production by Bovine Mammary Isolates of Staphylococcus aureus and Other Staphylococcus spp. from Europe and the United States

2000 ◽  
Vol 38 (8) ◽  
pp. 2998-3003 ◽  
Author(s):  
T. Tollersrud ◽  
K. Kenny ◽  
A. J. Reitz ◽  
J. C. Lee
Keyword(s):  
United States ◽  
Staphylococcus Aureus ◽  
Rational Design ◽  
Capsular Polysaccharide ◽  
Bovine Mastitis ◽  
The United States ◽  
Economic Losses ◽  
Enzyme Linked Immunosorbent Assay ◽  
Capsule Production ◽  
Many Sources

Bovine mastitis caused by Staphylococcus aureus is responsible for major economic losses to the dairy industry, and more-effective therapeutic or preventive approaches are sorely needed. The predominance of staphylococcal capsular polysaccharide types 5 and 8 among human isolates from many sources is well documented, but there seems to be a greater variation in the distribution of capsular serotypes among isolates from cows. A total of 636 isolates of S. aureus from cases of bovine mastitis in Sweden, Denmark, Finland, Iceland, Ireland, and the United States were investigated for production of capsular polysaccharide types 5 and 8. Approximately half of all the European isolates tested were of serotype 8, although variation among countries and among isolates of clinical and subclinical origin was observed. Sweden had the highest frequency (87%) of serotypeable isolates, and Finland had the lowest (48%). Capsule types 5 and 8 accounted for only 42% of the U.S. isolates tested. A few isolates showed weak reactivity with CP5 antiserum in a colony blot assay, and an enzyme-linked immunosorbent assay inhibition method confirmed that the levels of capsule produced by these strains were <10% of those produced by control strains. Fifty isolates that failed to react with capsular antisera all possessed the genes for production of capsular polysaccharide type 5 or 8. These results underscore the variability in capsule production by bovine isolates ofS. aureus from different geographic regions. This information is important for the rational design of a capsule-based vaccine to prevent S. aureus bovine mastitis.

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