Characterization of a high-affinity sialic acid-specific CBM40 from Clostridium perfringens and engineering of a divalent form

2016 ◽  
Vol 473 (14) ◽  
pp. 2109-2118 ◽  
Author(s):  
João P. Ribeiro ◽  
William Pau ◽  
Carlo Pifferi ◽  
Olivier Renaudet ◽  
Annabelle Varrot ◽  
...  
Keyword(s):  
Surface Plasmon Resonance ◽  
Clostridium Perfringens ◽  
Carbohydrate Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Affinity ◽  
Carbohydrate Binding Modules ◽  
Dimeric Form ◽  
Calorimetric Studies

CBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens. Glycan arrays revealed its preference towards α(2,3)-linked sialosides, which was confirmed and quantified by calorimetric studies. The CBM40 binds to α(2,3)-sialyl-lactose with a Kd of ∼30 μM, the highest affinity value for this class of proteins. Inspired by lectins' structure and their arrangement as multimeric proteins, we have engineered a dimeric form of the CBM, and using SPR (surface plasmon resonance) we have observed 6–11-fold binding increases due to the avidity affect. The structures of the CBM, resolved by X-ray crystallography, in complex with α(2,3)- or α(2,6)-sialyl-lactose explain its binding specificity and unusually strong binding.

scholarly journals Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family

2021 ◽  
Vol 12 ◽  
Author(s):  
James Stevenson ◽  
Maria Ngo ◽  
Alicia Brandt ◽  
Joel T. Weadge ◽  
Michael D. L. Suits
Keyword(s):  
Domain Architecture ◽  
Gene Clusters ◽  
Major Constituent ◽  
Carbohydrate Binding ◽  
Galactosidase Activity ◽  
Bacteroides Thetaiotaomicron ◽  
X Ray ◽  
X Ray Crystallography ◽  
Terminal Domain ◽  
Carbohydrate Binding Modules

Bacteroides thetaiotaomicron is a major constituent of the human gut microbiome and recognized as a prolific degrader of diverse and complex carbohydrates. This capacity is due to the large number of glycan-depolymerization and acquisition systems that are encoded by gene clusters known as polysaccharide utilization loci (PUL), with the starch utilization system (Sus) serving as the established model. Sharing features with the Sus are Sus-like systems, that require the presence of a specific membrane transporter and surface lipoprotein to be classified as Sus-like. Sus-like import loci are extremely varied with respect to any additional protein components encoded, that would effectively modify the functionality of the degradative and import action of each locus. Herein we have identified eight Sus-like systems in B. thetaiotaomicron that share the feature of a homologous SusE-like factor encoded immediately downstream from the transporter/lipoprotein duo susC/D. Two SusE-like proteins from these systems, BT2857 and BT3158, were characterized by X-ray crystallography and BT2857 was further analyzed by small-angle X-ray scattering. The SusE-like proteins were found to be composed of a conserved three domain architecture: a partially disordered N-terminal domain that is predicted to be proximal to the membrane and structurally homologous to an FN3-like bundle, a middle β-sandwich domain, and a C-terminal domain homologous to family 32 carbohydrate-binding modules, that bind to galactose. Structural comparisons of SusE with SusE-like proteins suggested only a small structural divergence has occurred. However, functional analyses with BT2857 and BT3158 revealed that the SusE-like proteins exhibited galactosidase activity with para-nitrophenyl-β-D-galactopyranoside and α-(1,4)-lactose substrates, that has not been demonstrated for SusE proteins. Using a series of domain truncations of BT2857, the predominant β-D-galactosidase activity is suggested to be localized to the C-terminal DUF5126 domain that would be most distal from the outer membrane. The expanded functionality we have observed with these SusE-like proteins provides a plausible explanation of how Sus-like systems are adapted to target more diverse groups of carbohydrates, when compared to their Sus counterparts.

scholarly journals Molecular determinants of ligand specificity in family 11 carbohydrate binding modules - an NMR, X-ray crystallography and computational chemistry approach

FEBS Journal ◽  
2008 ◽  
Vol 275 (10) ◽  
pp. 2524-2535 ◽  
Author(s):  
Aldino Viegas ◽  
Natércia F. Brás ◽  
Nuno M. F. S. A. Cerqueira ◽  
Pedro Alexandrino Fernandes ◽  
José A. M. Prates ◽  
...  
Keyword(s):  
Computational Chemistry ◽  
Carbohydrate Binding ◽  
Ligand Specificity ◽  
X Ray ◽  
X Ray Crystallography ◽  
Carbohydrate Binding Modules ◽  
Molecular Determinants

scholarly journals Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

2021 ◽  
Author(s):  
Shabana Noor ◽  
Richard Goddard ◽  
Fehmeeda Khatoon ◽  
Sarvendra Kumar ◽  
Rüdiger W. Seidel
Keyword(s):  
Molecular Structure ◽  
Schiff Base ◽  
Structural Characterization ◽  
Schiff Base Ligand ◽  
Crystal And Molecular Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

scholarly journals Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

2012 ◽  
Vol 13 (8) ◽  
pp. 10537-10552 ◽  
Author(s):  
Vincent J. B. Ruigrok ◽  
Mark Levisson ◽  
Johan Hekelaar ◽  
Hauke Smidt ◽  
Bauke W. Dijkstra ◽  
...  
Keyword(s):  
Protein Complexes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Alternative Approaches

Structural determination and characterization of copper and zinc bis-glycinates with X-ray crystallography and mass spectrometry

2010 ◽  
Vol 63 (19) ◽  
pp. 3335-3347 ◽  
Author(s):  
Sanjit Konar ◽  
Kevin Gagnon ◽  
Abraham Clearfield ◽  
Charles Thompson ◽  
Jennifer Hartle ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Determination ◽  
X Ray ◽  
X Ray Crystallography ◽  
Copper And Zinc

Synthesis and structural characterization of a magnesium phthalocyanine(3–) anion

2012 ◽  
Vol 16 (01) ◽  
pp. 154-162 ◽  
Author(s):  
Edwin W.Y. Wong ◽  
Daniel B. Leznoff
Keyword(s):  
Absorption Spectrum ◽  
Solid State ◽  
Single Crystal ◽  
Structural Characterization ◽  
Heterometallic Complex ◽  
State Structure ◽  
Solid State Structure ◽  
X Ray ◽  
X Ray Crystallography

The reduction of magnesium phthalocyanine (MgPc) with 2.2 equivalents of potassium graphite in 1,2-dimethoxyethane (DME) gives [K2(DME)4]PcMg(OH)(1) in 67% yield. Compound 1 was structurally characterized using single crystal X-ray crystallography and was found to be a monomeric, heterometallic complex consisting of a μ3-OH ligand that bridges a [MgIIPc3-]- anion to two potassium cations solvated by four DME molecules. An absorption spectrum of 1 confirms the Pc ligand is singly reduced and has a 3–charge. The solid-state structure of 1 does not indicate breaking of the aromaticity of the Pc ligand. Compound 1 is only the second Pc3- complex and the first reduced MgPc to be isolated and structurally characterized.

Preparation and characterization of a new series of Cr(II) hydroborates

1995 ◽  
Vol 73 (7) ◽  
pp. 1126-1134 ◽  
Author(s):  
Michel Dionne ◽  
Shoukang Hao ◽  
Sandro Gambarotta
Keyword(s):  
Trinuclear Complex ◽  
Synthesis And Characterization ◽  
Crystal Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Quadruple Bond ◽  
Quadruple Bonds ◽  
Reaction Proceeds

The synthesis and characterization of a new series of mono-, di-, and trinuclear Cr(II) borohydride compounds is described. The reaction of CrCl2(TMEDA) with two equivalents of NaBH4 afforded the thermally unstable (TMEDA)Cr(BH4)2 (1), which was converted by treatment with pyridine into the octahedral monomeric (Py)4Cr(BH4)2 (2). The reaction proceeds via formation of an intermediate trinuclear complex {[(TMEDA)(Py)Cr(η2-BH4)]2[(Py)2Cr(η2-BH4)2]}(µ,η1-BH4)2 (3), which was isolated and characterized by X-ray crystallography. Reaction of 1 and 2 with both CO2 and RN=C=NR (R = Cy, iPr) afforded hydride insertion and formation of the corresponding diamagnetic lantern-type Cr(II) formate (HCO2)4Cr2Py2 (4) and formamidinate compounds [RNC(H)NR]2Cr2(µ-BH)4 (R = Cy (5a), iPr (5b)), respectively, with supershort Cr—Cr quadruple bonds. The structures of 1, 2, 3, and 5b were elucidated by X-ray analysis. Crystal data are as follows. 1: C6H24N2B2Cr, monoclinic, Cc, a = 8.517(2) Å, b = 15.921(5) Å, c = 9.624(2) Å, β = 115.59(1)°, Z = 4, R = 0.022, Rw = 0.029; 2: C28H44N4B2O2Cr, monoclinic, P21/n, a = 12.021(1) Å, b = 15.555(1) Å, c = 15.723(1) Å, β = 90.13(2)°, Z = 4, R = 0.074, Rw = 0.086; 3: C32H76N8B6Cr3, monoclinic, P21/n, a = 8.515(1) Å, b = 14.525(1) Å, c = 18.286(2) Å, β = 91.38(1)°, Z = 2, R = 0.051, Rw = 0.060; 5b: C21H49N6BCr2, monoclinic, C2/c, a = 17.000(1) Å, b = 9.033(1) Å, c = 19.160(1) Å, β = 105.579(9)°, Z = 4, R = 0.069, Rw = 0.078. Keywords: divalent chromium, borohydride, Cr—Cr quadruple bond.

Synthesis and characterization of the binuclear diamido titanium chalcogenides [(Ar)NCH2CH2CH2N(Ar)]2Ti(µ-E)2 (E = Se, Te)

2002 ◽  
Vol 80 (11) ◽  
pp. 1524-1529 ◽  
Author(s):  
Tianle Zhang ◽  
Warren E Piers ◽  
Masood Parvez
Keyword(s):  
Solid State ◽  
Key Words ◽  
Synthesis And Characterization ◽  
Catalyst Precursor ◽  
Tellurium Atom ◽  
Titanium Complex ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atom Source

Reaction of McConville's chelating amido titanium complex [(Ar)NCH2CH2CH2N(Ar)]Ti(CH3)2 (Ar = 2,6-i-Pr2C6H3) with either elemental Se or the tellurium atom source Te=PBu3 resulted in the formation of bis-µ-chalcogenido dimers [(Ar)NCH2CH2CH2N(Ar)]2Ti(µ-E)2 (E = Se, 2; Te, 3) with concommitant loss of EMe2. The dimers 2 and 3 were characterized spectroscopically and via X-ray crystallography. The two compounds are isostructural in the solid state. The tellurido dimer 3 may also be synthesized by reduction of the diamido dichloride [(Ar)NCH2CH2CH2N(Ar)]2TiCl2 with Na–Hg amalgam followed by treatment with Te=PBu3. This dimer is unreactive toward further Te=PBu3 or stannanes such as HSnBu3. Unlike decamethyltitanocene derivatives, the diamido complex is not an effective catalyst precursor for the heterohydrodecoupling of Te=PBu3 and HSnBu3.Key words: diamido titanium complexes, selenides, tellurides.

scholarly journals Characterization of reactive organometallic species via MicroED

2019 ◽  
Author(s):  
Christopher Jones ◽  
Matthew Asay ◽  
Lee Joon Kim ◽  
Jack Kleinsasser ◽  
Ambarneil Saha ◽  
...  
Keyword(s):  
Transition Metal ◽  
Metal Complexes ◽  
Transition Metal Complexes ◽  
Cryogenic Cooling ◽  
Structural Determination ◽  
X Ray ◽  
X Ray Crystallography ◽  
Diamagnetic Transition

Here we apply microcrystal electron diffraction (MicroED) to the structural determination of transition metal complexes. We find that the simultaneous use of 300 keV electrons, very low electron doses, and an ultra-sensitive camera allows for the collection of data without cryogenic cooling of the stage. This technique reveals the first crystal structures of the classic zirconocene hydride, colloquially known as “Schwartz’s reagent”, a novel Pd(II) complex not amenable to solution-state NMR or X-ray crystallography, and five other paramagnetic or diamagnetic transition metal complexes.

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