Plasma cell rich acute rejection: Risk factors, treatment and outcomes.

Plasma cell-rich rejection is a rare and poorly defined entity. Its treatment is not clearly defined and has universally poor prognosis. More data should be published from various transplant centers around the world to identify the treatment that has the best outcomes and to formulate treatment guidelines for these cases. It is a retrospective analysis of kidney biopsies form 2008 to 2018. Four hundred biopsied were screened and 55 were found to have features of rejection and among them, 13 had plasma cell-rich rejection. Data of treatment given and the graft survival outcomes in these cases were retrieved by medical records. One patient had complete recovery, three had graft loss and the remaining nine had permanent decline in glomerular filtration rate. Decrease in immunosuppression and presence of infection are risk factors for plasma cell-rich acute rejection (PCAR). It can be acute cell-mediated rejection (ACR)/antibody-mediated rejection (AMR)/ACR+AMR. Resistant rejection, ACR+AMR, C4d positivity, and severe interstitial inflammation are poor prognostic factors. Overzealous decrease in immunosuppression should not be done. Management of immunosuppression during infection is most critical for the development of PCAR. Bortezomib is emerging as a therapeutic modality for the treatment of PCAR.

Two small, cysteine-rich and cationic antifungal proteins from Penicillium chrysogenum: A comparative study of PAF and PAFB.

The filamentous fungus Penicillium chrysogenum Q176 secretes the antimicrobial proteins (AMPs) PAF and PAFB, which share a compact disulfide-bond mediated, ß-fold structure rendering them highly stable. These two AMPs effectively inhibit the growth of human pathogenic fungi in micromolar concentrations and exhibit antiviral potential without causing cytotoxic effects on mammalian cells in vitro and in vivo. The antifungal mechanism of action of both AMPs is closely linked to - but not solely dependent on - the lipid composition of the fungal cell membrane and requires a strictly regulated protein uptake into the cell, indicating that PAF and PAFB are not canonical membrane active proteins. Variations in their antifungal spectrum and their killing dynamics point towards a divergent mode of action related to their physicochemical properties and surface charge distribution. In this review, we relate characteristic features of PAF and PAFB to the current knowledge about other AMPs of different sources. In addition, we present original data that have never been published before to substantiate our assumptions and provide evidences that help to explain and understand better the mechanistic function of PAF and PAFB. Finally, we underline the promising potential of PAF and PAFB as future antifungal therapeutics.

[New derivatives of eremomycin containing (15)n or f atoms for NMR study].

New semisynthetic derivatives of eremomycin containing (15)N or F atom were obtained for studying the antibiotic-target interaction in intact cells of Gram-positive bacteria by REDOR NMR method. Interaction of the terminal carboxyl group of amino acid 7 (AA7) of eremomycin with amines in the presence of PyBOP and TBTU reagents resulted in the corresponding [(15)N]-amide, p-fluorobenzylamide, p-fluorophenylpiperazide, and 6-N-(p-fluorobenzyl)aminohexylamide. A selective method of [(15)N]-amidation of carboxyl group of amino acid 3 (AA3) of carboxyeremomycin was developed, and the amide of eremomycin containing [(15)N] in AA3 amide group near the antibiotic binding pocket was obtained. Carboxyeremomycin bisamides substituted at AA3 and AA7 and containing two atoms of [(15)N] or F were obtained from carboxyeremomycin and [(15)N]NH4Cl or the corresponding p-fluorobenzylamine hydrochloride in the presence of PyBOP at pH ~8. The Edman degradation of eremomycin p-fluorobenzylamide gave de-(D-MeLeu)-eremomycin p-fluorobenzylamide, a hexapeptide derivative incapable of the antibiotic binding with -D-Ala-D-Ala fragment of growing cell wall peptidoglycan. Among the compounds studied, carboxyeremomycin bis-p-fluorobenzylamide showed the best activity against both the glycopeptides-sensitive and glycopeptides-resistant strains of staphylococci and enterococci.

The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition.

Human pancreatic ribonuclease (RNase 1) is expressed in many tissues; has several important enzymatic and biological activities, including efficient cleavage of single-stranded RNA, double-stranded RNA and double-stranded RNA-DNA hybrids, digestion of dietary RNA, regulation of vascular homeostasis, inactivation of the HIV, activation of immature dendritic cells and induction of cytokine production; and furthermore shows potential as an anti-tumor agent. The solution structure and dynamics of uncomplexed, wild-type RNase 1 have been determined by NMR spectroscopy methods to better understand these activities. The family of 20 structures determined on the basis of 6115 unambiguous nuclear Overhauser enhancements is well resolved (pairwise backbone RMSD=1.07 A) and has the classic RNase A type of tertiary structure. Important structural differences compared with previously determined crystal structures of RNase 1 variants or inhibitor-bound complexes are observed in the conformation of loop regions and side chains implicated in the enzymatic as well as biological activities and binding to the cytoplasmic RNase inhibitor. Multiple side chain conformations observed for key surface residues are proposed to be crucial for membrane binding as well as translocation and efficient RNA hydrolysis. (15)N-(1)H relaxation measurements interpreted with the standard and our extended Lipari-Szabo formalism reveal rigid regions and identify more dynamic loop regions. Some of the most dynamic areas are key for binding to the cytoplasmic RNase inhibitor. This finding and the important differences observed between the structure in solution and that bound to the inhibitor are indications that RNase 1 to inhibitor binding can be better described by the "induced fit" model rather than the rigid "lock-into-key" mechanism. Translational diffusion measurements reveal that RNase 1 is predominantly dimeric above 1 mM concentration; the possible implications of this dimeric state for the remarkable biological properties of RNase 1 are discussed.

Characterisation of two novel fork-head gene homologues of Schizosaccharomyces pombe: their involvement in cell cycle and sexual differentiation.

The fork-head type transcription factors are a class of regulators that function in a broad spectrum of cellular and developmental processes in many species ranging from yeasts to human. Previous data on yeast fork-head genes suggested roles for these regulators in the control of cell division, sexual differentiation and development. The genome of Schizosaccharomyces pombe has four genes that code for proteins containing fork-head domains (FKH), two of which have been characterised. Here we describe the remaining two genes, fhl1 and fkh2, that code for proteins containing fork-head-associated domains (FHA) besides their FKHs. Neither of them is essential for viability, although the deletion of either fhl1 (putative homologue of Saccharomyces cerevisiae FHL1) or fkh2 (similar to FKH1 and FKH2 of S. cerevisiae) reduced the growth rate and caused an extension of cell length due to delayed G2-to-M transition. Occasionally, multiseptate cells were also produced, indicating the involvement of fhl1 and fkh2 in efficient septum cleavage. The fkh2Delta cells were slightly more sensitive than the wild-type cells to certain environmental stresses, showed reduced fertility and occasional deficiencies in meiosis II, indicating that fkh2 might also act in stress response and sexual differentiation.

Structural and biochemical characterization of neuronal calretinin domain I-II (residues 1-100). Comparison to homologous calbindin D28k domain I-II (residues 1-93).

This study characterizes the calcium-bound CR I-II domain (residues 1-100) of rat calretinin (CR). CR, with six EF-hand motifs, is believed to function as a neuronal intracellular calcium-buffer and/or calcium-sensor. The secondary structure of CR I-II, defined by standard NMR methods on 13C,15N-labeled protein, contains four helices and two short interacting segments of extended structure between the calcium-binding loops. The linker between the two helix-loop-helix, EF-hand motifs is 12 residues long. Limited trypsinolysis at K60 (there are 10 other K/R residues in CR I-II) confirms that the linker of CR I-II is solvent-exposed and that other potential sites are protected by regular secondary structure. 45Ca-overlay of glutathione S-transferase (GST)-CR(1-60) and GST-CR(61-100) fusion proteins confirm that both EF-hands of CR I-II have intrinsic calcium-binding properties. The primary sequence and NMR chemical shifts, including calcium-sensitive glycine residues, also suggest that both EF-hand loops of CR I-II bind calcium. NMR relaxation, analytical ultracentrifugation, chemical cross-linking and NMR translation diffusion measurements indicate that CR I-II exists as a monomer. Calb I-II (the homologous domain of calbindin D28k) has the same EF-hand secondary structures as CR I-II, except that helix B is three residues longer and the linker has only four residues [Klaus, W., Grzesiek, S., Labhardt, A. M., Buckwald, P., Hunziker, W., Gross, M. D. & Kallick, D. A. (1999) Eur. J. Biochem. 262, 933-938]. In contrast, Calb I-II binds one calcium cation per monomeric unit and exists as a dimer. Despite close homology and similar secondary structures, CR I-II and Calb I-II probably have distinct tertiary structure features that suggest different cellular functions for the full-length proteins.

Synthesis of the alpha-L-Araf-(1-->2)-beta-D-Galp-(1-->6)-beta-D-Galp-(1-->6)-[alpha-L-Araf-(1-->2)]-beta-D-Galp-(1-->6)-D-Gal hexasaccharide as a possible repeating unit of the cell-cultured exudates of Echinacea purpurea arabinogalactan.

For the characterization of the supposed epitope of an arabinogalactan, isolated from the extract of the cell-cultured Echinacea purpurea, the title hexasaccharide was synthesized. The whole synthetic route was based on the 6-O-(methoxydimethyl)methyl ether (MIP) protecting group strategy. 2-O-Benzyl-3,4-O-isopropylidene-6-O-(methoxydimethyl)methyl-beta-D-galactopyranosyl-(1-->6)-1,2:3,4-di-O-isopropylidene-alpha-D-galactopyranose was used to prepare the desired glycosyl donor and glycosyl acceptor both carrying a persistent O-benzyl group at position 2'. Reaction of the digalactose donor and the digalactose acceptor resulted in a beta-(1-->6)-linked galactose-containing tetrasaccharide in which OH-2' and OH-2"' were substituted with benzyl groups. Hydrogenolytic removal of the benzyl groups of the tetragalactose compound gave the diol aglycon which was diarabinosylated in one step to furnish the protected target compound, whose deprotection led to the title hexasaccharide. All of the synthesized compounds were characterized by 1H and 13C NMR spectra, as well as by MALDI-TOF mass-spectrometry measurements.

A new mixed acetal-type substitution pattern for alpha-cyclodextrin. Preparation of hexakis (3-O-benzyl)- alpha-cyclodextrin.

alpha-CD was converted into hexakis[2,6-di-O-(methoxydimethyl)methyl]-alpha-CD by a proton-catalyzed reaction with 2-methoxypropene. Subsequent benzylation under Brimacombe conditions resulted in the fully protected compound, from which the acid-sensitive acetal groups were removed to obtain hexakis(3-O-benzyl)-alpha-cyclodextrin. The structure of all of the compounds synthesized was confirmed by 13C J-ECHO, COSY, HETCOR and HMBC NMR measurements.

J-modulated TROSY experiment extends the limits of homonuclear coupling measurements for larger proteins.

This paper describes the use of a TROSY experimental scheme and its variant extended with a scaled J-modulation spin-echo sequence for accurate and sensitive measurement of homonuclear 3J(H(N)H(alpha)) coupling constants in larger proteins with uniform 15N labeling. Exclusive selection of the most slowly relaxing component of a 15N-1H multiplet by the TROSY approach leads to substantial improvement in resolution; this is a prerequisite for accurate measurement of couplings from the 1H multiplets directly along the 1H frequency dimension or from the J-scaled doublets along the 15N frequency dimension.

Separating structure and dynamics in CSA/DD cross-correlated relaxation: a case study on trehalose and ubiquitin.

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of (13)C CSA and (13)C-(1)H dipolar coupling in a disaccharide, alpha,alpha-D-trehalose, at natural abundance of (13)C as well as interference of amide (15)N CSA and (15)N-(1)H dipolar coupling in uniformly (15)N-labeled ubiquitin. We demonstrate that the standard heteronuclear T(1), T(2), and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.

NMR spectroscopy, molecular dynamics, and conformation of a synthetic octasaccharide fragment of the O-specific polysaccharide of Shigella dysenteriae type 1.

A synthetic octasaccharide fragment (2) of the O-specific polysaccharide (1) of Shigella dysenteriae type 1 has been studied as its methyl glycoside by one- and two-dimensional homo- and heteronuclear NMR spectroscopy. Complete 1H and 13C NMR assignments have been generated, and the 13C spin-lattice relaxation times have been measured for the octasaccharide 2. A congener (6) of this octasaccharide containing one D-galactose residue with a specific 13C label at C-1 has been synthesized and used to measure interglycosidic 13C-1H coupling by the 2D J-resolved 1H NMR method. From the NMR data, three types of conformational restraints were developed: (a) 29 inter-residue, distance restraints; (b) 48 intra-residue, ring atom dihedral angle restraints, and (c) one heteronuclear, inter-residue dihedral angle restraint. The use of these restraints in a restrained molecular dynamics computation with simulated annealing yielded a conformation resembling a short, irregular spiral, with methyl substituents on the exterior.

Synthesis of the repeating unit of the O-specific polysaccharide of Shigella sonnei and quantitation of its serologic activity.

The chemical synthesis of the zwitterionic disaccharide 2 is described that corresponds to the repeating unit of the O-specific polysaccharide (1) of the gram-negative human pathogen Shigella sonnei. Passive hemolysis inhibition tests using a hyperimmune rabbit serum raised against S. sonnei showed that the serologic activity of the disaccharide 2 is nearly 2- to 3-fold higher than those of its component monosaccharides. NMR data of 2 are in support of the proposed structure of the O-specific polysaccharide.

A general scheme for suppression of ABX strong coupling signals in heteronuclear scalar and dipolar correlation experiments.

Enhanced versions of heteronuclear chemical shift correlation experiments which yield high-quality spectra with efficient suppression of extra peaks arising from strong coupling effects are proposed. The enhanced pulse sequences feature properly designed filtering schemes inserted during preparation, or prior to acquisition, or at both places depending on the particular experiment. These modifications extend the applicability of existing methods, since they exclude misinterpretation of spurious peaks and allow unambiguous assignment of the desired correlations. The general applicability of the filtering method is noteworthy; both scalar- and dipolar-correlated experiments with both X and 1H detection using phase cycling or gradient pulses for coherence selection can be freed of strong coupling artifacts.

A comparison of 1D and 2D (unbiased) experimental methods for measuring CSA/DD cross-correlated relaxation.

Conventional and enhanced 1D experiments and different NOESY experiments (the 2D unbiased method) were performed for measuring CSA/DD cross-correlated relaxation on trehalose, a compound which could be approximated as a spherical top, and on simple model compounds comprising C3v symmetry (CHCl3, triphenylsilane (TPSi)). The comparison gives experimental evidence for the equivalence of the methods within the limits of the two-spin approach. 1D data are evaluated with both the simple initial rate and the Redfield relaxation matrix approach. The 2D data are obtained from the so-called transfer matrix using the Perrin-Gipe eigenvalue/eigenvector method. For the improved performance of the 2D method, an X-filtered (HHH) NOESY is suggested at the natural abundance of 13C (or other dilute, low gamma species). Also, experimental parameters crucial for reliable CSA data are tested (e. g., the impact of insufficient relaxation delay). Error estimation is carried out for fair comparison of methods. Revised liquid state 1H and 13C (29Si) CSA data are presented for chloroform and TPSi.

Sensitivity- and gradient-enhanced hetero (omega1) half-filtered TOCSY experiment for measuring long-range heteronuclear coupling constants.

An enhanced version of the X (omega1) half-filtered TOCSY experiment for measurement of long-range heteronuclear coupling constants is proposed which yields high-quality spectra with substantially increased sensitivity and resolution. The modified method features gradient-enhanced X filtering sequences, broadband homonuclear decoupling during t1, optional 1JXH scaling in the F1 domain, and gradient coherence selection in combination with the sensitivity-enhanced protocol for the TOCSY transfer. These modifications extend the applicability of the method--coupling constants can be measured accurately for natural abundance samples at low concentrations and for compounds yielding complex spectra. Computer-aided analysis of E.COSY-type multiplets is applied for the determination of heteronuclear long-range coupling constants.

Chemical synthesis and structural study of lincomycin sulfoxides and a sulfone.

Oxidation of lincomycin with dimethyldioxirane resulted in the sulfoxide-glycosides 3a and 3b, whose treatment with osmium tetraoxide and N-methylmorpholine-N-oxide afforded the same sulfone; 4. According to FAB-MS and CD investigations, the absolute configuration of the sulfur atom in 3a and 3b is R and S, respectively. The new, unsaturated antibiotic analog (6) derived from clindamycin exists in the 4C1 conformation. The antibiotic activities of the synthesized compounds were also studied.

Syntheses of spacer-armed carbohydrate components of the Mycobacterium avium serocomplex serovar 8.

p-Nitrophenyl glycosides of 3-O-Me-beta-D-Glcp-(1-->3)-alpha-L-Rhap, alpha-L-Rhap-(1-->2)-6-deoxy-alpha-L-Talp, and 3-O-Me-beta-D-Glcp-(1-->3)-alpha-L-Rhap-(1-->2)-6-deoxy-alpha-L-++ +Talp have been prepared, related to Mycobacterium avium. Various glycosylation methods have been used for the formation of the interglycosidic linkages. The p-nitrophenyl derivatives were converted into p-isothiocyanatophenyl glycosides, capable of forming neoglycoproteins.