202 research outputs found
Crystal structure of human pFGE, the paralog of the C alpha-formylglycine-generating enzyme
No full textDickmanns A, Schmidt B, Rudolph MG, et al. Crystal structure of human pFGE, the paralog of the C alpha-formylglycine-generating enzyme. JOURNAL OF BIOLOGICAL CHEMISTRY. 2005;280(15):15180-15187.In eukaryotes, sulfate esters are degraded by sulfatases, which possess a unique C alpha-formylglycine residue in their active site. The defect in post-translational formation of the C alpha-formylglycine residue causes a severe lysosomal storage disorder in humans. Recently, FGE (formylglycine-generating enzyme) has been identified as the protein required for this specific modification. Using sequence comparisons, a protein homologous to FGE was found and denoted pFGE (paralog of FGE). pFGE binds a sulfatase-derived peptide bearing the FGE recognition motif, but it lacks formylglycine-generating activity. Both proteins belong to a large family of pro- and eukaryotic proteins containing the DUF323 domain, a formylglycine-generating enzyme domain of unknown three-dimensional structure. We have crystallized the glycosylated human pFGE and determined its crystal structure at a resolution of 1.86 angstrom. The structure reveals a novel fold, which we denote the FGE fold and which therefore serves as a paradigm for the DUF323 domain. It is characterized by an asymmetric partitioning of secondary structure elements and is stabilized by two calcium cations. A deep cleft on the surface of pFGE most likely represents the sulfatase polypeptide binding site. The asymmetric unit of the pFGE crystal contains a homodimer. The putative peptide binding site is buried between the monomers, indicating a biological significance of the dimer. The structure suggests the capability of pFGE to form a heterodimer with FGE
FIGURE 4 in Description of a new species, Toxorhynchites (Toxorhynchites) tyagii (Diptera: Culicidae), from Nilgiri hills, Western Ghats, southern India
No full textFIGURE 4. Male genitalia of Toxorhynchites tyagii, sp. n. A, Dorsal aspect; B, basal mesal lobe; C, tergum IX.Published as part of <i>Krishnamoorthy, R., Munirathinam, A., Dhananjeyan, K.J., Hiriyan, J., Mariappan, T., Samuel, P. Philip & Venkatesh, A., 2013, Description of a new species, Toxorhynchites (Toxorhynchites) tyagii (Diptera: Culicidae), from Nilgiri hills, Western Ghats, southern India, pp. 447-459 in Zootaxa 3701 (4)</i> on page 453, DOI: 10.11646/zootaxa.3701.4.4, <a href="http://zenodo.org/record/10099074">http://zenodo.org/record/10099074</a>
FIGURE 5 in Description of a new species, Toxorhynchites (Toxorhynchites) tyagii (Diptera: Culicidae), from Nilgiri hills, Western Ghats, southern India
No full textFIGURE 5. Pupa of Toxorhynchites tyagii, sp. n. A, terminal abdominal segments (dorsal); B, cephalothorax; C, metanotum.Published as part of <i>Krishnamoorthy, R., Munirathinam, A., Dhananjeyan, K.J., Hiriyan, J., Mariappan, T., Samuel, P. Philip & Venkatesh, A., 2013, Description of a new species, Toxorhynchites (Toxorhynchites) tyagii (Diptera: Culicidae), from Nilgiri hills, Western Ghats, southern India, pp. 447-459 in Zootaxa 3701 (4)</i> on page 454, DOI: 10.11646/zootaxa.3701.4.4, <a href="http://zenodo.org/record/10099074">http://zenodo.org/record/10099074</a>
Electrochemical performance of spinel-type Ni doped ZnCo2O4 mesoporous rods as an electrode for supercapacitors
No full textSynthesis, characterization, bioactivity and antibacterial studies of silver doped calcium borosilicate glass-ceramics
No full textResolution of C<SUB>2</SUB>-symmetric 9,10-dihydro-9,10-ethanoanthracene-11,12-dicarboxylic acid and 2,3-diphenylsuccinic acid using (S)-proline
No full textRacemic 9,10-dihydro-9,10-ethanoanthracene-11,12-dicarboxylic acid is resolved to obtain the corresponding (S,S)-isomer in 96±2% ee and the (R,R)-isomer in 97±2% ee through complexation with (S)-proline in methanol. The racemic 2,3-diphenylsuccinic acid has been resolved to obtain the (S,S)-isomer in 93% ee using (S)-proline in methanol
Quality of bladder cancer surgery – improving outcomes
No full textBackground: At the time of diagnosis, approximately 75% of all bladder cancers are
Non-Muscle Invasive Bladder Cancers (NMIBC) - the standard treatment for these
cancers is a Transurethral Resection of the Bladder Tumour (TURBT). Although, the
vast majority of these cancers are not life-threatening, they have a high risk of
recurrence (and progression, particularly in higher risk NMIBC), despite the use of
adjuvant intravesical chemotherapy. Consequently, patients are kept on long term
cystoscopic surveillance with endoscopic removal if recurrences are detected – this
impacts on patients’ quality of life and contributes to the high cost for the healthcare
provider.
Aims: The fundamental aim of this series of clinical studies, spanning 12 years, was
to identify and implement, means of improving the efficiency in both processing and
operating on patients with NMIBC to not only reduce recurrence, but also to reduce
the duration of follow up and repeat operations. It was an evolutionary process where
the findings in the preceding studies formed the basis of the subsequent one - while
the aim of the individual studies were different, there was a clear link to the essential
principles, thus forming a coherent collection of studies.
Methods and results: The project was carried out in 3 phases (with 2 or 3 main studies
in each phase, augmented by 1 to 2 linked studies – making the entire submission for
PhD by publications a series of 12 studies, to date):
Phase 1 (5 studies in this phase): The aim was to demonstrate the natural history of
non-invasive bladder cancer and identify sub-categories of patients who could be
discharged from surveillance at 5 years. This was initially achieved by evaluating a
prospectively maintained cohort of non-invasive bladder cancer patients diagnosed
between 1978 and 1984 at the Western General Hospital, Edinburgh. This study
identified the importance of the recurrence rate at the first follow up cystoscopy
(RRFFC) as an essential prognostic marker. This finding was further validated using
2 separate cohorts from a different Centre (the Royal Infirmary, Edinburgh) managed
in the 80s and the 90’s, respectively. The data confirmed that over the decades,
recurrence patterns do change, possibly as a result of differing techniques and
improvements in optics and instruments; however, what remained the same was the
prognostic value of the RRFFC.
Phase 2 (3 studies in this phase): The early recurrence was deemed to be the result of
missed and tumours left behind at the initial TURBT, i.e. a marker of quality.
However, RRFFC was only known 3 months after the initial surgery. Since the RRFFC
was such an important prognostic factor, the aim of this phase was to determine the
surgical factors contributing to the quality of TURBT and subsequently implement
changes to the principles in carrying out the surgery to improve this quality. This was
achieved by prospective collection of information regarding all patients undergoing
TURBT for new bladder cancers, recording the tumour features, surgeon experience,
if the resection was deemed to have been complete or not, and the pathological results.
We identified that the detrusor muscle in the resected specimen and the experience of
the surgeon were independent determinants of TURBT quality. This finding was
validated in a further study using cohorts from another time period and another Centre
– this allowed me to develop the concept of Good Quality White Light TURBT
(GQWLTURBT) as the benchmark for the white light TURBT. Phase 3 (4 studies in this phase): Photodynamic Diagnosis assisted TURBT (PDDTURBT)
was demonstrated in randomised controlled trials as a technique that reduces
the recurrences in NMIBC. In the absence of evidence with this technique in the ‘real
life’ setting nor comparisons with standardised, benchmarked white light TURBT
technique, we performed a prospective controlled study comparing PDD-TURBT and
GQ-WLTURBT, evaluating early and delayed recurrence rates in 2 separate studies. I
also performed a multicentre UK study on the outcomes with PDD-TURBT and
collaborated with other experts in Europe in producing a review article around
Photodynamic Diagnosis and the cost effectiveness of this technique.
Summary: This coherent series of studies has contributed to knowledge in bladder
cancer surgery by, among others: (a) mapping the individual patient natural history of
non-invasive bladder cancer; (b) confirming the importance of early recurrence as a
strong prognostic indicator; (c) identifying predictors of this early recurrence and the
quality of TURBT; (d) introducing the concept of the benchmark Good Quality White
Light TURBT and (e) demonstrating the benefits of photodynamic diagnosis within a
‘real life’ setting
Copper(I) catalysis: synthesis of N,N'-diarylated and N-aryl,N'-formylated chiral C<SUB>2</SUB>-symmetric diamines
No full textChiral N,N'-diaryl C2-symmetric diamines and N-aryl,N'-formyl-trans-(1R,2R)-diaminocyclohexane are readily accessed by copper catalyzed N,N'-diarylation and N-aryl,N'-formylation of trans-(1R,2R)-diaminocyclohexane with aryl bromides. N,N'-diarylation using (R)-1,1'-binaphthyl-2,2'-diamine and iodobenzene gave the corresponding (R)-N,N'-diphenyl-1,1'-binaphthyl-2,2'-diamine derivative in 83% yield
Computational Studies on the Mechanical Inhomogeneity of Tropomyosin, and the Directed and Cooperative Motility of the Ncd Motor
No full textAlpha-helical coiled-coils are common protein structural motifs with varied mechanical roles, such as, tropomyosin in muscle contraction or neck-stalks of kinesins and myosins, in motor proteins. Using computer simulations, we characterized elastic properties of coiled-coils both, globally and locally. Normal mode analysis for global elastic properties revealed a buckling instability due to inherently present weak non-bonded forces. We characterized this using a critical buckling length (lc). For coiled-coils, lc was significantly less than their persistence length thereby governing the filament conformation. We also found that mutations to the hydrophobic residues at the knob-into-hole interface affect elasticity of coiled-coils significantly. We built a flexibility map of tropomyosin using a local fluctuation analysis and found regional variations in flexibilities due to such breaks in the knob-into-hole packing. Overall, flexibility varies by more than twofold and increases towards the C-terminal region of the molecule. Actin binding sites in zones and broken core regions due to acidic residues at the hydrophobic face such as, the Asp137 and the Glu218, are found to be the most labile with moduli for splay and broad face bending as 70 nm and 116 nm, respectively. Such variations in flexibility could be relevant to the tropomyosin function, especially for moving across the non-uniform surface of F-actin to regulate myosin binding.
Non-claret disjunction (Ncd), is a Kinesin-14 family protein that walks to the microtubule's minus end. Although available structures show its alpha-helical coiled-coil neck in either pre- or post-stroke orientations, little is known about the transition between these two states. Using a combination of molecular dynamics simulations and structural analyses, we find that the neck travel is a guided diffusion involving sequential intermediate contacts with the motor head. The post-stroke is at a higher free-energy minimum than the pre-stroke. The importance of intermediate contacts correlates with the existing motility data including those of mutant Ncds and other members of the kinesin-14 family. While the forward motion has a ~4.5 kBT (kB: Boltzmann constant, T = 300 K) free energy barrier, recovery stroke goes nearly downhill in free energy. The hysteresis in forward and reverse neck motion energetics arises from the mechanical compliance of the protein, and together with guided diffusion, it may be key for the directed motility of Ncd.
Although it is known that neighboring Ncds on a microtubule (MT) have an attractive interaction and a group of Ncds act cooperatively, the physical basis of neither this attraction nor the cooperativity is known. From structural analysis of Ncd neighbors on an MT lattice we find that steric hindrances between the coiled-coil neck-stalks of longitudinal neighbors drive synchrony among a group of Ncds on a single protofilament. Across lateral dimers, surface loop L2 of the motor-head (MH) that is not bound to the MT (unbound-MH) in a pre-stroke dimer, is seen to have strong attraction to the nucleotide pocket in the MH that is bound to MT (bound-MH) of its off-axis neighbor. Such an attraction will however impede the motility in both the dimers. We hence propose rules that drive motor binding to an MT site in the presence of immediate neighbors such that motility of the group is not compromised. The unbound-MH, whose role in the walking step of an Ncd was unclear, is thus seen to regulate MT decoration
Synthesis and antiproliferative activity of Naphtalenyl substituted 1,2-dihydropyrazol-5-one and related fused tetrazine
No full textIn recent years, besides the main field of nonsteroidal anti-inflammatory agents, the interest towards pyrazolone derivatives has been renewed because of their wide biological and pharmacological applications [1]. Currently, particular attention is focused on such a class of compounds due to the affinity with sigma receptor and their relationship with cancer [2].To these purposes we planned to design, synthesize and evaluate the antiproliferative activity (MTS assays) of a new series of 3-methyl-2-(1-R-naphthalen-2-yl)-1,2-dihydropyrazol-3-one derivatives 1 against HeLa, MCF-7, LAN-5, Caco2 in order to explore their anticancer potential. Additionally, further elaboration of the amino derivative 1 led to the tetracycle 2, possessing a reactive tetrazinone core which conferred valuable antiproliferative activity as previously reported [3]. Synthesis and biological results will be presented.
[1] G. Mariappan, B.P. Saha, L. Sutharson, Anki, S. Garg, L. Pandey, D. Kumar, J. Pharm. Res., 2010, 3(12), 2856.
[2] E. Aydar, C.P. Palmer, M. B. A. Djamoz, Cancer Res., 2004, 64, 5029.
[3] A.M., Almerico, F. Mingoia, P. Diana, P. Barraja, A. Lauria, A. Montalbano, G Cirrincione, G. Dattolo, J. Med. Chem., 2005, 48, 2859
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