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1.
De-Kuan Chang Vinodh B. Kurella Subhabrata Biswas Yuval Avnir Jianhua Sui Xueqian Wang 《MABS-AUSTIN》2016,8(4):787-798
In 10–20% of the cases of chronic lymphocytic leukemia of B-cell phenotype (B-CLL), the IGHV1-69 germline is utilized as VH gene of the B cell receptor (BCR). Mouse G6 (MuG6) is an anti-idiotypic monoclonal antibody discovered in a screen against rheumatoid factors (RFs) that binds with high affinity to an idiotope expressed on the 51p1 alleles of IGHV1-69 germline gene encoded antibodies (G6-id+). The finding that unmutated IGHV1-69 encoded BCRs are frequently expressed on B-CLL cells provides an opportunity for anti-idiotype monoclonal antibody immunotherapy. In this study, we first showed that MuG6 can deplete B cells encoding IGHV1-69 BCRs using a novel humanized GTL mouse model. Next, we humanized MuG6 and demonstrated that the humanized antibodies (HuG6s), especially HuG6.3, displayed ~2-fold higher binding affinity for G6-id+ antibody compared to the parental MuG6. Additional studies showed that HuG6.3 was able to kill G6-id+ BCR expressing cells and patient B-CLL cells through antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Finally, both MuG6 and HuG6.3 mediate in vivo depletion of B-CLL cells in NSG mice. These data suggest that HuG6.3 may provide a new precision medicine to selectively kill IGHV1-69-encoding G6-id+ B-CLL cells. 相似文献
2.
Carolyn M. Kelly Peter J. Zeiger Vinodh Narayanan Keri Ramsey Holger Sondermann 《The Journal of biological chemistry》2022,298(1)
Hereditary spastic paraplegia (HSP) comprises a heterogeneous group of neuropathies affecting upper motor neurons and causing progressive gait disorder. Mutations in the gene SPG3A/atlastin-1 (ATL1), encoding a dynamin superfamily member, which utilizes the energy from GTP hydrolysis for membrane tethering and fusion to promote the formation of a highly branched, smooth endoplasmic reticulum (ER), account for approximately 10% of all HSP cases. The continued discovery and characterization of novel disease mutations are crucial for our understanding of HSP pathogenesis and potential treatments. Here, we report a novel disease-causing, in-frame insertion in the ATL1 gene, leading to inclusion of an additional asparagine residue at position 417 (N417ins). This mutation correlates with complex, early-onset spastic quadriplegia affecting all four extremities, generalized dystonia, and a thinning of the corpus callosum. We show using limited proteolysis and FRET-based studies that this novel insertion affects a region in the protein central to intramolecular interactions and GTPase-driven conformational change, and that this insertion mutation is associated with an aberrant prehydrolysis state. While GTPase activity remains unaffected by the insertion, membrane tethering is increased, indicative of a gain-of-function disease mechanism uncommon for ATL1-associated pathologies. In conclusion, our results identify a novel insertion mutation with altered membrane tethering activity that is associated with spastic quadriplegia, potentially uncovering a broad spectrum of molecular mechanisms that may affect neuronal function. 相似文献
3.
Rodrigo Cilla Vinodh Mechery Beatriz Hernandez de Madrid Steven Del Signore Ivan Dotu Victor Hatini 《PLoS computational biology》2015,11(4)
Epithelial morphogenesis generates the shape of tissues, organs and embryos and is fundamental for their proper function. It is a dynamic process that occurs at multiple spatial scales from macromolecular dynamics, to cell deformations, mitosis and apoptosis, to coordinated cell rearrangements that lead to global changes of tissue shape. Using time lapse imaging, it is possible to observe these events at a system level. However, to investigate morphogenetic events it is necessary to develop computational tools to extract quantitative information from the time lapse data. Toward this goal, we developed an image-based computational pipeline to preprocess, segment and track epithelial cells in 4D confocal microscopy data. The computational pipeline we developed, for the first time, detects the adherens junctions of epithelial cells in 3D, without the need to first detect cell nuclei. We accentuate and detect cell outlines in a series of steps, symbolically describe the cells and their connectivity, and employ this information to track the cells. We validated the performance of the pipeline for its ability to detect vertices and cell-cell contacts, track cells, and identify mitosis and apoptosis in surface epithelia of Drosophila imaginal discs. We demonstrate the utility of the pipeline to extract key quantitative features of cell behavior with which to elucidate the dynamics and biomechanical control of epithelial tissue morphogenesis. We have made our methods and data available as an open-source multiplatform software tool called TTT (http://github.com/morganrcu/TTT) 相似文献
4.
Stabilization of collagen through bioconversion: An insight in protein–protein interaction
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Nagarajan Usharani Gladstone Christopher Jayakumar Swarna Vinodh Kanth Jonnalagadda Raghava Rao 《Biopolymers》2014,101(8):903-911
Collagen is a natural protein, which is used as a vital biomaterial in tissue engineering. The major concern about native collagen is lack of its thermal stability and weak resistance to proteolytic degradation. In this scenario, the crosslinking compounds used for stabilization of collagen are mostly of chemical nature and exhibit toxicity. The enzyme mediated crosslinking of collagen provides a novel alternative, nontoxic method for stabilization. In this study, aldehyde forming enzyme (AFE) is used in the bioconversion of hydroxylmethyl groups of collagen to formyl groups that results in the formation of peptidyl aldehyde. The resulted peptidyl aldehyde interacts with bipolar ions of basic amino acid residues of collagen. Further interaction leads to the formation of conjugated double bonds (aldol condensation involving the aldehyde group of peptidyl aldehyde) within the collagen. The enzyme modified collagen matrices have shown an increase in the denaturation temperature, when compared with native collagen. Enzyme modified collagen membranes exhibit resistance toward collagenolytic activity. Moreover, they exhibited a nontoxic nature. The catalytic activity of AFE on collagen as a substrate establishes an efficient modification, which enhances the structural stability of collagen. This finds new avenues in the context of protein–protein stabilization and discovers paramount application in tissue engineering. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 903–911, 2014. 相似文献
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Identification of somatic chromosomal abnormalities in hypothalamic hamartoma tissue at the GLI3 locus
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Craig DW Itty A Panganiban C Szelinger S Kruer MC Sekar A Reiman D Narayanan V Stephan DA Kerrigan JF 《American journal of human genetics》2008,82(2):366-374
Hypothalamic hamartomas (HH) are rare, benign congenital tumors associated with intractable epilepsy. Most cases are sporadic and nonsyndromic. Approximately 5% of HH cases are associated with Pallister-Hall syndrome (PHS), which is caused by haploinsufficiency of GLI3. We have investigated the possibility that HH pathogenesis in sporadic cases is due to a somatic (tumor-only) mutation in GLI3. We isolated genomic DNA from peripheral blood and surgically resected HH tissue in 55 patients with sporadic HH and intractable epilepsy. A genome-wide screen for loss of heterozygosity (LOH) and chromosomal abnormalities was performed with parallel analysis of blood and HH tissue with Affymetrix 10K SNP microarrays. Additionally, resequencing and fine mapping with SNP genotyping were completed for the GLI3 gene with comparisons between peripheral blood and HH tissue pairs. By analyzing chromosomal copy-number data for paired samples on the Affymetrix 10K array, we identified a somatic chromosomal abnormality on chromosome 7p in one HH tissue sample. Resequencing of GLI3 did not identify causative germline mutations but did identify LOH within the GLI3 gene in the HH tissue samples of three patients. Further genotyping of 28 SNPs within and surrounding GLI3 identified five additional patients exhibiting LOH. Together, these data provide evidence that the development of chromosomal abnormalities within GLI3 is associated with the pathogenesis of HH lesions in sporadic, nonsyndromic patients with HH and intractable epilepsy. Chromosomal abnormalities including the GLI3 locus were seen in 8 of 55 (15%) of the resected HH tissue samples. These somatic mutations appear to be highly variable. 相似文献
8.
Vinodh B. Kurella Jessica M. Richard Courtney L. Parke Louis F. LeCour Jr. Henry D. Bellamy David K. Worthylake 《The Journal of biological chemistry》2009,284(22):14857-14865
IQGAP1 is a 190-kDa molecular scaffold containing several domains required
for interaction with numerous proteins. One domain is homologous to Ras
GTPase-activating protein (GAP) domains. However, instead of accelerating
hydrolysis of bound GTP on Ras IQGAP1, using its GAP-related domain (GRD)
binds to Cdc42 and Rac1 and stabilizes their GTP-bound states. We report here
the crystal structure of the isolated IQGAP1 GRD. Despite low sequence
conservation, the overall structure of the GRD is very similar to the GAP
domains from p120 RasGAP, neurofibromin, and SynGAP. However, instead of the
catalytic “arginine finger” seen in functional Ras GAPs, the GRD
has a conserved threonine residue. GRD residues 1099–1129 have no
structural equivalent in RasGAP and are seen to form an extension at one end
of the molecule. Because the sequence of these residues is highly conserved,
this region likely confers a functionality particular to IQGAP family GRDs. We
have used isothermal titration calorimetry to demonstrate that the isolated
GRD binds to active Cdc42. Assuming a mode of interaction similar to that
displayed in the Ras-RasGAP complex, we created an energy-minimized model of
Cdc42·GTP bound to the GRD. Residues of the GRD that contact Cdc42 map
to the surface of the GRD that displays the highest level of sequence
conservation. The model indicates that steric clash between threonine 1046
with the phosphate-binding loop and other subtle changes would likely disrupt
the proper geometry required for GTP hydrolysis.The small GTPase Ras functions as a binary switch in cell signaling
processes. When bound to GTP, Ras is able to interact with effector proteins,
including Raf kinase, and alter their activities. Ras signaling is terminated
when bound GTP is hydrolyzed to GDP and inorganic phosphate. The basal rate of
GTP hydrolysis on Ras is quite slow (∼1.2 × 10–4
s–1), but this rate of hydrolysis can be enhanced
∼105-fold by interaction with a GTPase-activating protein
(GAP)2
(1). Several RasGAPs have been
identified to date including p120 RasGAP and neurofibromin (NF1). The Rho
family of Ras-related small GTPases also function as binary switches in cell
signaling processes. Whereas the intrinsic rate of GTP hydrolysis on Rho
proteins is faster than Ras, this rate can also be stimulated by interaction
with a RhoGAP. Examination of the structures of the GAP domains of p120RasGAP
(2), neurofibromin
(3), SynGAP
(4), and the GAP domains from
the RhoGAPs p50 RhoGAP and the Bcr homology domain of phosphatidylinositol
3-kinase (5,
6) indicates that although
ostensibly different, these all-helical domains are structurally related
(7).IQGAP1 was discovered by chance during an attempt to isolate novel matrix
metalloproteinases (8).
Analysis reveals that the protein contains several discrete domains and motifs
including a region containing four isoleucine- and glutamine-rich motifs (IQ
repeats) and a region with sequence homology to the Ras-specific GAP domains
of p120RasGAP, NF1, and SynGAP
(2–4,
8). Subsequently, two homologs,
IQGAP2 and IQGAP3, have been discovered. The IQ repeats have been shown to
mediate binding to calmodulin and calmodulin-like proteins (e.g.
S100, myosin essential light chain), whereas the GAP-related domain (GRD) does
not appear to bind to Ras but instead is necessary for binding to the Rho
family GTPases Cdc42 and Rac1, primarily in their active forms
(9–11).
However, instead of accelerating hydrolysis of GTP, IQGAP1 preserves the
activated states of Cdc42 and Rac1 to the extent that overexpression of IQGAP1
in cells increases the levels of active GTPase
(12). Because IQGAP1
expression increases the level of activated Cdc42, initially there was some
confusion as to whether the protein might not represent a novel guanine
nucleotide exchange factor. However it now appears that IQGAP1 is an effector
of Cdc42 and Rac1 and preserves their activated states by tightly binding to
the GTPases and stabilizing them in a conformation not conducive to GTP
hydrolysis. IQGAP1 appears to be such an important effector for Cdc42 that
abrogation of binding to IQGAP1 not only reduces the levels of active Cdc42,
it also reduces membrane-localized Cdc42 and the cellular response to
bradykinin (12).A growing body of evidence implicates IQGAP1 in carcinogenesis. Expression
of IQGAP1 increases during the transition from a minimally to a highly
metastastic form of melanoma, and IQGAP1 has been found to be overexpressed in
ovarian, breast, lung, and colorectal cancers
(13–17).
In vitro, overexpressed IQGAP1 enhances cell motility and
invasiveness in a process that requires Cdc42 and Rac
(18). β-Catenin is one of
the many binding partners of IQGAP1 identified to date. IQGAP1 has been shown
to bind to β-catenin and interfere with β-catenin binding to
α-catenin, an interaction necessary for stable cell-cell adhesion
(19). Another study found that
IQGAP2 knock-out mice overexpress IQGAP1 and developage-dependent liver cancer
and apoptosis (20).To better understand how a protein domain homologous to others that
accelerate GTP hydrolysis can function as an effector and preserve the
GTP-bound state, we have determined the x-ray structure of the IQGAP1 GRD.
Despite low sequence identity, the GRD structure is quite similar to the GAP
domains of p120, neurofibromin, and SynGAP; however, unlike those domains, the
GRD possesses a conserved threonine in place of the catalytic arginine finger
and has a 31-residue insertion that projects from one end of the molecule.
Using the coordinates of Ras·GDP·AlF3 in complex with
the GAP domain of p120, we built a model of Cdc42·GTP bound to the GRD.
The model indicates that a steric clash between the conserved
Thr1046 and the phosphate-binding loop of Cdc42 and other subtle
changes within the active site would likely preclude nucleotide hydrolysis.
Sequence conservation mapped to the surface of the GRD indicates that the
surface with the highest degree of conservation overlaps with the surface that
makes contacts to Cdc42 in the model. 相似文献
9.
Spatial molecular epidemiology of carbapenem‐resistant and New Delhi metallo beta‐lactamase (blaNDM)‐producing Escherichia coli in the piglets of organized farms in India
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10.
Swarna Vinodh Kanth Rajangam Venba Gladstone Christopher Jayakumar Narasimhan Kannan Chandrababu 《Bioresource technology》2009,100(8):2430-2435
In the present investigation, kinetics of dyeing involving pretreatment with acid protease has been presented. Application of acid protease in dyeing process resulted in increased absorption and diffusion of dye into the leather matrix. Enzyme treatment at 1% concentration, 60 min duration and 50 °C resulted in maximum of 98% dye exhaustion and increased absorption rate constants. The final exhaustion (C∞) for the best fit of CI Acid Black 194 dye has been 98.5% with K and r2 values from the modified Cegarra-Puente isotherm as 0.1033 and 0.0631. CI Acid Black 194 being a 2:1 metal complex acid dye exhibited higher absorption rate than the acid dye CI Acid Black 210. A reduction in 50% activation energy calculated from Arrhenius equation has been observed in enzyme assisted dyeing process of both the dyes that substantiates enhanced dye absorption. The absorption rate constant calculated with modified Cegarra-Puente equation confirm higher rate constants and faster kinetics for enzyme assisted dyeing process. Enzyme treated leather exhibited richness of color and shade when compared with control. The present study substantiates the essential role of enzyme pretreatment as an eco-friendly leather dyeing process. 相似文献