No description available.

This thesis describes the cloning and characterisation of a novel human gene and its protein products, which have been designated SAPK- and Ras-interacting protein (SinRIP). SinRIP shares identity with JC310, a partial human cDNA that was previously identified a candidate Ras-inhibitor (Colicelli et al., 1991, Proc Natl Acad Sci USA 88, p. 2913). In this study, it was shown that SinRIP is a member of an orthologous family of proteins that is conserved from yeast to mammals and contains proteins involved in Ras- and SAPK-mediated signalling pathways. Comparison of this family of proteins showed that human SinRIP contains a potential Ras-binding domain (RBD; residues 279-354), a PH-like domain (PHL; 376-487), and a highly conserved novel region designated the CRIM (134-265). Several other potential targeting sites, such as nuclear localisation signals and target sites for kinases, were identified within the SinRIP sequence. The human SinRIP gene is unusually large (>280 kbp) and is located on chromosome 9 at 9q34. SinRIP mRNA was detected in a wide variety of tissue-types and cell lines by RT-PCR, and the SinRIP sequences in the EST database were derived from an diverse array of tissues, suggesting a widespread or ubiquitous expression. Northern blot analysis revealed the highest levels in skeletal muscle and heart tissue. However, the steady-state levels of SinRIP mRNA vary greatly from cell to cell, and SinRIP expression is likely to be regulated at multiple post-transcriptional levels. It was shown that SinRIP mRNA is likely to be translated inefficiently by the normal cap-scanning mechanism, due to the presence of a GC-rich and structured 5’-UTR, which also contains upstream ORFs. Alternative polyadenylation signals in the SinRIP 3’-UTR can be used, resulting in the expression of short and long SinRIP mRNA isoforms. Several potential A/T-rich regulatory elements were also identified in SinRIP mRNA, which may target specific SinRIP mRNA isoforms for rapid degradation. Importantly, it was shown that SinRIP mRNA is alternatively spliced, resulting in the production of distinct SinRIP protein isoforms. Three isoforms, SinRIP2-4, were definitively identified by RT-PCR and full-length cloning. The SinRIP isoforms contain deletions in conserved regions, and are likely to have biochemical characteristics that are different to full-length SinRIP1. SinRIP2 is C-terminally truncated and lacks the PHL domain and part of the RBD, and relatively high levels of SinRIP2 expression arelikely to occur in kidneys. The RBD is disrupted in SinRIP3, but all other domains are intact, and RT-PCR analyses suggest that SinRIP3 is present in some cells at levels comparable to SinRIP1. A rabbit polyclonal antiserum against SinRIP was generated and detected endogenous SinRIP proteins. Using the anti-SinRIP antibody in immunoblots, multiple SinRIP isoforms were observed in most cell types. SinRIP1 and another endogenous SinRIP protein, likely to be SinRIP3, were detected in most cell lines, and appear to be are the major SinRIP proteins expressed in most cells. The subcellular localisation of both recombinant and endogenous SinRIP proteins was investigated by immunofluorescence assays and biochemical fractionation. Recombinant SinRIP1 protein was found in the cytoplasm and associated with the plasma membrane. In contrast, the SinRIP2 protein was predominantly nuclear, with only low-level cytoplasmic staining observed. The endogenous SinRIP proteins, likely to comprise these and other SinRIP isoforms, were found in both the nucleus and cytoplasm. SinRIP1 interacted with GTP-bound (active) Ras, but not GDP-bound (inactive) Ras, in an in vitro assay, and also co-localised with activated H- and K-Ras in cells. The binding profile observed is typical of Ras-effectors, and SinRIP did not inhibit signalling by the Ras proteins, suggesting that it is not likely to be a Ras-inhibitor. It was also shown that SinRIP1 and SinRIP2 both interact and colocalise with c-Jun NH2- terminal kinase (JNK). Both SinRIP proteins were able to recruit JNK to their respective sub-cellular compartments. These interactions suggest an adaptor role for SinRIP in the Ras and/or JNK pathways. In addition, Sam68 was isolated as a SinRIP-binding protein in a yeast two-hybrid screen. Sam68 was shown to colocalise with SinRIP2 and endogenous SinRIP proteins, but not SinRIP1. Further colocalisation studies showed that endogenous SinRIP proteins localise in nuclear structures that may be associated with pre-mRNA splicing. Likely functions for SinRIP, as indicated by experimental results and studies of the orthologues of SinRIP in other species, are discussed.

Aquesta tesi tracta de la creació d'un nou programari de codi obert i d'una interfície de programació (API) per realitzar simulacions (bio) moleculars, així com de a la seva aplicació posterior a problemes biològics. El nou programa, Adun, es focalitza en les àrees clau del càlcul d'energies lliures, el desenvolupament ràpid de programari i la productivitat d'alt rendiment. Mètodes com SCAAS, EVB i Born generalitzat han estat implementats per tal d'assolir el primer objectiu. La presencia d'aquestes tècniques, a m´es d'altres, mostra la velocitat de desenvolupament d'Adun. Totes les característiques s´on accessibles mitjanant una interfície gràfica d'usuari avançada que proveeix de noves capacitats, com el tractament de dades integrat o la compartició de dades i de càlculs distribuïts. La capacitat d'Adun de tractar problemes biològics és il·lustrada amb la investigació de la dinàmica de la proteïna Ras i el desenvolupament, implementació i demostració d'un nou mètode per a la determinació de camins de transició. A més, per tal de demostrar el potencial del programa Adun, aquests estudis també proporcionen una visió avançada sobre l'ús de la informació dinàmica en determinar la unció de les proteïnes. L'estat actual del programa i els resultats dels dos estudis és, doncs, discutit, i es donen indicacions dels objectius i direccions futurs. Finalment s'examina el paper dels científics computacionals com desenvolupadors d'eines, per a ells mateixos o per a tota la comunitat científica. / This thesis deals with the creation of a new open-source program and API for biomolecular simulation and its subsequent application to biological problems. The program, Adun, focuses on the key areas of biological free-energy calculations, rapid development and highperformance productivity. Methods such as SCAAS, EVB and switched Generalised-Born have been implemented to realise the first aim. The presence of these techniques, along with a multitude of others, verifies Adun's rapid development potential. All these features are united by an advanced graphical user interface which provides novel capabilities such as inbuilt data management, and distributed datasharing and computation. Adun's ability to tackle biological problems is illustrated with an investigation of Ras dynamics and the development, implementation and testing of a novel method for determining transition paths. In addition to concretely demonstrating Adun's potential these studies also provide insight into the use of dynamic information in elucidating protein function. The current state of the program and the results of the two studies is discussed and indications of future aims and directions given. In addition the role of computational scientists as developers of tools, for themselves and the wider scientific community, is examined.

Diss. (sammanfattning) Umeå : Univ., 2007. / Härtill 4 uppsatser.

Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Vita. Bibliography: References located at the end of each chapter.

Pancreatic cancer is the 4th leading cause of cancer related death in the United States with a median survival time of less than 6 months. Pancreatic ductal adenocarcinoma (PDAC) accounts for greater than 85% of all pancreatic cancers, and is marked by early and frequent mutation of the KRAS oncogene, with activating KRAS mutations present in over 90% of PDAC. To date, though, targeting activated KRAS for cancer treatment has been very difficult, and targeted therapies are currently being sought for the downstream effectors of activated KRAS. Activation of KRAS stimulates multiple signaling pathways, including the MEK-ERK and PI3K-AKT signaling cascades, but the role of downstream effectors in pancreatic tumor initiation and progression remains unclear. I therefore used primary pancreatic ductal epithelial cells (PDECs), the putative cell of origin for PDAC, to determine the role of specific downstream signaling pathways in KRAS activated pancreatic tumor initiation. As one third of KRAS wild type PDACs harbor activating mutations in BRAF , and KRAS and BRAF mutations appear to be mutually exclusive, I also sought to determine the effect of activated BRAF (BRAF V600E ) expression on PDECs and the signaling requirements downstream of BRAF. I found that both KRAS G12D and BRAF V600E expressing PDECs displayed increased proliferation relative to GFP expressing controls, as well as increased PDEC survival after challenge with apoptotic stimuli. This survival was found to depend on both the MEK-ERK and PI3K-AKT signaling cascades. Surprisingly, I found that this survival is also dependent on the IGF1R, and that activation of PI3K/AKT signaling occurs downstream of MEK/ERK activation, and is dependent on signaling through the IGF1R. Consistent with this, I find increased IGF2 expression in KRAS G12D and BRAF V600E expressing PDECs, and show that ectopic expression of IGF2 rescues survival in PDECs with inhibited MEK, but not PI3K. Finally, I showed that the expression of KRAS G12D or BRAF V600E in PDECs lacking both the Ink4a/Arf and Trp53 tumor suppressors is sufficient for tumor formation following orthotopic transplant of PDECs, and that IGF1R knockdown impairs KRAS and BRAF-induced tumor formation in this model. In addition to these findings within PDECs, I demonstrate that KRAS G12D or BRAF V600E expressing tumor cell lines differ in MEK-ERK and PI3K-AKT signaling from PDECs. In contrast to KRAS G12D or BRAF V600E expressing PDECs, activation of AKT at serine 473 in the KRAS G12D or BRAF V600E expressing tumor cell lines does not lie downstream of MEK, and only the inhibition of PI3K alone or both MEK and the IGF1R simultaneously results in loss of tumor cell line survival. However, inhibition of MEK, PI3K, or the IGF1R in KRAS G12D or BRAF V600E expressing tumor cell lines also resulted in decreased proliferation relative to DMSO treated cells, demonstrating that all three signaling cascades remain important for tumor cell growth and are therefore viable options for pancreatic cancer therapeutics.

Die Fusion von Membranen erfordert die Verschmelzung von zwei Phospholipiddoppel-schichten, wobei dies über dieselben Zwischenschritte abzulaufen scheint. Eine lokale Störung (‚Stalk’) stellt eine erste Verbindung der äußeren Membranhälften dar, die anschließend lateral expandiert und ein Hemifusionsdiaphragma (HD) bildet. Das Öffnen einer Fusionspore im HD führt zur vollständigen Fusion. Mittels konfokaler Mikroskopie wurde die Fusion von Giant unilamellar vesicles (GUVs) mit negativ geladenen Lipiden und transmembranen (TM) Peptiden in Anwesenheit von zweiwertigen Kationen beobachtet, wobei die Peptide bei der HD Entstehung völlig verdrängt wurden. Eine detaillierte Analyse zeigte, dass es sich bei diesem Mikrometer-großen Bereich um ein HD handelt, dessen Größe von der Lipidzusammensetzung und Peptidkonzentration in den GUVs abhängt. Laterale Lipiddomänen gelten als entscheidend für Signal- und Sortierungsprozesse in der Zelle. Liquid ordered (Lo) Domänen in Modellsystemen wie GUVs ähneln den mit Sphingo-lipiden und Cholesterol angereicherten biologischen Raft-Domänen, allerdings scheinen Membraneigenschaften wie die Lipidpackung sich von biologischen Membranen zu unterscheiden. In diesem Zusammenhang wird die Sortierung des TM-verankerten Hemag-glutinin (HA) des Influenzavirus und von lipidverankerten Ras-Proteinen in GUVs wie auch in abgelösten Plasmamembran-Ausstülpungen (GPMVs) untersucht. HA Protein und TM-Pepitde von HA wurden ausschließlich (GUVs) bzw. vorwiegend (GPMVs) in der liquid disordered (Ld) Domäne gefunden. K-Ras wurde inmitten der Ld detektiert, während N-Ras zur Lo/Ld Grenzlinie diffundierte. Diese Ergebnisse werden im Zusammenhang mit den Unterschieden der Lipidpackung innerhalb der verschiedenen membranverankerten Systeme diskutiert. Es ist wahrscheinlich, dass die Bildung, Größe und Stabilität sowie die physikalischen Eigenschaften der Lipiddomänen in biologischen Membranen stark von Protein-Lipid-Wechsel-wirkungen beeinflusst werden. / Membrane fusion is ubiquitous in life and requires remodelling of two phospholipid bilayers. Fusion likely proceeds through similar sequential intermediates. A stalk between the contacting leaflets forms and radially expands into a hemifusion diaphragm (HD) wherein finally a fusion pore opens up. Direct experimental verification of this key structure is difficult due to its transient nature. Confocal microscopy was used to visualize the fusion of giant unilamellar vesicles (GUVs) comprising negatively charged phosphatidylserine and fluorescent transmembrane (TM) entities in the presence of divalent cations. A complete displacement of TM peptides preceded full fusion. This is consistent with HD formation. Detailed analysis provided proof that the micrometer sized structures are in fact HDs. HD size is dependent on lipid composition and peptide concentration. Lateral lipid domain formation is believed to be essential for sorting and signalling processes in the cell. Liquid ordered (Lo) domains in model systems like GUVs resemble biological rafts enriched in sphingolipids and cholesterol, but their physical properties seem distinct from biological membranes as judged by e.g. lipid order and packing. In this context the sorting of TM anchored influenza virus hemagglutinin (HA) and different lipid anchored Ras proteins is studied in GUVs and giant plasma membrane derived vesicles (GPMVs). Authentic HA or the TM domain peptides were sorted exclusively (GUVs) or predominantly (GPMVs) to the liquid disordered (Ld) domains. Whereas K-Ras was found in the bulk Ld domains, N-Ras diffuses to the Lo/Ld interface. These results are discussed with respect to differences in lipid packing in the different membrane systems and regarding the membrane anchors and their hydrophobic matching. The results suggest that the formation, size and stability as well as the physical properties of lipid domains in biological membranes are tightly regulated by protein-lipid interactions.

Dissulfeto isomerase proteica como a PDIA1 tem sido implicada na progressão do câncer, porém os mecanismos envolvidos ainda não foram claramente identificados. Previamente, nós demonstramos um importante efeito da PDIA1 induzindo a superexpressão da Nox1 NADPH oxidase, associada à geração de espécie reativas de oxigênio (ROS). Uma vez que a perda na regulação de ROS envolve o crescimento tumoral, nós propusemos que a PDIA1 atua como um mecanismo regulador proximal na produção de ROS em tumores. No presente estudo, nós focamos no câncer colorretal (CRC) com distintos efeitos na ativação de KRas. Resultados provenientes de bancos de dados de RNAsec e validação direta, indicam um significante aumento na expressão de PDIA1 em CRC com alta ativação constitutiva da Kras (HCT116) vs. ativação intermediária (HKE3) ou basal (Caco2). A PDIA1 sustenta a produção de superóxido dependente da Nox1 em CRC; entretanto, observamos pela primeira vez uma ação dupla da PDIA1 correlacionada ao nível de ativação da Ras: em células Caco2 e HKE3, experimentos de perda de função indicam que o PDIA1 sustenta a produção de superóxido dependente de Nox1; no entanto, em células HCT116, PDIA1 limita a produção de superóxido pela Nox1. Este comportamento da PDIA1 é associado ao aumento da expressão / atividade da Rac1. A transfecção do mutante constitutivamente ativo Rac1G12V em células HKE3 faz com que a PDIA1 se torne restritiva a produção de superóxido dependente de Nox1, paralelamente, em células HCT116 tratadas com inibidor da Rac1, PDIA1 se torna favorável à produção de superóxido. Um screening em importantes vias de sinalização celular em HKE3 mostrou que a perda de função da PDIA1 promove inativação da GSK3? em paralelo à diminuicão da ativacção de Stat3; em HCT116 em estado basal, GSK3beta é inativada enquanto Stat3 está ativa, já o silenciamento da PDIA1 não resulta em nenhum efeito adicional. As implicações funcionais do silenciamento da PDIA1 incluíram uma diminuição da proliferação e migração celular em HKE3, não detectável em HCT116. Além disso, a PDIA1 parece sustentar a transição epitélio-mesenquimal (EMT), uma vez que após o silenciamento da PDIA1, observamos um aumento da expressão da E-caderina em HKE3 e uma diminuição em HCT116. Assim, a superativação da Ras se associa a uma alteração no padrão de regulação da Nox1 pela PDIA1. A supressão do efeito regulador da PDIA1 pela Kras é provavelmente devido a uma ativação sustentada da Rac1. Portanto, PDIA1 pode exercer um papel redox-dependente adaptativo crucial relacionado à progressão tumoral / Protein disulfide isomerases such as PDIA1 have been implicated in cancer progression, but the underlying mechanisms are unclear. We showed previously important PDIA1 effects enabling vascular Nox1 NADPH oxidase expression and associated generation of reactive oxygen species (ROS). Since deregulated ROS production underlies tumor growth, we proposed that PDIA1 acts as an upstream regulatory mechanism of tumor-associated ROS production. We focused on colorectal cancer (CRC) with distinct levels of KRas activation. Our results from RNAseq databanks and direct validation indicate significant increase in PDIA1 expression in CRC with constitutive high (HCT116) vs. moderate (HKE3) or basal (e.g. Caco2) Ras activity. PDIA1 supported Nox1-dependent superoxide production in CRC; however, we observed for the first time a dual effect correlated with Ras level activity: in Caco2 and HKE3 cells, loss-of-function experiments indicate that PDIA1 sustains Nox1-dependent superoxide production; however, in HCT116 cells, PDIA1 restricted Nox1-dependent superoxide production. This PDIA1 behavior in HCT116 is associated with increased Rac1 expression/activity. Transfection of Rac1G12V active mutant into HKE3 cells induced PDIA1 to become restrictive of Nox1-dependent superoxide; accordingly, in HCT116 cells treated with Rac1 inhibitor, PDIA1 became supportive of superoxide production. Screening of cell signaling routes affected by PDIA1 silencing showed induced GSK3beta inactivation and parallel decrease of active Stat3 in HKE3 cells; in baseline HCT116 cells, GSK3beta was inactivated and Stat3 active, whereas PDIA1 silencing had no further effect. Functional implications of PDIA1 silencing included a decrease of cell proliferation and migration in HKE3, not detectable in HCT116 cells. Also, PDIA1 may support epithelial-mesenchymal transition (EMT), since after PDIA1 silencing, E-cadherin expression increased in HKE3 and decreased in HCT116. Thus, Ras overaction associates with a switched in PDIA1 pattern regulation of Nox1. Ras-induced PDIA1 bypass may involve direct Rac1 activation. Therefore, PDIA1 may be a crucial regulator of redox-dependent adaptive processes related to cancer progression

Dissulfeto isomerase proteica como a PDIA1 tem sido implicada na progressão do câncer, porém os mecanismos envolvidos ainda não foram claramente identificados. Previamente, nós demonstramos um importante efeito da PDIA1 induzindo a superexpressão da Nox1 NADPH oxidase, associada à geração de espécie reativas de oxigênio (ROS). Uma vez que a perda na regulação de ROS envolve o crescimento tumoral, nós propusemos que a PDIA1 atua como um mecanismo regulador proximal na produção de ROS em tumores. No presente estudo, nós focamos no câncer colorretal (CRC) com distintos efeitos na ativação de KRas. Resultados provenientes de bancos de dados de RNAsec e validação direta, indicam um significante aumento na expressão de PDIA1 em CRC com alta ativação constitutiva da Kras (HCT116) vs. ativação intermediária (HKE3) ou basal (Caco2). A PDIA1 sustenta a produção de superóxido dependente da Nox1 em CRC; entretanto, observamos pela primeira vez uma ação dupla da PDIA1 correlacionada ao nível de ativação da Ras: em células Caco2 e HKE3, experimentos de perda de função indicam que o PDIA1 sustenta a produção de superóxido dependente de Nox1; no entanto, em células HCT116, PDIA1 limita a produção de superóxido pela Nox1. Este comportamento da PDIA1 é associado ao aumento da expressão / atividade da Rac1. A transfecção do mutante constitutivamente ativo Rac1G12V em células HKE3 faz com que a PDIA1 se torne restritiva a produção de superóxido dependente de Nox1, paralelamente, em células HCT116 tratadas com inibidor da Rac1, PDIA1 se torna favorável à produção de superóxido. Um screening em importantes vias de sinalização celular em HKE3 mostrou que a perda de função da PDIA1 promove inativação da GSK3? em paralelo à diminuicão da ativacção de Stat3; em HCT116 em estado basal, GSK3beta é inativada enquanto Stat3 está ativa, já o silenciamento da PDIA1 não resulta em nenhum efeito adicional. As implicações funcionais do silenciamento da PDIA1 incluíram uma diminuição da proliferação e migração celular em HKE3, não detectável em HCT116. Além disso, a PDIA1 parece sustentar a transição epitélio-mesenquimal (EMT), uma vez que após o silenciamento da PDIA1, observamos um aumento da expressão da E-caderina em HKE3 e uma diminuição em HCT116. Assim, a superativação da Ras se associa a uma alteração no padrão de regulação da Nox1 pela PDIA1. A supressão do efeito regulador da PDIA1 pela Kras é provavelmente devido a uma ativação sustentada da Rac1. Portanto, PDIA1 pode exercer um papel redox-dependente adaptativo crucial relacionado à progressão tumoral / Protein disulfide isomerases such as PDIA1 have been implicated in cancer progression, but the underlying mechanisms are unclear. We showed previously important PDIA1 effects enabling vascular Nox1 NADPH oxidase expression and associated generation of reactive oxygen species (ROS). Since deregulated ROS production underlies tumor growth, we proposed that PDIA1 acts as an upstream regulatory mechanism of tumor-associated ROS production. We focused on colorectal cancer (CRC) with distinct levels of KRas activation. Our results from RNAseq databanks and direct validation indicate significant increase in PDIA1 expression in CRC with constitutive high (HCT116) vs. moderate (HKE3) or basal (e.g. Caco2) Ras activity. PDIA1 supported Nox1-dependent superoxide production in CRC; however, we observed for the first time a dual effect correlated with Ras level activity: in Caco2 and HKE3 cells, loss-of-function experiments indicate that PDIA1 sustains Nox1-dependent superoxide production; however, in HCT116 cells, PDIA1 restricted Nox1-dependent superoxide production. This PDIA1 behavior in HCT116 is associated with increased Rac1 expression/activity. Transfection of Rac1G12V active mutant into HKE3 cells induced PDIA1 to become restrictive of Nox1-dependent superoxide; accordingly, in HCT116 cells treated with Rac1 inhibitor, PDIA1 became supportive of superoxide production. Screening of cell signaling routes affected by PDIA1 silencing showed induced GSK3beta inactivation and parallel decrease of active Stat3 in HKE3 cells; in baseline HCT116 cells, GSK3beta was inactivated and Stat3 active, whereas PDIA1 silencing had no further effect. Functional implications of PDIA1 silencing included a decrease of cell proliferation and migration in HKE3, not detectable in HCT116 cells. Also, PDIA1 may support epithelial-mesenchymal transition (EMT), since after PDIA1 silencing, E-cadherin expression increased in HKE3 and decreased in HCT116. Thus, Ras overaction associates with a switched in PDIA1 pattern regulation of Nox1. Ras-induced PDIA1 bypass may involve direct Rac1 activation. Therefore, PDIA1 may be a crucial regulator of redox-dependent adaptive processes related to cancer progression