54 research outputs found
DNA triple helix formation at target sites containing several pyrimidine interruptions: stabilization by protonated cytosine or 5-(1-propargylamino)dU.
No full textDNase I footprinting has been used to study the formation of parallel triplexes at oligopurine target sequences which are interrupted by pyrimidines at regular intervals. TA interruptions are targeted with third strand oligonucleotides containing guanine, generating G x TA triplets, while CG base pairs are targeted with thymine, forming T x CG triplets. We have attempted to optimize the stability of these complexes by varying the base composition and sequence arrangement of the target sites, and by replacing the third strand thymines with the positively charged analogue 5-(1-propargylamino)dU (U(P)). For the target sequence (AAAT)(5)AA, in which pyrimidines are positioned at every fourth residue, triplex formation with TG-containing oligonucleotides is only detected in the presence of a triplex-binding ligand, though stable triplexes were detected at the target site (AAAAAT)(3)AAAA. Triplex stability at targets containing pyrimidines at every fourth residue is increased by introducing guanines into the duplex repeat unit using the targets (AGAT)(5)AA and (ATGA)(5)AA. In contrast, placing C(+) x GC triplets on the 5'-side of G x TA, using the target (AGTA)(5)TT, produces complexes of lower stability. We have attempted further to increase the stability of these complexes by using the positively charged thymine base analogue U(P), and have shown that (TU(P)TG)(5)TT forms a more stable complex with target (AAAT)(5)AA than the unmodified third strand, generating a footprint in the absence of a triplex-binding ligand. Triplex formation at (AGTA)(5)AA is improved by using the modified oligonucleotide (TCGU(P))(5)TT, generating a complex in which the charged triplets C(+) x GC and U(P) x AT alternate with uncharged triplets. In contrast, placing U(P) x AT triplets adjacent to C(+) x GC, using the third strand oligonucleotide (U(P)CGT)(5)TT, reduces triplex formation, while the third strand with both substitutions, (U(P)CGU(P))(5)TT, produces a complex with intermediate stability. It appears that, although adjacent U(P) x AT triplets form stable triplexes, placing U(P) x AT adjacent to C(+) x GC is unfavorable. Similar results were obtained with fragments containing CG inversions within the oligopurine tract, though triplexes at (AAAAAC)(3)AA were only detected in the presence of a triplex-binding ligand. Placing C(+) x GC on the 5'-side of T x CG triplets also reduces triplex formation, while a 3'-C(+) x GC produces complexes with increased stability
Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins
No full textMultifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP2 lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP2 lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle
Enabling Data Marketplaces with Multi-Party Computation (MPC): An Exploratory Study investigating the Implication of the Maturation of Multi-Party Computation (MPC) technology to the Architecture and the Threat Landscape of the Data Marketplaces
No full textThe emergence of the Data Marketplaces is the latest iteration in the phenomenon of data-driven transformation of the world. Data marketplaces have emerged as a new form of data-driven business models which enable trading of data between the data owners/providers and data consumers by providing the necessary technological and non-technological infrastructure. These features present an alternative to the cumbersome logistics currently involved in searching, buying and selling data; thus, simplify the data supply chains between the data-driven business entities. However, they suffer to take off into mainstream success because of a myriad of reasons. Of all the reasons, 2 of them are focused in this thesis. Firstly, the difficulty involved in architecturally enabling a data marketplace platform as the prospective enabling technologies are still immature. Secondly, the uncertainty associated with the commodification of data which comprises of the intellectual property enforcement of data (data ownership), privacy and confidentiality breach (threats), regulatory ignorance (implication of GDPR), reluctance of businesses from participating because of the previous reasons et cetera. This reason is collectively referred as due to the uncertainty around the threat landscape of the data marketplaces. Multi-Party Computation (MPC) technology provide a solution to these problems. Through its capabilities to preserve the confidentiality of data architecturally and thereby securing the interests of the data actors with respect to the uncertainty of the threat landscape around data, MPC can enable safe and secure data sharing between data actors. This characteristic of MPC can help data marketplaces to overcome their challenges and foster their realisation. However, since MPC cannot handle the scale of real-life application, it is not mature enough yet to be incorporated into real-life data marketplaces. An EU funded project called SafeDEED: Safe Data-Enabled Economic Development, proposes to overcome the scalability issue and intends to achieve the maturation of MPC for real-life application. Building upon this forecast, a research was conducted to investigate the implication of the maturation of MPC technology towards the 2 problems faced by data marketplaces, architectural and threat landscape; and the same is documented in this thesis.Safe-DEEDManagement of Technology (MoT
Novel Concepts in Cardiac Energy Metabolism: From Biology to Disease
No full textThis eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contac
The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation
No full text
- …
