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Citation - WoS: 17
Aggregatibacter actinomycetemcomitans: GroEL protein promotes conversion of human CD4+T cells into IFNγ IL10 producing Tbet+Th1 cells
(Public Library Science, 2012) Saygili, Tahsin; Akincilar, Semih Can; Akgul, Bunyamin; Nalbant, Ayten; Akgül, Bünyamin
One of the heat shock family protein (Hsp) expressing bacteria is the gram negative, periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa). A. actinomycetemcomitans' Hsp is a 64-kDa GroEL-protein, which has been shown to influence the host cells. In this study we used recombinant A. actinomycetemcomitans GroEL (rAaGroEL) protein as a model antigen to study GroEL-mediated T cell immune response. Human peripheral mononuclear cells (PBMCs), when stimulated with recombinant rAaGroEL, expressed early activation marker CD69 and IL-2R (CD25). CD25 and CD69 expressions were higher in CD4+ T cells compared to CD8+ T cells. rAaGroEL-responding CD4+ T cells expressed IL-10, IFN gamma and TNF alpha cytokines. Interestingly, there were also IL-10 and IFN gamma double cytokine producing CD4+ T cells. Additionally, IFN gamma expressing CD4+ T cells were also T-bet positive. Altogether the results suggest that rAaGroEL protein affects CD4+ T cells to differentiate into IFN gamma IL10-secreting T-bet+ Th1 cells.
Citation - WoS: 4
Citation - Scopus: 9
End-to-end security implementation for mobile devices using TLS protocol
(Springer France, 2006) Kayayurt, Baris; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
End-to-end security has been an emerging need for mobile devices with the widespread use of personal digital assistants and mobile phones. Transport Layer Security Protocol (TLS) is an end-to-end security protocol that is commonly used on the Internet, together with its predecessor, SSL protocol. By implementing TLS protocol in the mobile world, the advantage of the proven security model of this protocol can be utilized. The main design goals of mobile end-to-end security protocol are maintainability and extensibility. Cryptographic operations are performed with a free library, Bouncy Castle Cryptography Package. The object oriented architecture of proposed end-to-end security protocol implementation makes the replacement of this library with another cryptography package easier. The implementation has been experimented with different cases, which represent use of different cryptographic algorithms.
Citation - WoS: 73
Evidence for water-tuned structural differences in proteins: an approach emphasizing variations inlocal hydrophilicity
(Public Library Science, 2012) Akdogan, Yasar; Reichenwallner, Joerg; Hinderberger, Dariush
We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands' points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.
Citation - WoS: 5
Heme binding constricts the conformational dynamics of the cytochrome: Heme binding cavity
(Amer Chemical Soc, 2012) Akdogan, Yasar; Anbazhagan, Veerappan; Hinderberger, Dariush; Schneider, Dirk
Cytochrome b(559)' is a transmembrane protein formed by homodimerization of the 44-residue PsbF polypeptide and noncovalent binding of a heme cofactor. The PsbF polypeptide can dimerize in the absence and presence of heme. To monitor structural alterations associated with binding of heme to the apocytochrome, we analyzed the apo- and holo-cytochrome structure by electron paramagnetic resonance spectroscopy. Spin labeling of amino acids located close to the heme binding domain of the cytochrome revealed that the structure of the heme binding domain is unconstrained in the absence of heme. Heme binding restricts the conformational dynamics of the heme binding domain, resulting in the structurally more constricted holo-cytochrome structure.

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