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The peroxidation of cardiolipins by reactive oxygen species (ROS), which is regulated and enhanced by cytochrome c (cyt c), is a critical signaling event in mitochondrial apoptosis. We probe the molecular underpinnings of this mitochondrial death signal through structural and functional studies of horse heart cyt c binding to mixed-lipid membranes containing cardiolipin with mono- and polyunsaturated acyl chains. Lipidomics reveal the selective oxidation of polyunsaturated fatty acid (PUFA) cardiolipin, while multidimensional solid state NMR (ssNMR) probes the structure and dynamics of the membrane and the peripherally bound protein. The hydrophilic milieu at the membrane interface stabilizes a native-like fold, but also leads to localized flexibility at the membrane-interacting protein face. PUFA CL acts as both a preferred substrate and a dynamic regulator by impacting the dynamics of the cyt c N70-I85 omega loop, which covers the heme cavity.

This study explores the relationships among cultural identity, accentedness, and the attitudes that native Greek speakers hold towards English pronunciation. Advanced Greek speakers of English responded to a questionnaire and completed three pronunciation tasks related to Greek identity and pronunciation. Subjects’ performance on pronunciation tasks was evaluated by three native English speakers. Findings indicate that Greek speakers dissociate their cultural identity from their preference for standard native/native-like models of English pronunciation., Selected papers on theoretical and applied linguistics, Vol 22 (2017): Selected Papers on Theoretical and Applied Linguistics from ISTAL, Thessaloniki 24-26 April 2015

A variety of enzymes have been found to interact with double-stranded RNA (dsRNA) in order to carry out its functions. We have endeavored to prepare the covalently crosslinked native-like duplex RNA, which could be useful for biochemical studies and RNA nanotechnology. In this study, the interstrand covalently linked duplex RNA was formed by a crosslinking reaction between vinylpurine (VP) and the target cytosine or uracil in RNA. We measured melting temperatures and CD spectra to identify the properties of the VP crosslinked duplex RNA. The crosslinking formation increased the thermodynamic stability without disturbing the natural conformation of dsRNA. In addition, a competitive binding experiment with the duplex RNA binding enzyme, ADAR2, showed the crosslinked dsRNA bound the protein with nearly the same binding affinity as the natural dsRNA, confirming that it has finely preserved the natural traits of duplex RNA.

Item does not contain fulltext Transient structures in unfolded proteins are important in elucidating the molecular details of initiation of protein folding. Recently, native and non-native secondary structure have been discovered in unfolded A. vinelandii flavodoxin. These structured elements transiently interact and subsequently form the ordered core of an off-pathway folding intermediate, which is extensively formed during folding of this alpha-beta parallel protein. Here, site-directed spin-labelling and paramagnetic relaxation enhancement are used to investigate long-range interactions in unfolded apoflavodoxin. For this purpose, glutamine-48, which resides in a non-native alpha-helix of unfolded apoflavodoxin, is replaced by cysteine. This replacement enables covalent attachment of nitroxide spin-labels MTSL and CMTSL. Substitution of Gln-48 by Cys-48 destabilises native apoflavodoxin and reduces flexibility of the ordered regions in unfolded apoflavodoxin in 3.4 M: GuHCl, because of increased hydrophobic interactions in the unfolded protein. Here, we report that in the study of the conformational and dynamic properties of unfolded proteins interpretation of spin-label data can be complicated. The covalently attached spin-label to Cys-48 (or Cys-69 of wild-type apoflavodoxin) perturbs the unfolded protein, because hydrophobic interactions occur between the label and hydrophobic patches of unfolded apoflavodoxin. Concomitant hydrophobic free energy changes of the unfolded protein (and possibly of the off-pathway intermediate) reduce the stability of native spin-labelled protein against unfolding. In addition, attachment of MTSL or CMTSL to Cys-48 induces the presence of distinct states in unfolded apoflavodoxin. Despite these difficulties, the spin-label data obtained here show that non-native contacts exist between transiently ordered structured elements in unfolded apoflavodoxin. 01 maart 2010

It is important to understand the conformational features of the unfolded state in equilibrium with folded state under physiological conditions. In this paper, we consider a short peptide model LMYKGQPM from staphylococcal nuclease to model the conformational equilibrium between a hairpin conformation and its unfolded state using molecular dynamics simulation under NVT conditions at 300K using GROMOS96 force field. The free energy landscape has overall funnel-like shape with hairpin conformations sampling the minima. The "unfolded" state has a higher free energy of approximately 12kJ/mol with respect to native hairpin minimum and occupies a plateau region. We find that the unfolded state has significant contributions from compact conformations. Many of these conformations have hairpin-like topology. Further, these compact conformational forms are stabilized by hydrophobic interactions. Conversion between native and non-native hairpins occurs via unfolded states. Frequent conversions between folded and unfolded hairpins are observed with single exponential kinetics. We compare our results with the emerging picture of unfolded state from both experimental and theoretical studies.

Bu çalışma, kültürel kimlik ve aksan arasındaki ilişkiyi incelemektedir. Çalışmanın odağı anadili İngilizce olan ve uzun süredir Türkiye?de yaşayan 20 kişinin kimlik algıları ve anadili gibi yakınlığı açısından Türkçe aksanları arasındaki ilişkdir. Katılımcılara bir kültürel kimlik anketi uygulanmış, birkaç Türk pasajların yüksek sesle okumaları kaydedilmiş, ve dört katılımcı ile takip görüşmeler yapılmıştır.Bu çalışmanın bulguları, kültürel kimlik ve aksan arasında bir ilişki olduğunu göstermiştir. Bu anlamda katılımcıların kendilerini Türk olarak gördükçe aksan skoları da o kadar 'anadili gibi' olduğu görülmektedir. Bu bulgu kültürel kimlik ve vurgu arasında bir ilişki olduğunu öne süren önceki literatürü (örneğin; Gatbonton , Trofimovich, & Magid, 2005; Jones, 2001; Marx, 2002; Rindal, 2010) doğrulamaktadır.Bulgular, katılımcıların konuşma sunumu yerine anlaşılırlığa öncelik gösterme eğilimi olduğunu göstermiştir. Pedagojik düzeyde, bu çalışma ikinci dil öğretmenlerin kendi öğretim uygulamaları sırasında, dil öğrencileri ile arasında uyumsuzlukları önlemek için, dil öğrencilerinin hedeflerinin farkında olmaları gerektiğini hatırlatmaktadır.Anahtar sözcükler: kültürel kimlik, kimlik, aksan, ana dili gibi This study investigates the relationship between cultural identity and accent. The focus is on the relationship between the identity perceptions of 20 native speakers of English, who have been living in Turkey for a long period of time, and their Turkish accent in terms of nativelikeness. The participants were administered a cultural identity questionnaire, their reading aloud of a few Turkish passages was recorded, and follow-up interviews were conducted with four of the participants.The findings of this study showed that there is a relationship between cultural identity and accent, in the sense that the more the participants identified themselves as Turkish the more `native-like? their accent score was. This finding confirms the previous literature (e.g., Gatbonton, Trofimovich, & Magid, 2005; Jones, 2001; Marx, 2002; Rindal, 2010), suggesting a relationship between cultural identity and accent. The findings further indicated that the participants tended to prioritize comprehensibility over presentation of speech. At the pedagogical level, this is a reminder that during their practices, second language teachers need to be aware of the language learners? goals in order to avoid mismatches.Key words: cultural identity, identity, accent, native-like 104