Sequence-based prediction of protein binding mode landscapes.

Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred (http://protdyn-fuzpred.org) algorithm to predict the range of context-dependent binding modes of proteins from their amino acid sequences. As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways

A comparative study of femtosecond pulsed laser ablation of meloxicam in distilled water and in air

The increasing prevalence of water insoluble or poorly soluble drugs calls for the development of new formulation methods. Common approaches include the reduction of particle size and degree of crystallinity. Pulsed laser ablation is a clean technique for producing sub-micrometre sized drug particles and has the potential to induce amorphization. We studied the effect of femtosecond pulsed laser ablation (ELI ALPS THz pump laser system: λ c = 781 nm, τ = 135 fs) on meloxicam in distilled water and in air. The ablated particles were characterized chemically, morphologically and in terms of crystallinity. We demonstrated that femtosecond laser ablation can induce partial amorphization of the particles in addition to a reduction in particle size. In the case of femtosecond pulsed laser ablation in air, the formation of pure meloxicam spheres showed that this technique can produce amorphous meloxicam without the use of excipients, which is a unique result. We also aimed to describe the ablation processes in both investigated media

Interobserver agreement and diagnostic accuracy of shearwave elastography for the staging of hepatitis C virus-associated liver fibrosis

Abstract PURPOSE: Our study aimed to evaluate the technical success rate, interobserver reproducibility, and accuracy of shearwave elastography (SWE) in the staging of hepatitis C virus (HCV)-associated liver fibrosis. METHODS: A total of 10 healthy controls and 49 patients with chronic liver disease were enrolled prospectively. Two examiners performed point shearwave elastography (pSWE) and two-dimensional shearwave elastography (2D-SWE) measurements with an RS85A ultrasound scanner using the S-Shearwave application (Samsung Medison, Hongcheon, Korea). The performance of S-Shearwave in the staging (METAVIR F0-F4) of liver fibrosis was compared with prior transient elastography (TE) with receiver operating characteristic (ROC) curve analysis. RESULTS: The interobserver reproducibility was excellent with pSWE (ICC = 0.92, 95% CI: 0.86-0.95, P < .001). A very good agreement was found between pSWE and TE measurements (ICC =0.85, 95% CI: 0.78-0.89, P < .001). The ROC analysis determined the optimal cut-off values of pSWE for the staging of chronic hepatitis C-associated fibrosis (F2, 1.46 m/s; F3, 1.63 m/s; F4, 1.95 m/s). Both observers achieved excellent diagnostic accuracy (AUROC: 94% vs 97%) in the detection of significant (≥F2) liver fibrosis. CONCLUSION: The interobserver agreement is excellent with S-Shearwave pSWE, and observers can diagnose significant liver fibrosis with a comparable accuracy to TE

Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis

: During muscle cell differentiation, the alternatively spliced, acidic β-domain potentiates transcription of Myocyte-specific Enhancer Factor 2 (Mef2D). Sequence analysis by the FuzDrop method indicates that the β-domain can serve as an interaction element for Mef2D higher-order assembly. In accord, we observed Mef2D mobile nuclear condensates in C2C12 cells, similar to those formed through liquid-liquid phase separation. In addition, we found Mef2D solid-like aggregates in the cytosol, the presence of which correlated with higher transcriptional activity. In parallel, we observed a progress in the early phase of myotube development, and higher MyoD and desmin expression. In accord with our predictions, the formation of aggregates was promoted by rigid β-domain variants, as well as by a disordered β-domain variant, capable of switching between liquid-like and solid-like higher-order states. Along these lines, NMR and molecular dynamics simulations corroborated that the β-domain can sample both ordered and disordered interactions leading to compact and extended conformations. These results suggest that β-domain fine-tunes Mef2D higher-order assembly to the cellular context, which provides a platform for myogenic regulatory factors and the transcriptional apparatus during the developmental process

Fabry-betegség - Diagnosztikai útmutató

A Fabry-kór a lizoszomális tárolási betegségek csoportjába tartozó, X-kromoszómához kötötten, recesszív módon öröklődő betegség, amely a globotriaosylceramid felhalmozódásához vezet a szervezet legkülönbözőbb szöveteiben. A betegség első tünetei többnyire gyermekkorban jelentkeznek, a progresszió során a betegek súlyos szervi károsodásokkal és korai halálozással számolhatnak. Elsősorban fiúk és férfiak érintettek, azonban a betegség tüneteit heterozigóta nők esetében is megfigyelhetjük, de náluk a kórkép súlyossága változó, általában enyhébb lefolyású. Az enzimpótló kezelések megjelenése szükségessé tette, hogy részletes diagnosztikus és terápiás protokollt dolgozzunk ki. A jelen dolgozatban megjelenő ajánlásokat egy, a magyarországi Fabry-betegek kezelésében aktívan részt vevő orvosokból, a diagnosztika területén dolgozó biológosukból és egyéb szakemberekből álló multidiszciplináris munkacsoport foglalta össze. A munkacsoport áttekintette a korábbi klinikai tanulmányokat, a publikált vizsgálatokat és a közelmúltban megjelent nemzetközi és nemzeti útmutatókat. | Fabry disease is a rare, X-linked lysosomal storage disorder that leads to accumulation of globotriaosylceramide in different tissues of the body. The disease is progressive, first symptoms usually present in childhood. Consequencies of the diseases are disability and premature death. The disease in females could be as severe as in males although women may also be asymptomatic. The possibility of enzyme replacement therapy has made it necessary to elaborate a comprehensive guideline for the diagnosis and treatment follow-up. The guideline was established by a Hungarian multi-disciplinary working group, consisting of physicians who are involved in health care of Fabry patients. Previous clinical studies, published materials, and recently established international treatment guidelines were reviewed by the group

The role of protein dynamics in enzyme evolution

Az enzimek evolúciójának molekuláris mechanizmusát a mai napig nem sikerült teljes mértékben feltárni. A dolgozat az enzimatikus evolúció jobb megértéséhez szeretne hozzájárulni az eddig elért egyik legsikeresebb laboratóriumi evolúciós funkcióváltó kísérlet - a Pseudomonas diminuta foszfotriészteráz enzim arilészterázzá történő teljes aktivitásváltása, majd az eredeti aktivitás helyreállítása- adatainak bioinformatikai elemzésével. Az evolúciós intermedierek szekvenciájából való fehérje rendezetlenség becsléssel és a röntgenkrisztallográfiás szerkezetek elemzésével vizsgálja az aktivitásváltás során végbement dinamikai és szerkezeti változásokat, ezek kapcsolatát egymással illetve az aktivitásváltozással, feltételezhető szerepüket az evolúciós folyamatokban. A vizsgálatok eredményei arra utalnak, hogy a kísérlet kezdetén beépülő neutrális mutációk, melyek elindítják a funkcióváltást, a fehérje aktiv helyének és az azt koordináló oldalláncok flexibilitásának növeléséhez nagy mértékben járulnak hozzá, míg a specializációt a fehérje általános stabilizációja jellemzi. A későbbiekben a kutatás eredményei alapjául szolgálhatnak egy funkcióváltó mutációkat megjósolni képes prediktív algoritmus kidolgozásához.MSc/MABiotechnológia MScg

Sequence-based prediction of protein binding mode landscapes

Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred (http://protdyn-fuzpred.org) algorithm to predict the range of context-dependent binding modes of proteins from their amino acid sequences. As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways