crystal structure classification
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... Contents -- Protein Structure -- Part 1 Basic Structural Principles -- 1. ... ... Motifs of Protein Structure -- Few general principles emerged from the first protein structure -- The ... ... -- Topology diagrams are useful for classification of protein structures -- Secondary structure elements ... ... 72 -- The hemagglutinin polypeptide chain folds into a complex structure 72 -- The subunit structure ... ... is necessary for prediction of tertiary structure 251 -- Prediction methods for secondary structure ...
xv, 302 stran : ilustrace ; 28 cm
BACKGROUND: A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with dinucleotide steps exhibiting a substantial flexibility in a sequence-dependent manner. An analysis of the conformational space of the DNA backbone and the enhancement of our understanding of the conformational dependencies in DNA are therefore important for full comprehension of DNA structural polymorphism. RESULTS: A detailed classification of local DNA conformations based on the technique of Fourier averaging was published in our previous work. However, this procedure requires a considerable amount of manual work. To overcome this limitation we developed an automatic classification method consisting of the combination of supervised and unsupervised approaches. A proposed workflow is composed of k-NN method followed by a non-hierarchical single-pass clustering algorithm. We applied this workflow to analyze 816 X-ray and 664 NMR DNA structures released till February 2013. We identified and annotated six new conformers, and we assigned four of these conformers to two structurally important DNA families: guanine quadruplexes and Holliday (four-way) junctions. We also compared populations of the assigned conformers in the dataset of X-ray and NMR structures. CONCLUSIONS: In the present work we developed a machine learning workflow for the automatic classification of dinucleotide conformations. Dinucleotides with unassigned conformations can be either classified into one of already known 24 classes or they can be flagged as unclassifiable. The proposed machine learning workflow permits identification of new classes among so far unclassifiable data, and we identified and annotated six new conformations in the X-ray structures released since our previous analysis. The results illustrate the utility of machine learning approaches in the classification of local DNA conformations.
- MeSH
- algoritmy MeSH
- DNA chemie MeSH
- G-kvadruplexy MeSH
- klasifikace metody MeSH
- konformace nukleové kyseliny MeSH
- krystalografie rentgenová MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- průběh práce MeSH
- shluková analýza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.
Lichen-inhabiting fungi are highly specialized mycoparasites, commensals or rarely saprotrophs, that are common components of almost every ecosystem, where they develop obligate associations with lichens. Their relevance, however, contrasts with the relatively small number of these fungi described so far. Recent estimates and ongoing studies indicate that a significant fraction of their diversity remains undiscovered and may be expected in tropical regions, in particular in hyperdiverse fog-exposed montane forests. Here, we introduce the new genus Zhurbenkoa, from South America and Europe, for three lichenicolous fungi growing on thalli of the widespread lichen genus Cladonia (Lecanorales). Phylogenetic analyses based on combined sequence data of mt and nuc rDNA obtained from Andean populations (Bolivia) placed Zhurbenkoa as a member of Malmideaceae, a recently introduced family of lichen-forming fungi in the class Lecanoromycetes. Zhurbenkoa is closely related to the genera Savoronala and Sprucidea. The new genus is characterized by the development of grayish brown to almost black apothecia lacking an evident margin, an epihymenium interspersed with crystals (often seen as pruina), a strongly conglutinated hymenium made of noncapitate and sparsely branched paraphyses, a colorless exciple composed of radially arranged hyphae, a Lecanora/Micarea-like ascus type, and aseptate or 1-septate ellipsoidal colorless ascospores. Zhurbenkoa includes two Neotropical (Z. cladoniarum, Z. latispora) and one widespread (Z. epicladonia) species. The lichenicolous trophic mode is documented for the first time in the Malmideaceae, which until now included only lichen-forming associations between fungi and green algae.
- MeSH
- Ascomycota klasifikace cytologie genetika MeSH
- fylogeneze MeSH
- interakce mikroorganismu a hostitele fyziologie MeSH
- klasifikace MeSH
- lišejníky mikrobiologie MeSH
- ribozomální DNA genetika MeSH
- symbióza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Jižní Amerika MeSH
... Dendritic Cells and Adaptive Immunity 307 -- Madhav Dhodapkar, Crystal L. Mackali, and Ralph M. ... ... Structure and Composition of the Erythrocyte -- Narla Mohandas -- 32. ... ... Classification and Clinical Manifestations of -- Neutrophil Disorders 983 -- Marshall A. ... ... Structure, Receptors, and Functions of Monocytes and -- Macrophages 1045 -- Steven D. ... ... The Structure of Lymphocytes and Plasma Cells 1137 -- Natarajan Muthusamy and Michael A. ...
Ninth edition xi, 2505 stran , ilustrace
- MeSH
- hematologie metody MeSH
- krevní nemoci * MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- hematologie a transfuzní lékařství
... Epidemiologic concepts and classification of rheumatic and 25. ... ... Bone structure and function -- David B. Burr, Teresita Bellido, Kenneth E. White 7. ... ... Other crystal-related arthropathies Lan X. Chen, H. ... ... Epidemiology and classification of osteoporosis -- 180. ... ... Renal osteodystrophy -- CRYSTAL-RELATED ARTHROPATHIES Paul D. Miller 206. ...
6th ed. 2 sv. : il., tab. ; 31 cm
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- revmatologie
- NLK Publikační typ
- kolektivní monografie
- učebnice vysokých škol
Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD) in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.
... STRUCTURE -- 2.1. Meaning, Factorization, Internal Coordinates. Isomers 11 -- 2.2. ... ... Determination of Structure 24 -- 2.6. A Priori Calculation of Structure 32 -- 2.7. ... ... Separation of Enantiomers by Crystallization 298 a. Crystal Picking. Triage 298 b. ... ... Preferential Crystallization 304 d. ... ... Preferential Crystallization in the Presence of Additives 311 e. ...
1267 s.
Úvod: Moderní medicína k dosažení miniinvazivity a dodržení radikality léčby využívá řadu technicky vyspělých přístrojů. Naším cílem bylo stanovit přínos laserové medicíny do miniivazivity v oblasti tonzilektomií a její srovnání s klasickou tonzilektomií. Materiál a metoda: Do roku 2014 jsme měli možnost pracovat na ORL klinice v Plzni s celkem 10 laserovými systémy. V této práci jsme srovnávali Ho:YAG laser s klasickou tonzilektomií a novým typem krystalického laseru (Er,Cr:YSGG). Pacienti byli rozděleni do 2 skupin po 10 respondentech. Levostranná tonzilektomie byla prováděna klasicky, pravostranná zkoušenými přístroji. U každého pacienta bylo hodnoceno peroperační krvácení, doba operace a pooperační průběh bolesti (pro každou stranu zvlášť). Histologicky byla ověřena šířka ireverzibilního termického poškození tkáně. Výsledky: Průměrná doba operace byla proti klasické tonzilektomii zkrácena u Ho:YAG laseru o 2 min. a naopak prodloužena o 4,3 min. u Er,Cr:YSGG laseru. Výrazná redukce peroperačního krvácení byla pozorována u Ho:YAG laseru. U obou laserů byla statisticky signifikantně vyšší bolestivost v pooperačním průběhu oproti klasické tonzilektomii. Závěr: Oba lasery nabízejí bezpečnou, nekomplikovanou metodu pro provedení tonzilektomie srovnatelnou se “zlatým standardem” (klasickou tonzilektomií), avšak z celkového nadhledu bez zásadního profitu pro pacienta.
Introduction: Modern medicine uses a whole range of technically developed devices to reach mini invasiveness and to keep radicality of therapy. Our aim was to determine the benefit of laser medicine to mini invasiveness related to tonsillectomies and its comparison with classic tonsillectomy. Material and methodology: Until 2014, it was possible to work with ten laser systems at the ENT department of University hospital in Pilsen. In this study, Ho:YAG laser was compared with classic tonsillectomy and a new type of crystal laser (Er,Cr:YSGG). Patients were divided into two groups of ten respondents. Left-sided tonsillectomy was performed in a classic way. In case of right-sided tonsillectomy, it was realized by using tested devices. Peroperative bleeding, duration of operation as well as postoperative pain were evaluated in each patient (by each side separately). The width of irreversible tissue thermal damage was histologically verified. Results: Compared to classic tonsillectomy, the average duration of operation using Ho:YAG laser was shortened by two minutes. Regarding Er,Cr:YSGG laser, it was prolonged by 4.3 minutes. The considerable reduction of perioperative bleeding could be seen in case of Ho:YAG laser. Contrary classic tonsillectomy, postoperative pain was significantly stronger in case of using both lasers. Conclusion: Both lasers (Ho:YAG and Er,Cr:YSGG) offer a safe non-complicated method to perform tonsillectomy which is comparable with gold standard (classic tonsillectomy). But overall, it brings no essential benefits to the patient. .
- MeSH
- dospělí MeSH
- infračervené záření terapeutické užití MeSH
- laserová terapie * metody využití MeSH
- lasery pevnolátkové využití MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- peroperační doba MeSH
- prospektivní studie MeSH
- statistika jako téma MeSH
- tonzilektomie * využití MeSH
- výsledky a postupy - zhodnocení (zdravotní péče) MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
Formation of transient complexes of cytochrome P450 (P450) with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates the catalytic activities of several P450s. Therefore, we examined formation and binding modes of the complex of human P450 1A2 with cyt b5. Docking of soluble domains of these proteins was performed using an information-driven flexible docking approach implemented in HADDOCK. Stabilities of the five unique binding modes of the P450 1A2-cyt b5 complex yielded by HADDOCK were evaluated using explicit 10 ns molecular dynamics (MD) simulations in aqueous solution. Further, steered MD was used to compare the stability of the individual P450 1A2-cyt b5 binding modes. The best binding mode was characterized by a T-shaped mutual orientation of the porphyrin rings and a 10.7 Å distance between the two redox centers, thus satisfying the condition for a fast electron transfer. Mutagenesis studies and chemical cross-linking, which, in the absence of crystal structures, were previously used to deduce specific P450-cyt b5 interactions, indicated that the negatively charged convex surface of cyt b5 binds to the positively charged concave surface of P450. Our simulations further elaborate structural details of this interface, including nine ion pairs between R95, R100, R138, R362, K442, K455, and K465 side chains of P450 1A2 and E42, E43, E49, D65, D71, and heme propionates of cyt b5. The universal heme-centric system of internal coordinates was proposed to facilitate consistent classification of the orientation of the two porphyrins in any protein complex.
