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Density functional theory investigation of 3d, 4d, and 5d 13-atom metal clusters

PIOTROWSKI, Mauricio J.; PIQUINI, Paulo; SILVA, Juarez L. F. Da
Fonte: AMER PHYSICAL SOC Publicador: AMER PHYSICAL SOC
Tipo: Artigo de Revista Científica
ENG
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46.07%
The knowledge of the atomic structure of clusters composed by few atoms is a basic prerequisite to obtain insights into the mechanisms that determine their chemical and physical properties as a function of diameter, shape, surface termination, as well as to understand the mechanism of bulk formation. Due to the wide use of metal systems in our modern life, the accurate determination of the properties of 3d, 4d, and 5d metal clusters poses a huge problem for nanoscience. In this work, we report a density functional theory study of the atomic structure, binding energies, effective coordination numbers, average bond lengths, and magnetic properties of the 3d, 4d, and 5d metal (30 elements) clusters containing 13 atoms, M(13). First, a set of lowest-energy local minimum structures (as supported by vibrational analysis) were obtained by combining high-temperature first- principles molecular-dynamics simulation, structure crossover, and the selection of five well-known M(13) structures. Several new lower energy configurations were identified, e. g., Pd(13), W(13), Pt(13), etc., and previous known structures were confirmed by our calculations. Furthermore, the following trends were identified: (i) compact icosahedral-like forms at the beginning of each metal series...

Um estudo da aplicação de algoritmos genéticos na predição da estrutura 3-D aproximada de proteínas; Study of Application of Genetic Algorithms in Predicting Approximate 3-D Structure of Proteins

Gonçalves, William Wolmann
Fonte: Universidade Federal do Rio Grande do Sul Publicador: Universidade Federal do Rio Grande do Sul
Tipo: Trabalho de Conclusão de Curso Formato: application/pdf
POR
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46.15%
O Problema da Predição da Estrutura Tridimensional de Proteínas (3D-PSP, sigla em inglês) é um dos mais importantes problemas em Bioinformática Estrutural. Diversos algoritmos têm sido propostos ao longo dos últimos anos. Entretanto, o problema continua desafiante por causa da complexidade e dimensionalidade do espaço de busca conformacional das proteínas. A estrutura nativa de uma proteína dita sua função bioquímica em um organismo. Conhecer sua estrutura 3D implica em também conhecer a sua função. Assim, conhecendo a sua estrutura é possível interferir ativando ou inibindo a sua função, como em doenças onde os alvos dos fármacos são as proteínas. Neste trabalho de diplomação é apresentado um estudo da aplicação de algoritmos genéticos com população estruturada no 3D-PSP. Diferentes estratégias de seleção e organização populacional são utilizadas com a finalidade de garantir diversidade de indivíduos e convergência das conformações preditas. A eficácia dos métodos estudados é conferida com a execução de seis estudos de caso.; The Protein 3D Structure Prediction problem (3D-PSP) is one of the most important problems in Structural Bioinformatics. Several algorithms have been proposed over the last years. However...

Hybrid 3D structure of poly(d,l-lactic acid) loaded with chitosan/chondroitin sulfate nanoparticles to be used as carriers for biomacromolecules in tissue engineering

Santo, Vitor E.; Duarte, Ana Rita C.; Gomes, Manuela E.; Mano, J. F.; Reis, R. L.
Fonte: Elsevier Publicador: Elsevier
Tipo: Artigo de Revista Científica
Publicado em //2010 ENG
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46.05%
In the tissue engineering (TE) field, the concept of producing multifunctional scaffolds, capable not only of acting as templates for cell transplantation but also of delivering bioactive agents in a controlled manner, is an emerging strategy aimed to enhance tissue regeneration. In this work, a complex hybrid release system consisting in a three-dimensional (3D) structure based on poly(d,l-lactic acid) (PDLLA) impregnated with chitosan/chondroitin sulfate nanoparticles (NPs) was developed. The scaffolds were prepared by supercritical fluid foaming at 200 bar and 35 "C, and were then characterized by scanning electron microscopy (SEM) and micro-CT. SEM also allowed to assess the distribution of the NPs within the structure, showing that the particles could be found in different areas of the scaffold, indicating a homogeneous distribution within the 3D structure. Water uptake and weight loss measurements were also carried out and the results obtained demonstrated that weight loss was not significantly enhanced although the entrapment of the NPs in the 3D structure clearly enhances the swelling of the structure. Moreover, the hybrid porous biomaterial displayed adequate mechanical properties for cell adhesion and support. The possibility of using this scaffold as a multifunctional material was further evaluated by the incorporation of a model protein...

MMDB: Entrez’s 3D-structure database

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamas
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/01/2002 EN
Relevância na Pesquisa
46.18%
Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure.

MMDB: 3D structure data in Entrez

Wang, Yanli; Addess, Kenneth J.; Geer, Lewis; Madej, Thomas; Marchler-Bauer, Aron; Zimmerman, Diane; Bryant, Stephen H.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/01/2000 EN
Relevância na Pesquisa
46.11%
Three-dimensional structures are now known for roughly half of all protein families. It is thus quite likely, in searching sequence databases, that one will encounter a homolog with known structure and be able to use this information to infer structure–function properties. The goal of Entrez’s 3D structure database is to make this information accessible and useful to molecular biologists. To this end, Entrez’s search engine provides three powerful features: (i) Links between databases; one may search by term matching in Medline®, for example, and link to 3D structures reported in these articles. (ii) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view a combined molecular-graphic and alignment display, to infer approximate 3D structure. Entrez’s MMDB (Molecular Modeling DataBase) may be accessed at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html

Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties

Tong, Wenxu; Wei, Ying; Murga, Leonel F.; Ondrechen, Mary Jo; Williams, Ronald J.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.11%
A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures, an important current challenge in genomics. The input consists of electrostatic and geometric properties derived from the 3D structure of the query protein alone. Sequence-based conservation information, where available, may also be incorporated. Electrostatics features from THEMATICS are combined with multidimensional isotonic regression to form maximum likelihood estimates of probabilities that specific residues belong to an active site. This allows likelihood ranking of all ionizable residues in a given protein based on THEMATICS features. The corresponding ROC curves and statistical significance tests demonstrate that this method outperforms prior THEMATICS-based methods, which in turn have been shown previously to outperform other 3D-structure-based methods for identifying active site residues. Then it is shown that the addition of one simple geometric property, the size rank of the cleft in which a given residue is contained, yields improved performance. Extension of the method to include predictions of non-ionizable residues is achieved through the introduction of environment variables. This extension results in even better performance than THEMATICS alone and constitutes to date the best functional site predictor based on 3D structure only...

Automated 3D structure composition for large RNAs

Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.06%
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently...

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard
Fonte: Elsevier Publicador: Elsevier
Tipo: Artigo de Revista Científica
Publicado em /12/2013 EN
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Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background...

Inferring 3D Structure with a Statistical Image-Based Shape Model

Grauman, Kristen; Shakhnarovich, Gregory; Darrell, Trevor
Fonte: MIT - Massachusetts Institute of Technology Publicador: MIT - Massachusetts Institute of Technology
Formato: 17 p.; 6362014 bytes; 9371703 bytes; application/postscript; application/pdf
EN_US
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We present an image-based approach to infer 3D structure parameters using a probabilistic "shape+structure' model. The 3D shape of a class of objects may be represented by sets of contours from silhouette views simultaneously observed from multiple calibrated cameras. Bayesian reconstructions of new shapes can then be estimated using a prior density constructed with a mixture model and probabilistic principal components analysis. We augment the shape model to incorporate structural features of interest; novel examples with missing structure parameters may then be reconstructed to obtain estimates of these parameters. Model matching and parameter inference are done entirely in the image domain and require no explicit 3D construction. Our shape model enables accurate estimation of structure despite segmentation errors or missing views in the input silhouettes, and works even with only a single input view. Using a dataset of thousands of pedestrian images generated from a synthetic model, we can perform accurate inference of the 3D locations of 19 joints on the body based on observed silhouette contours from real images.

A Statistical Image-Based Shape Model for Visual Hull Reconstruction and 3D Structure Inference

Grauman, Kristen
Fonte: MIT - Massachusetts Institute of Technology Publicador: MIT - Massachusetts Institute of Technology
Formato: 60 p.; 14619811 bytes; 42799632 bytes; application/postscript; application/pdf
EN_US
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We present a statistical image-based shape + structure model for Bayesian visual hull reconstruction and 3D structure inference. The 3D shape of a class of objects is represented by sets of contours from silhouette views simultaneously observed from multiple calibrated cameras. Bayesian reconstructions of new shapes are then estimated using a prior density constructed with a mixture model and probabilistic principal components analysis. We show how the use of a class-specific prior in a visual hull reconstruction can reduce the effect of segmentation errors from the silhouette extraction process. The proposed method is applied to a data set of pedestrian images, and improvements in the approximate 3D models under various noise conditions are shown. We further augment the shape model to incorporate structural features of interest; unknown structural parameters for a novel set of contours are then inferred via the Bayesian reconstruction process. Model matching and parameter inference are done entirely in the image domain and require no explicit 3D construction. Our shape model enables accurate estimation of structure despite segmentation errors or missing views in the input silhouettes, and works even with only a single input view. Using a data set of thousands of pedestrian images generated from a synthetic model...

Determinação da estrutura terciária do peptídeo Cn-AMP1 isolado da água do coco verde, por Ressonância Magnética Nuclear (RMN); Determining the tertiary structure of the peptide Cn-AMP1 isolated from coconut water by Nuclear Magnetic Resonance (NMR)

Santana, Mábio João
Fonte: Universidade Federal de Goiás; Brasil; UFG; Programa de Pós-graduação em Química (IQ); Instituto de Química - IQ (RG) Publicador: Universidade Federal de Goiás; Brasil; UFG; Programa de Pós-graduação em Química (IQ); Instituto de Química - IQ (RG)
Tipo: Dissertação Formato: application/pdf
POR
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56.06%
This study aims to determine and analyze the three-dimensional structure in the lowest energy conformation of the peptide Cn-AMP1, isolated from green coconut water by 1H NMR. The determination of the 3D structure of the peptide under study was performed by homonuclear 2D 1H NMR experiments COSY, TOCSY and NOESY, using a 1 mM solution of the peptide Cn-AMP1 on Bruker AVANCE III 500 MHz (for 1H). The analysis of the correlation maps were made using the software NMRView, and the methodology adopted was the allocation sequence described by Wüthrich, where 200 structures were generated and selected the 20 lowest energy conformations to represent the overall three-dimensional structure Cn-AMP1 peptide. The peptide showed helical structure between residues Ser-1and Ala-6 in SDS- d25 micelles, 100 mM being structured randomly between residues Gln-7 and Met-9. However, under conditions of physiological pH, as in the absence of SDS micelles d25, the peptide showed no helix structure, predominating is randomly.; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES; O presente trabalho tem como objetivo determinar e analisar a estrutura tridimensional em conformação de menor energia do peptídeo Cn-AMP1, isolado da água de coco verde por RMN de 1H. A determinação da estrutura 3D do peptídeo em estudo foi realizada através de experimentos de RMN de 1H homonuclear de COSY...

3D mapping of the SPRY2 domain of ryanodine receptor 1 by single-particle Cryo-EM

Perálvarez-Marín, Alex; Tae, HanShen; Board, Philip G.; Casarotto, Marco G.; Dulhunty, Angela F.; Samsó, Montserrat
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica Formato: 7 pages
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The type 1 skeletal muscle ryanodine receptor (RyR1) is principally responsible for Ca(2+) release from the sarcoplasmic reticulum and for the subsequent muscle contraction. The RyR1 contains three SPRY domains. SPRY domains are generally known to mediate protein-protein interactions, however the location of the three SPRY domains in the 3D structure of the RyR1 is not known. Combining immunolabeling and single-particle cryo-electron microscopy we have mapped the SPRY2 domain (S1085-V1208) in the 3D structure of RyR1 using three different antibodies against the SPRY2 domain. Two obstacles for the image processing procedure; limited amount of data and signal dilution introduced by the multiple orientations of the antibody bound in the tetrameric RyR1, were overcome by modifying the 3D reconstruction scheme. This approach enabled us to ascertain that the three antibodies bind to the same region, to obtain a 3D reconstruction of RyR1 with the antibody bound, and to map SPRY2 to the periphery of the cytoplasmic domain of RyR1. We report here the first 3D localization of a SPRY2 domain in any known RyR isoform.; The authors want to thank the Brigham and Women’s Hospital Biomedical Research Institute (to MS), the Australian National Health and the Medical Research Council (471418 to AD...

Étude structurale conformationnelle des toxines de l’anthrax par cryo-microscopie et dynamique moléculaire

Fabre, Lucien
Fonte: Université de Montréal Publicador: Université de Montréal
Tipo: Thèse ou Mémoire numérique / Electronic Thesis or Dissertation
FR
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46.09%
Les toxines de l’anthrax font partie de la famille des toxines A-B dans laquelle la moitié B se fixe à la membrane de la cellule permettant par la suite la translocation de la moitié A. Dans le cas de l’anthrax, la moitié B est représentée par le Protective Antigen (PA) et la moitié A par les deux protéines Edema Factor (EF) et Lethal Factor (LF). Après le recrutement par les récepteurs cellulaires (CMG2 et TEM8), PA s’organise en heptamère. Il peut fixer jusqu'à 3 ligands (EF et LF) avant d'être endocyté. Les modèles actuels de PA suggèrent que la baisse de pH à l’intérieur des endosomes permet un changement de conformation de la forme pré-pore vers la forme pore et que les ligands EF et LF passeraient au travers le pore pour entrer dans le cytoplasme. Cependant, le diamètre du pore est environ dix fois inférieur à celui des ligands (10 Å contre 100 Å). Un processus de folding/unfolding a été proposé mais demeure controversé. Afin d'identifier le processus de passage des facteurs EF et LF dans le cytoplasme, nous avons déterminé par cryo-microscopie électronique combinée avec l’analyse d’image les structures tridimensionnelles des complexes formés par PA et LF aux étapes prépore et pore. Par la suite...

MMDB: Entrez's 3D structure database.

Marchler-Bauer, A; Addess, K J; Chappey, C; Geer, L; Madej, T; Matsuo, Y; Wang, Y; Bryant, S H
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 01/01/1999 EN
Relevância na Pesquisa
46.07%
The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The goal of Entrez's 3D-structure database is to make this information accessible and usable by molecular biologists (http://www.ncbi.nlm.nih.gov/Entrez). To this end Entrez provides two major analysis tools, a search engine based on sequence and structure 'neighboring' and an integrated visualization system for sequence and structure alignments. From a protein's sequence 'neighbors' one may rapidly identify other members of a protein family, including those where 3D structure is known. By comparing aligned sequences and/or structures in detail, using the visualization system, one may identify conserved features and perhaps infer functional properties. Here we describe how these analysis tools may be used to investigate the structure and function of newly discovered proteins, using the PTEN gene product as an example.

MMDB: annotating protein sequences with Entrez's 3D-structure database

Wang, Yanli; Addess, Kenneth J.; Chen, Jie; Geer, Lewis Y.; He, Jane; He, Siqian; Lu, Shennan; Madej, Thomas; Marchler-Bauer, Aron; Thiessen, Paul A.; Zhang, Naigong; Bryant, Stephen H.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.16%
Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The ‘Related Structure’ service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB ().

3D Continuum radiative transfer in complex dust configurations around young stellar objects and active nuclei II. 3D Structure of the dense molecular cloud core Rho Oph D

Steinacker, J.; Bacmann, A.; Henning, Th.; Klessen, R.; Stickel, M.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.11%
Constraints on the density and thermal 3D structure of the dense molecular cloud core Rho Oph D are derived from a detailed 3D radiative transfer modeling. Two ISOCAM images at 7 and 15 micron are fitted simultaneously by representing the dust distribution in the core with a series of 3D Gaussian density profiles. Size, total density, and position of the Gaussians are optimized by simulated annealing to obtain a 2D column density map. The projected core density has a complex elongated pattern with two peaks. We propose a new method to calculate an approximate temperature in an externally illuminated complex 3D structure from a mean optical depth. This T(tau)-method is applied to a 1.3 mm map obtained with the IRAM 30m telescope to find the approximate 3D density and temperature distribution of the core Rho Oph D. The spatial 3D distribution deviates strongly from spherical symmetry. The elongated structure is in general agreement with recent gravo-turbulent collapse calculations for molecular clouds. We discuss possible ambiguities of the background determination procedure, errors of the maps, the accuracy of the T(tau)-method, and the influence of the assumed dust particle sizes and properties.; Comment: 16 pages, 12 figures

Single-shot 3D structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

Xu, Rui; Jiang, Huaidong; Song, Changyong; Rodriguez, Jose A.; Huang, Zhifeng; Chen, Chien-Chun; Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Kim, Sangsoo; Kim, Sunam; Suzuki, Akihiro; Takayama, Yuki; Oroguchi, Tomotaka; Takahashi, Yukio; Fan, J
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 31/10/2013
Relevância na Pesquisa
46.08%
Coherent diffraction imaging (CDI) using synchrotron radiation, X-ray free electron lasers (X-FELs), high harmonic generation, soft X-ray lasers, and optical lasers has found broad applications across several disciplines. An active research direction in CDI is to determine the structure of single particles with intense, femtosecond X-FEL pulses based on diffraction-before-destruction scheme. However, single-shot 3D structure determination has not been experimentally realized yet. Here we report the first experimental demonstration of single-shot 3D structure determination of individual nanocrystals using ~10 femtosecond X-FEL pulses. Coherent diffraction patterns are collected from high-index-faceted nanocrystals, each struck by a single X-FEL pulse. Taking advantage of the symmetry of the nanocrystal, we reconstruct the 3D structure of each nanocrystal from a single-shot diffraction pattern at ~5.5 nm resolution. As symmetry exists in many nanocrystals and virus particles, this method can be applied to 3D structure studies of such particles at nanometer resolution on femtosecond time scales.; Comment: 18 pages, 4 figures

Does 2D-Histologic Identification of Villous Types of Human Placentas at Birth Enable Sensitive and Reliable Interpretation of 3D Structure?

Haeussner, Eva; Aschauer, Beate; Burton, Graham J.; Huppertz, Berthold; von Koch, Franz Edler; M?ller-Starck, Jens; Salafia, Carolyn; Schmitz, Christoph; Frank, Hans-Georg
Fonte: Elsevier Publicador: Elsevier
Tipo: Article; published version
EN
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66.07%
This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.placenta.2015.10.003; Introduction: The villous tree of human placentas is a complex three-dimensional (3D) structure which enables fetomaternal exchange. Current concepts of microscopic analyses are based on the analysis of two-dimensional (2D) histologic sections. For this approach, the assessment of the stromal core of sectioned villi is of key importance. The classification of stromal properties of sectioned villi allows allocation of villous sections to villous types which are named by their expected position in villous trees (terminal, intermediate, and stem villi). Method: The present study takes these current concepts of placental histology as hypothesis and validates them against predetermined 3D positions of branches of villous trees. The 3D positions were determined prior to histologic sectioning using a recently introduced 3D-microscopic approach. Individual histologic sections of villi were classified by their stromal structures and inter rater variability of these histologic assessments were determined. Results/disscussion: Inter rater variability was high and indicates substantial observer influence on the outcome of histologic assessments. Cross-match of villous types with the predetermined positions of villous branches of villous trees revealed substantial mismatch between the outcome of stromal classification and 3D-position of the sectioned villi in the placental villous trees.; DFG...

RNA 3D Structure Analysis and Validation, and Design Algorithms for Proteins and RNA

Jain, Swati
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Dissertação
Publicado em //2015
Relevância na Pesquisa
55.95%

RNA, or ribonucleic acid, is one of the three biological macromolecule types essential for all known life forms, and is a critical part of a variety of cellular processes. The well known functions of RNA molecules include acting as carriers of genetic information in the form of mRNAs, and then assisting in translation of that information to protein molecules as tRNAs and rRNAs. In recent years, many other kinds of non-coding RNAs have been found, like miRNAs and siRNAs, that are important for gene regulation. Some RNA molecules, called ribozymes, are also known to catalyze biochemical reactions. Functions carried out by these recently discovered RNAs, coupled with the traditionally known functions of tRNAs, mRNAs, and rRNAs make RNA molecules even more crucial and essential components in biology.

Most of the functions mentioned above are carried out by RNA molecules associ- ating themselves with proteins to form Ribonucleoprotein (RNP) complexes, e.g. the ribosome or the splicesosome. RNA molecules also bind a variety of small molecules, such as metabolites, and their binding can turn on or off gene expression. These RNP complexes and small molecule binding RNAs are increasingly being recognized as potential therapeutic targets for drug design. The technique of computational structure-based rational design has been successfully used for designing drugs and inhibitors for protein function...

Visualization of protein 3D structures in reduced representation with simultaneous display of intra and inter-molecular interactions

Sheth, Vrunda
Fonte: Rochester Instituto de Tecnologia Publicador: Rochester Instituto de Tecnologia
Tipo: Tese de Doutorado
EN_US
Relevância na Pesquisa
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Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require. Currently there is no available method of protein 3D structure representation which captures enough chemical information from the protein sequence and clearly shows the intra-molecular and the inter-molecular H-bonds and VDW interactions at the same time. This project aims to reduce the 3D structure of a protein and display the reduced representation along with inter-molecular and the intra-molecular H-bonds and van der Waals interactions. A reduced protein representation has a significantly lower "atomicity" (i.e., number of the coordinates) than one which is in all-atom representation. In this work, we transform the protein structure from 'all- atom representation' (AAR) to 'double-centroid reduced representation' (DCRR), which contains amino acid backbone (N, C[alpha], C', O) and side chain (C[beta] and beyond) centroid coordinates instead of atomic coordinates. Another aim of this project is to develop a visualization interface for the reduced representation. This interface is implemented in MATLAB and displays the protein in DCRR along with its inter-molecular...