811 research outputs found
Biodegradable containers from green waste materials
No full textNovel biodegradable polymeric materials based on protein hydrolysate (PH), derived from waste products of the leather industry, and poly(ethylene glycol) diglycidyl ether (PEG) or epoxidized soybean oil (ESO) were obtained and their physico-chemical properties and mechanical behaviour were evaluated. Different processing conditions and the introduction of fillers of natural origin, as saw dust and wood flour, were used to tailor the mechanical properties and the environmental durability of the product. The biodegradable products, which are almost completely manufactured from renewable-based raw materials, look promising for several applications, particularly in agriculture for the additional fertilizing action of PH or in packaging. © 2016 Author(s)
Conservation and specialization in PAS domain dynamics
No full textThe PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2α and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies. © The Author 2005. Published by Oxford University Press. All rights reserved
The work of design for distance learning (DL) in the convergence of educational modalities: between knowledge, thoughts and activities in practice communities
No full textTese de Doutoramento em Ciências da Educação (Especialidade em Tecnologia Educativa)Esta investigação desenvolveu um estudo de caso de tendência etnográfica sobre o trabalho do Design
da EaD realizado por professores e designers instrucionais que atuam em colaboração no Laboratório
de Desenho e Produção de Material Didático para a EaD – Multi.Lab.EaD. As atividades deste trabalho
incidem sobre o desenho e desenvolvimento de ações para a construção das salas online e de
materiais para os Cursos de Licenciatura do CEAD, vinculados ao Sistema Universidade Aberta do
Brasil, da Universidade do Estado de Santa Catarina (UDESC). A problemática de investigação traz ao
centro das finalidades a análise dos saberes, dos modos de pensar e das atividades envolvidas no
trabalho do Design da EaD, protagonizado em Comunidade de Prática. Estão envolvidas nessas
questões problematizadoras e finalidades de pesquisa as formas de ideação, criação e implementação
das atividades que envolvem as escolhas e decisões frente às tarefas necessárias ao Design da EaD
para os cursos supracitados. A decisão do estudo de caso de tendência etnográfica ocorreu em virtude
de se tratar de um grupo específico que atua em Comunidade de Prática, por princípios profissionais, e
situado no interior de uma Universidade, a qual integra um sistema de universidades públicas
brasileiras. Os participantes são professores e designers vinculados aos Cursos de Licenciatura na
modalidade a distância, que estivessem em ação ou que tenham atuado em algum momento nos
cursos na proposta de Comunidade de Prática. A coleta de dados foi realizada utilizando-se o método
de triangulação de fontes sugerida por Yin (2005) e por Minayo (1994), e as técnicas utilizadas foram a
observação, o questionário, a entrevista, o grupo focal (GF), a análise documental e a produção de um
artefato. O registro dos dados foi realizado com o auxílio de diários de campo, gravações em áudio,
vídeos e fotografias. Para o tratamento dos dados foi adotada a análise de conteúdo, inspirada no
método de Bardin (2004), e foi aplicada como prática a perspectiva da análise categorial temática
proposta por Minayo (1994), Minayo e Minayo-Gómez (2003), Minayo, Assis e Souza (2010) e Gomes
(1994). A abordagem teórica utilizada nesta investigação foi a sócio-histórica, cujo representante mais
expressivo é Lev S. Vygotsky, acompanhada de uma articulação com autores contemporâneos de
tendência social. Outro autor e tendência expressiva é a humanista, cujo nome central é Paulo Freire.
Ambas as abordagens foram propostas como expressão da valorização humana e social no contexto
social e profissional, tendo como base o “ser em situação” envolto de condicionantes presentes na
sociedade e nos contextos específicos. A abordagem de Design que se vinculou a pensamentos de
tendência situada e contextualizada, as quais consideram que o produto de Design é parte dos desejos
e da ação humana e do meio sobre a solução. As análises de dados se nutriram da análise documental
para situar e compreender os princípios do trabalho realizado no contexto do laboratório, e os
resultados finais das análises trouxeram evidências de um modelo único de Design e de um conceito
em transição, o qual, nesta tese, denominamos CoDesign.This investigation developed a case study of ethnographic tendency on the work of design for distance
learning (DL) carried out by teachers and instructional designers who work in collaboration in the
Laboratory of Design and Production of Didactic Material for DL - Multi.Lab.EaD. The activities of this
work focus on design and development of actions for the construction of online rooms and resources for
degree courses at the Distance Learning Center of Santa Catarina State University (CEAD/UDESC),
linked to the Universidade Aberta do Brasil System (UAB). The research problems bring to the center of
the purposes the analysis of the knowledge, the ways of thinking and the activities involved in the work
of designing for DL, in the community of practice. The ways of ideation, creation and implementation of
activities that involve the choices and decisions facing the tasks required for DL Design for the
aforementioned courses are involved in these problematic questions and research purposes. The
decision choice of an ethnographic trend study was due to the fact that it is a specific group that works
in a community of practice based on professional principles and located within an university, which is
part of a system of Brazilian public universities. Participants are professors and designers linked to
distance learning undergraduate courses, who were in action or who have acted at some point in the
courses in the proposed community of practice. Data collection was performed using the sources
triangulation method suggested by Yin (2005) and Minayo (1994), and the techniques used were
observation, the questionnaire, the interview, the focus group (FG), the document analysis and the
production of na artifact. Data were recorded with the help of field diaries, audio recordings, videos and
photographs. For data treatment, content analysis was adopted, inspired by the method of Bardin
(2004), and the perspective of thematic categorical analysis proposed by Minayo (1994), Minayo and
Minayo-Gómez (2003), Minayo, Assis and Souza (2010) and Gomes (1994) was applied as practice.
The theoretical approach used in this investigation was the social-historical one whose most expressive
representative is Lev S. Vygotski in conjunction with contemporary authors, all of them with a social
tendency. Another author and expressive trend for this study is the humanist whose central name is
Paulo Freire. Both approaches were proposed as an expression of human and social valorization in the
social and professional context, based on “the being in a situation” surrounded by constraints present
in society and in specific contexts. The design approach linked to these thoughts was the situated and
contextualized tendency which considers that the design product is part of the desires and actions of
the human beings and the environment on the solution. The analysis was based on documentary
analysis to situate and understand the principles of the work carried out in the context of the laboratory,
and the final results of the analysis brought evidence of a unique Design model and a concept in
transition, which, in this thesis, we call it CoDesign
Detecting similarities among distant homologous proteins by comparison of domain flexibilities
No full textAim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable. © 2007 The Author(s)
GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet
No full textMotivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact: alessandro.pandini@kcl. ac.uk or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press
PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations
No full textCopyright © 2022 The Author(s). Understanding the process of ligand–protein recognition is important to unveil biological mechanisms and to guide drug discovery and design. Enhanced-sampling molecular dynamics is now routinely used to simulate the ligand binding process, resulting in the need for suitable tools for the analysis of large data sets of binding events. Here, we designed, implemented, and tested PathDetect-SOM, a tool based on self-organizing maps to build concise visual models of the ligand binding pathways sampled along single simulations or replicas. The tool performs a geometric clustering of the trajectories and traces the pathways over an easily interpretable 2D map and, using an approximate transition matrix, it can build a graph model of concurrent pathways. The tool was tested on three study cases representing different types of problems and simulation techniques. A clear reconstruction of the sampled pathways was derived in all cases, and useful information on the energetic features of the processes was recovered. The tool is available at https://github.com/MottaStefano/PathDetect-SOM.Leverhulme Trust (An integrated computational-experimental method to redesign protein dynamics, RPG-2017-222)
MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations
No full textData availability: A sample of the trajectory data is included in the GitHub repository. The data underpinning this publication can be accessed from Brunel University London's data repository under CC BY license: https://doi.org/10.17633/rd.brunel.c.6620539 .Supplementary information: Supplementary data are available at Bioinformatics online at https://academic-oup-com.ezproxytest.brunel.ac.uk/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad427/7221036?searchresult=1#supplementary-data .Copyright © The Author(s) 2023.. Motivation:
Molecular dynamics (MD) simulations have become routine tools for the study of protein dynamics and function. Thanks to faster GPU-based algorithms, atomistic and coarse-grained simulations are being used to explore biological functions over the microsecond timescale, yielding terabytes of data spanning multiple trajectories, thereby extracting relevant protein conformations without losing important information is often challenging.
Results:
We present MDSubSampler, a Python library and toolkit for a posteriori subsampling of data from multiple trajectories. This toolkit provides access to uniform, random, stratified, weighted sampling and bootstrapping sampling methods. Sampling can be performed under the constraint of preserving the original distribution of relevant geometrical properties. Possible applications include simulations post-processing, noise reduction and structures selection for ensemble docking.
Availability:
MDSubSampler is freely available at https://github.com/alepandini/MDSubSampler, along with guidance on installation and tutorials on how it can be used.NO is supported by a scholarship from Brunel University London EPSRC DTP (grant no. EP/T518116/1). This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (https://www.hecbiosim.ac.uk), supported by EPSRC (grant no. EP/X035603/1)
Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics
No full textAllostery offers a highly specific way to modulate protein function. Therefore, understanding this mechanism is of increasing interest for protein science and drug discovery. However, allosteric signal transmission is difficult to detect experimentally and to model because it is often mediated by local structural changes propagating along multiple pathways. To address this, we developed a method to identify communication pathways by an information- theoretical analysis of molecular dynamics simulations. Signal propagation was described as information exchange through a network of correlated local motions, modeled as transitions between canonical states of protein fragments. The method was used to describe allostery in two-component regulatory systems. In particular, the transmission from the allosteric site to the signaling surface of the receiver domain NtrC was shown to be mediated by a layer of hub residues. The location of hubs preferentially connected to the allosteric site was found in close agreement with key residues experimentally identified as involved in the signal transmission. The comparison with the networks of the homologues CheY and FixJ highlighted similarities in their dynamics. In particular, we showed that a preorganized network of fragment connections between the allosteric and functional sites exists already in the inactive state of all three proteins. © The Author(s)
PyCoM: a python library for large-scale analysis of residue-residue coevolution data
No full textThe version currently archived on this institutional repository is an accepted manuscript, the PDF version of the author’s final manuscript, as accepted for publication by the journal but prior to copyediting or typesetting. They can be cited using the author(s), article title, journal title, year of online publication, and DOI. They will be replaced by the final typeset articles, which may therefore contain changes. The DOI will remain the same throughout.Data availability The data underpinning this publication can be accessed from Brunel University London's data repository under CC BY license: Coevolution matrix database https://brunel.figshare.com/articles/dataset/PyCoM_ProCoM_Database_of_coevolu tion_matrices/23735613 and protein database https://brunel.figshare.com/articles/dataset/PyCoM_ProCoM_Curated_UniProt_pro tein_database/23733309 .Availability and implementation
PyCoM code is freely available from https://github.com/scdantu/pycom and PyCoMdb and the Jupyter Notebook tutorials are freely available from https://pycom.brunel.ac.uk .Supplementary information:
Supplementary data are available at Bioinformatics online at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae166/7635577#supplementary-data .Motivation:
Computational methods to detect correlated amino acid positions in proteins have become a valuable tool to predict intra and inter-residue protein contacts, protein structures, and effects of mutation on protein stability and function. While there are many tools and webservers to compute coevolution scoring matrices, there is no central repository of alignments and coevolution matrices for large-scale studies and pattern detection leveraging on structural and biological annotation already available in UniProt.
Results:
We present a Python library, PyCoM, which enables users to query and analyse coevolution matrices and sequence alignments of 457,622 proteins, selected from UniProtKB/Swiss-Prot database (length ≤ 500 residues), from a pre-compiled coevolution matrix database (PyCoMdb). PyCoM facilitates the development of statistical analyses of residue coevolution patterns using filters on structural and biological annotation from UniProtKB/Swiss-Prot, with simple access to PyCoMdb for both novice and advanced users, supporting Jupyter Notebooks, Python scripts, and a web API access. The resource is open source and will help in generating data-driven computational models and methods to study and understand protein structures, stability, function, and design.This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1). Philipp Bibik was funded by Department of Computer Science, Brunel University London, summer internship programme
- …
