Готові списки джерел за темами / Proteins crowding

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Добірка наукової літератури з теми "Proteins crowding"

Автор: Grafiati

Опубліковано: 10 березня 2023

Оновлено: 6 вересня 2023

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Статті в журналах з теми "Proteins crowding"

Zhou, Huan-Xiang. "Crowding Effects of Membrane Proteins." Journal of Physical Chemistry B 113, no. 23 (June 11, 2009): 7995–8005. http://dx.doi.org/10.1021/jp8107446.

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Rhoades, Elizabeth. "Proteins: Disorder, Folding, and Crowding." Biophysical Journal 117, no. 1 (July 2019): 3–4. http://dx.doi.org/10.1016/j.bpj.2019.06.014.

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Snead, Wilton T., Carl C. Hayden, Avinash K. Gadok, Chi Zhao, Eileen M. Lafer, Padmini Rangamani, and Jeanne C. Stachowiak. "Membrane fission by protein crowding." Proceedings of the National Academy of Sciences 114, no. 16 (April 3, 2017): E3258—E3267. http://dx.doi.org/10.1073/pnas.1616199114.

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Membrane fission, which facilitates compartmentalization of biological processes into discrete, membrane-bound volumes, is essential for cellular life. Proteins with specific structural features including constricting rings, helical scaffolds, and hydrophobic membrane insertions are thought to be the primary drivers of fission. In contrast, here we report a mechanism of fission that is independent of protein structure—steric pressure among membrane-bound proteins. In particular, random collisions among crowded proteins generate substantial pressure, which if unbalanced on the opposite membrane surface can dramatically increase membrane curvature, leading to fission. Using the endocytic protein epsin1 N-terminal homology domain (ENTH), previously thought to drive fission by hydrophobic insertion, our results show that membrane coverage correlates equally with fission regardless of the hydrophobicity of insertions. Specifically, combining FRET-based measurements of membrane coverage with multiple, independent measurements of membrane vesiculation revealed that fission became spontaneous as steric pressure increased. Further, fission efficiency remained equally potent when helices were replaced by synthetic membrane-binding motifs. These data challenge the view that hydrophobic insertions drive membrane fission, suggesting instead that the role of insertions is to anchor proteins strongly to membrane surfaces, amplifying steric pressure. In line with these conclusions, even green fluorescent protein (GFP) was able to drive fission efficiently when bound to the membrane at high coverage. Our conclusions are further strengthened by the finding that intrinsically disordered proteins, which have large hydrodynamic radii yet lack a defined structure, drove fission with substantially greater potency than smaller, structured proteins.

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Zosel, Franziska, Andrea Soranno, Karin J. Buholzer, Daniel Nettels, and Benjamin Schuler. "Depletion interactions modulate the binding between disordered proteins in crowded environments." Proceedings of the National Academy of Sciences 117, no. 24 (June 2, 2020): 13480–89. http://dx.doi.org/10.1073/pnas.1921617117.

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Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of macromolecular crowding on the interactions of IDPs with their cellular targets. Here, we investigate the influence of crowding on the interaction between two IDPs that fold upon binding, with polyethylene glycol as a crowding agent. Single-molecule spectroscopy allows us to quantify the effects of crowding on a comprehensive set of observables simultaneously: the equilibrium stability of the complex, the association and dissociation kinetics, and the microviscosity, which governs translational diffusion. We show that a quantitative and coherent explanation of all observables is possible within the framework of depletion interactions if the polymeric nature of IDPs and crowders is incorporated based on recent theoretical developments. The resulting integrated framework can also rationalize important functional consequences, for example, that the interaction between the two IDPs is less enhanced by crowding than expected for folded proteins of the same size.

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Wei, Jiachen, and Fan Song. "Association equilibria for proteins interacted with crowders of short-range attraction in crowded environment." International Journal of Modern Physics B 31, no. 03 (January 23, 2017): 1750007. http://dx.doi.org/10.1142/s0217979217500072.

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Based on a very simple coarse-grained colloidal model, here we implement an effective hard-sphere theory and numerical simulation to capture the general features of the association equilibria for globular proteins in crowded environment. We measure the activity coefficient, i.e., the deviation from ideal behavior of protein solution, and the crowding factor, i.e., the contribution of crowders to the association equilibria, for proteins in macromolecular crowding. The results show that the association balance in macromolecular crowding depends sensitively on the magnitude of protein–crowder attraction and the relative size of reactant to crowding agent. Since our coarse-grained model is irrelevant to the microscopic details of the molecules, it can be applied to the control of the association equilibria of many globular proteins such as bovine serum albumin, crystallin and lysozyme.

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Horton, Margaret R., Felix Höfling, Joachim O. Rädler, and Thomas Franosch. "Development of anomalous diffusion among crowding proteins." Soft Matter 6, no. 12 (2010): 2648. http://dx.doi.org/10.1039/b924149c.

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Banks, Daniel S., and Cécile Fradin. "Anomalous Diffusion of Proteins Due to Molecular Crowding." Biophysical Journal 89, no. 5 (November 2005): 2960–71. http://dx.doi.org/10.1529/biophysj.104.051078.

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Makowski, Lee, Diane J. Rodi, Suneeta Mandava, David D. L. Minh, David B. Gore, and Robert F. Fischetti. "Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins." Journal of Molecular Biology 375, no. 2 (January 2008): 529–46. http://dx.doi.org/10.1016/j.jmb.2007.07.075.

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Candotti, Michela, and Modesto Orozco. "The Differential Response of Proteins to Macromolecular Crowding." PLOS Computational Biology 12, no. 7 (July 29, 2016): e1005040. http://dx.doi.org/10.1371/journal.pcbi.1005040.

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Perham, Michael, Loren Stagg, and Pernilla Wittung-Stafshede. "Macromolecular crowding increases structural content of folded proteins." FEBS Letters 581, no. 26 (October 1, 2007): 5065–69. http://dx.doi.org/10.1016/j.febslet.2007.09.049.

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Дисертації з теми "Proteins crowding"

Candotti, Michela. "Environment matters : the impact of urea and macromolecular crowding on proteins." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/403839.

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This work aims to analytically understand the impact of two diametric opposite environments on protein structure and dynamics and compared them to the most common solvent on earth: water. The first environment is a popular denaturing solution (urea 8M), which has served for years in protein-science laboratories to investigate protein stability; still many open questions regarding its mechanism of action remained unclear. The second environment instead moves towards a more physiological representation of proteins. The cell interior, in fact, is a crowded solution highly populated prevalently by proteins, but studies on protein structure and dynamics have lead so far to confusing or even opposite observations. The lack of a consensus view in both phenomena possibly derives from the bias of the system under study. This work is an attempt of a comparative study using the most general systems: a diverse spectrum of proteins folds, different stages along the reaction path (early stages or end-point) and/or different protein force-fields. Our main objective was to derive common pattern and general rules valid at proteome level, focusing on three major aspects of proteins: the structure, the dynamic and the interactions with the solvent molecules. Molecular dynamics simulation appeared then as the most suitable tool because of its ability to i) analyze proteins at broad range of resolutions; ii) access the direct time-resolved dynamic of the system and iii) dissect the specific interactions that arise in the new settings. Specifically, the case of urea-induced unfolding needs a system for which is possible to clearly identify folded and unfolded state – globular proteins are then the most suitable ones. We extracted general rules on the folded/unfolded transition by studying independently the two end-points of folded/unfolded reaction. We simulated the urea-induced unfolded state of a model protein, ubiquitin to understand the energetics stabilizing unfolded structures in urea. We found that the unfolded ubiquitin in 8M urea is fully extend and flexible and capturing efficiently urea molecules to the first solvation shell. Dispersion, rather than electrostatic, appear the main energetic contribution to explain the stabilization of the unfolded state. We then simulated the early stages of urea-induced unfolding on a large dataset of folded proteins, which represent the major folds of globular proteins, aiming also to investigate the kinetic role of urea in triggering the protein unfolding. We found that partially unfolded proteins expose the apolar residues buried in the protein interior, mainly via cavitation. Similar to the unfolded state, it is the dispersion interactions that drive urea accumulation in the solvation shell but here urea molecules take advantage of microscopic unfolding events to penetrate the protein interior. Macromolecular crowding instead is a phenomenon that universally affects all the proteins. We simulated a system that included as crowding agents proteins with different conformational landscapes (a globular protein, an intrinsically disordered proteins and a molten globule) arranged to reach cell-like concentrations. We conclude that the universal effect of crowding, valid for all the proteins types, is exerted via the aspecific interactions and favors open and moderately extended conformations with higher secondary structure content. This phenomenon counterbalances the volume-exclusion, which prevails at higher crowding concentrations. The impact of crowding is proportional to the degree of disorder of the protein and for folded protein crowding favors structural rearrangements while unfolded structures experience a stronger stabilization and a higher secondary structures content. The synthetic crowder PEG doesn’t reproduce any of these effects, arising concerns about its employment in study cell-like environments.

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Toyooka, Tsuguyoshi. "Photoreaction Dynamics of Blue Light Sensor Proteins and Application to Crowding Environments." 京都大学 (Kyoto University), 2011. http://hdl.handle.net/2433/142398.

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Roos, Matthias [Verfasser], Kay [Akademischer Betreuer] Saalwächter, Wolfgang [Akademischer Betreuer] Paul, and Frank [Akademischer Betreuer] Schreiber. "Brownian dynamics of globular proteins under macromolecular crowding as studied by NMR : [kumulative Dissertation] / Matthias Roos ; Kay Saalwächter, Wolfgang Paul, Frank Schreiber." Halle, 2016. http://d-nb.info/1123998612/34.

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Ping, Guanghui Yuan Jian-Min. "Effects of confinement and macromolecular crowding on protein stability and protein folding dynamics /." Philadelphia, Pa. : Drexel University, 2005. http://dspace.library.drexel.edu/handle/1860/491.

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Li, X. F. "Investigation of protein-protein interactions : multibody docking, association/dissociation kinetics and macromolecular crowding." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1302277/.

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Анотація:

Protein-protein interactions are central to understanding how cells carry out their wide array of functions and metabolic procedures. Conventional studies on specific protein interactions focus either on details of one-to-one binding interfaces, or on large networks that require a priori knowledge of binding strengths. Moreover, specific protein interactions, occurring within a crowded macromolecular environment, which is precisely the case for interactions in a real cell, are often under-investigated. A macromolecular simulation package, called BioSimz, has been developed to perform Langevin dynamics simulations on multiple protein-protein interactions at atomic resolution, aimed at bridging the gaps between structural, kinetic and crowding studies on protein-protein interactions. Simulations on twenty-seven experimentally determined protein-protein interactions, indicated that the use of contact frequency information of proteins forming specific encounters can guide docking algorithms towards the most likely binding regions. Further evidence from eleven benchmarked protein interactions showed that the association rate constant of a complex, kon, can be estimated, with good agreement to experimental values, based on the retention time of its specific encounter. Performing these simulations with ten types of environmental protein crowders, it suggests, from the change of kon, that macromolecular crowding improves the association kinetics of slower-binding proteins, while it damps the association kinetics of fast, electrostatics-driven protein-protein interactions. It is hypothesised, based on evidence from docking, kinetics and crowding, that the dynamics of specific protein-protein encounters is vitally important in determining their association affinity. There are multiple factors by which encounter dynamics, and subsequently the kon, can be influenced, such as anchor residues, long-range forces, and environmental steering via crowders’ electrostatics and/or volume exclusion. The capacity of emulating these conditions on a common platform not only provides a holistic view of interacting dynamics, but also offers the possibility of evaluating and engineering protein-protein interactions from aspects that have never been opened before.

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Lu, Cheng [Verfasser], and Gerhard [Akademischer Betreuer] Stock. "Modeling protein dynamics in solution: effects of ligand binding and crowding." Freiburg : Universität, 2016. http://d-nb.info/1119452643/34.

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Cao, Yang. "Macromolecular crowding effects on the activity of the extracellular signal regulated kinase 2 /." View abstract or full-text, 2008. http://library.ust.hk/cgi/db/thesis.pl?CHEM%202008%20CAO.

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Aguilar, Ximena. "Folding and interaction studies of subunits in protein complexes." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-84726.

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Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis. Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements. The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%). The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25. The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

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Christiansen, Alexander. "Effects of Macromolecular Crowding on Protein Folding : - in-vitro equilibrium and kinetic studies on selected model systems." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-82059.

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Protein folding is the process during which an extended and unstructured polypeptide converts to its compact folded structure that is most often the functional state. The process has been characterized extensively in dilute buffer in-vitro during the last decades but the actual biological place for this process is the inside of living cells. The cytoplasm of a cell is filled with a plethora of different macromolecules that together occupy up to 40% of the total volume. This large amount of macromolecules restricts the available space to each individual molecule, which has been termed macromolecular crowding. Macromolecular crowding results in excluded volume effects and also increases chances for non-specific interactions. Macromolecular crowding should favor reactions that lead to a decrease in the total occupied volume by all molecules, such as folding reactions. Theoretical models have predicted that the stability of protein folded states should increase in presence of macromolecular crowding due to unfavorable effects on the extended unfolded state. To understand protein folding and function in living systems, we need to have a defined quantitative link between in-vitro dilute conditions (where most biophysical experiments are made) and in-vivo crowded conditions. An important question is thus how macromolecular crowding modifies the biophysical properties of a protein. The work underlying this thesis focused on how macromolecular crowding tunes protein equilibrium stability and kinetic folding processes. To mimic the crowded cellular environment, synthetic sugar-based polymers (Dextrans of different sizes and Ficoll 70) were used as crowding agents (crowders) in controlled in-vitro experiments. In contrast to previous studies which often have focused on one protein and one crowder at a time, the goal here was to make systematic analyses of how size, shape and concentration of the crowders affect both equilibrium and kinetic properties of structurally-different proteins. Three model proteins (cytochrome c, apoazurin and apoflavodoxin) were investigated under crowding by Ficoll 70 and different-size Dextrans, using various spectroscopic techniques such as far-UV circular dichroism and intrinsic tryptophan fluorescence. Thermodynamic models were applied to explain the experimental results. It was discovered that equilibrium stability of all three proteins increased in presence of crowding agents in a crowder concentration dependent manner. The stabilization effect was around 2-3 kJ/mol, larger for the various Dextrans than for Ficoll 70 at the same g/l, but independent of Dextran size (in the range 20 to 70 kDa). To further investigate the cause for the stabilization a theoretical crowding model was applied. In this model, Dextran and Ficoll were modeled as elongated rods and the protein was represented as a sphere, where the folded sphere representation was smaller than the unfolded sphere representation. It is notable that the observed stability changes could be reproduced by this model taking only steric interactions into account. This correlation showed that when using sugar-based crowding agents, excluded volume effects could be studied in isolation and there were no contributions from nonspecific interactions. Time-resolved experiments with apoazurin and apoflavodoxin revealed an increase in the folding rate constants while the unfolding rates were invariant in the presence of crowding agents. For apoflavodoxin and cytochrome c, the presence of crowding agents also altered the folding pathway such that it became more homogeneous (cytochrome c) and it gave less misfolding (apoflavodoxin). These results showed that macromolecular crowding restricts the conformational space of the unfolded polypeptide chain, makes the conformations more compact which, in turn, eliminates access to certain pathways. The results from kinetic and equilibrium measurements on three model proteins, together with available data from the literature, demonstrate that macromolecular crowding effects due to volume exclusion are in the order of a few kJ/mol. Considering the numerous concentration balances and cross-dependent reactions of the cellular machinery, small changes in energetics/kinetics of the magnitudes found here can still have dramatic consequences for cellular fitness. In fact local and transient changes in macromolecular crowding levels may be a way to tune biochemical reactions without invoking gene expression.

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Köhn, Birgit Anna Luise [Verfasser]. "Characterizing the Effects of Macromolecular Crowding on Protein Stability, Dynamics and Function / Birgit Anna Luise Köhn." Konstanz : KOPS Universität Konstanz, 2020. http://d-nb.info/1233203436/34.

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Частини книг з теми "Proteins crowding"

Uversky, Vladimir N. "Conformational Behavior of Intrinsically Disordered Proteins: Effects of Strong Denaturants, Temperature, PH, Counterions, and Macromolecular Crowding." In Instrumental Analysis of Intrinsically Disordered Proteins, 545–68. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2010. http://dx.doi.org/10.1002/9780470602614.ch19.

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Casati, Diego F. Gómez, Miguel A. Aon, and Alberto A. Iglesias. "Molecular Crowding and Cytoskeletal Proteins Affect the Allosteric Regulatory Properties of ADP Glucose Pyrophosphorylase." In Photosynthesis: Mechanisms and Effects, 3695–98. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-3953-3_861.

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Varela, Daniel, and José Santos. "Crowding Differential Evolution for Protein Structure Prediction." In From Bioinspired Systems and Biomedical Applications to Machine Learning, 193–203. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-19651-6_19.

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Ellis, R. John. "Protein Aggregation: Opposing Effects of Chaperones and Crowding." In Folding for the Synapse, 9–34. Boston, MA: Springer US, 2010. http://dx.doi.org/10.1007/978-1-4419-7061-9_2.

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Rösgen, Jörg. "Molecular Crowding and Solvation: Direct and Indirect Impact on Protein Reactions." In Methods in Molecular Biology, 195–225. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-367-7_9.

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Chitara, Dheeraj, and Prashant Kumar. "Insights from Molecular Dynamics Studies: The Effects of Molecular Crowding on the Human Argonaute Protein." In Proceedings of the NIELIT's International Conference on Communication, Electronics and Digital Technology, 561–76. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-1699-3_39.

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Pandey, Mukesh, Jahangir Nabi, Nahida Tabassum, Faheem Hyder Pottoo, Renuka Khatik, and Niyaz Ahmad. "Molecular Chaperones in Neurodegeneration." In Quality Control of Cellular Protein in Neurodegenerative Disorders, 354–79. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-1317-0.ch014.

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Анотація:

Cellular chaperones are essential players to this protein quality control network that functions to prevent protein misfolding, refold misfolded proteins, or degrade them, thereby maintaining neuronal proteostasis. Moreover, overexpression of cellular chaperones is considered to inhibit protein aggregation and apoptosis in various experimental models of neurodegeneration. Alterations or downregulation of chaperone machinery by age-related decline, molecular crowding, or genetic mutations are regarded as key pathological hallmarks of neurodegenerative disorders like Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and Prion diseases. Therefore, chaperones may serve as potential therapeutic targets in these diseases. This chapter presents a generalized view of misfolding and aggregation of proteins in neurodegeneration and then critically analyses some of the known cellular chaperones and their role in several neurodegenerative disorders.

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Musiani, F., and A. Giorgetti. "Protein Aggregation and Molecular Crowding." In International Review of Cell and Molecular Biology, 49–77. Elsevier, 2017. http://dx.doi.org/10.1016/bs.ircmb.2016.08.009.

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Pittas, Theodoros, Weiyan Zuo, and Arnold J. Boersma. "Engineering crowding sensitivity into protein linkers." In Methods in Enzymology. Elsevier, 2020. http://dx.doi.org/10.1016/bs.mie.2020.09.007.

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Gupta, Munishwar Nath, and Vladimir N. Uversky. "Macromolecular crowding: how it affects protein structure, disorder, and catalysis." In Structure and Intrinsic Disorder in Enzymology, 353–76. Elsevier, 2023. http://dx.doi.org/10.1016/b978-0-323-99533-7.00016-9.

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Тези доповідей конференцій з теми "Proteins crowding"

Truskett, Thomas M. "How Concentration and Crowding Impact Protein Stability: Insights From a Coarse-Grained Model." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-192239.

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Much of the current understanding of the protein folding problem derives from studies of proteins in dilute solutions. However, in many systems of scientific and engineering interest, proteins must fold in concentrated, heterogeneous environments. Cells are crowded with many molecular species, and chaperones often sequester proteins and promote rapid folding. Proteins are also present in high concentrations in the manufacture, storage, and delivery of biotherapeutics. How does crowding generally affect the stability of the native state? Are all crowding agents created equal? If not, can generic structural or chemical features forecast their effects on protein stability?

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Bernaschi, Massimo, Mauro Bisson, Massimiliano Fatica, and Simone Melchionna. "20 petaflops simulation of proteins suspensions in crowding conditions." In SC13: International Conference for High Performance Computing, Networking, Storage and Analysis. New York, NY, USA: ACM, 2013. http://dx.doi.org/10.1145/2503210.2504563.

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Dias, André, Mateus Boiani, and Rafael Parpinelli. "Aplicação de Evolução Diferencial em GPU Para o Problema de Predição de Estrutura de Proteínas com Modelo 3D AB Off-Lattice." In XXI Simpósio em Sistemas Computacionais de Alto Desempenho. Sociedade Brasileira de Computação, 2020. http://dx.doi.org/10.5753/wscad.2020.14080.

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A função que uma proteína exerce está diretamente relacionada com a sua estrutura tridimensional. Porém, para a maior parte das proteínas atualmente sequenciadas ainda não se conhece sua forma estrutural nativa. Este artigo propõe a utilização do algoritmo de Evolução Diferencial (DE) desenvolvido na plataforma NVIDIA CUDA aplicado ao modelo 3D AB Off-Lattice para Predição de Estrutura de Proteínas. Uma estratégia de nichos e crowding foi implementada no algoritmo DE combinada com técnicas de autoajuste de parâmetros, rotinas para reinicialização da população, dois níveis de otimização e busca local. Quatro proteínas reais foram utilizadas para experimentação e os resultados obtidos se mostram competitivos com o estado-da-arte. A utilização de paralelismo massivo através da GPU ressalta a aplicabilidade desses recursos a esta classe de problemas atingindo acelerações de 708.78x para a maior cadeia proteica.

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Rocha, Gregório Kappaun, Fábio Lima Custódio, Helio J. C. Barbosa, and Laurent Emmanuel Dardenne. "Using Crowding-Distance in a Multiobjective Genetic Algorithm for Protein Structure Prediction." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2931717.

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Rocha, Gregorio Kappaun, Fabio Lima Custodio, Helio Jose Correa Barbosa, and Laurent Emmanuel Dardenne. "A multiobjective approach for protein structure prediction using a steady-state genetic algorithm with phenotypic crowding." In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2015. http://dx.doi.org/10.1109/cibcb.2015.7300284.

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Звіти організацій з теми "Proteins crowding"

Stachowiak, Jeanne C., Carl C. Hayden, Oscar Negrete, Ryan Wesley Davis, and Darryl Y. Sasaki. Towards understanding of Nipah virus attachment protein assembly and the role of protein affinity and crowding for membrane curvature events. Office of Scientific and Technical Information (OSTI), October 2013. http://dx.doi.org/10.2172/1096477.

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Noga, Edward J., Angelo Colorni, Michael G. Levy, and Ramy Avtalion. Importance of Endobiotics in Defense against Protozoan Ectoparasites of Fish. United States Department of Agriculture, September 2003. http://dx.doi.org/10.32747/2003.7586463.bard.

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Infectious disease is one of the most serious causes of economic loss in all sectors of aquaculture. There is a critical need to understand the molecular basis for protection against infectious disease so that safer, more reliable and more cost-effective strategies can be designed for their control. As part of this effort, the major goal of our BARD project was to determine the importance of endobiotics as a defense against protozoan ectoparasites in fish. Endobiotics, or antimicrobial polypeptides, are peptides and small proteins that are increasingly recognized as having a vital role in the innate defense of virtually all animals. One objective of our BARD project was to determine the antiparasitic potency of one specific group of endobiotics that were isolated from hybrid striped bass (Morone saxatilis x M chrysops). We found that these endobiotics, which we had previously named histone-like proteins (HLPs), exhibited potent activity against Amyloodinium and that the putative levels of HLPs in the skin were well within the levels that we found to be lethal to the parasite in vitro. We also found evidence for the presence of similar antibiotics in sea bream (Sparus aurata) and Mediterranean sea bass (Dicentrarchus labrax). We also examined the effect of chronic stress on the expression of HLP in fish and found that HLP levels were dramatically decreased after only one week of a crowding/high ammonia sublethal stress. We also began to explore the feasibility of upregulating endobiotics via immunostimulation. However, we did not pursue this objective as fully as we originally intended because we spent a much larger effort than originally anticipated on the last objective, the attempted isolation of novel endobiotics from hybrid striped bass. In this regard, we purified and identified four new peptide endobiotics. These endobiotics, which we have named piscidins (from "Pisces" meaning fish), have potent, broad-spectrum activity against a number of both fish and human pathogens. This includes not only parasites but also bacteria. We also demonstrated that these peptides are present in the mast cell. This was the first time that the mast cell, the most common tissue granulocyte in vertebrates, was shown to possess any type of endobiotic. This finding has important implications in explaining the possible function of mast cells in the immune response of vertebrates. In summary, the research we have accomplished in this BARD project has demonstrated that endobiotics in fish have potent activity against many serious pathogens in aquaculture and that there is considerable potential to use these compounds as stress indicators in aquaculture. There is also considerable potential to use some of these compounds in other areas of medicine, including treatment of serious infectious diseases of humans and animals.

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