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Measurement and Numerical Modeling of Cell-Free Protein Synthesis: Combinatorial Block-Variants of the PURE System
2018
Data
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We report and share the kinetic traces of the enhanced Green Fluorescent Protein (eGFP) synthesis in bulk aqueous phase, for 27 combinatorial block-variants. ...
In order to verify that the variation of TX–TL components concentration brings about a variation of produced protein rate and yield, here we directly measure the performances of the 'PURE system' TX–TL ...
providing the PURE system in the context of the HFSP Project RGP0033/2007-C. ...
doi:10.3390/data3040041
fatcat:5ut7cyi4svepjmp6ljdkv5q4pq
Integration of Combinatorial Synthesis, Rapid Screening, and Computational Modeling in Biomaterials Development
2004
Macromolecular rapid communications
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Financial support was also provided by NIH Grant HL-60416 and the New Jersey Center for Biomaterials. Dr. Wise Young, Dr. ...
Acknowledgements: This work was supported by seed funds provided by Rutgers University, by NIH grant R01 EB00286, and by ''RESBIO -The National Resource for Polymeric Biomaterials'' funded under NIH grant ...
The successful prediction of protein adsorption and cell growth on different polymeric surfaces by a computational model presents a significant breakthrough and illustrates that the integration of combinatorial ...
doi:10.1002/marc.200300193
fatcat:x2iy6lixirhmfjyoiwiqouejka
Toward Automated Oligosaccharide Synthesis
2011
Angewandte Chemie International Edition
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system for the synthesis of oligosaccharide and glycoconjugates. ...
in numerous biological processes, including viral and bacterial infection, angiogenesis and tumor cell metastasis, toxin interaction, inflammation and immune response, cell growth and proliferation, and ...
doi:10.1002/anie.201100125
pmid:22127846
fatcat:gbxknalhefc5zbffrok6fd5tly
Miniaturized and Automated Synthesis of Biomolecules—Overview and Perspectives
2019
Advanced Materials
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Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. ...
Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. ...
Numerous groups have used MALDI to investigate the interactions of proteins to glycans immobilized on arrays [94, 117] and also to measure enzyme activity; for example, studies with glycosyltransferase ...
doi:10.1002/adma.201806656
pmid:31033052
fatcat:i4qioyn7vbdlrinhl2frxs5gsy
In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles
2014
Accounts of Chemical Research
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for their function and delivery in cell culture and animal models. ...
Also of importance is the delivery of the RNA NPs to the cells of interest in vitro or in vivo. ...
( Figure 5 ), suggested reasons for the measured melting temperature differences for the cube variants, and offered more insight into the observed assembly yield differences ...
doi:10.1021/ar400329z
pmid:24758371
pmcid:PMC4066900
fatcat:kpkaakvo6ffujj4tgfosht5vji
Combinatorial chemistry. Facing the challenge of chemical genomics
2001
Pure and Applied Chemistry
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In this new operating model, called "combinatorial chemical genomics", an optimal combination of the marker and high-quality libraries provides a novel synergy for the drug discovery process at a very ...
In the age of high-throughput screening and combinatorial chemistry, the focus of drug discovery is to replace the sequential approach with the most effective parallel approach. ...
ACKNOWLEDGMENTS The authors thank to Péter Krajcsi, István Bágyi (ComGenex), András Guttman (Syngenta), and Klára Valkó (GlaxoSmithKline) for their contribution. ...
doi:10.1351/pac200173091487
fatcat:fz3zoed6hfcefpz7q34e35ei7y
Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes
2021
Nature Communications
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AbstractWe apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP ...
To verify our model and experimental findings, we design several non-repetitive binding site cassettes and validate their functionality in mammalian cells. ...
Acknowledgements The authors would like to acknowledge the Technion's LS&E staff (Dr. Tal Katz-Ezov, Anastasia Diviatis) for help with sequencing and for Dr. Shay Kirzner for help with FACS-sorting. ...
doi:10.1038/s41467-021-21578-6
pmid:33707432
fatcat:nomprmgbyncshhyt2wsvdaktuy
Recent Advances in Biocatalysis for Drug Synthesis
2022
Biomedicines
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Here we highlight some of the most recent developments to add to the portfolio of biocatalysis with special relevance for the synthesis and late-stage functionalization of APIs, in order to bypass pure ...
This is especially true for the advances in the field of nonribosomal peptide synthesis and enzyme cascades that are expanding the capabilities for the discovery and synthesis of new bioactive compounds ...
Rolf et al. demonstrated the identification of novel KDOs utilizing cell-free protein synthesis, which has the potential to drastically speed up the screening of enzymes [47, 48] . ...
doi:10.3390/biomedicines10050964
fatcat:3s2kskm2jjeftluywpjxui2t4q
Microwave heating in solid-phase peptide synthesis
2012
Chemical Society Reviews
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The highly refined organic chemistry in solid-phase synthesis has made it the method of choice not only to assemble peptides but also small proteins -mainly on a laboratory scale but increasingly also ...
synthesis of, for example, phosphopeptides, glycopeptides, and N-methylated peptides. ...
The methodology makes it ideal for automated and combinatorial synthesis. ...
doi:10.1039/c1cs15214a
pmid:22012213
fatcat:2z2yshkzynckxlub2fi7p75mae
Genetic Synthesis of Software Architecture
[chapter]
2008
Lecture Notes in Computer Science
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The chosen genetic construction of software architectures is based on a model which contains information of a set of responsibilities and dependencies between them. ...
An implementation using this model is presented, as well as test results achieved from a case study made on a sketch of an electronic home control system. ...
As for the evaluation of interfaces and using the dispatcher, there are no metrics found so far for pure numerical measurement. ...
doi:10.1007/978-3-540-89694-4_57
fatcat:bckme2qcbvh7fnmaqvutgqo4d4
A genetic shift in an escaped transmitted/founder virus guides combinatorial vaccine design against HIV-1
[article]
2021
bioRxiv
pre-print
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Given the occurrence of conformational dynamism in the V2 region, combinatorial V2 vaccine candidates consisting of numerous conformational variants in the natural HIV-1 diversity were designed and tested ...
These libraries, especially the Y173 variant libraries that also contained a V1 loop deletion showed increased breadth and cross-reactivity to diverse HIV-1 Env proteins. ...
Briefly, viral RNA was isolated from cell-free plasma using the 707 QIAamp viral RNA isolation kit (Qiagen) and quantitated. ...
doi:10.1101/2021.06.16.448593
fatcat:yryyufy2ubbz7npnemxyjdhkqi
Canthaxanthin, a Red-Hot Carotenoid: Applications, Synthesis, and Biosynthetic Evolution
2020
Plants
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We review the de novo synthesis of canthaxanthin and the functional β-carotene ketolase enzyme across organisms, supported by a protein-sequence-based phylogenetic analysis. ...
Also reviewed and discussed are the properties of canthaxanthin, its natural producers, and various strategies for its chemical synthesis. ...
Our approach is the exploitation of cell cultures from model plants, since they offer tangible advantages when compared with traditional systems, in terms of cost reduction, safety, and growth in a controlled ...
doi:10.3390/plants9081039
pmid:32824217
fatcat:4z6vhsi4ejax5nqj3bhdj7gijq
High Throughput Methods in the Synthesis, Characterization, and Optimization of Porous Materials
2020
Advanced Materials
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Synthesis, characterization, and pre- and post-synthetic computer simulations are mostly carried out in a piecemeal and ad hoc manner. ...
Porous materials are widely employed in a large range of applications, in particular, for storage, separation, and catalysis of fine chemicals. ...
Acknowledgements B.S. would like to thank EPSRC for funding the programme grant EP/ N004884/1 and a CASE studentship and a doctoral training centre studentship (with Johnson Matthey) which have helped ...
doi:10.1002/adma.202002780
pmid:32954550
fatcat:43qjqaflprfrtlz6y3z5lmkh74
Design and Creativity in Synthesis of Multivalent Neoglycoconjugates
[chapter]
2010
Advances in Carbohydrate Chemistry and Biochemistry
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A systematic description of glycocluster and glycodendrimer synthesis follows, starting from the simplest architectures and ending in the most complex ones. ...
This chapter briefly surveys the concept of multivalency involved in carbohydrate-protein interactions. ...
When the crystallographic structures of the protein or carbohydrate-ligated proteins are known, it is possible to model multivalent oligosaccharide inhibitors. ...
doi:10.1016/s0065-2318(10)63006-5
pmid:20381707
pmcid:PMC7112031
fatcat:5uiqzcl6ijdxfbgrsdon6s5ihe
Mini-review: In vitro Metabolic Engineering for Biomanufacturing of High-value Products
2017
Computational and Structural Biotechnology Journal
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In brief, by reconstituting a biosynthetic pathway in a cell-free environment with the supplement of cofactors and substrates, the performance of each biosynthetic pathway could be evaluated and optimized ...
This mini-review summarizes the recent progresses on the emerging topic of in vitro metabolic engineering and comments on the potential application of cell-free technology to speed up the "design-build-test ...
Acknowledgments This study was supported by a start-up fund (#175323) and the ICTAS Junior Faculty Award from Virginia Tech. ...
doi:10.1016/j.csbj.2017.01.006
pmid:28179978
pmcid:PMC5288458
fatcat:l23636737bebtmq2i37r5632ge
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