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Measurement and Numerical Modeling of Cell-Free Protein Synthesis: Combinatorial Block-Variants of the PURE System

Paolo Carrara, Emiliano Altamura, Francesca D'Angelo, Fabio Mavelli, Pasquale Stano
2018 Data  
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

Jack R. Smith, Agnieszka Seyda, Norbert Weber, Doyle Knight, Sascha Abramson, Joachim Kohn
2004 Macromolecular rapid communications  
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

Che-Hsiung Hsu, Shang-Cheng Hung, Chung-Yi Wu, Chi-Huey Wong
2011 Angewandte Chemie International Edition  
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

Daniela S. Mattes, Nicole Jung, Laura K. Weber, Stefan Bräse, Frank Breitling
2019 Advanced Materials  
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

Kirill A. Afonin, Wojciech K. Kasprzak, Eckart Bindewald, Maria Kireeva, Mathias Viard, Mikhail Kashlev, Bruce A. Shapiro
2014 Accounts of Chemical Research  
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

Ferenc Darvas, Gyorgy Dorman, Laszlo Urge, Istvan Szabo, Zsolt Ronai, Maria Sasvari-Szekely
2001 Pure and Applied Chemistry  
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

Noa Katz, Eitamar Tripto, Naor Granik, Sarah Goldberg, Orna Atar, Zohar Yakhini, Yaron Orenstein, Roee Amit
2021 Nature Communications  
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

Alina Kinner, Philipp Nerke, Regine Siedentop, Till Steinmetz, Thomas Classen, Katrin Rosenthal, Markus Nett, Jörg Pietruszka, Stephan Lütz
2022 Biomedicines  
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

Søren L. Pedersen, A. Pernille Tofteng, Leila Malik, Knud J. Jensen
2012 Chemical Society Reviews  
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]

Outi Räihä, Kai Koskimies, Erkki Mäkinen
2008 Lecture Notes in Computer Science  
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]

Swati Jain, Gherman Uritskiy, Marthandan Mahalingam, Himanshu Batra, Subhash Chand, Hung Trinh, Charles Beck, Woong-Hee Shin, Wadad AlSalmi, Gustavo Kijak, Leigh Anne Eller, Jerome Kim (+6 others)
2021 bioRxiv   pre-print
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

Bárbara A. Rebelo, Sara Farrona, M. Rita Ventura, Rita Abranches
2020 Plants  
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

Ivan G Clayson, Daniel Hewitt, Martin Hutereau, Tom Pope, Ben Slater
2020 Advanced Materials  
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]

Yoann M. Chabre, René Roy
2010 Advances in Carbohydrate Chemistry and Biochemistry  
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

Weihua Guo, Jiayuan Sheng, Xueyang Feng
2017 Computational and Structural Biotechnology Journal  
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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