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Biomolecular engineering for nanobio/bionanotechnology

Teruyuki Nagamune
2017 Nano Convergence  
This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with  ...  Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials.  ...  Random mutagenesis With random mutagenesis, point mutations are introduced at random positions in a gene of interest, typically through error-prone PCR mutagenesis, in which MnCl 2 is added to the reaction  ... 
doi:10.1186/s40580-017-0103-4 pmid:28491487 pmcid:PMC5401866 fatcat:xa4yixjnd5d2fh6mzc6qub7ylu

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A Marti-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2007 BMC Bioinformatics  
Acknowledgements: This work is funded by an RO1 from the NHGRI and by a Presidential Early Career Award for Scientists and Engineers from the National Science Foundation.  ...  The geometric potential can distinguish ligand binding sites from non-ligand-binding site with high confidence.  ...  -gated ion channel (VIC) superfamily is the largest and possibly the oldest of the recognized transporter protein families.  ... 
doi:10.1186/1471-2105-8-s4-s4 pmid:17570147 pmcid:PMC1892083 fatcat:o5p5c46emzbhxlmq27vqibskdi

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
Wigley for the contribution to this work with the x-ray structure of the protein ligand to the GR1222222.  ...  Furthermore, the conducted docking studies elucidated the possible alternative binding mode of the ligands into the ATP binding cleft and assigned their physicochemical and structural features which promote  ...  The results for the same experiments using Random Forests were 93%, 90% and 68%.  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

Gains from no real PAINS: Where 'Fair Trial Strategy' stands in the development of multi-target ligands

Jianbo Sun, Hui Zhong, Kun Wang, Na Li, Li Chen
2021 Acta Pharmaceutica Sinica B  
Additionally, these in silico approaches may inappropriately label a ligand as PAINS.  ...  More than 80% of the initial hits can be identified as PAINS by the filters if appropriate biochemical tests are not used resulting in false positive data that are unacceptable for medicinal chemists in  ...  Acknowledgments This work was financially supported by National Natural Science  ... 
doi:10.1016/j.apsb.2021.02.023 pmid:34900527 pmcid:PMC8642439 fatcat:qrbrayfj75hqfbzlr4fvfclutq

LC–MS Based Detection of Differential Protein Expression

Leepika Tuli, Habtom W. Ressom
2009 Journal of Proteomics & Bioinformatics  
Moreover, automation and robotics for sample handling process permit multiple sampling with high throughput.  ...  While several techniques are available in proteomics, LC-MS based analysis of complex protein/peptide mixtures has turned out to be a mainstream analytical technique for quantitative proteomics.  ...  Acknowledgements This work was supported in part by the National Science Foundation Grant IIS-0812246, the National Cancer Institute (NCI) R21CA130837 Grant, NCI Early Detection Research Network Associate  ... 
doi:10.4172/jpb.1000102 pmid:20473349 pmcid:PMC2867618 fatcat:weyv7yegwjhlnotanbmsm7fjca

Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases

Rahil Taujale, Aarya Venkat, Liang-Chin Huang, Zhongliang Zhou, Wayland Yeung, Khaled M Rasheed, Sheng Li, Arthur S Edison, Kelley W Moremen, Natarajan Kannan
2020 eLife  
Using evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 90% accuracy and deployed it for the annotation of understudied  ...  Further, a Random forest model trained using features from only the donor binding residues performs with an accuracy of only 75%, indicating the importance of features other than those directly involved  ...  Machine learning model training: We first trained random forest models by using an R package "randomForest" (68) with limited number of trees (ntree = 300) and limited maximum number of terminal nodes  ... 
doi:10.7554/elife.54532 pmid:32234211 pmcid:PMC7185993 fatcat:fhrnw7put5bdzbm7a666l6fxoy

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

Andrew Currin, Neil Swainston, Philip J. Day, Douglas B. Kell
2015 Chemical Society Reviews  
Improving enzymes by directed evolution requires the navigation of very large search spaces; we survey how to do this intelligently.  ...  proteins, also comes with incorporation of additional structural features beyond the primary sequence, like disulphide linkages, metal ions, 11 cofactors and post-translational modifications, and the  ...  NNK) to a small subset of residues with a particular physicochemical property (e.g. NTN for nonpolar residues only).  ... 
doi:10.1039/c4cs00351a pmid:25503938 pmcid:PMC4349129 fatcat:4alcgtju6jfdrj7ditdnurs4qq

1 Keynote address by Nobel Laureate Phillip A. Sharp the 21st century opened with a revolution in RNA biology

Phillip A. Sharp
2015 Journal of Biomolecular Structure and Dynamics  
PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation. Molecular Carcinogenesis. (Epub ahead of print).  ...  AS was supported by the This research was supported by an NIH grant, CA077712, from the National Cancer Institute to P.C.H. Belotserkovskii, B. P., & Hanawalt, P. C. (2014).  ...  Such subtle amino acid preferences were next encoded into a machine learning algorithm, driven by Random Forest for its training, to predict proteins that are likely to be engaged in domain swapping from  ... 
doi:10.1080/07391102.2015.1032624 fatcat:w7iil7k3ize77bjkthcyi52ohy

Award Winners and Abstracts of the 31st Annual Symposium of The Protein Society, Montreal, Canada, July 24-27, 2017

2017 Protein Science  
Grouping by Topics Pages  ...  by imaging of the ACTN4 protein expression pattern with conventional light microscopy.  ...  ExPath enables morphological and protein imaging and analysis of tissue microarrays, by providing $70nm resolution imaging of proteins in any type of human tissues, using optical microscopes (currently  ... 
doi:10.1002/pro.3349 pmid:29280217 fatcat:jrxtwzblare37gxsvc5szbwuhu

The 28th Annual Symposium of The Protein Society: Program & Abstracts

2014 Protein Science  
A second round of design identified a series of candidate proteins in which octahedral binding sites were formed from Bpy-ala, two scaffold based metal liganding residues, and two water molecules.  ...  To assess the current state of protein-ligand interface design, we benchmarked the computer algorithm Rosetta on a diverse set of 43 protein-ligand complexes.  ...  Thus any molecules, able to change kinetics or alter the pathway of protein aggregation, can potentially interfere with diseases.  ... 
doi:10.1002/pro.2504 pmid:25043257 pmcid:PMC4116645 fatcat:yjhug3aif5futn3icovvrkgebm

Thirty-seventh Annual Meeting February 14-18, 1993 Washington Convention Center Washington, D.C. Thursday Symposia and Posters, Part II

1993 Biophysical Journal  
Protein-protein interactions and their effects on membrane properties have been characterized both experimentally and theoretically.  ...  Biological membranes can contain up to 75% protein and thus should be viewed as nonideal fluids in which protein-protein Interactions can profoundly affect both protein organization and mobility.  ...  We have studied the interaction of metal ions, netropsin (a minor groove ligand) and ethidium (an intercalator) to DNA molecules of known sequence.  ... 
doi:10.1016/s0006-3495(93)81413-9 fatcat:i5k6hqq2bbfszejbftrbj22jpm

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt, Christine A. Orengo
2010 PLoS Computational Biology  
By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms.  ...  Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products.  ...  By using Random Forest classifiers, they also predicted the sub-subclass of EC reactions with accuracies up to 85% [90] .  ... 
doi:10.1371/journal.pcbi.1000700 pmid:20300652 pmcid:PMC2837397 fatcat:gzf6fvbshzh6xcg5xuxargqs4i


2018 Seibutsu Butsuri  
In this symposium, each speaker will make 10-minute presentation followed by 3-minute discussion as the second round of screening.  ...  Up to five awardees of the Early Career Award in Biophysics will be selected and announced at the banquet 3SEA-5 光遺伝子操作による単一の糸球体の活性により誘因される恐怖行動の探索 Immobility responses are induced by photoactivation of  ...  induced by metal-ion binding.  ... 
doi:10.2142/biophys.58.s1 fatcat:6slkwnu64fen7cjixehxrcmdzm

EMBnet.journal 18 Suppl. A

EMBnet Journal
2012 EMBnet journal  
Protein Structure and Function Acknowledgments This work was supported by NFSR of Bulgaria project DVU 01/197.  ...  Random Forests has been considered standard 'tool-box of methods' for class prediction and gene selection with microarray data. We outperform Random Forests approach.  ...  Results We have evaluated five methods: PDBinder, Concavity and Fpocket for the prediction of protein binding pockets and Pfinder and FINDSITE _ metal for the prediction of phosphate and metals binding  ... 
doi:10.14806/ej.18.a.497 fatcat:2aexioifkfgfnipbo3btxqwvia

Thirtieth Annual Meeting 9–13 February 1986 Brooks Hall/Convention Center, San Francisco, California

1986 Biophysical Journal  
rather 9han by producing a generalized permeability increase. (3) Duramycin is a potent inhibitor of Ca release triggered by palmitoyl-CoA; Ca2+ release is eliminated at 40 pg duramycin/mg protein.  ...  We assume that protons can be transferred to adsorbed S-13 anions by three mechanisms: 1) a proton in the aqueous phase combines with an adsorbed anion with a rate constant kR9 2) a buffer molecule in  ...  The absence of tyrosine reduces the ambiguity in interpretation of the fluorescence emission properties of tryptophan in this protein. The protein binds Ca2+ and lanthanide ions with high affinity.  ... 
doi:10.1016/s0006-3495(86)83675-x fatcat:ueksbiqtg5gezldbdltnznp6ei
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