Arnold World March 2023

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Science (New York, N.Y.)

Enzyme function prediction using contrastive learning.

2023-03-30

PubMed:36996195; DOI:10.1126/science.adf2465

Tianhao Yu¹, Haiyang Cui¹, Jianan Canal Li², Yunan Luo³, Guangde Jiang¹, Huimin Zhao¹

Affiliations

Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
National Science Foundation Molecule Maker Lab Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30308, USA

Excited to share our latest research published at Science! We developed CLEAN, an AI tool based on contrastive learning for enzyme function prediction.
Check out our paper for more details!

2023-03-31

In annotation’s realm, a challenge profound,
Enzyme functions, mysteries to expound,
Computational tools emerge with might,
Yet for less-known proteins, a challenging fight,
CLEAN shines bright, its accuracy renowned.

Contrastive learning’s prowess it employs,
EC numbers assigned with confident voice,
Understudied enzymes find their place,
Mislabeled ones, it helps to retrace,
Promiscuous enzymes it skillfully deploys.

Through in silico and in vitro tests,
CLEAN’s power shines, its strength attests,
Annotating functions, a potent art,
Unveiling enzymes’ codes, each part,
In genomics and beyond, it manifests.

Nature communications

Genome mining unveils a class of ribosomal peptides with two amino termini.

2023-03-23

PubMed:36959188; DOI:10.1038/s41467-023-37287-1

Hengqian Ren¹, Shravan R Dommaraju², Chunshuai Huang², Haiyang Cui², Yuwei Pan³, Marko Nesic², Lingyang Zhu⁴, David Sarlah², Douglas A Mitchell⁵, Huimin Zhao⁶

Affiliations

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Our work on the discovery of a new class of ribosomal peptides that contain two positively charged termini was just published (https://nature.com/articles/s41467-023-37287-1…). A related news release was also just published (https://igb.illinois.edu/article/researchers-discover-new-class-ribosomal-peptide-hemolytic-activity…). Congrats to Hengqian, Shravan, and the rest of team!

2023-03-24

Congrats Huimin and team.

2023-03-28

synbio-meteng

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ACS synthetic biology

Marine Biofilm Engineered to Produce Current in Response to Small Molecules.

2023-03-16

PubMed:36926839; DOI:10.1021/acssynbio.2c00417

Lina J Bird¹, Dagmar H Leary¹, Judson Hervey¹, Jaimee Compton¹, Daniel Phillips², Leonard M Tender¹, Christopher A Voigt³, Sarah M Glaven¹

Affiliations

Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375, United States
Biochemistry Branch, Oak Ridge Institute for Science and Education/US Army DEVCOM Chemical Biological Center, Aberdeen Proving Grounds, Maryland 21005, United States
Department of Biological Engineering and the Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States

Interesting paper @ACSSynBio
@Geneticdesigner

2023-04-29

ACS synthetic biology

Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis.

2023-03-21

PubMed:36943773; DOI:10.1021/acssynbio.2c00607

Jong Hyun Park¹, Marcelo C Bassalo¹, Geng-Min Lin¹, Ye Chen¹, Hamid Doosthosseini¹, Joep Schmitz², Johannes A Roubos², Christopher A Voigt¹

Affiliations

Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, Massachusetts 02139, United States
DSM Science & Innovation, Biodata & Translational Sciences, P.O. Box 1, 2600 MA Delft, The Netherlands

evolutionary-engineering–proteins

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Chemical communications (Cambridge, England)

First and second sphere interactions accelerate non-native N -alkylation catalysis by the thermostable, methanol-tolerant B 12 -dependent enzyme MtaC.

2023-03-31

PubMed:37000588; DOI:10.1039/d3cc01071f

Amardeep Kumar¹, Xinhang Yang¹, Jianbin Li¹, Jared C Lewis¹

Affiliations

Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.

This study shows that MtaC activates B12 toward aniline alkylation; the cofactor alone is unreactive. Scaffold activation facilitates evolution, giving us a way to generate variants for other reactions that cannot be readily screened.

2023-04-26

way to go amardeep and team!

2023-03-24

Journal of the American Chemical Society

MicroED Structure of a Protoglobin Reactive Carbene Intermediate.

2023-03-22

PubMed:36948184; DOI:10.1021/jacs.2c12004

Emma Danelius¹, Nicholas J Porter², Johan Unge¹, Frances H Arnold², Tamir Gonen¹

Affiliations

Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States

Great collaboration with @gonenlab, who caught the reactive carbene inside the enzyme. Congrats to Nick Porter @NJP_Chem and @EmmaDanelius. Interesting that #AlphaFold got the overall structure, but not the effects of the mutations that conferred activity with #diazirines.

2023-03-24

@EmmaDanelius @francesarnold @NJP_Chem amazing team and amazing results. Time resolved novel enzymatic dynamics determined by #MicroED

2023-03-23

Chirality

Asymmetric catalysis by flavin-dependent halogenases.

2023-03-14

PubMed:36916449; DOI:10.1002/chir.23550

Yuhua Jiang¹, Jared C Lewis¹

Affiliations

Department of Chemistry, Indiana University, Bloomington, Indiana, USA

PLoS computational biology

Inferring protein fitness landscapes from laboratory evolution experiments.

2023-03-01

PubMed:36857380; DOI:10.1371/journal.pcbi.1010956

Sameer D’Costa¹, Emily C Hinds¹, Chase R Freschlin¹, Hyebin Song², Philip A Romero¹

Affiliations

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
Department of Statistics, Pennsylvania State University, State College, Pennsylvania, United States of America

Angewandte Chemie (International ed. in English)

A Flow Cytometry-Based Ultrahigh-Throughput Screening Method for Directed Evolution of Oxidases.

2023-03-02

PubMed:36861784; DOI:10.1002/anie.202214999

Lilin Feng¹, Liang Gao¹, Volkan Besirlioglu¹, Khalil Essani¹, Malte Wittwer¹, Tetiana Kurkina¹, Yu Ji¹, Ulrich Schwaneberg¹

Affiliations

Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany

General flow cytometry-based screening platform FlOxi developed integrating oxidation/Fenton rxn cascade, Fe3+ mediated #eGFPHis decoration & validated by evolution of 2 #oxidases by #Ultrahigh-ThroughputScreening @SchwanebergG #openaccess #projektDEAL https://onlinelibrary.wiley.com/doi/10.1002/anie.202214999…

2023-04-26

evolution-physiology

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Chemical communications (Cambridge, England)

Chemical control of phase separation in DNA solutions.

2023-03-13

PubMed:36911995; DOI:10.1039/d2cc06901f

Samuel Hauf¹, Yohei Yokobayashi¹

Affiliations

Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan 904-0495, Japan.

This article is #openaccess

Stay up to date with the latest research like ‘Chemical control of phase separation in DNA solutions’ by Yohei Yokobayashi & Samuel Hauf @OISTedu

2023-03-26

Chemical control of phase separation in DNA solutions

2023-03-08

Briefings in bioinformatics

A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding.

2023-03-23

PubMed:36951499; DOI:10.1093/bib/bbad110

Sumit Mukherjee¹, Matan Drory Retwitzer¹, Sara M Hubbell², Michelle M Meyer², Danny Barash¹

Affiliations

Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA

Molecular pharmaceutics

Glycan-Controlled Human PD-1 Variants Displaying Broad-Spectrum High Binding to PD-1 Ligands Potentiate T Cell.

2023-03-10

PubMed:36897183; DOI:10.1021/acs.molpharmaceut.3c00003

Ji Yeon Ha¹, Kwang-Jin Chun², Sanghwan Ko³, Ho Won Lee⁴, Ok Kyung Hwang⁴, Chung Su Lim⁴, Kyungsoo Ha⁴, Byoung Joon Ko⁵, Sang Taek Jung¹

Affiliations

Department of Biomedical Sciences, Graduate School, Korea University, Seoul 02842, Republic of Korea
Neuracle Science, Seoul 02841, Republic of Korea
Institute of Human Genetics, Korea University College of Medicine, Seoul 02842, Republic of Korea
New Drug Development Center, Osong Medical Innovation Foundation, 123, Cheongju, Chungcheongbuk-do 28160, Republic of Korea
School of Biopharmaceutical and Medical Sciences, Sungshin Women’s University, Seoul 02844, Republic of Korea

human-physiology

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Journal of the American Chemical Society

Small-Molecule Aptamer for Regulating RNA Functions in Mammalian Cells and Animals.

2023-03-29

PubMed:36991533; DOI:10.1021/jacs.2c12332

Keisuke Fukunaga¹, V Dhamodharan¹, Nao Miyahira¹, Yoko Nomura¹, Kamila Mustafina¹, Yasuaki Oosumi², Kosuke Takayama², Akira Kanai², Yohei Yokobayashi¹

Affiliations

Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
Applied Research & Operations, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305 0841, Japan

Open access in this week’s Issue: researchers have developed a new toolkit that uses small molecules to control the activity of a piece of synthetic RNA, and ultimately regulate gene expression

Learn more here

2023-04-16

kedalionlabs.com

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