A. James Link
Contact
ajlink@princeton.eduResearch Area
Biochemistry, Biophysics & Structural BiologyResearch Focus
Protein engineering and chemical biologyEngineering high-affinity inhibitors of anti-apoptotic proteins
The molecular cause of several cancers is an imbalance between pro-apoptotic and anti-apoptotic proteins. It is postulated that the excess anti-apoptotic protein sequesters all of the pro-apoptotic protein thus preventing execution of apoptosis (programmed cell death). One potential treatment for cancers of this type is a high-affinity competitive inhibitor to the anti-apoptotic protein. We are pursuing several different natural proteins as scaffolds for such an inhibitor as well as completely de novo library designs.
Evolving higher efficacy antimicrobial peptides
Some classes of antimicrobial peptides are used by microbes as a defense mechanism against other species. These peptides represent an avenue of treatment for multidrug resistant (MDR) bacterial infections that has not been thoroughly explored yet. We will utilize naturally occurring antimicrobial peptides and apply directed evolution in order to engineer molecules with higher efficacies and broader spectra of activity. Synthetic biology principles are also being investigated in order to generate novel methods of delivering antimicrobial peptides to infection sites.
Biotechnological uses of E. coli: understanding the cellular response
Protein engineers often use host organisms such as E. coli simply as factories with little regard for the physiological state of the cell. We plan to use transcriptional reporters along with genomic and proteomic approaches (including BONCAT) to catalog the response of the cell to biotechnological uses of E. coli such as heterologous protein expression and unnatural amino acid incorporation. The knowledge and insights gained from these large-scale studies will subsequently be used to inform strain engineering experiments to develop host strains of E. coli that are more useful in biotech contexts.
Analyzing differential proteomes with BONCAT (Bio-Orthogonal Non-Canonical Amino Acid Tagging)
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. Translational Fusion to Hmp Improves Heterologous Protein Expression. Microorganisms. 2022 ;10(2).
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. The Shuttling Cascade in Lasso Peptide Benenodin-1 is Controlled by Non-Covalent Interactions. Chemistry. 2022 ;28(5):e202103615.
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. Phenotype-Guided Comparative Genomics Identifies the Complete Transport Pathway of the Antimicrobial Lasso Peptide Ubonodin in . ACS Chem Biol. 2022 ;17(8):2332-2343.
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. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol. 2021 ;48(3-4).
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. Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides. Nat Chem. 2021 ;13(9):850-857.
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. Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-Translational Modification. J Am Chem Soc. 2021 ;143(30):11690-11702.
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. Local accumulation of extracellular matrix regulates global morphogenetic patterning in the developing mammary gland. Curr Biol. 2021 ;31(9):1903-1917.e6.
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. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep. 2021 ;38(1):130-239.
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. Introduction to Special Issue on "Frontiers in Industrial Microbiology and Biotechnology 2020". J Ind Microbiol Biotechnol. 2020 ;47(9-10):621-622.
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. Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex. Chembiochem. 2020 ;21(9):1335-1340.
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. Synergy Screening Identifies a Compound That Selectively Enhances the Antibacterial Activity of Nitric Oxide. Front Bioeng Biotechnol. 2020 ;8:1001.
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. Genome mining for lasso peptides: past, present, and future. J Ind Microbiol Biotechnol. 2019 ;46(9-10):1371-1379.
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. Pandonodin: A Proteobacterial Lasso Peptide with an Exceptionally Long C-Terminal Tail. ACS Chem Biol. 2019 ;14(12):2783-2792.
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. Discovery and structure of the antimicrobial lasso peptide citrocin. J Biol Chem. 2019 ;294(17):6822-6830.
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. Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc Natl Acad Sci U S A. 2019 ;116(4):1273-1278.
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. ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism. Proc Natl Acad Sci U S A. 2019 ;116(3):826-834.
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. Albusnodin: an acetylated lasso peptide from Streptomyces albus. Chem Commun (Camb). 2018 ;54(11):1339-1342.
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. Cyclic and Lasso Peptides: Sequence Determination, Topology Analysis, and Rotaxane Formation. Angew Chem Int Ed Engl. 2018 ;57(21):6150-6154.
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. Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch. J Am Chem Soc. 2017 ;139(30):10403-10409.
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. Lasso Peptide Biosynthetic Protein LarB1 Binds Both Leader and Core Peptide Regions of the Precursor Protein LarA. ACS Cent Sci. 2016 ;2(10):702-709.
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. Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and Their Modifications. ACS Chem Biol. 2016 ;11(3):782-91.
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. Construction of Lasso Peptide Fusion Proteins. ACS Chem Biol. 2016 ;11(1):61-8.
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. Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. J Am Chem Soc. 2016 ;138(50):16452-16458.
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. Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3. ACS Chem Biol. 2016 ;11(11):3043-3051.
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. Self-Assembly of Catenanes from Lasso Peptides. J Am Chem Soc. 2016 ;138(43):14214-14217.
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. Mapping the binding interface of ERK and transcriptional repressor Capicua using photocrosslinking. Proc Natl Acad Sci U S A. 2015 ;112(28):8590-5.
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. Elucidating the Specificity Determinants of the AtxE2 Lasso Peptide Isopeptidase. J Biol Chem. 2015 ;290(52):30806-12.
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. Biosynthesis: Leading the way to RiPPs. Nat Chem Biol. 2015 ;11(8):551-2.