Isaac S. Carrico

Stony Brook University

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Co-Authors

Daniel P. Raleigh

Stony Brook University

P. S. Banerjee

Novartis (India)

Humeyra Taskent‐Sezgin

Izmir Institute of Technology

Bruce H. Lipshutz

University of California, Santa Barbara

Juah Chung

Stony Brook University

Yoon Hyeun Oum

Emory University

David A. Tirrell

California Institute of Technology

Ivan Peran

St. Jude Children's Research Hospital

Shelly Vance

University of California, Santa Barbara

Carolyn R. Bertozzi

Stanford University

Cooperative Institutions

Stony Brook University

State University of New York

University of California, Berkeley

Howard Hughes Medical Institute

California Institute of Technology

University of California, Santa Barbara

Massachusetts Institute of Technology

Lawrence Berkeley National Laboratory

University of Wisconsin–Madison

Stony Brook Medicine

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Interpretation of p-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-Chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study

Biochemistry (2009)

Humeyra Taskent‐Sezgin Juah Chung Vadim Patsalo Shigeki J. Miyake-Stoner Andrew M. Miller

The use of noncoded amino acids as spectroscopic probes of protein folding and function is growing rapidly, in large part because of advances in the methodology for their incorporation. Recently p-cyanophenylalanine has been employed as a fluorescence and IR probe, as well as a FRET probe to study protein folding, protein−membrane interactions, protein−protein interactions and amyloid formation. The probe has been shown to be exquisitely sensitive to hydrogen bonding interactions involving the cyano group, and its fluorescence quantum yield increases dramatically when it is hydrogen bonded. However, a detailed understanding of the factors which influence its fluorescence is required to be able to use this popular probe accurately. Here we demonstrate the recombinant incorporation of p-cyanophenylalanine in the N-terminal domain of the ribosomal protein L9. Native state fluorescence is very low, which suggests that the group is sequestered from solvent; however, IR measurements and molecular dynamics simulations show that the cyano group is exposed to solvent and forms hydrogen bonds to water. Analysis of mutant proteins and model peptides demonstrates that the reduced native state fluorescence is caused by the effective quenching of p-cyanophenylalanine fluorescence via FRET to tyrosine side-chains. The implications for the interpretation of p-cyanophenylalanine fluorescence measurements and FRET studies are discussed.

Folding (DSP implementation)

Side chain

10.1021/bi900938z

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Citations (79)

Light-Activated Staudinger–Bertozzi Ligation within Living Animals

Journal of the American Chemical Society (2016)

Lisa Shah Scott T. Laughlin Isaac S. Carrico

The ability to regulate small molecule chemistry in vivo will enable new avenues of exploration in imaging and pharmacology. However, realization of these goals will require reactions with high specificity and precise control. Here we demonstrate photocontrol over the highly specific Staudinger-Bertozzi ligation in vitro and in vivo. Our simple approach, photocaging the key phosphine atom, allows for the facile production of reagents with photochemistry that can be engineered for specific applications. The resulting compounds, which are both stable and efficiently activated, enable the spatial labeling of metabolically introduced azides in vitro and on live zebrafish.

10.1021/jacs.5b13401

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Citations (74)

A general strategy for the bioorthogonal incorporation of strongly absorbing, solvation-sensitive infrared probes into proteins

F1000Research (2014)

Ivan Peran Tracey A. Oudenhoven Ann Marie Woys Matthew D. Watson Tianqi O. Zhang

Open peer review

Bioorthogonal Chemistry

10.7490/f1000research.1097006.1

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Citations (0)

Unexpected N-terminal editing: a cysteine protease that cuts and pastes

Nature Chemical Biology (2008)

Isaac S. Carrico

Cysteine protease

10.1038/nchembio0908-525

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Citations (1)

Compartment-Specific Labeling of Bacterial Periplasmic Proteins by Peroxidase-Mediated Biotinylation

ACS Infectious Diseases (2018)

Uday S. Ganapathy Lu Bai Linpeng Wei Kathryn A. Eckartt Clarissa M. Lett

The study of the bacterial periplasm requires techniques with sufficient spatial resolution and sensitivity to resolve the components and processes within this subcellular compartment. Peroxidase-mediated biotinylation has enabled targeted labeling of proteins within subcellular compartments of mammalian cells. We investigated whether this methodology could be applied to the bacterial periplasm. In this study, we demonstrated that peroxidase-mediated biotinylation can be performed in mycobacteria and Escherichia coli. To eliminate detection artifacts from natively biotinylated mycobacterial proteins, we validated two alternative labeling substrates, tyramide azide and tyramide alkyne, which enable biotin-independent detection of labeled proteins. We also targeted peroxidase expression to the periplasm, resulting in compartment-specific labeling of periplasmic versus cytoplasmic proteins in mycobacteria. Finally, we showed that this method can be used to validate protein relocalization to the cytoplasm upon removal of a secretion signal. This novel application of peroxidase-mediated protein labeling will advance efforts to characterize the role of the periplasm in bacterial physiology and pathogenesis.

Compartment (ship)

10.1021/acsinfecdis.8b00044

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Citations (17)

Simulations and Experiments Provide a Convergent View of Protein Unfolded States under Folding Conditions

Biophysical Journal (2017)

Alex S. Holehouse Ivan Perana Isaac S. Carrico Osman Bilsel Daniel P. Raleigh

Folding (DSP implementation)

Random coil

Folding funnel

Chain (unit)

Conformational ensembles

Molten globule

Intrinsically Disordered Proteins

10.1016/j.bpj.2016.11.1709

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Citations (1)

Targeted and armed oncolytic adenovirus via chemoselective modification

Bioorganic & Medicinal Chemistry Letters (2011)

P. S. Banerjee Edison S. Zuniga Iwao Ojima Isaac S. Carrico

Taxoid

Oncolytic adenovirus

10.1016/j.bmcl.2011.05.039

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Citations (13)

General Strategy for the Bioorthogonal Incorporation of Strongly Absorbing, Solvation-Sensitive Infrared Probes into Proteins

The Journal of Physical Chemistry B (2014)

Ivan Peran Tracey A. Oudenhoven Ann Marie Woys Matthew D. Watson Tianqi O. Zhang

A high-sensitivity metal-carbonyl-based IR probe is described that can be incorporated into proteins or other biomolecules in very high yield via Click chemistry. A two-step strategy is demonstrated. First, a methionine auxotroph is used to incorporate the unnatural amino acid azidohomoalanine at high levels. Second, a tricarbonyl (η(5)-cyclopentadienyl) rhenium(I) probe modified with an alkynyl linkage is coupled via the Click reaction. We demonstrate these steps using the C-terminal domain of the ribosomal protein L9 as a model system. An overall incorporation level of 92% was obtained at residue 109, which is a surface-exposed residue. Incorporation of the probe into a surface site is shown not to perturb the stability or structure of the target protein. Metal carbonyls are known to be sensitive to solvation and protein electrostatics through vibrational lifetimes and frequency shifts. We report that the frequencies and lifetimes of this probe also depend on the isotopic composition of the solvent. Comparison of the lifetimes measured in H2O versus D2O provides a probe of solvent accessibility. The metal carbonyl probe reported here provides an easy and robust method to label very large proteins with an amino-acid-specific tag that is both environmentally sensitive and a very strong absorber.

Bioorthogonal Chemistry

10.1021/jp5008279

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Citations (29)

Altering Adenoviral Tropism via Click Modification with ErbB Specific Ligands

Bioconjugate Chemistry (2012)

Yoon Hyeun Oum Isaac S. Carrico

Methods for targeting oncolytic viruses can increase efficacy and accelerate development. Genetic engineering, the predominant method for changing vector tropism, is limited in scope and often represents the bottleneck for vector development. Metabolic incorporation of an unnatural azido sugar, O-GlcNAz, at a specific site on the adenoviral surface allows chemoselective attachment of affibodies for Her2 or EGF receptors. Modification with these high-affinity, high-selectivity proteins is straightforward and readily generalizable, demonstrates minimal impact on virus physiology, and affords significant increases in gene delivery to cancer cells. As a result, this method has significant potential to increase the efficacy of next-generation viral vectors.

Tissue tropism

10.1021/bc200477z

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Citations (9)

Chemoselective modification of proteins: hitting the target

Chemical Society Reviews (2008)

Isaac S. Carrico

The use of synthetic molecules to modulate and track biological events is a central component of chemical biology. As a result, the precise, covalent modification of biomolecules is a key goal for this field. Several strategies have emerged that allow specific tailoring of polypeptides through either endogenous residues or introduced functionality. This tutorial review discusses these recent advances in the context of in vitro and in vivo applications.

Biomolecule

Component (thermodynamics)

Chemical Biology

Posttranslational modification

10.1039/b703364h

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Citations (128)