Scholars@Duke
Pranam D. Chatterjee

Pranam D. Chatterjee

Assistant Professor of Biomedical Engineering
Biomedical Engineering
pranam.chatterjee@duke.edu
101 Science Drive, CIEMAS 2353A, Durham, NC 27705
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Selected Publications

Programmable Protein Stabilization with Language Model-Derived Peptide Guides.

Conference Res Sq · July 26, 2024 Dysregulated protein degradation via the ubiquitin-proteasomal pathway can induce numerous disease phenotypes, including cancer, neurodegeneration, and diabetes. Stabilizing improperly ubiquitinated proteins via target-specific deubiquitination is thus a c ... Full text Link to item Cite

Generative design of therapeutics that bind and modulate protein states

Journal Article Current Opinion in Biomedical Engineering · December 1, 2023 Numerous therapeutic approaches have been developed to enable interrogation and modulation of protein isoforms, but often require laborious experimental development or screening of binders to targets of interest. In this article, we focus on efficient, sta ... Full text Cite

PAM-flexible genome editing with an engineered chimeric Cas9.

Journal Article Nature communications · October 2023 CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a b ... Full text Cite

SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders.

Journal Article Communications biology · October 2023 Protein-protein interactions (PPIs) are critical for biological processes and predicting the sites of these interactions is useful for both computational and experimental applications. We present a Structure-agnostic Language Transformer and Peptide Priori ... Full text Cite

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag.

Journal Article Nature methods · June 2023 Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-c ... Full text Cite

PAM-Flexible Genome Editing with an Engineered Chimeric Cas9.

Journal Article Res Sq · March 7, 2023 CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a b ... Full text Link to item Cite

Directed differentiation of human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression.

Journal Article eLife · February 2023 An in vitro model of human ovarian follicles would greatly benefit the study of female reproduction. Ovarian development requires the combination of germ cells and several types of somatic cells. Among these, granulosa cells play a key role in follicle for ... Full text Cite

MegaGate: A toxin-less gateway molecular cloning tool.

Journal Article STAR protocols · December 2021 Gateway cloning employs the use of the ccdb toxin and has low colony numbers, making it difficult to apply at scale to clone libraries of cDNA vectors. In this protocol, we describe MegaGate, a toxin-less Gateway technology capable of robust cDNA li ... Full text Cite

An integrated pipeline for mammalian genetic screening.

Journal Article Cell reports methods · October 2021 With the recent advancements in genome editing, next-generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a ... Full text Cite

Programmable Protein Stabilization with Language Model-Derived Peptide Guides.

Conference Res Sq · July 26, 2024 Dysregulated protein degradation via the ubiquitin-proteasomal pathway can induce numerous disease phenotypes, including cancer, neurodegeneration, and diabetes. Stabilizing improperly ubiquitinated proteins via target-specific deubiquitination is thus a c ... Full text Link to item Cite

Generative design of therapeutics that bind and modulate protein states

Journal Article Current Opinion in Biomedical Engineering · December 1, 2023 Numerous therapeutic approaches have been developed to enable interrogation and modulation of protein isoforms, but often require laborious experimental development or screening of binders to targets of interest. In this article, we focus on efficient, sta ... Full text Cite

PAM-flexible genome editing with an engineered chimeric Cas9.

Journal Article Nature communications · October 2023 CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a b ... Full text Cite

SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders.

Journal Article Communications biology · October 2023 Protein-protein interactions (PPIs) are critical for biological processes and predicting the sites of these interactions is useful for both computational and experimental applications. We present a Structure-agnostic Language Transformer and Peptide Priori ... Full text Cite

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag.

Journal Article Nature methods · June 2023 Prime editors have a broad range of potential research and clinical applications. However, methods to delineate their genome-wide editing activities have generally relied on indirect genome-wide editing assessments or the computational prediction of near-c ... Full text Cite

PAM-Flexible Genome Editing with an Engineered Chimeric Cas9.

Journal Article Res Sq · March 7, 2023 CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a b ... Full text Link to item Cite

Directed differentiation of human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression.

Journal Article eLife · February 2023 An in vitro model of human ovarian follicles would greatly benefit the study of female reproduction. Ovarian development requires the combination of germ cells and several types of somatic cells. Among these, granulosa cells play a key role in follicle for ... Full text Cite

MegaGate: A toxin-less gateway molecular cloning tool.

Journal Article STAR protocols · December 2021 Gateway cloning employs the use of the ccdb toxin and has low colony numbers, making it difficult to apply at scale to clone libraries of cDNA vectors. In this protocol, we describe MegaGate, a toxin-less Gateway technology capable of robust cDNA li ... Full text Cite

An integrated pipeline for mammalian genetic screening.

Journal Article Cell reports methods · October 2021 With the recent advancements in genome editing, next-generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a ... Full text Cite

Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions.

Journal Article Communications biology · November 2020 The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has elicited a global health crisis of catastrophic proportions. With only a few vaccines approved for early or limited use, there is a critical need for effective antiviral strategies. In ... Full text Cite

An engineered ScCas9 with broad PAM range and high specificity and activity.

Journal Article Nature biotechnology · October 2020 CRISPR enzymes require a protospacer-adjacent motif (PAM) near the target cleavage site, constraining the sequences accessible for editing. In the present study, we combine protein motifs from several orthologs to engineer two variants of Streptococcus can ... Full text Cite

Publisher Correction: An engineered ScCas9 with broad PAM range and high specificity and activity.

Journal Article Nature biotechnology · October 2020 An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Full text Cite

A Cas9 with PAM recognition for adenine dinucleotides

Journal Article Nature Communications · May 18, 2020 AbstractCRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical e ... Full text Cite

Minimal PAM specificity of a highly similar SpCas9 ortholog.

Journal Article Science advances · October 2018 RNA-guided DNA endonucleases of the CRISPR-Cas system are widely used for genome engineering and thus have numerous applications in a wide variety of fields. CRISPR endonucleases, however, require a specific protospacer adjacent motif (PAM) flanking the ta ... Full text Cite

PD-1 alters T-cell metabolic reprogramming by inhibiting glycolysis and promoting lipolysis and fatty acid oxidation.

Journal Article Nature communications · March 2015 During activation, T cells undergo metabolic reprogramming, which imprints distinct functional fates. We determined that on PD-1 ligation, activated T cells are unable to engage in glycolysis or amino acid metabolism but have an increased rate of fatty aci ... Full text Cite