About

Alanna Schepartz is a principal investigator at UC Berkeley, leading the Schepartz Laboratory. Her research focuses on chemical biology, particularly on the development of innovative molecular tools and techniques to study biological systems. She has a background in chemistry and molecular biology, and her work contributes to understanding the mechanisms of biomolecular interactions and designing new therapeutic strategies. As a prominent figure in her field, she is dedicated to advancing scientific knowledge through her research and mentoring students and postdoctoral scientists in her lab.

Research topics

• Biology
• Biochemistry
• Chemistry
• Biophysics
• Materials science
• Optoelectronics
• Combinatorial chemistry
• Genetics
• Computational biology
• Optics
• Physics
• Nanotechnology

Selected publications

• Co-Translational Incorporation of <i>(R)</i> - and <i>(S)</i> -β ² -Hydroxy Acids <i>In Vitro</i> : A Structural and Biochemical Study on the <i>E. coli</i> Ribosome

  Journal of the American Chemical Society · 2026-02-27

  articleOpen accessSenior authorCorresponding

  Engineering the translation apparatus to accept backbone-modified amino acid analogues would enable the programmed synthesis of sequence-defined biopolymers with tunable properties. β-Hydroxy acids are of particular interest because they could support the programmed biosynthesis of both biocompatible polyester materials as well as natural product-like depsipeptides. Previous work has reported that both enantiomers of β2-hydroxy-Nε-Boc-lysine (β2-OH-BocK) are in vitro substrates for the orthogonal M. alvi pyrrolysyl-tRNA synthetase (PylRS)/tRNA pair, but only one enantiomer is introduced into protein in vivo. Here we make use of high-resolution cryogenic electron microscopy (cryo-EM) to determine the structural basis for this observation. These structures reveal both β2-OH-BocK isomers equally well-positioned within the ribosomal A site regardless of stereochemistry. Consistent with this observation, in vitro translation reactions charged with tRNAs acylated with (R)- or (S)-β2-OH-BocK produced roughly equal amounts of translated product when quantified on the basis of either mass spectrometry or luminescence. Together, these experiments imply that the substantial preferential in vivo incorporation of one enantiomer over the other observed previously results primarily from deficiencies in the steps that precede bond formation by the E. coli ribosome. Indeed, as predicted by this work and demonstrated in an accompanying paper (Soni, C. Co-Translational Incorporation of (R)- and (S)-β2-Hydroxyacids In Vivo: Directed Evolution of Efficient Aminoacyl-tRNA Synthetases. J. Am. Chem. Soc. 2026, 148, 10.1021/jacs.5c18595), when cells are provided with an active and orthogonal aminoacyl-tRNA synthetase/tRNA pair that accepts both (R)- and (S)-β2-OH-BocK as substrates, both monomers are introduced into protein in good yield and with high fidelity.

  PublisherDOI

• Co-translational incorporation of (R) and (S) β2 -hydroxyacids in vivo: Directed evolution of efficient aminoacyl-tRNA synthetases

  Zenodo (CERN European Organization for Nuclear Research) · 2026-02-09

  datasetOpen access

  This is the dataset for the publication in the Journal of American Chemical Society. This dataset includes raw data for PacBio sequencing and Illumina sequencing, as well as intermediate and final analysis files.

  PublisherDOI

• BPS2026 – Proteins with new-to-nature backbones

  Biophysical Journal · 2026-02-01

  article1st authorCorresponding
  PublisherDOI

• Bioinformatics-Guided Discovery of a Thermostable and Highly Promiscuous RiPP Cyclodehydratase

  ChemRxiv · 2026-05-05

  articleOpen accessSenior author

  Ribosomally synthesized and post-translationally modified peptides (RiPPs) often contain backbone-embedded oxazoline/thiazoline heterocycles that are installed by enzymes known as cyclodehydratases. These enzymes are of great interest as biocatalysts for biotechnology applications, as embedded oxazoline/thiazoline heterocycles can induce non-subtle structural and functional changes that alter bioactivity both directly and indirectly. However, the toolkit of existing cyclodehydratases with robust activity, stability, and well-defined sequence specificity is extremely limited. Herein, we apply a genome mining approach to discover two novel cyclodehydratases: TcuD (from Thermomonospora curvata) and TteD (from Thermocatellispora tengchongensis) with improved thermostability; TcuD also displays exceptional substrate scope. Specifically, TcuD showed remarkable tolerance to mutations, insertions, and deletions to its substrate precursor peptide, TcuA, and it could easily modify a diverse set of substrates whose sequences were derived from α-helical regions of structurally characterized proteins. This work expands the repertoire of cyclodehydratases available for biotechnology applications.

  PublisherDOI

• Co-Translational Incorporation of ( <i>R</i> )- and ( <i>S</i> )-β ² -Hydroxyacids <i>In Vivo</i> : Directed Evolution of Efficient Aminoacyl-tRNA Synthetases

  Journal of the American Chemical Society · 2026-02-27

  articleOpen access

  Expanding the genetic code of living cells with noncanonical monomers (ncMs) relies on engineered aminoacyl-tRNA synthetases (aaRS) and their cognate tRNAs. Conventional aaRS engineering strategies rely on translation-dependent selection systems, limiting their utility for ncMs that are poorly accommodated by the native translational machinery. To address this limitation, we recently developed START, a translation-independent platform that selects Methanomethylophilus alvus pyrrolysyl-synthetase (MaPylRS) mutants based on their ability to acylate cognate tRNAMaPyl. START uses barcoded tRNAs to encode the identity of distinct aaRS mutants in a library. Acylation by active aaRS mutants protects the corresponding tRNAs from periodate oxidation, and their identity is retrieved subsequently through sequencing. START was previously applied to genetically encode noncanonical α-amino acids. Here, we successfully applied START to engineer MaPylRS mutants capable of acylating tRNAMaPyl with diverse non-α-amino acid substrates with good efficiency and fidelity, including (R) and (S) enantiomers of a β2-hydroxy acid, a β2-amino acids, and a malonate. Several mutants exhibit notable polyspecificity across noncanonical backbones while maintaining selectivity against their α-amino acid counterparts. Using these novel enzymes, we demonstrate the ribosomal incorporation of both (R)- and (S)-β2-hydroxy acids into a luciferase reporter protein expressed in Escherichia coli with good efficiency and fidelity. These results imply that highly active engineered aaRS/tRNA pairs can overcome the recently established limitations of EF-Tu with respect to non-α-amino acid substrates. The engineered MaPylRS mutants also enabled the successful incorporation of both (R)- and (S)-β2-hydroxy acids into a protein expressed in mammalian cells, demonstrating for the first time that eukaryotic translation can accommodate non-α-backbones.

  PublisherOA PDFDOI

• Co-translational incorporation of (R) and (S) β2 -hydroxyacids in vivo: Directed evolution of efficient aminoacyl-tRNA synthetases

  Open MIND · 2026-02-09

  dataset

  This is the dataset for the publication in the Journal of American Chemical Society. This dataset includes raw data for PacBio sequencing and Illumina sequencing, as well as intermediate and final analysis files.

  DOI

• Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems

  Nucleic Acids Research · 2026-02-24 · 1 citations

  articleOpen access

  Transfer RNAs (tRNAs) are utilized by the ribosome to decode the nucleic acid alphabet. tRNA structure, stability, aminoacylation efficiency, and decoding efficacy are governed by their extensive post-transcriptional modifications. In most studies, individual tRNAs are generated using in vitro transcription, which produces tRNAs devoid of these critical site-specific modifications, negatively affecting translation yields and fidelity. To address this challenge, we have developed a purification method that couples tRNA overexpression to DNA hybridization-based purification. Using this approach, we produced native tRNAs from Escherichia coli in high yield and purity while retaining their complement of native post-transcriptional modifications and translational activity. We extend this technique to the purification of Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}$, tRNAs of critical importance for genetic code expansion. We confirmed that both Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}$ contain native E. coli post-transcriptional modifications and provide the first complete modification profiles of each. Moreover, we found that in vivo-generated Mj-$tRNA_{CUA}^{Opt}$ and Ma-$tRNA_{CUA}^{Pyl}\ $significantly outperform their in vitro-generated counterparts in amber codon suppression in cell-free translation reactions. Finally, we purified an engineered variant of E. coli$tRNA_{CCA}^{Trp}$, extending our studies to synthetic tRNAs. We present a flexible method that generates modified tRNAs in high yield and purity, addressing a critical and persistent challenge in RNA biochemistry.

  PublisherDOI

• Expanding the multiplexing capability of HIDE probes via fluorescence lifetime imaging microscopy

  Methods in enzymology on CD-ROM/Methods in enzymology · 2026-01-01

  book-chapterOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• Drug Delivery: Built by Biochemistry

  Biochemistry · 2025-06-17

  editorial1st authorCorresponding
  PublisherDOI

• Abstract 1528 A mutation to the exit tunnel of the E. coli ribosome improves translation of polyproline sequences with implications for incorporation of cyclic β-amino acids

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access

  Incorporation of β-amino acids into peptides imparts proteolytic stability, unique architectures, and membrane permeability as demonstrated by β-amino acid containing natural products. Additionally, cyclic β-amino acids can act as turn inducers, and multiple incorporations can generate foldamers with rigid helical structures. However, incorporation efficiency and number of residues incorporated is highly dependent on the stereochemistry of the cyclic β-amino acid. We sought to improve incorporation of cyclic β-amino acids through structure guided mutations of the E.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01GM043501

  NIH · $1.8M · 1998

• NIH Grant R01GM131372

  NIH · $299k · 2021

• NSF Center for Genetically Encoded Materials

  NSF · $19.8M · 2020–2026

• Fluorescence tools that illuminate biology and inspire translation

  NIH · $4.0M · 2020–2030

• NIH Grant R01GM053829

  NIH · $881k · 2000

Frequent coauthors

• Scott J. Miller

  NextFlex

  118 shared

• William L. Jorgensen

  Yale University

  91 shared

• M. G. Finn

  Georgia Institute of Technology

  85 shared

• Paul S. Weiss

  California NanoSystems Institute

  85 shared

• Courtney C. Aldrich

  University of Minnesota System

  85 shared

• Marc A. Hillmyer

  University of Minnesota

  85 shared

• Jillian M. Buriak

  University of Alberta

  85 shared

• Stuart J. Rowan

  University of Chicago

  85 shared

Labs

• Schepartz LaboratoryPI

  A chemical and synthetic biology research group at UC Berkeley

Education

• Ph.D., Chemistry

  Columbia University

  1986

• B.S., Chemistry

  State University of New York

  1982

Awards & honors

• Ralph F. Hirschmann Award in Peptide Chemistry (2020)
• Inspiring Yale Award, Yale University (2018)
• Wheland Medal, University of Chicago (2015)
• Elected Member, National Academy of Sciences (2014)
• ACS Ronald Breslow Award for Achievement in Biomimetic Chemi…