About

Karen Allen is a Professor of Chemistry and Materials Science and Engineering at Boston University. Her research group, The Allen Group, investigates the structure, function, mechanisms of catalysis, and evolution of enzymes. Their work provides insights into these essential proteins, guiding the design of specialized molecules and enzymes to aid in drug discovery and protein studies. The group employs techniques such as X-ray crystallography, kinetics, enzymology, and bioinformatics, collaborating with leading laboratories at other universities. Their studies include elucidating the determinants of substrate and membrane interaction of enzymes in the phosphoglycosyl transferase and glycosyl transferase families, which are involved in biosynthetic pathways leading to complex glycoconjugates that provide mechanical stability to microorganisms and mediate interactions among bacteria and with human hosts. Additionally, her group focuses on drug discovery efforts, including developing small-molecule inhibitors against neurotoxins produced by Clostridium botulinum, which are significant for both clinical applications and biological security. The research also extends to exploring protein-protein interactions to enhance structure-based ligand discovery. Dr. Allen holds a B.S. in Biology from Tufts University and a Ph.D. in Biochemistry from Brandeis University, with postdoctoral training in X-ray crystallography at MIT and Brandeis. Her work is supported by state-of-the-art facilities, including advanced X-ray crystallography suites and supercomputers for bioinformatics, and she actively collaborates with national research centers to utilize specialized facilities at Brookhaven, Argonne, and Stanford. Graduates of her group have pursued careers in academia, industry, and research institutes, demonstrating the broad applicability of her research expertise.

Research topics

• Chemistry
• Biochemistry
• Biology
• Stereochemistry
• Computational biology
• Crystallography
• Microbiology
• Biophysics
• Nuclear physics
• Optics
• Internal medicine
• Medicine
• Immunology
• Nanotechnology
• Combinatorial chemistry
• Pediatrics
• Genetics

Selected publications

• Detergent Exchange from Lipid Nanoparticles into Detergent Micelles Unlocks a Tool for Biochemical and Kinetic Characterization of Membrane Proteins

  Biochemistry · 2026-03-26

  articleSenior authorCorresponding

  Bacterial membrane proteins make up ∼ 30% of the prokaryotic genome and play key roles in infection and virulence. Membrane protein chemistry has advanced in recent years, including purification strategies that mimic nativelike lipid environments, such as lipid nanoparticles, amphipols, and nanodiscs. The use of styrene maleic acid copolymers (SMALPs) to form a lipid nanoparticle has become increasingly common in membrane protein purification, especially for proteins which are not amenable to detergent extraction from the cellular membrane fraction. Yet, for some biochemical and biophysical methods, it is preferable to use detergent-solubilized protein. Here we show a general exchange screening method to transfer membrane proteins from lipid nanoparticles to detergent micelles while retaining protein fold, homogeneity, and function. Conditions were first optimized for copolymer dispersion and recovery into detergents, and analytical methods were employed to assess activity and quality of detergent-solubilized proteins. Thirteen protein targets were purified in copolymer based on a 16-polymer screen. This selection was followed by an eight-detergent screen in the presence of calcium and magnesium ions for optimal dissolution of the nanoparticle, producing detergent-stabilized protein. In all membrane proteins assessed, homogeneity and folding were retained from the initial purification in lipid nanoparticles through a detergent-exchange protocol. For membrane enzymes that have proven to be experimentally intractable when detergent solubilized, we were able to observe catalytic activity using the detergent-exchanged material. The use of this protocol to purify membrane proteins provides greater versatility for biochemical and kinetic characterization than was previously accessible.

  PublisherDOI

• Initial Responses of Riparian Vegetation and Wetland Functions to Stage 0 Restoration of Whychus Creek, Oregon

  Land · 2026-03-19

  articleOpen access

  Floodplain disconnection caused by channel incision and/or levee construction has led to widespread loss of riparian habitats and ecosystem functions globally. Restoring full stream–floodplain connectivity is increasingly promoted, yet evidence of ecological outcomes remains limited. This study evaluates the initial performance of two Stage 0 restoration projects on Whychus Creek, Oregon, which reconnected incised channels to their historical floodplains in 2012 and 2016. We combined pre- and post-restoration vegetation surveys along fixed transects with hydrogeomorphic-based riparian and wetland function assessments and applied quantitative analyses, including Kruskal–Wallis tests, Jaccard correlations, Sorensen similarity indices, and factor analysis, to compare changes in plant assemblages and ecosystem functions across restored, transitional, and unrestored reaches. Our research results indicate that two years post-restoration, the active riparian area expanded 2.5-fold, species richness and structural diversity increased significantly, and riparian and wetland functions such as water storage, sediment retention, and habitat support for fish and amphibians improved markedly. Numbers of anadromous salmonids also increased markedly. This is important as salmon recovery is a regional stream restoration goal. Comparisons with a reach restored six years earlier suggest a positive trajectory toward mature, resilient ecosystems. These findings demonstrate that Stage 0 restoration can rapidly reestablish complex habitat mosaics and enhance ecosystem services critical for biodiversity, water quality, and flood resilience. Practically, this evidence supports process-based restoration strategies that prioritize full floodplain reconnection as a cost-effective approach to reversing long-term ecological degradation. Continued monitoring is essential to guide adaptive management and strengthen the evidence base for the wide-scale implementation of valley-floor wide stream restoration.

  PublisherDOI

• A nicotine biosensor derived from microbial screening

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-13

  articleOpen access

  Abstract Physiologically relevant biosensors are in increasingly high demand, yet existing ones are severely limited in the number and type of biomarkers that are detected. The lack of biorecognition elements for most medically relevant biomarkers restricts the development of next generation single and continuous use monitors. Over billions of years, microbes have evolved a vast array of proteins to sense and metabolize small molecules, including those pertinent to human health. Of particular interest to us is the identification and subsequent integration of new microbial redox enzymes into electronic biosensors building off the established electrochemical technology of the continuous glucose monitor. Here we deploy genomic screening to identify analyte specific redox enzymes for biosensor development. As a proof of concept, we report the first electrochemical enzyme-based nicotine biosensor from a novel microbial enzyme, and use a variant with improved catalytic performance to enhance sensor performance. The biosensor detects nicotine over 0.4-100 μM, a range relevant to nicotine concentrations present in active smoker sweat, saliva, gastric juice, and urine. This microbial mining approach for discovering redox enzymes expands the sensing parts toolbox available over conventional antibodies and aptamers.

  PublisherDOI

• Rare skeletal condition caused by enzyme’s failure to rescue a catalytic cycle

  Nature · 2025-08-20

  article1st authorCorresponding
  PublisherDOI

• Selection of nanobodies against liponanoparticle-embedded membrane proteins by yeast surface display

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-23 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Single-domain antibodies, known as nanobodies (Nbs), are widely used in structural biology, therapeutics, and as molecular probes in biology and biotechnology. Nbs towards soluble proteins are routinely developed via alpaca immunization or directed evolution in yeast cell-surface display. However, for membrane proteins, the targets are generally detergent-solubilized, and there remains a need for Nb development methods against membrane proteins in a native-like membrane environment. To address this need, we present a protocol for Nb selection via extraction of membrane proteins into amphiphilic polymers such as styrene-maleic acid to produce purified membrane proteins in stable liponanoparticles. Proof of generality is demonstrated by applying the pipeline to four membrane-resident enzymes of differing fold, oligomerization state, and membrane topology (reentrant membrane helix, transmembrane, membrane-associated). Following screening for optimal stabilization into liponanoparticles, Nbs were selected against four target proteins from glycoconjugate biosynthesis pathways. The selected Nbs showed high affinity and selectivity towards their target proteins with K D apparent values ranging from 15 nM to 200 nM, depending on the Nb-protein conjugate. In accordance with their tight binding, various Nb-protein complexes were found to be stable to size-exclusion chromatography purification. The Nbs were also amenable to sortase-mediated ligation, enabling their conversion into molecular probes for the target membrane protein. The ability to select for such high-affinity Nb against membrane proteins in SMALP will facilitate their widespread application in cell biology and biomedical applications.

  PublisherOA PDFDOI

• Unmanned Aerial Systems and Violent Non-state Actors in Africa: Proliferation, Adaptation and Use

  Southern space studies · 2025-01-01

  book-chapter1st authorCorresponding
  PublisherDOI

• Initial Responses of Riparian Vegetation and Wetland Functions to Stage 0 Restoration of Whychus Creek, Oregon

  Preprints.org · 2025-10-22

  preprintOpen access

  Floodplain disconnection caused by anthropogenically-triggered channel incision or artificial levee construction, has led to widespread loss of riparian habitat and ecosys-tem functions in river systems across the globe. Restoring connectivity is now consid-ered essential to recover lost biodiversity and improve water quality, yet evidence for the ecological outcomes of full reconnection remains limited. This study evaluates the ecological effectiveness of two Stage 0 restoration projects on Whychus Creek, Oregon, which reestablished stream–floodplain connectivity across the entire valley floor in 2012 and 2016, respectively. We used pre- and post-restoration vegetation surveys along fixed transects to assess changes in plant assemblages and compared these with an unre-stored reach and a reach restored six years earlier. Two years after the restoration was carried out, the active riparian area had expanded 2.5-fold and supported a patchy, shifting mosaic of aquatic, wetland, riparian, mesic, and upland habitats. Species rich-ness and structural diversity increased significantly. We also saw found improvements in key wetland functions such as water storage, sediment retention and nutrient cycling – evidence of healthy, heterogenous habitats that can support a wide range of species. Our results show that Stage 0 restoration can rapidly reestablish complex habitat net-works and deliver diverse ecological benefits. Continued monitoring is essential to as-sess the long-term trajectories of post-restoration succession and resilience. This study contributes to the growing evidence base for process-based restoration that pri-oritizes full floodplain reconnection in anthropogenically-incised rivers.

  PublisherOA PDFDOI

• Conformational changes in ketohexokinase are conserved across isozymes and species

  Acta Crystallographica Section F Structural Biology Communications · 2025-09-30

  article

  Ketohexokinase (KHK) catalyses the initial step in fructose metabolism, converting the furanose form of D-fructose to fructose 1-phosphate in an ATP-dependent reaction. Given its central role in metabolic pathways, KHK has emerged as a target for pharmacological intervention in the treatment of non-alcoholic fatty liver disease, metabolic syndrome, type 2 diabetes and obesity. KHK exists as two isoforms, A and C, which arise from alternative splicing of exon 3, resulting in a differing 45-amino-acid sequence within the 298-amino-acid primary structure of the enzyme. KHK is a biological homodimer, with each subunit adopting an α/β-fold architecture that interlocks with a β-clasp domain. In the case of KHK-C at least two distinct conformations of the β-clasp domain have been identified, whereas this conformational flexibility had not been observed in KHK-A. Here, X-ray crystallographic structural investigations of unliganded murine KHK-A refined to 1.37 Å resolution revealed the adoption of two conformations similar to those adopted by the human ortholog, suggesting that this structural feature is conserved across species. The functional significance of these conformational changes in KHK-A is of particular interest as this isoform has been implicated in cancer metastasis through a `moonlighting' protein kinase activity. Understanding the mechanistic role of conformational shifts in KHK-A may provide insights into its broader physiological functions and therapeutic potential.

  PublisherDOI

• Using structure and informatics to probe the mechanism of enzymes in the flavin amine oxidase superfamily

  Structural Dynamics · 2025-03-01

  articleOpen accessSenior author

  Flavoenzymes, which use a flavin adenine dinucleotide (FAD) cofactor, feature a wide range of activities and substrate specificities. This includes the ability to act as oxidases, relying on molecular oxygen (O2) as a co-substrate, or as dehydrogenases wherein the FAD is redox-cycled not by O2, but by other redox-active proteins or small-molecule substrates. Nicotine oxidoreductase (NicA2) is a flavin-dependent enzyme that provides a useful model system for interrogating structure-function relationships: first characterized as an oxidase, NicA2 has been proven to be a true dehydrogenase, with a native cytochrome c redox partner that greatly stimulates activity. Out of the 9,000 members of the flavin amine oxidase (FAO) superfamily, NicA2 and its downstream homolog pseudooxynicotine amine oxidase (Pnao) are the only members experimentally characterized as using a cytochrome c as an electron acceptor. This finding raises the question of whether other members may function similarly, and thus might in fact be unrecognized dehydrogenases. Additionally, NicA2 is structurally similar to known oxidases, for example Corynebacterium ammoniagenes monoamine oxidase (caMAO) (RMSD value of 1.89), therefore the molecular switch to convert an enzyme from a dehydrogenase to an oxidase may lie in a few key residues. Our bioinformatics analysis identifies dozens of genomes in which a cytochrome c is immediately downstream or upstream of a NicA2 homolog and one case of a larger molecular weight enzyme annotated as both a FAO and cytochrome c. Using the genome neighborhood network, many likely uncharacterized dehydrogenases were found that may have cytochrome c or cytochrome p450 cofactors. Upon further sequence and structural analysis, the dually annotated enzyme is a naturally occurring fusion: a NicA2 homolog fused to a cytochrome c at the enzyme's C-terminus, and its expression is currently in progress. Eight rationally designed variants based on conserved residues in known oxidases have been selected for mutagenesis and steady state kinetics. Additional information about the first half reaction with flavin has been elucidated by x-ray crystallography of a nicotine analog inhibitor complex. The structure, refined to 2.88 Å, shows good correspondence between positioning in the analog complex and the substrate complex structure which validates that the charge-transfer complex and spectral shift revealed in spectroscopic studies are mirroring steps along the reaction coordinate. Overall our study will elucidate how NicA2 and other cytochrome-dependent family members have evolved to interact with a cytochrome instead of O2, paving the way for the use of flavin-dependent enzymes in biosensing and bioremediation.

  PublisherDOI

• Abstract 2343 Functional Characterization and Inhibitor Screening of the Monotopic Phosphoglycosyl Transferase Superfamily Using a Novel Protein-Purification-Free Approach for Antibiotic Drug Discovery

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access

  The rise of antibiotic resistance has intensified the need for new bacterial targets for therapeutic intervention. Monotopic phosphoglycosyl transferases (monoPGTs), a class of exclusively prokaryotic membrane proteins that remain poorly understood, represent promising targets for pharmacological intervention against human pathogens, including Campylobacter jejuni and Streptococcus pneumoniae. MonoPGTs play a key role in glycoconjugate synthesis, which is crucial for bacterial pathogenesis. These enzymes initiate glycan biosynthesis by transferring a sugar-phosphate from a soluble nucleotide diphosphate sugar to a polyprenol phosphate acceptor in the membrane.

  PublisherOA PDFDOI

Recent grants

• Trehalose-6-phosphate phosphatase inhibitors as anti-helminthics

  NIH · $512k · 2016–2018

• Collaborative Research-Lanthanide Binding Tags: Chemical Tools for Investigating Protein Structure and Function

  NSF · $791k · 2008–2012

• NIH Grant P41RR012408

  NIH · $17.2M · 2013

• NIH Grant R01GM061099

  NIH · $3.2M · 2011

• MRI: Acquisition of Circular Dichroism (CD) Spectrometer

  NSF · $101k · 2011–2014

Frequent coauthors

• Debra Dunaway‐Mariano

  University of New Mexico

  106 shared

• Federico Martinón‐Torres

  Centro de Investigación Biomédica en Red de Enfermedades Respiratorias

  64 shared

• Barbara Imperiali

  Massachusetts Institute of Technology

  53 shared

• Michiel van der Flier

  53 shared

• N.R. Silvaggi

  University of Wisconsin–Milwaukee

  43 shared

• Ronald de Groot

  42 shared

• Michael Levin

  Royal College of Paediatrics and Child Health

  33 shared

• Marieke Emonts

  Newcastle University

  32 shared

Labs

• Allen GroupPI

Education

• Post-doctoral Associate, Chemistry

  Massachusetts Institute of Technology

  1990

• Ph.D., Biochemistry

  Brandeis University

  1989

• B.S., Biology

  Tufts University

  1984