About

Keisha-Khan Y. Perry is the Africana Studies Graduate Chair and the Presidential Penn Compact Associate Professor of Africana Studies at the University of Pennsylvania. She previously served as an Associate Professor of Africana Studies at Brown University. Her research focuses on race, gender, and politics in the Americas, urban geography, questions of citizenship, intellectual history, disciplinary formation, and the interrelationship between scholarship, pedagogy, and political engagement. Her first book, Black Women against the Land Grab: The Fight for Racial Justice in Brazil, received the 2014 National Women’s Studies Association Gloria Anzaldúa Book Prize. She is currently working on her second book, which examines how state violence limits activist research and writing.

Research topics

• Biochemistry
• Biology
• Chemistry
• Immunology
• Cell biology
• Genetics
• Virology
• Computational biology

Selected publications

• RAPD2: Rapid Automated Processing of Macromolecular Crystallographic Data 2

  Structural Dynamics · 2025-09-01

  articleOpen access

  RAPD2 is a modular package of programs written for the automated processing of macromolecular crystallographic data at the NE-CAT beamlines. It monitors for collected data, processes snapshots to create strategies for data collection, processes data runs for structure solution, and can then solve the structure using molecular replacement or single-wavelength anomalous diffraction with results stored in a MongoDB. Most of the backend code is written in Python3 with an AngularJS based frontend. This allows users to login with a web browser to view results, modify settings and rerun jobs, or launch additional pipelines (see Kay Perry). The RAPD2 code is designed to be modular on multiple levels. With a variety of possible experimental and computing environments in mind, RAPD2 is separated into several interdependent modules. At the highest level, X-Ray source monitoring (Monitors), core data handling and archiving (Control), and job launching (Launch) can be started through the Control or separated into distinct programs that communicate by passing Python objects over standard TCP sockets or Redis Streams. This allows flexibility in setup; for example, RAPD was developed on a single computer, so the Control and the Launch programs initially ran on a single machine; when a computational cluster was later acquired, the Launch module was moved with minimal changes to either program. On a deeper level, the code is divided into functionally distinct modules. For example, each pipeline is self-contained and called by a launch adapter when needed, allowing nimble development (i.e. bug fixes) that do not require any program restarting to take effect. Additional benefits of the built-in modularity are that all site-specific settings and functions are isolated as much as possible to one module (Site), so adapting RAPD to a new experimental environment is relatively simple. At NE-CAT, Redis Streams are used for communication between the beamline and the RAPD2 Monitors; however this can be modified to suit different environments at other facilities. The Monitors save the beamline information in MongoDB and pass it to Control, where the strategy or data processing commands are generated. These commands are sent to a Launch manager that decides where to launch the job based on Site settings. This provides flexibility in launching jobs on specific machines using a shell launch adapter or on a computer cluster with launch adapters for various cluster workload managers including SLURM, SGE, and PBS. For strategy commands, the index pipeline is launched, where six Labelit autoindexing jobs are started simultaneously with different peak pick settings, each optimized for different types of diffraction data. Once the best solution is determined, Raddose is run to calculate radiation damage parameters, which are input to BEST for the regular and anomalous data collection strategies. This pipeline takes approximately 30s to complete, and results are displayed in the UI. The index pipeline is modular, so other auto-index, radiation damage, or strategy programs can be launched through different plugins. For data runs, the integration pipeline is launched running XDS multiple times to optimize the results. This pipeline takes a few minutes to finish, and results are displayed in the UI. A new mintegrate pipeline will additionally launch data processing in autoPROC, Fast DP, and XIA2, with results from all 4 data processing programs displayed in the UI for comparison.

  PublisherOA PDFDOI

• A nut-and-bolt assembly of the bimodular large progenitor botulinum neurotoxin complex

  Science Advances · 2025-08-27 · 2 citations

  articleOpen access

  Botulinum neurotoxin serotype A (BoNT/A) is naturally produced by bacteria along with four nontoxic neurotoxin-associated proteins (NTNH, HA70, HA33, and HA17), forming a bimodular large progenitor toxin complex (L-PTC). The BoNT/A-NTNH complex protects the toxin from adverse environment, while the complex consisting of HA proteins facilitates toxin absorption during oral intoxication. How these two independent modules assemble into the L-PTC remains unclear. Here, we report the crystal structure of the BoNT/A-NTNH-HA70 complex at ~2.9-Å resolution. The structure reveals that the BoNT/A-NTNH complex is anchored into a concentric double β-barrel channel of trimeric HA70 through a short β-hairpin of NTNH (termed nLoop), resembling a nut-and-bolt attachment. We find that the nLoop of NTNH is strictly conserved across HA-containing BoNT complexes and that NTNH-HA70 binding is interchangeable among them. Furthermore, we demonstrate that the nLoop functions as a minimal motif enabling attachment of a protein-of-interest to the HA complex, with potential applications in oral biologics delivery.

  PublisherDOI

• Structural and Functional Characterization of a Novel Class A Flavin Monooxygenase from <i>Bacillus niacini</i>

  Biochemistry · 2024-09-12

  articleOpen access

  A gene cluster responsible for the degradation of nicotinic acid (NA) in Bacillus niacini has recently been identified, and the structures and functions of the resulting enzymes are currently being evaluated to establish pathway intermediates. One of the genes within this cluster encodes a flavin monooxygenase (BnFMO) that is hypothesized to catalyze a hydroxylation reaction. Kinetic analyses of the recombinantly purified BnFMO suggest that this enzyme catalyzes the hydroxylation of 2,6-dihydroxynicotinic acid (2,6-DHNA) or 2,6-dihydroxypyridine (2,6-DHP), which is formed spontaneously by the decarboxylation of 2,6-DHNA. To understand the details of this hydroxylation reaction, we determined the structure of BnFMO using a multimodel approach combining protein X-ray crystallography and cryo-electron microscopy (cryo-EM). A liganded BnFMO cryo-EM structure was obtained in the presence of 2,6-DHP, allowing us to make predictions about potential catalytic residues. The structural data demonstrate that BnFMO is trimeric, which is unusual for Class A flavin monooxygenases. In both the electron density and coulomb potential maps, a region at the trimeric interface was observed that was consistent with and modeled as lipid molecules. High-resolution mass spectral analysis suggests that there is a mixture of phosphatidylethanolamine and phosphatidylglycerol lipids present. Together, these data provide insights into the molecular details of the central hydroxylation reaction unique to the aerobic degradation of NA in Bacillus niacini.

  PublisherOA PDFDOI

• An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa

  Proceedings of the National Academy of Sciences · 2024-07-10 · 13 citations

  articleOpen access

  Hemostasis relies on a reaction network of serine proteases and their cofactors to form a blood clot. Coagulation factor IXa (protease) plays an essential role in hemostasis as evident from the bleeding disease associated with its absence. RNA aptamers specifically targeting individual coagulation factors have potential as anticoagulants and as probes of the relationship between structure and function. Here, we report X-ray structures of human factor IXa without a ligand bound to the active site either in the apo-form or in complex with an inhibitory aptamer specific for factor IXa. The aptamer binds to an exosite in the catalytic domain and allosterically distorts the active site. Our studies reveal a conformational ensemble of IXa states, wherein large movements of Trp 215 near the active site drive functional transitions between the closed (aptamer-bound), latent (apo), and open (substrate-bound) states. The latent state of the apo-enzyme may bear on the uniquely poor catalytic activity of IXa compared to other coagulation proteases. The exosite, to which the aptamer binds, has been implicated in binding VIIIa and heparin, both of which regulate IXa function. Our findings reveal the importance of exosite-driven allosteric modulation of IXa function and new strategies to rebalance hemostasis for therapeutic gain.

  PublisherOA PDFDOI

• Structural basis for antibody recognition of the proximal MUC16 ectodomain

  Journal of Ovarian Research · 2024-02-19 · 6 citations

  articleOpen access

  Abstract Background Mucin 16 (MUC16) overexpression is linked with cancer progression, metastasis, and therapy resistance in high grade serous ovarian cancer and other malignancies. The cleavage of MUC16 forms independent bimodular fragments, the shed tandem repeat sequence which circulates as a protein bearing the ovarian cancer biomarker (CA125) and a proximal membrane-bound component which is critical in MUC16 oncogenic behavior. A humanized, high affinity antibody targeting the proximal ectodomain represents a potential therapeutic agent against MUC16 with lower antigenic potential and restricted human tissue expression. Results Here, we demonstrate the potential therapeutic versatility of the humanized antibody as a monoclonal antibody, antibody drug conjugate, and chimeric antigen receptor. We report the crystal structures of 4H11-scFv, derived from an antibody specifically targeting the MUC16 C-terminal region, alone and in complex with a 26-amino acid MUC16 segment resolved at 2.36 Å and 2.47 Å resolution, respectively. The scFv forms a robust interaction with an epitope consisting of two consecutive β-turns and a β-hairpin stabilized by 2 hydrogen bonds. The V H -V L interface within the 4H11-scFv is stabilized through an intricate network of 11 hydrogen bonds and a cation-π interaction. Conclusions Together, our studies offer insight into antibody-MUC16 ectodomain interaction and advance our ability to design agents with potentially improved therapeutic properties over anti-CA125 moiety antibodies.

  PublisherOA PDFDOI

• Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2

  Nature Communications · 2023-04-24 · 20 citations

  articleOpen access

  Abstract Botulinum neurotoxin E (BoNT/E) is one of the major causes of human botulism and paradoxically also a promising therapeutic agent. Here we determined the co-crystal structures of the receptor-binding domain of BoNT/E (H C E) in complex with its neuronal receptor synaptic vesicle glycoprotein 2A (SV2A) and a nanobody that serves as a ganglioside surrogate. These structures reveal that the protein-protein interactions between H C E and SV2 provide the crucial location and specificity information for H C E to recognize SV2A and SV2B, but not the closely related SV2C. At the same time, H C E exploits a separated sialic acid-binding pocket to mediate recognition of an N-glycan of SV2. Structure-based mutagenesis and functional studies demonstrate that both the protein-protein and protein-glycan associations are essential for SV2A-mediated cell entry of BoNT/E and for its potent neurotoxicity. Our studies establish the structural basis to understand the receptor-specificity of BoNT/E and to engineer BoNT/E variants for new clinical applications.

  PublisherOA PDFDOI

• Ligand bound structure of a 6‐hydroxynicotinic acid 3‐monooxygenase provides mechanistic insights

  Archives of Biochemistry and Biophysics · 2023-12-15 · 2 citations

  articleOpen access
  PublisherOA PDFDOI

• Crystal structures of <scp>OrfX1</scp>, <scp>OrfX2</scp> and the <scp>OrfX1</scp>–<scp>OrfX3</scp> complex from the <scp><i>orfX</i></scp> gene cluster of botulinum neurotoxin <scp>E1</scp>

  FEBS Letters · 2023-01-19 · 11 citations

  articleOpen access

  Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A-G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1-OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

  PublisherOA PDFDOI

• Advancing crystallography research: the latest progress and future directions of NE-CAT beamlines at the Advanced Photon Source

  Acta Crystallographica Section A Foundations and Advances · 2023-07-07

  articleOpen access

  The Northeastern Collaborative Access Team (NE-CAT) designs and operates synchrotron X-ray beamlines for solving technically challenging structural biology problems.Our state-of-the-art instrumentation and expertise provide critical resources for the national and international research community.Currently, we operate two undulator beamlines: a tunable energy beamline (24-ID-C) that can deliver X-rays from 6-22 keV, and a single-energy beamline (24-ID-E) that operates at 12.662 keV.Both beamlines are designed for remote operations and are equipped with MD2 micro diffractometers, custom-built ALS-style robotic sample automounters with dewars capable of holding up to 14 pucks, and a locally developed software suite RAPD, which provides data collection strategies, integration, scaling, and a simple automated MR/SAD.Our experienced NE-CAT team supports our users 24/7, and they can securely download their data using Globus, sftp, or a custom Python script.The Advanced Photon Source upgrade (APS-U) is underway, and our goal is to provide a faster, more flexible, and reliable data collection experience for the structural biology community.To achieve this, we are implementing several upgrades during the APS-U period, including a new monochromator for the C-beamline, MD3 micro diffractometers, a custom-built sample automounter with a 30-puck capacity, a more flexible design for the remote user interface with fully automated data collection, and RAPDv2, a faster and redesigned data processing software suite.Additionally, we are increasing our capabilities for room-temperature data collection experiments.

  PublisherOA PDFDOI

• Abstract 1256: The surface-specific antigenic peptide designs of HPIV-type 2 Hemagglutinin-Neuraminidase and Fusion protein for anti-viral immunotherapy drug development

  Journal of Biological Chemistry · 2023-01-01 · 1 citations

  articleOpen accessSenior author
  PublisherDOI

Frequent coauthors

• Rongsheng Jin

  University of California, Irvine

  49 shared

• Kwok Ho Lam

  30 shared

• Gregory D. Van Duyne

  University of Pennsylvania

  28 shared

• Andreas Rummel

  Medizinische Hochschule Hannover

  27 shared

• Min Dong

  Boston Children's Hospital

  24 shared

• Kwangkook Lee

  Massachusetts General Hospital

  18 shared

• Guorui Yao

  13 shared

• Kanagalaghatta R. Rajashankar

  Cornell University

  13 shared

Awards & honors

• 2014 National Women’s Studies Association Gloria Anzaldúa Bo…