About

Dan Kahne is the Higgins Professor of Chemistry and Chemical Biology at Harvard University and serves as the Department Chair of the Department of Chemistry and Chemical Biology. His research group is focused on addressing the problem of antibiotic resistance by developing new approaches to treat resistant bacterial infections. The group investigates the protein machines responsible for assembling the outer membrane that protects Gram-negative bacteria from toxic molecules. They have identified many components of these assembly machines and seek to elucidate their functions. A long-term goal of Kahne's research is to discover molecules that interfere with the assembly of the outer membrane, with particular interest in protein translocation, trafficking and assembly of lipopolysaccharide and beta barrel proteins, and cell wall biosynthesis.

Research topics

• Chemistry
• Biochemistry
• Biology
• Cell biology
• Biophysics
• Nanotechnology
• Materials science
• Crystallography
• Organic chemistry

Selected publications

• Structures of folding intermediates on BAM show diverse substrates fold by a conserved mechanism

  Proceedings of the National Academy of Sciences · 2026-04-02

  articleOpen accessSenior authorCorresponding

  The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multisubunit machines. In bacteria, the β-barrel assembly machine (BAM) folds over a hundred compositionally different substrates into barrels that vary greatly in size. Some larger barrels require globular proteins to plug the barrel lumen. How a single machine can assemble such different barrels is unknown. Here we report three structures representing progressively folded stages of a 16-stranded barrel engaged with BAM, as well as the structure of a late-stage folding intermediate of a 26-stranded substrate folding around its soluble lipoprotein plug on BAM. We find that BAM catalyzes folding of these substrates by a uniform mechanism in which BAM undergoes major distortions to accommodate the nascent barrel.

  PublisherDOI

• Structures of folding intermediates on BAM show diverse substrates fold by a uniform mechanism

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-17 · 1 citations

  preprintOpen accessSenior authorCorresponding

  The outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria contain β-barrel membrane proteins that are assembled by conserved multi-subunit machines. In bacteria, the β-barrel assembly machine (BAM) folds over a hundred compositionally different substrates into barrels that vary greatly in size. Some larger barrels require globular proteins to plug the barrel lumen. How a single machine can assemble such different barrels is unknown. Here we report three structures representing progressively folded stages of a 16-stranded barrel engaged with BAM, as well as the structure of a late-stage folding intermediate of a 26-stranded substrate folding around its soluble lipoprotein plug on BAM. We find that BAM catalyzes folding of these substrates by a uniform mechanism in which BAM undergoes major distortions to accommodate the nascent barrel.

  PublisherOA PDFDOI

• Inhibiting Lipopolysaccharide Biogenesis: The More You Know the Further You Go

  Annual Review of Biochemistry · 2025-06-20 · 10 citations

  reviewOpen accessSenior author

  Gram-negative bacteria are intrinsically resistant to many antibiotics because they are surrounded by an outer membrane that creates a robust permeability barrier. The outer membrane has an unusual asymmetric structure with a periplasmic leaflet composed of phospholipids and an outer leaflet composed of lipopolysaccharides. Because lipid biosynthesis is completed in the inner membrane of these didermic bacteria, these components must be transported across the cell envelope and properly assembled to expand the outer membrane during growth and division. Lipopolysaccharide molecules are transported over a multi-protein transenvelope bridge that is powered by ATP hydrolysis in the cytoplasm. This review discusses how this bridge is assembled and functions and how lipopolysaccharide transport is regulated to ensure balanced growth of all envelope layers. A combination of approaches and new experimental tools have significantly advanced our understanding of this molecular machine and contributed to the development of new antimicrobials that interfere with transport.

  PublisherDOI

• Determination of Initial Rates of Lipopolysaccharide Transport

  Biochemistry · 2024-09-12 · 2 citations

  articleOpen accessCorresponding

  Nonvesicular lipid trafficking pathways are an important process in every domain of life. The mechanisms of these processes are poorly understood in part due to the difficulty in kinetic characterization. One important class of glycolipids, lipopolysaccharides (LPS), are the primary lipidic component of the outer membrane of Gram-negative bacteria. LPS are synthesized in the inner membrane and then trafficked to the cell surface by the lipopolysaccharide transport proteins, LptB2FGCADE. By characterizing the interaction of a fluorescent probe and LPS, we establish a quantitative assay to monitor the flux of LPS between proteoliposomes on the time scale of seconds. We then incorporate photocaged ATP into this system, which allows for light-based control of the initiation of LPS transport. This control allows us to measure the initial rate of LPS transport (3.0 min–1 per LptDE). We also find that the rate of LPS transport by the Lpt complex is independent of the structure of LPS. In contrast, we find the rate of LPS transport is dependent on the proper function of the LptDE complex. Mutants of the outer membrane Lpt components, LptDE, that cause defective LPS assembly in live cells display attenuated transport rates and slower ATP hydrolysis compared to wild type proteins. Analysis of these mutants reveals that the rates of ATP hydrolysis and LPS transport are correlated such that 1.2 ± 0.2 ATP are hydrolyzed for each LPS transported. This correlation suggests a model where the outer membrane components ensure the coupling of ATP hydrolysis and LPS transport by stabilizing a transport-active state of the Lpt bridge.

  PublisherDOI

• Author Correction: A new antibiotic traps lipopolysaccharide in its intermembrane transporter

  Nature · 2024-01-10 · 3 citations

  erratumOpen accessSenior author
  PublisherOA PDFDOI

• Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-05-09

  preprintOpen accessSenior authorCorresponding

  Abstract The assembly of β-barrel proteins into membranes is mediated by the evolutionarily conserved BAM complex. In Escherichia coli , BAM folds numerous substrates which vary considerably in size and shape. How BAM is able to efficiently fold such a diverse array of β-barrel substrates is not clear. Here, we develop a disulfide crosslinking method to trap native substrates in vivo as they fold on BAM. By placing a cysteine within the luminal wall of the BamA barrel as well as in the substrate β-strands, we can compare the residence time of each substrate strand within the BamA lumen. We validated this method using two defective, slow-folding substrates. We used this method to characterize stable intermediates which occur during folding of two structurally different native substrates. Strikingly, these intermediates occur during identical stages of folding for both substrates: soon after folding has begun, and just before folding is completed. We suggest that these intermediates arise due to barriers to folding that are common between β-barrel substrates, and that the BAM catalyst is able to fold so many different substrates because it addresses these common challenges. Significance Statement The outer membrane of Gram-negative bacteria is a barrier which protects these organisms from many antimicrobial agents. Here, we study the machine responsible for folding and inserting integral β-barrel proteins into the membrane: BAM. Outer membrane integrity and cell viability is dependent on the proper function of BAM. Here we show that stable intermediates exist on the folding pathway of native substrates. We also show that mutant substrates that increase the stability of these native intermediates can stall during folding. This creates permeability defects that can be exploited by antibiotics that normally do not cross the outer membrane. These observations could enable the design of strategies to combat Gram-negative pathogens.

  PublisherOA PDFDOI

• Author Correction: A novel antibiotic class targeting the lipopolysaccharide transporter

  Nature · 2024-07-11 · 3 citations

  erratumOpen access
  PublisherOA PDFDOI

• Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex

  Proceedings of the National Academy of Sciences · 2024-10-08 · 9 citations

  articleOpen accessSenior author

  , BAM folds numerous substrates which vary considerably in size and shape. How BAM is able to efficiently fold such a diverse array of β-barrel substrates is not clear. Here, we develop a disulfide crosslinking method to trap native substrates in vivo as they fold on BAM. By placing a cysteine within the luminal wall of the BamA barrel as well as in the substrate β-strands, we can compare the residence time of each substrate strand within the BamA lumen. We validated this method using two defective, slow-folding substrates. We used this method to characterize stable intermediates which occur during folding of two structurally different native substrates. Strikingly, these intermediates occur during identical stages of folding for both substrates: soon after folding has begun and just before folding is completed. We suggest that these intermediates arise due to barriers to folding that are common between β-barrel substrates, and that the BAM catalyst is able to fold so many different substrates because it addresses these common challenges.

  PublisherOA PDFDOI

• A new antibiotic traps lipopolysaccharide in its intermembrane transporter

  Nature · 2024-01-03 · 149 citations

  articleOpen accessSenior author

  Abstract Gram-negative bacteria are extraordinarily difficult to kill because their cytoplasmic membrane is surrounded by an outer membrane that blocks the entry of most antibiotics. The impenetrable nature of the outer membrane is due to the presence of a large, amphipathic glycolipid called lipopolysaccharide (LPS) in its outer leaflet 1 . Assembly of the outer membrane requires transport of LPS across a protein bridge that spans from the cytoplasmic membrane to the cell surface. Maintaining outer membrane integrity is essential for bacterial cell viability, and its disruption can increase susceptibility to other antibiotics 2–6 . Thus, inhibitors of the seven lipopolysaccharide transport (Lpt) proteins that form this transenvelope transporter have long been sought 7–9 . A new class of antibiotics that targets the LPS transport machine in Acinetobacter was recently identified. Here, using structural, biochemical and genetic approaches, we show that these antibiotics trap a substrate-bound conformation of the LPS transporter that stalls this machine. The inhibitors accomplish this by recognizing a composite binding site made up of both the Lpt transporter and its LPS substrate. Collectively, our findings identify an unusual mechanism of lipid transport inhibition, reveal a druggable conformation of the Lpt transporter and provide the foundation for extending this class of antibiotics to other Gram-negative pathogens.

  PublisherOA PDFDOI

• Author Correction: A new antibiotic traps lipopolysaccharide in its intermembrane transporter

  Nature · 2024-07-11 · 1 citations

  erratumOpen accessSenior author
  PublisherOA PDFDOI

Recent grants

• NIH Grant R01GM042733

  NIH · $3.0M · 2002

• NIH Grant R01GM066174

  NIH · $8.9M · 2019

• Outer Membrane Biogenesis: New Antibiotic Targets

  NIH · $9.5M · 2008–2029

• Discovery and characterization of new bacterial cell wall targets and inhibitors to treat resistant infections

  NIH · $5.5M · 2020–2029

• Innovative Platforms for Antimicrobial Therapy and Vaccine Development

  NIH · $50.4M · 2014–2019

Frequent coauthors

• Suzanne Walker

  Harvard University

  86 shared

• Christopher T. Walsh

  Met Office

  55 shared

• Markus Oberthür

  HAW Hamburg

  42 shared

• Thomas J. Silhavy

  Princeton University

  31 shared

• Catherine Leimkuhler

  Harvard University

  31 shared

• Natividad Ruiz

  The Ohio State University

  30 shared

• Thomas G. Bernhardt

  Howard Hughes Medical Institute

  17 shared

• Wei Lü

  Shanghai Jiao Tong University

  16 shared

Labs

• Kahne GroupPI

Education

• Ph.D., Chemistry

  Harvard University

  1995

• B.S., Chemistry

  University of California, Berkeley

  1990