Harris D. Bernstein, Ph.D.

Senior Investigator

Protein Biogenesis Section, Genetics & Biochemistry Branch


Building NIHBC 05, Room B1-20
5 Memorial Dr
Bethesda, MD 20892

+1 301 402 4770


Research Topics

My laboratory has a long-standing interest in understanding how proteins are inserted into or transported across the cell membranes of both pathogenic and non-pathogenic bacteria.

Current Research

In one project we are investigating the assembly (folding and membrane insertion) of proteins that reside in the outer membrane of Gram-negative bacteria. While most integral membrane proteins contain one or more α-helical membrane spanning segments, bacterial outer membrane proteins are anchored to the membrane by a single amphipathic β sheet that folds into a distinctive closed cylindrical structure called a “β barrel”. Previous studies have shown that a highly conserved and essential heterooligomer (the barrel assembly machinery or “Bam” complex) catalyzes the integration of β barrels into the outer membrane, but the mechanism by which it promotes insertion is unknown. Several lines of evidence indicate that the BamA subunit, an integral outer membrane protein that contains both a β barrel and several periplasmic domains that tether the other subunits, plays a central role in the insertion reaction. To gain further insight into outer membrane protein biogenesis, we recently developed a method to arrest the assembly of a native β barrel before it dissociates from the Bam complex and solved the structure of the purified Bam complex-substrate supercomplex by cryo-EM. The results showed that the BamA β barrel binds to the C-terminus of the substrate and then promotes its progressive conversion from an open β sheet to a barrel-like structure in a remarkable process that is influenced by membrane tension. Although we have focused on the assembly of a specific class of outer membrane proteins produced by pathogenic bacteria called “autotransporters” that contain a large N-terminal extracellular domain that encodes a virulence function in addition to a C-terminal β barrel, we are interested in studying the assembly of other classes of outer membrane proteins using biochemical, genetic and structural methods.

In a second project we are studying protein secretion by the Bacteroides, a genus of experimentally tractable Gram-negative bacteria that are highly abundant in the human gut microbiome. Although recent studies have suggested that these organisms influence human health significantly, their biology remains poorly understood. We recently found that one member of the Bacteroides genus, B. fragilis, utilizes a very different range of secretion strategies than well characterized Gram-negative bacteria such as E. coli. B. fragilis lacks several of the secretion pathways found in E. coli, and unlike E. coli transports a large number of lipoproteins to the cell surface. We also found that B. fragilis secretes a variety of unique proteins of unknown function. Presumably many of these proteins play important roles in colonization, persistence or communication with other microorganisms. By studying protein secretion in the Bacteroides we hope to gain insight into the remarkable ability of these organisms to thrive in a complex and potentially hostile environment.

Applying our Research

Both natural and synthetic compounds that exhibit strong antimicrobial activity have recently been described that inhibit the activity of the Bam complex and provide a “proof of concept” that this essential factor is a promising target for the development of a novel class of antibiotics that could help to combat the rise of multidrug-resistant Gram-negative “superbugs”. Our studies may lead to strategies to isolate additional Bam complex inhibitors and to optimize the lead compounds that have already been isolated. Furthermore, our work on autotransporters may accelerate the development of vaccines against specific bacterial pathogens. Autotransporters are excellent vaccine candidates because they contain a large extracellular domain, and one autotransporter (pertactin) is already in use in pertussis vaccines. Our studies on autotransporters may also lead to improvements in “autodisplay” technology, a method in which autotransporters are used for the cell surface presentation of heterologous peptides or proteins. Autodisplay has proven to be a valuable alternative to phage-display technology and may ultimately be useful as a method to present antigens to induce immune protection. Finally, our work on Bacteroides may facilitate the construction of genetically engineered strains that secrete beneficial proteins into the colon and that can be used to treat illnesses such as inflammatory bowel disease.


  • Ph.D., Massachusetts Institute of Technology, 1987
  • B.A., Harvard University, 1980

Selected Publications

  1. Doyle MT, Jimah JR, Dowdy T, Ohlemacher SI, Larion M, Hinshaw JE, Bernstein HD. Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. Cell. 2022;185(7):1143-1156.e13.
  2. Sikdar R, Peterson JH, Anderson DE, Bernstein HD. Folding of a bacterial integral outer membrane protein is initiated in the periplasm. Nat Commun. 2017;8(1):1309.
  3. Roman-Hernandez G, Peterson JH, Bernstein HD. Reconstitution of bacterial autotransporter assembly using purified components. Elife. 2014;3:e04234.

Related Scientific Focus Areas

This page was last updated on Wednesday, May 1, 2024