Publications by authors named "Barbara T Amann"

5 Publications

  • Page 1 of 1

SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins.

Proc Natl Acad Sci U S A 2020 11 22;117(45):28026-28035. Epub 2020 Oct 22.

Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218;

The periplasmic chaperone network ensures the biogenesis of bacterial outer membrane proteins (OMPs) and has recently been identified as a promising target for antibiotics. SurA is the most important member of this network, both due to its genetic interaction with the β-barrel assembly machinery complex as well as its ability to prevent unfolded OMP (uOMP) aggregation. Using only binding energy, the mechanism by which SurA carries out these two functions is not well-understood. Here, we use a combination of photo-crosslinking, mass spectrometry, solution scattering, and molecular modeling techniques to elucidate the key structural features that define how SurA solubilizes uOMPs. Our experimental data support a model in which SurA binds uOMPs in a groove formed between the core and P1 domains. This binding event results in a drastic expansion of the rest of the uOMP, which has many biological implications. Using these experimental data as restraints, we adopted an integrative modeling approach to create a sparse ensemble of models of a SurA•uOMP complex. We validated key structural features of the SurA•uOMP ensemble using independent scattering and chemical crosslinking data. Our data suggest that SurA utilizes three distinct binding modes to interact with uOMPs and that more than one SurA can bind a uOMP at a time. This work demonstrates that SurA operates in a distinct fashion compared to other chaperones in the OMP biogenesis network.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2008175117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668074PMC
November 2020

Identification of nucleic acid binding residues in the FCS domain of the polycomb group protein polyhomeotic.

Biochemistry 2011 Jun 12;50(22):4998-5007. Epub 2011 May 12.

Department of Biochemistry, University of Texas Health Science Center at San Antonio, MSC 7760, San Antonio, Texas 78229-3990, United States.

Polycomb group (PcG) proteins maintain the silent state of developmentally important genes. Recent evidence indicates that noncoding RNAs also play an important role in targeting PcG proteins to chromatin and PcG-mediated chromatin organization, although the molecular basis for how PcG and RNA function in concert remains unclear. The Phe-Cys-Ser (FCS) domain, named for three consecutive residues conserved in this domain, is a 30-40-residue Zn(2+) binding motif found in a number of PcG proteins. The FCS domain has been shown to bind RNA in a non-sequence specific manner, but how it does so is not known. Here, we present the three-dimensional structure of the FCS domain from human Polyhomeotic homologue 1 (HPH1, also known as PHC1) determined using multidimensional nuclear magnetic resonance methods. Chemical shift perturbations upon addition of RNA and DNA resulted in the identification of Lys 816 as a potentially important residue required for nucleic acid binding. The role played by this residue in Polyhomeotic function was demonstrated in a transcription assay conducted in Drosophila S2 cells. Mutation of the Arg residue to Ala in the Drosophila Polyhomeotic (Ph) protein, which is equivalent to Lys 816 in HPH1, was unable to repress transcription of a reporter gene to the level of wild-type Ph. These results suggest that direct interaction between the Ph FCS domain and nucleic acids is required for Ph-mediated repression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi101487sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938326PMC
June 2011

The design of functional DNA-binding proteins based on zinc finger domains.

Chem Rev 2004 Feb;104(2):789-99

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/cr020603oDOI Listing
February 2004

Solution structure of a CCHHC domain of neural zinc finger factor-1 and its implications for DNA binding.

Biochemistry 2004 Feb;43(4):898-903

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

The structure of a CCHHC zinc-binding domain from neural zinc finger factor-1 (NZF-1) has been determined in solution though the use of NMR methods. This domain is a member of a family of domains that have the Cys-X(4)-Cys-X(4)-His-X(7)-His-X(5)-Cys consensus sequence. The structure determination reveals a novel fold based around a zinc(II) ion coordinated to three Cys residues and the second of the two conserved His residues. The other His residue is stacked between the metal-coordinated His residue and a relatively conserved aromatic residue. Analysis of His to Gln sequence variants reveals that both His residues are required for the formation of a well-defined structure, but neither is required for high-affinity metal binding at a tetrahedral site. The structure suggests that a two-domain protein fragment and a double-stranded DNA binding site may interact with a common two-fold axis relating the two domains and the two half-sites of the DNA-inverted repeat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi035159dDOI Listing
February 2004

A Cys3His zinc-binding domain from Nup475/tristetraprolin: a novel fold with a disklike structure.

Biochemistry 2003 Jan;42(1):217-21

Department of Biophysics and Biophysical Chemistry, 713 WBSB, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

Nup475 (also known as tristetraprolin and TIS11) includes two zinc-binding domains of the form Cys-X8-Cys-X5-Cys-X3-His. These domains are required for rapid degradation of tumor necrosis factor (TNF) and other mRNAs through the interaction with AU-rich elements in their 3'-untranslated regions. The three-dimensional solution structure of the first domain was determined by multidimensional nuclear magnetic resonance spectroscopy, revealing a novel fold around a central zinc ion. The core structure is disk-like with a diameter of approximately 25 A and a width of approximately 12 A. This structure provides a basis for evaluating the role of individual residues for structural stability and for nucleic acid binding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi026988mDOI Listing
January 2003