Research

The Berndsen lab is interested in two areas: the enzymatic mechanisms of acyl transfer and viral tethering by the protein Tetherin. Lab projects on these topics use a variety of techniques and approaches from measurement of enzyme activity to observing protein structure through X-ray crystallography and computational methods.

We also work with collaborators on and off campus to help answer questions involving protein structure and function.

There are several opportunities for undergraduate students to perform research in the lab both during the academic year and summer, please contact Dr. Berndsen for more information.

A complete list of publications from the Berndsen lab.

The Berndsen lab is also associated with the JMU Center for Genome and Metagenome Studies.

Enzymatic Mechanism of Acyl Transfer

Cellular proteins are often modified with chemical moieties such as phosphate or methyl groups in order to alter the function of these proteins in response to changes in the environment or during the cell cycle. Two of these post-translational modifications, acetylation and ubiquitination, involve a reaction of a thioester with an amine. While the reaction chemistry is straightforward, the enzymatic mechanism of transfer is not clear and there are a variety of protein structures that can do this chemistry. We aim to determine the catalytic mechanism of these enzymes via biochemical and structural methods to understand:

• how substrates bind
• the enzyme increases the rate of the reaction
• the role of changes in the enzyme structure in the reaction chemistry
• how substrate specificity is encoded by the enzyme.

Current projects are focused on ubiquitin/ubiquitin-like activating enzymes, cleavage of ubiquitin precursors, and enzymatic modification of protein lysines by acetyltransferases.

Previous work by the lab on this project:

(undergraduate authors are indicated by a *)

Padala P, Oweis W, Mashahreh B, Soudah N, Cohen-Kfir E, Todd EA*, Berndsen CE, Wiener R. Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Sci Rep. 2017 Mar 30;7(1):508. doi: 10.1038/s41598-017-00610-0. PubMed PMID: 28360427

Young BH*, Caldwell TA*, McKenzie AM*, Kokhan O, Berndsen CE. (2016) Characterization of the structure and catalytic activity of Legionella pneumophila VipF. Proteins. Oct;84(10):1422-30. doi: 10.1002/prot.25087. PMID: 27315603

Oweis W, Padala P, Hassouna F, Cohen-Kfir E, Gibbs DR*, Todd EA*, Berndsen CE, Wiener R. (2016) Trans-Binding Mechanism of Ubiquitin-like Protein Activation Revealed by a UBA5-UFM1 Complex. Cell Rep. Sep 20;16(12):3113-20. doi: 10.1016/j.celrep.2016.08.067. PMID: 27653677

Viral Tethering by human Tetherin

All humans contain a simple protein known as BST-2 or Tetherin which has the innate ability to latch onto budding viruses and tether the virus to the host cell membrane. Other than a mechanical tether, there are no known functions for Tetherin and it is not exactly clear how this protein functions. We combine biophysical and computational approaches to determine the structural mechanism of viral tethering and how viral antagonists block the function of Tetherin

Previous work by the lab on this project:

(undergraduate authors are indicated by a *)

Ozcan KA*, Berndsen CE Bending of the BST-2 coiled-coil during viral budding. (2017) Proteins. 2017 Aug 4. doi: 10.1002/prot.25362.

Du Pont KE*, McKenzie AM*, Kokhan O, Sumner I, Berndsen CE. (2016) The Disulfide Bonds within BST-2 Enhance Tensile Strength during Viral Tethering. Biochemistry. Feb 16;55(6):940-7. doi: 10.1021/acs.biochem.5b01362.

Welbourn S, Kao S, Du Pont KE*, Andrew AJ, Berndsen CE, Strebel K. (2015) Positioning of cysteine residues within the N-terminal portion of the BST-2/tetherin ectodomain is important for functional dimerization of BST-2. J Biol Chem. Feb 6;290(6):3740-51. doi: 10.1074/jbc.M114.617639. PMID: 25525265

Support and Funding from

• National Science Foundation
• Jeffress Memorial Trust for Interdisciplinary Research
• 4-VA organization
• Hamilton Syringe Company
• U.S.-Israel Binational Science Foundation