One if by editing, two if by roadblock: Human protein fights HIV as monomer and dimer

October 12, 2017, Northeastern University
Research recently published in Nature Communications examines the capabilities of a human protein that inhibits HIV-1, APOBEC3G (A3G). The paper highlights the work of Northeastern Physics Professor and Chair Mark Williams, postdoctoral researcher Mike Morse, Professor Linda Chelico, University of Saskatchewan in Canada, and Ioulia Rouzina, Ohio State University. Credit: Mike Morse/Northeastern University

Fifteen years ago, a class of proteins was discovered, which give humans innate immunity to HIV-1. Unfortunately, HIV-1 is a smart virus and has evolved to battle these proteins. Northeastern researchers, with help from their collaborators, have been studying these proteins for several years to help further understand their function and mechanisms in the hopes to be better prepared against HIV-1.

The research, published in Nature Communications, highlights the work of Northeastern Physics Professor and Chair Mark Williams, postdoctoral researcher Mike Morse, Professor Linda Chelico, University of Saskatchewan in Canada, and Ioulia Rouzina, Ohio State University. The paper examines on the capabilities of a human protein that inhibits HIV-1, APOBEC3G (A3G).

Their findings determined that when the A3G protein grows from a single protein (monomer) to a two-protein complex (dimer), its function is transformed from being an editing protein that mutates viral DNA to acting as a roadblock for further replication of the virus.

"I was completely surprised by the result that dimers were sufficient to do this," said Williams. "We got our data, and the data told us this, but it took us a long time to realize that the only way to understand this data is that dimers must be the model for the protein's properties to suddenly change."

The Williams Laboratory for Single Molecule Biophysics specializes in instruments called optical tweezers that study molecules such as single DNA molecules or DNA-protein complexes. This tool holds DNA or RNA between two polystyrene beads to look at interactions with the DNA by observing changes in its length and tension. Using this technique, the lab studies many different biological systems including HIV-1 replication. A combination of these biophysical methods with the enzyme activity experiments and creation of mutant forms of A3G by the Chelico lab allowed for Williams and Morse to compare the original form of the protein with different mutants containing structural changes. This allowed for the isolation of the process that resulted in stably bound dimerized protein.

For the past 12 years, the Williams lab has been studying HIV-1 replication with help from an NIH grant. Their most recent project involves understanding the innate immune proteins that give humans immunity to HIV-1. There are seven proteins in the APOBEC3 family, some of which battle retroviruses like HIV-1, while others battle retrotransposons, which are genetic elements that amplify themselves within a genome and have potential to cause disease.

All APOBEC proteins are cytidine deaminases, allowing them to modify single-stranded DNA to replace bases, causing mutations when the strand is replicated. However, A3G also has another function that does quite the opposite. Rather than quickly zipping along the genome making edits, it can become a stable binding protein that inhibits the reverse transcription process from occurring, preventing HIV-1 replication. This happens because of a process called oligomerization, where single protein units (monomers) join together to create multi-protein complexes or oligomers.

"The idea that you could be zooming along and making these changes, and yet also be blocking something else from moving, didn't really make sense," said Williams. "That's why the oligomerization is so important. As they start off fast and move along, over time they oligomerize and become very slow."

This team of researchers discovered the oligomerization as published in their 2014 paper in Nature Chemistry. Their study showed that the growth of a multi-protein complex caused the protein to slow down, but it was not known how many proteins were required to make a slow complex. If the number was high, the results might not be relevant for viral replication. In addition, they could show that the complexes were slow, but they could not tell if the slow complexes had enzyme activity. But now their new research has found the answers to these two critical questions.

"Between our experiments where we directly observed the binding of proteins onto DNA, and Professor Chelico's work looking into the enzymatic activity of A3G, we found that on short time scales in the monomeric form, the protein binds and dissociates very rapidly from DNA and has high enzymatic activity," said Morse. "But once you let it form these oligomers, the binding is much more stable, and doesn't dissociate as readily. Professor Chelico was able to find that the enzymatic activity actually decreases when this process occurs so you have these two functions - the which occurs on one-time scale, and in one form, and this secondary function that, due to the oligomerization, occurs on another timescale."

Their research showed that this happens even if just two proteins come together, forming a dimer. The dimer is enough to make the protein complex stable and alter the protein's function. Since only a dimer is needed, multiple roadblocks could be acting to prevent reverse transcription from occurring. Now, this important function is more likely to be biologically relevant.

"Knowing how something inhibits HIV-1 could be a guide to helping design new methods for anti-HIV drugs. The HIV-1 virus has developed its own protein to trick the cell into degrading APOBEC proteins, so if we can figure out how to stop that degradation, maybe we'd be able to enhance the ability of this to inhibit HIV-1," Williams said.

The Williams Lab at Northeastern University plans on continuing to study the different APOBEC proteins, others of which inhibit HIV-1 or retrotransposons. Through studying these proteins with their unique biophysical measurement tools, their lab hopes to understand the proteins' regulation, activity, and processes to help us to be further prepared against HIV and other related diseases.

Explore further: A new way to battle HIV: 3 questions with Mark Williams

More information: Michael Morse et al, Dimerization regulates both deaminase-dependent and deaminase-independent HIV-1 restriction by APOBEC3G, Nature Communications (2017). DOI: 10.1038/s41467-017-00501-y

Related Stories

A new way to battle HIV: 3 questions with Mark Williams

December 3, 2013

More than 35 million people around the world now live with HIV/AIDS. While drug discovery efforts to combat the disease have been successful, multiple treatments are required because the virus mutates and develops resistance ...

Bonding together to fight HIV

November 25, 2013

A collaborative team led by a Northeastern University professor may have altered the way we look at drug development for HIV by uncovering some unusual properties of a human protein called APOBEC3G (A3G).

Self-assembling cyclic protein homo-oligomers

May 10, 2017

Cyclic proteins that assemble from multiple identical subunits (homo-oligomers) play key roles in many biological processes, including cell signaling and enzymatic catalysis and protein function. Researchers in Berkeley Lab's ...

Team identifies structure of tumor-suppressing protein

August 20, 2015

An international group of researchers led by Carnegie Mellon University physicists Mathias Lösche and Frank Heinrich have established the structure of an important tumor suppressing protein, PTEN. Their findings provide ...

Sendai virus defends against a threat

October 15, 2015

A research group at Hiroshima University demonstrated the mechanism by which the Sendai virus (SeV) escapes the host immune system. The researchers examined the crystal structure of the complex of SeV C protein and transcription ...

Recommended for you

Wearable device measures cortisol in sweat

July 20, 2018

The hormone cortisol rises and falls naturally throughout the day and can spike in response to stress, but current methods for measuring cortisol levels require waiting several days for results from a lab. By the time a person ...

Researchers report two-faced Janus membrane applications

July 20, 2018

Named for the mythical god with two faces, Janus membranes—double-sided membranes that serve as gatekeepers between two substances—have emerged as a material with potential industrial uses. Creating two distinct "faces" ...

Chemists characterize the fatal fungus among us

July 19, 2018

Life-threatening fungal infections affect more than two million people worldwide. Effective antifungal medications are very limited. Until now, one of the major challenges is that the fungal cell wall is poorly understood, ...

Infrared sensor as new method for drug discovery

July 19, 2018

Using an infrared sensor, biophysicists at Ruhr-Universität Bochum (RUB) have succeeded in analysing quickly and easily which active agents affect the structure of proteins and how long that effect lasts. Thus, Prof Dr. ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.