Our group reveals details of how HIV-1 becomes infectious.

The article “Dynamic Regulation of HIV-1 Capsid Interaction with the Restriction Factor TRIM5α” was published Oct. 17 in the Proceedings of the National Academy of Sciences.

In addition to Quinn, Polenova and Perilla, the authors are Mingzhang Wang, Matthew P. Fritz, Brent Runge and Chaoyi Xu, all doctoral students at UD, and Jinwoo Ahn and Angela M. Gronenborn of the Pittsburgh Center for HIV Protein Interactions and the Department of Structural Biology at the University of Pittsburgh School of Medicine.

Gronenborn is a University of Pittsburgh School of Medicine Rosalind Franklin Professor and chair of the Department of Structural Biology. She is the director of the National Institutes of Health-funded Pittsburgh Center for HIV Protein Interactions, which brings together high-caliber scientists and facilities to study the HIV virus and its interactions with host cell proteins.

Our group is awarded the best HPC collaboration at SuperComputing 18

Our group has been recognized in the annual HPCwire
Readers’ and Editors’ Choice Awards, presented at the 2018 International Conference for High Performance
Computing, Networking, Storage and Analysis (SC18), in Dallas, Texas. Specifically we have been awarded the price for our collaborations with researchers at the Pittsburgh Center for HIV Protein Interactions, and in collaboration with D.E. Shaw Research and PSC, discover how drugs stop HIV maturation (Nature Communications).

The coveted annual HPCwire Readers’ and Editors’ Choice Awards are determined through a

nomination and voting process with the global HPCwire community, as well as selections from the HPCwire
editors. The awards are an annual feature of the publication and constitute prestigious recognition from the HPC
community. These awards are revealed each year to kick off the annual supercomputing conference, which
showcases high performance computing, networking, storage, and data analysis.

Our work is nominated to the HPC Wire reader's award

These annual awards are a way for our community to recognize the best and brightest innovators within the global HPC community.

We were nominated in the Best HPC Collaboration (Academia/Government/Industry) by the Pittsburgh Super Computing center.

Work performed by Juan R. Perilla, has previously won the 2013 HPCWire Reader's award for Best Use of HPC Application in Life Sciences.

The 2018 Categories Include the Following:

* Best Use of HPC Application in Life Sciences
* Best Use of HPC in Physical Sciences
* Best Use of HPC in Manufacturing
* Best Use of HPC in Energy
* Best Use of HPC in Automotive
* Best Use of HPC in Entertainment
* Best Use of HPC in Financial Services
* Best Use of High Performance Data Analytics
* Best Use of AI (Deep Learning/Machine Learning)
* Best Use of HPC in the Cloud (Use Case)
* Best Cloud Platform for HPC
* Best HPC Server Product or Technology
* Best HPC Visualization Product or Technology
* Best HPC Interconnect Product or Technology
* Best HPC Programming Tool or Technology
* Best HPC Cluster Solution or Technology
* Best AI Product or Technology
* Top 5 New Products or Technologies to Watch
* Best HPC Collaboration (Academia/Government/Industry)
* Top Supercomputing Achievement
* Top HPC-Enabled Scientific Achievement
* Top Energy-Efficient HPC Achievement
* Top 5 Vendors to Watch
* Workforce Diversity Leadership Award
* Outstanding Leadership in HPC (Individual)

Nominations are accepted from readers, users, vendors – virtually anyone who is connected to the HPC community and is a reader of HPCwire.

Supercomputer Simulations show new target in HIV-1 replication

Scientists from the group found the naturally-occurring compound a hexakisphosphate (IP6) promotes both assembly and maturation of HIV-1. We discovered, in collaboration with other researchers, that HIV uses this small molecule to complete its function. This is a molecule that's extremely available in human cells and in other mammalian cells. HIV has evolved to make use of these small molecules present in our cells to essentially be infectious. Our study was published in the journal Nature in August 2018.

More information.

Postdoctoral researcher position

The Department of Chemistry & Biochemistry at the University of Delaware invites applications for a Postdoctoral Researcher position beginning September 1, 2018 (a later start can be negotiated). The primary function of this position is to conduct research regarding the molecular architecture of the HIV-1 virus in the research group of Prof. Juan R. Perilla (http://perilla.chem.udel.edu).  The U.S. National Institutes of Health-funded project is on the design, development and execution of computer simulations of biomedically relevant systems including, but not limited to, the HIV-1 virus. Preference will be given to applicants with expertise in 1) protein dynamics; 2) molecular dynamics simulations; and 3) high-performance computing environments. Prior programming experience is preferred but not required. The Postdoctoral Researcher will design, perform, and develop new scientific tools for the analysis of long-time and/or large-scale molecular dynamics simulations in collaboration with the PI. The selected candidate will also participate in the development, testing and implementation of novel computational methods, the preparation of technical reports and peer-reviewed publications, and the dissemination of project results at professional meetings.  Within the Department of Chemistry and Biochemistry, the successful candidate will benefit from excellent core laboratories and a vibrant and supportive intellectual environment.

Applicant must hold a PhD in biophysics, biochemistry, chemistry, physics, or related area.  Potential applicants are strongly encouraged to contact Prof. Juan R. Perilla (biophysics-positions@udel.edu) prior to submission.  Candidates should submit a cover letter, CV, and the names, phone numbers and email addresses of three references through the University of Delaware Jobs website.  The initial appointment is for one year with the possibility of renewal, based on the availability of funding and contingent upon satisfactory performance.  This position includes full UD benefits (www.udel.edu/benefits).  Review of applications will begin immediately and will continue until the position is filled.

Apply here

The biophysical society spoke with us on the world hepatitis day

July 28 is World Hepatitis Day. The Biophysical Society spoke with us regarding our work on Hepatitis B. Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). It can cause chronic infection and puts people at high risk of death from cirrhosis and liver cancer. According to the World Health Organization, an estimated 257 million people are living with hepatitis B virus infection. 

More on the society's blog :  Biophysics on world hepatitis day.

MD simulations shed light on Hepatitis B virus

Hepatitis B virus (HBV) causes severe liver disease. Although a vaccine to prevent HBV is available, there is no cure to treat people who are already infected. Researchers aim to design new drugs against HBV that target its capsid, a protein shell at the core of the virus that encloses its genetic blueprint. During infection, the capsid drives delivery of the blueprint to the host cell nucleus, where it is used to generate new copies of the virus. While the structure of the HBV capsid had been previously determined, its motion, which underlies its role in HBV infection, had not been characterized at the atomic level until recently.

HBV capsid simulation system

HBV capsid simulation system, 6M atoms

In a study published in eLife, we used molecular dynamics simulations on the microsecond timescale to observe the motion of the HBV capsid and its influence on surrounding water molecules and ions. We learned that the capsid is extremely flexible, and that this is likely the reason experimental microscopes have not been able to obtain high-resolution images of the capsid. We also learned that the capsid can distort asymmetrically, which may be important for the capsid to accommodate the asymmetric blueprint it encloses, or to squeeze through the nuclear pore into the host cell nucleus.

Finally, we learned that the capsid translocates ions across its surface through triangular-shaped pores, and that positively-charged ions translocate five times faster than negatively-charged ions. In the human body, the capsid proteins include positively-charged tails that expose themselves to the capsid surface, which signals the host cell to transport the capsid towards its nucleus. Our observations suggest that the tails are exposed through the capsid’s triangular pores, not through hexameric pores as previously thought, and that the capsid can control this exposure based on changes in tail charge that also occur during infection.

By revealing details about how the HBV capsid functions, our results imply new strategies to target the capsid with drugs. For example, drugs designed to rigidify the capsid could inhibit asymmetric distortion, and drugs designed to block triangular pores could inhibit cellular signaling. Importantly, our results also indicate that cryo-electron microscopy, which recently won the 2017 Nobel Prize in Chemistry, may be limited in reaching atomic resolution for biomolecules as flexible as the HBV capsid.

Lab researchers study the HIV-1 maturation process in the millisecond regime

Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag
via an orchestrated series of proteolytic cleavage events. A longstanding question concerns
the structure of the C-terminal region of CA and the peptide SP1 (CA–SP1), which represents
an intermediate during maturation of the HIV-1 virus. Employing enhanced sampling techniques in the Anton2 super computer researchers were able to observe the milisecond dynamics of the so-called SP1 domain. By integrating NMR, cryo-EM, and
molecular dynamics simulations, we show that SP1 acts as a maturation switch. In particular, we show that the SP1 peptide
exists in a dynamic helix–coil equilibrium, and that the addition of the maturation inhibitors
causes stabilization of a helical form of SP1.  Moreover, the
maturation-arresting SP1 mutation T8I also induces helical structure in SP1 and further global
dynamical and conformational changes in CA. Overall, our results show that dynamics of CA
and SP1 are critical for orderly HIV-1 maturation and that small molecules can inhibit maturation by perturbing molecular motions.  Results are published in the journal Nature Communications.

Our group uses the most powerful super computers

The list of World's most powerful supercomputers is out, and some of the computers employed by the group are listed in the Top500. Our research was higlighted as one of the key results from SuperComputers (see article here).

CryoEM, a core technique in our lab wins the 2017 Chemistry Nobel prize

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry 2017 to

Jacques Dubochet

University of Lausanne, Switzerland

Joachim Frank

Columbia University, New York, USA


Richard Henderson

MRC Laboratory of Molecular Biology, Cambridge, UK

"for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution"

Our lab continuosly develop novel techniques for cryoEM structure determination and refinement (see our list of Publications). 

For a list of cryo-EM structures derived by our researchers please see :

List of PDB entries by Perilla et al.