|The HIV envelope protein has long been considered one of the most difficult targets in structural biology and of great value for medical science — particularly for HIV/AIDS vaccine development. Using advanced techniques in both cryo-EM and x-ray crystallography, researchers from The Scripps Research Institute and Weill Cornell Medical College have now determined the structure of this protein, shown here bound by broadly neutralizing antibodies against two distinct sites of vulnerability.
Courtesy of The Scripps Research Institute.
The new data provide the most detailed picture yet of the AIDS-causing virus’s complex envelope, including sites that future vaccines will try to mimic to elicit a protective immune response.
“Most of the prior structural studies of this envelope complex focused on individual subunits, but we’ve needed the structure of the full complex to properly define the sites of vulnerability that could be targeted, for example with a vaccine,” said Dr. Ian A. Wilson, the Hansen Professor of Structural Biology at TSRI and a senior author of the new research with biologists Drs. Andrew Ward and Bridget Carragher of TSRI and virologist and immunologist Dr. John Moore of Weill Cornell.
The findings were published in two papers in Science Express, the early online edition of the journal Science, on October 31, 2013.
A Difficult Target
HIV, the human immunodeficiency virus, infects about 34 million people globally, 10 percent of whom are children, according to World Health Organization estimates. Although antiviral drugs are now used to manage many HIV infections, especially in developed countries, scientists have long sought a vaccine that can prevent new infections and would help perhaps to ultimately eradicate the virus from the human population.
However, none of the HIV vaccines tested so far has come close to providing adequate protection. This failure is due largely to the challenges posed by HIV’s envelope protein, known to virologists as Env.
HIV’s Env is not a single, simple protein but rather a “trimer” made of three identical, loosely connected structures with a stalk-like subunit, gp41, and a cap-like region, gp120. Each trimer resembles a mushroom and about 15 of these Env trimers sprout from the membrane of a typical virus particle, ready to latch onto susceptible human cells and facilitate viral entry.
Although Env in principle is exposed to the immune system, in practice it has evolved highly effective strategies for evading immune attack. It frequently mutates its outermost “variable loop” regions, for example, and also coats its surfaces with hard-to-grip sugar molecules called glycans.
Even so, HIV vaccine designers might have succeeded by now had they been able to study the structure of the entire Env protein at atomic-scale — in particular, to fully characterize the sites where the most effective virus-neutralizing antibodies bind. But Env’s structure is so complex and delicate that scientists have had great difficulty obtaining the protein in a form that is suitable for atomic-resolution imaging.
“It tends to fall apart, for example, even when it’s on the surface of the virus, so to study it we have to engineer it to be more stable,” said Dr. Ward, who is an assistant professor in TSRI’s Department of Integrative Structural and Computational Biology.
The key goal in this area has been to engineer a version of the Env trimer that has the stability and other properties needed for atomic-resolution imaging, yet retains virtually all of the complex structural characteristics of native Env.
After many years in pursuit of this goal, Drs. Moore, Rogier W. Sanders and their colleagues at Weill Cornell, working with Drs. Wilson, Ward and others at TSRI, recently managed to produce a version of the Env trimer (called BG505 SOSIP.664 gp140) that is suitable for atomic-level imaging work — and includes all of the trimer structure that normally sits outside the viral membrane. The TSRI researchers then evaluated the new Env trimer using advanced versions of two imaging methods, X-ray crystallography and electron microscopy. The X-ray crystallography study was the first ever of an Env trimer, and both methods resolved the trimer structure to a finer level of detail than has been reported before.
“The new data are consistent with the findings on Env subunits over the last 15 years, but also have enabled us to explain many prior observations about HIV in structural terms for the first time,” said Dr. Jean-Philippe Julien, a senior research associate in the Wilson laboratory at TSRI, who was first author of the X-ray crystallography study.
The data illuminated the complex process by which the Env trimer assembles and later undergoes radical shape changes during infection and clarified how it compares to envelope proteins on other dangerous viruses, such as flu and Ebola.
Arguably the most important implications of the new findings are for HIV vaccine design. In both of the new studies, Env trimers were imaged while bound to broadly neutralizing antibodies against HIV. Such antibodies, isolated from naturally infected patients, are the very rare ones that somehow bind to Env in a way that blocks the infectivity of a high proportion of HIV strains.
Ideally an HIV vaccine would elicit large numbers of such antibodies from patients, and to achieve that, vaccine designers would like to know the precise structural details of the sites where these antibodies bind to the virus — so that they can mimic those viral “epitopes” with the vaccine.
“It’s been a privilege for us to work with the Scripps’ team on this project,” said Dr. Moore, a professor of microbiology and immunology at Weill Cornell. “Now we all need to harness this new knowledge to design and test next-generation trimers and see if we can induce the broadly active neutralizing antibodies that an effective vaccine is going to need.”
“One surprise from this study was the revelation of the complexity and the relative inaccessibility of these neutralizing epitopes,” Dr. Julien added. “It helps to know this for future vaccine design, but it also makes it clear why previous structure-based HIV vaccines have had so little success.”
“We found that these neutralizing epitopes encompass features such as the variable loop regions and glycans that were excluded from previous studies of individual Env subunits,” said Dmitry Lyumkis, first author of the electron microscopy study, who is a graduate student at TSRI participating in the NIH-funded National Resource for Automated Molecular Microscopy. “We observed, too, that neutralizing antibody binding to gp120 can be influenced by the neighboring gp120 structure within the trimer — another complication that was not apparent when we were not studying the whole trimer.”
Having provided these valuable structural insights, the new Env trimer is now being put to work in vaccine development. “We and others are already injecting the trimer into animals to elicit antibodies,” Dr. Ward said. “We can look at the antibodies that are generated and if necessary modify the Env trimer structure and try again. In this iterative way, we aim to refine and increase the antibody response in the animals and eventually, humans.”
Other contributors to the studies, “Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 Env trimer,” and “Crystal structure of a soluble cleaved HIV-1 envelope trimer in complex with a glycan-dependent broadly neutralizing antibody,” included TSRI’s Natalia de Val, Devin Sok, Drs. Robyn L. Stanfield and Marc C. Deller; and Weill Cornell Medical College’s Albert Cupo and Dr. Per-Johan Klasse. In addition to Drs. Wilson, Ward and Carragher, senior participants at TSRI included Drs. Clinton S. Potter and Dennis Burton.
The research was supported in part by the National Institutes of Health (HIVRAD P01 AI82362, R01 AI36082, R01 AI084817, R37 AI36082, R01 AI33292), the NIH’s National Institute of General Medical Sciences (GM103310) and the International AIDS Vaccine Initiative Neutralizing Antibody Consortium. IAVI has filed a patent that includes WCMC and TSRI authors on the development of the BG505 SOSIP.664 trimers as vaccine antigens.
Weill Cornell Medical College
Weill Cornell Medical College, Cornell University’s medical school located in New York City, is committed to excellence in research, teaching, patient care and the advancement of the art and science of medicine, locally, nationally and globally. Physicians and scientists of Weill Cornell Medical College are engaged in cutting-edge research from bench to bedside, aimed at unlocking mysteries of the human body in health and sickness and toward developing new treatments and prevention strategies. In its commitment to global health and education, Weill Cornell has a strong presence in places such as Qatar, Tanzania, Haiti, Brazil, Austria and Turkey. Through the historic Weill Cornell Medical College in Qatar, the Medical College is the first in the U.S. to offer its M.D. degree overseas. Weill Cornell is the birthplace of many medical advances — including the development of the Pap test for cervical cancer, the synthesis of penicillin, the first successful embryo-biopsy pregnancy and birth in the U.S., the first clinical trial of gene therapy for Parkinson’s disease, and most recently, the world’s first successful use of deep brain stimulation to treat a minimally conscious brain-injured patient. Weill Cornell Medical College is affiliated with NewYork-Presbyterian Hospital, where its faculty provides comprehensive patient care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center. The Medical College is also affiliated with Houston Methodist. For more information, visit weill.cornell.edu.