The HIVE Center characterizes assemblies of HIV and host molecules in multiple states and their transitions, by combining structural studies of HIV protein interactions with chemical and evolutionary probes and computational modeling to elucidate macromolecular interactions and mechanisms critical for the viral life cycle. Previous work by Center structural biologists have characterized all of the HIV enzymes, with over 300 unique structure depositions in the PDB, and the work within HIVE will reveal their interaction and maturation from viral polyproteins, and their interactions within the viral lifecycle. HIVE laboratories are approaching this challenge with a variety of experimental methods. The evolution of HIV under the selection pressure of small molecule effectors provides a functional window on the underlying macromolecular interactions. Chemistry gives us the capability to design and refine new atomic level probes to explore mechanism. Computational modeling guides the establishment of structural hypotheses and enables the integration of multi-scale dynamic data into a coherent physical picture.

HIVE Center Team Members

Stefan G. Sarafianos has more than 20 years of experience in retroviral structural biology, biochemistry, and virology. His lab has contributed to the development of potent antivirals that act by novel mechanisms of action by characterizing their mechanisms of inhibition and resistance. His group solved the elusive crystal structure of the first native (uncrosslinked) hexameric HIV capsid protein, which serves as a model system for the identification and characterization of novel compounds targeting HIV capsid. He has also recently developed an imaging/microscopy assay (MICDDRP) to visualize viral RNA, DNA, and protein. Collaborations in the HIVE Center include structural and biophysical studies on APOBEC3G complexes with Michael Malim and Arnold, Griffin, Lyumkis, Musier-Forsyth, and Olson; kinetic characterization of HIV RT initiation complexes with Arnold, Millar, Musier-Forsyth, and Lyumkis; reactive docking of novel compounds as probes targeting HIV capsid with Olson and Sharpless; MICDDRP microscopy assays to visualize various aspects of the HIV life cycle with Engelman and Torbett.

Bruce E. Torbett has 15 years of experience in the studies of the biochemical and structural roles of drug resistance mutations in HIV protease and Gag, their macromolecular interplay, and contributions in altering virological fitness. The Torbett group has utilized small molecule protease inhibitors as chemical probes to structurally and mechanistically define the macromolecular interplay during the acquisition of protease inhibitor resistance.

The Group’s expertise will facilitate active and extensive participation among the HIVE Center investigators and projects. The use of the novel protease/Gag assays, developed by the Torbett group, will be integral for undertaking low- and high-resolution studies of protease and Gag polyprotein interaction, small molecule screening, and resistance studies with HIVE Center Investigators. The use of the novel protease/Gag assays, and proteins generated from various protease/Gag constructs will be integral for undertaking low- and high-resolution studies of protease and Gag interaction, necessary to glean insights into the topology of the Gag-Pol polyprotein and its macromolecular partners. Moreover, the Torbett group’s expertise in the identification of chemical probes and the generation of drug resistant viral mutants for interrogating protease and Gag macromolecular interaction is a strong asset for the Center. In this regard, the Gag assay will afford small molecule screening as proposed by Center Investigators.

Eddy Arnold has been studying HIV-1 RT structure and its implications for function, ligand binding, drug design, and drug resistance since 1987. In a long-term collaboration with Stephen Hughes at NCI Frederick, the Arnold lab has solved the structure of wild-type and mutant HIV-1 RT in many functional states, including complexes with DNA, RNA/DNA, and inhibitors. The Arnold group contributed to the discovery of two anti-AIDS drugs, TMC125/etravirine/Intelence and TMC278/rilpivirine/Edurant, in a multidisciplinary structure-based drug design effort. Key areas of focus within the HIVE Center are structural (cryo-EM with Lyumkis, and crystallographic) and functional studies of the HIV-1 RT initiation complex (HIV-1 RT/vRNA/tRNA), HIV Gag-Pol and Pol polyproteins, prototype foamy virus (PFV) PR-RT and Pol polyprotein, and crystallographic fragment screening of multiple HIV targets. Collaborations within the HIVE Center have included: study of IN-ALLINI interaction and structure-guided fragment-based inhibitor design with Kvaratskhelia, Engelman, Fuchs, Olson, and Levy; structural, biophysical, functional, and expression studies of retroviral polyproteins, including PFV PR-RT, PFV PR-RT complex with DNA, and HIV-1 Gag-Pol and Pol, and PFV Pol, with Marcotrigiano, Torbett, Musier-Forsyth, Hughes, and Lyumkis; hydrogen-deuterium exchange studies to probe RT dynamics and interactions with inhibitors, DNA, and RNA with Griffin, DeStefano, and Musier-Forsyth; chemical labeling using SuFEx and click chemistry of HIV-1 RT and other HIVE targets with Sharpless, Olson, Sample, and Forli; and use of DNA aptamers for structure determination of HIV-1 RT with DeStefano.

Jeffrey DeStefano works on understanding the process of reverse transcription including fidelity, recombination, protein-nucleic acid interactions, and design of novel inhibitors. HIVE-related research has focused on developing nucleic acid aptamers that bind with high affinity to retroviral proteins and can aid in structural analysis as well as serve as potential inhibitors or diagnostics. A primer-template mimicking aptamer to HIV RT helped produce (with the Arnold group) the first RT structure with a nucleic acid in the absence of cross-linking agents.

Alan Engelman has >30 years of experience studying retrovirology and >25 years of experience studying HIV DNA integration. Seminal contributions to the integration field include deciphering the mechanisms of IN 3’ processing and strand transfer activities, the roles of LEDGF and CPSF6 in guiding PICs to favored integration sites in the human genome, the initial structure of the IN-LEDGF complex, the fact that ALLINIs inhibit HIV-1 particle maturation, and several intasome structures. Engelman moreover coined the class I and class II terminology to distinguish the different phenotypic effects of IN mutations on HIV-1 replication. Collaborations within the HIVE Center have included: elucidation of the mechanism of action of ALLINIs with Kvaratskhelia; discovery and characterization of new IN inhibitors with Kvaratskhelia, Arnold, Fuchs, Levy and Olson; and structure of integrase and intasomes with Lyumkis.

James Fuchs has expertise in the synthesis of small molecules for the treatment of diseases. He successfully collaborated with HIVE labs as a CDP awardee to develop functional probes and lead compounds for the exploration of HIV-1 IN function. Within the HIVE Center, he will undertake the synthesis of various ALLINIs, including thiophene-based derivatives.

Pat Griffin has a broad background in drug discovery and development, as well as the study of protein structure with approaches to modulating protein function via synthetic small molecules that spans the last 20+ years. His research is focused on structure-function and chemical biology studies of nuclear receptors and GPCRs. His laboratory has built an automated platform to profile protein:protein and protein:ligand interactions by hydrogen/deuterium exchange (HDX) mass spectrometry. In the HIVE Center, he serves as a HDX Core Director, providing HDX support to all the Center members, as well as guidance on assay development and using the Fast Track mechanism to transfer assays into the MLPCN network.

Wei-Shau Hu studies how retroviruses transfer genetic information to the next generation, including the transport and trafficking of the viral RNA, packaging of the viral RNA genome, virus assembly, reverse transcription, and recombination. She uses molecular biology and biochemical approaches in combination with state-of-the-art microscopy techniques to study these topics.

Stephen Hughes is a prominent retrovirologist with long-standing interests in RT and IN. He studies the mechanisms that underlie drug resistance, and using that information, to develop more effective anti-HIV drugs. He is, in both the RT and IN Projects, doing experiments that are intended to better understand the roles that these enzymes play in viral replication. Hughes’ recent studies focus on HIV integration in patients, and on using redirected HIV integration as a tool to investigate chromatin structure and function.

Mamuka Kvaratskhelia investigates the structure and function of retroviral integrase as a therapeutic target. Some seminal findings include revealing a role of BET proteins in targeting gamma-retroviral integration to transcription start sites, binding of LEDGF/p75 to mononucleosomes containing a specific histone mark (H3K36me3), and a non-catalytic function of integrase in HIV-1 biology as it binds and encapsidates the viral RNA genome during virion morphogenesis. Within the HIVE Center, his collaborative work with Engelman, Arnold, Griffin, Levy, Olson and Fuchs have allowed these investigators to dissect the unexpected mode of action of quinoline-based allosteric integrase inhibitors (ALLINIs) that are currently in clinical trials and to identify entirely new ALLINIs with unique structural scaffolds through fragment-based screening of HIV-1 integrase inhibitors.

Ron Levy brings to the HIVE Center more than thirty years of experience and leadership in the development and application of molecular simulation methods to study the structure, folding, and dynamics of proteins and their complexes. Levy works on problems involving the interplay between computational models in structural biology and experiments at different levels of resolution and different time scales. The group uses their multi-scale modeling approaches with experimental restraints provided by HIVE collaborators to elucidate the thermodynamic and kinetic processes by which ALLINIs promote multimerization of HIV integrase, and to build structural models for Gag-Pol polyproteins. Novel high throughput free energy simulations refine the results of protein-ligand docking carried out by HIVE collaborators in order to assist in the design of potent inhibitors of HIV integrase and reverse transcriptase. The Levy group is developing information-theoretic (Potts) statistical inference techniques to identify correlated patterns of resistance mutations on HIV proteins and their partners. In collaboration with other HIVE investigators, Levy is integrating these tools with biophysical and biochemical data and structural models to map the fitness landscapes of HIV proteins, in order to assess how correlated mutations facilitate the development and evolution of drug resistance.

Dmitry Lyumkis brings to the HIVE Center nearly a decade of expertise in the field of single-particle cryo-EM. He has contributed numerous technical advances that broadly aim to improve cryo-EM methods and to resolve increasingly more complex and structurally heterogeneous macromolecular assemblies. He continues to develop tools for pushing the technological capabilities of cryo-EM to gain a deeper understanding into macromolecular structure and function. He also has broad interests in HIV structural biology, and in particular integration. In collaboration with HIVE Center researchers, he solved groundbreaking structures of several intasome complexes, from HIV and related retroviruses.

Michael Malim is the Head of the Department of Infectious Diseases at King’s College London. He has >25 years of research experience investigating the molecular pathogenesis of HIV. He has described the anti-viral properties of the human restriction factors APOBEC3G (A3G), a cytidine deaminase that edits viral DNA, and MX2, a dynamin-like GTPase. He will actively participate in the study of the A3G/RT interactions and on the mechanism of RT inhibition by APOBEC3 proteins.

Gregory Melikian has more than 30 years of experience in viral entry and fusion steps of infection. His laboratory has studied HIV-1 entry intermediates and pathways, using a number of functional and live cell imaging techniques. More recently, his laboratory has focused on visualization of single HIV-1 uncoating, docking at the nuclear pore complex, nuclear import and intranuclear trafficking steps of infection.

David Millar has pioneered the application of single-molecule fluorescence methods in HIV-1. He will develop new single-molecule methods to monitor Gag polyprotein assembly, both in a defined in vitro system and in cells and will contribute to real-time visualization of intasome assembly and single-molecule analyses of integrase-vRNA interactions and the RT initiation complex.

Karin Musier-Forsyth focuses on understanding RNA structure and RNA-protein interactions that are critical for retrovirus replication. Areas of expertise in the lab include RNA structure probing by SHAPE, RNA SAXS analysis, and RNA-protein interactions. An overarching goal is to identify new targets and novel strategies for anti-retroviral therapy. Current research in the lab related to the specific objectives of the HIVE Center includes: structural analysis of the reverse transcription initiation complex (RTIC), assembly and packaging of genomic RNA into HIV-1 by retroviral Gag proteins, and polyprotein structure and function. As a HIVE CDP awardee, exciting collaborations have been established with Arnold (RTIC structure), Lyumkis and Kvaratskhelia (structural analysis of RNA and RNA-IN complexes by Cryo-EM), Griffin (HDX of Gag-RNA complexes), and Levy and Olson (modeling of Gag).

Arthur Olson brings to the Center decades of research and development in computational docking and virtual screening, and the largest distributed-computing resource currently addressing HIV biology: FightAIDS@Home. The Olson laboratory focuses on developing and applying computational methods to understand the nature of HIV structure and mechanism and to improve drug design methodology within the context of the evolution of viral drug resistance. Recently the lab is bringing systems biology and structural biology together by integrating proteomics and other bioinformatics with data from structural information at multiple scales. For this task, the lab is developing the autoPACK/cellPACK software, automated tools to construct complex cellular environments at molecular and atomic detail, such as whole virion models of HIV at the molecular level. Collaborations within the HIVE Center have included: an inhibitor design cycle targeting protease resistance with Elder, Finn, Torbett and Stout; development of improved methods for free energy prediction with Levy, and modeling of high-order integrase assemblies with Kvaratskhelia and Engelman.

Barry Sharpless is a highly innovative Nobel Laureate (2001who developed click chemistry and recently produced an application termed Sulfur (VI) Fluoride Exchange (SuFEx). He has had a long-standing interest in infectious disease and development of chemical reagents to serve as probes and therapeutic agents for HIV. SuFEx compounds are very stable in aqueous solutions near neutral conditions, but become reactive upon encountering a specific protein partner. When the correct SVI–F motif is incorporated into the correct small organic molecule, it may selectively and covalently react with protein targets. Sharpless’s significant contribution to the HIVE Center is to develop novel small-molecule libraries using the SuFEx chemistry for HIV polyprotein and virion screening.

Jamie Williamson has extensive experience with biophysical studies of RNA folding and RNP assembly, using NMR, X-ray crystallography, single molecule fluorescence, electron microscopy, and mass spectrometry (MS) to study the process of ribosome assembly. A key feature of this approach is the use of quantitative MS to study the protein composition of intermediates, and the use of stable isotope pulse labeling to study the dynamics of intermediates. This broadly based approach will now be brought to bear on the process of HIV assembly.

Daniel Adu-Ampratwum, Research Scientist, PhD, Division of Medicinal Chemistry and Pharmacognosy, Ohio State University. CDP Title: “Design and Synthesis of Small Molecules That Target CA to Serve as Probes to Provide New Insight into HIV-1 CA Biology and Gag Polyprotein Degradation”

Robert A. Dick, PhD, Research Associate, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY. CDP Title: “Structure Determination of HIV Capsid Cores Via cryo-Electron Tomography and Subtomogram Averaging with a Focus on Drug Binding and CA Pentamers”

Bridget Carragher, Director, and Clint Potter, Co-Director, National Resource for Automated Molecular Microscopy, TSRI, will provide automated imaging techniques for solving the three-dimensional structures of Gag, Gag-Pol, and Pol complexes using cryoTEM, evaluating the monodispersity of HIV polyproteins in conjunction with crystallization, and visualizing microcrystals in the lipidic cubic phase.

David Looney MD, University of California San Diego School of Medicine, UCSD/VMRF CFAR Molecular Biology Core, has provided a clinical perspective in the TSRI HIV Program Project. He has been instrumental in compiling, annotating, and analyzing clinical data from Southern California VA Healthcare System and CFAR Network of Integrated Clinical Systems, which provides the primary support for work on pathways of resistance mutation. Within the Center, he will continue to provide new clinical data on resistance mutations to all inhibitors.

Jason Okulicz MD, MC, USAF, is on the Infectious Disease Service Staff at Lackland Air Force Base, Texas, will provide clinical data and sera/plasma/cell samples from participates in the U.S. Military HIV Natural History Study. Okulicz will participate within the Center on the antiretroviral-mediated viral co-evolution studies by providing viral samples from individuals for protease and gag sequencing. The sequence information from viral samples will be crucial for modeling the acquisition of resistance mutations.

Alan Rein, Director of the Retroviral Assembly Section, NCI-Frederick, and staff scientist Sid Datta will collaborate on studies of HIV Gag and Gag-Pol polyprotein precursors. Using a defined assembly system that he and his colleagues have developed, Rein and Datta will work with Center investigators to map specific Gag-Gag interactions by HDX and to explore Gag and Gag-Pol interactions in assembly. Their broad expertise in studying retroviral assembly will help to place the Center’s studies of HIV polyproteins in the broader context of HIV assembly and maturation.

Doug Richman MD, Director of UC San Diego Center for AIDS Research, will provide resources from the CFAR, including core services in flow cytometry, molecular biology, translation virology, bioinformatics and genomics, protein expression and proteomics, and as well as clinic investigations. Utilizing the available CFAR Cores will leverage valuable research and clinical services for all Center grant participants.

Robin Wilner, Vice President for Global Community Initiatives, IBM World Community Grid, will continue a long-standing collaboration on the FightAIDS@Home project, which provides a distributed network of over two million internet shared processors for use in docking and drug design.


Stefan Sarafianos, Emory University
Bruce Torbett, University of Washington


Arthur Olson, TSRI La Jolla

Collaborative Development Program

Karen Kirby, Emory University
Arthur Olson, TSRI La Jolla
Stefan Sarafianos, Emory University
Bruce Torbett, University of Washington


David Goodsell, TSRI La Jolla

Management of the Center builds upon over 25 years of experience in the Structural Biology of HIV program. Stefan Sarafianos and Bruce Torbett will act as Co-directors of the Center. Both have been centrally involved in the previous cycle of HIVE Center funding. Arthur Olson led the HIVE Center during its first cycle, as well as the previous TSRI program project for three funding cycles, building a highly collaborative program that effectively combined structure, biology, chemistry and computation into a full drug discovery cycle. Olson will continue administration of the HIVE Center, acting as coordinator of HIVE Center activities.

The HIVE Collaborative Development Program efforts is led by Karen Kirby, building on the program that was built by Edward Arnold, in consultation with Center Directors Torbett and Sarafianos toward the continued success of the program.

David Goodsell creates materials for outreach to the research and educational communities. For the past 18 years, he has been centrally involved in outreach at the RCSB Protein Data Bank, creating materials for educators, students, and the general public. In collaboration with education researchers at the Milwaukee School of Engineering, he has helped to create innovative teaching materials that combine physical models, printed material and interactive online materials. In addition, he has provided materials for science museums and the news media, as well as coordinating outreach efforts to local high schools.

Douglas D. Richman, M. D.
Distinguished Professor
Director of the AIDS Research Institute, Veteran’s Administration
Department of Pathology, UC San Diego School of Medicine

John Coffin, Ph. D.
American Cancer Society Professor of Molecular Biology
Tufts University

Jack Johnson, Ph. D.
Professor Emeritus
Department of Integrative Structural and Computational Biology, The Scripps Research Institute

Rommie Amaro, Ph. D.
Professor and Shuler Scholar
Director of the National Biomedical Computation Resource
Department of Chemistry and Biochemistry, UC San Diego

Anna Marie Pyle, Ph. D
William Edward Gilbert Professor of Molecular, Cellular & Developmental Biology
Investigator Howard Hughes Medical Institute
Professor of Chemistry
Yale University