Salk Institute

Lyumkis Lab
Lyumkis Lab

Lyumkis Lab - Research

Biological macromolecules such as proteins and nucleic acids, together with their macromolecular assemblies, govern cellular function and are necessary for life. We are generally interested in understanding how macromolecules are assembled and how their structures influence and describe macromolecular function. To study macromolecular structure at resolutions ranging from nanometer to near-atomic, we use a technique called single-particle cryo-electron microscopy (cryoEM). This technique enables us to observe large macromolecular assemblies under near native conditions, characterize structurally heterogeneous components within them, and define regions that are necessary for function. We have several ongoing directions in the lab, described below.

We are interested in understanding how retroviruses, such as HIV-1, can gain access to target host cells, evade the immune system, and establish permanent viral infection. To this end, some of the lab’s effort is geared toward unraveling the structural biology of macromolecular assemblies within HIV-1 and related retroviruses. For example, our structure of the HIV-1 Envelope (Env) trimer provided key insights into the mechanism of HIV entry into immune cells, and represents a platform that is currently guiding multiple vaccine design efforts. We have ongoing efforts to understand the molecular mechanisms governing retroviral integration, which is the point at which the virus catalytically inserts its complementary viral DNA into target host cells and establishes permanent and irreversible infection. This point-of-no-return also underlies some of the difficulties in combating the HIV/AIDS pandemic. A recent highlight was the structural and functional characterization of a novel form of macromolecular retroviral integration complex (called an “intasome”) from the Mouse Mammary Tumor Virus, which reveals an unexpected mechanism of intasome oligomerization while maintaining positional conservation of the catalytic protein domains. We are expanding these efforts to now study the molecular mechanisms of HIV-1 integration. Broadly speaking, these efforts have the potential to define and detail, with atomic level precision, novel molecular surfaces for the development of improved therapies against HIV.

We are interested in understanding how the immune system activates pro-inflammatory molecular signaling networks under conditions of stress or in response to pathogen invasion. Inflammation as a whole is an enormously complex and highly intricate process that involves crosstalk between numerous signaling pathways. Among the many participants, the IKK proteins and their downstream NF-kB effectors have emerged as some of the key players in and mediators of pro-inflammatory cellular response. NF-kB activity promotes transcription of a wide range of genes, and dysregulation of proper NF-κB activity is associated with different pathological conditions, including chronic inflammatory and metabolic diseases, autoimmune disorders, and cancer. Although these proteins have been especially studied for their oncogenic properties, as they are upregulated in many different types of tumors, they also play prominent roles in viral infections, including HIV. We aim to define some of the structural signatures governing NF-kB activation in order to better understand the molecular mechanisms underlying inflammation, as well as pathogen-host interactions. In turn, we hope that our efforts will provide novel paradigms for understanding molecular signaling networks and for designing therapeutics against a range of diseases.

To address increasingly complex questions in structural biology, we are additionally interested in advancing cryoEM methodologies and pushing its technological capabilities. For example, one limitation of cryoEM is that the structure of small proteins (<100 kDa) is very challenging to resolve using this technique. One of our goals is to establish a more general methodology that will enable structural characterization of small proteins by single-particle cryoEM to a resolution that is sufficient for interpreting atomic structure through molecular model building. We are also interested in expanding current capabilities to address increasingly more heterogeneous systems. The ability to fully describe and characterize heterogeneous macromolecules and macromolecular assemblies has the potential to address increasingly complex questions pertaining to macromolecular dynamics, assembly pathways, and relationships between distinct constituent components. These combined efforts, in turn, can provide a deeper understanding into the molecular mechanisms governing macromolecular assembly and function.

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