Michelle W. Lee

Molecular basis of Tank-binding kinase 1 activation by transautophosphorylation.

Tank-binding kinase (TBK)1 plays a central role in innate immunity: it serves as an integrator of multiple signals induced by receptor-mediated pathogen detection and as a modulator of IFN levels. Efforts to better understand the biology of this key immunological factor have intensified recently as growing evidence implicates aberrant TBK1 activity in a variety of autoimmune diseases and cancers. Nevertheless, key molecular details of TBK1 regulation and substrate selection remain unanswered. Here, structures of phosphorylated and unphosphorylated human TBK1 kinase and ubiquitin-like domains, combined with biochemical studies, indicate a molecular mechanism of activation via transautophosphorylation. These TBK1 structures are consistent with the tripartite architecture observed recently for the related kinase IKKβ, but domain contributions toward target recognition appear to differ for the two enzymes. In particular, both TBK1 autoactivation and substrate specificity are likely driven by signal-dependent colocalization events.

Helical antimicrobial polypeptides with radial amphiphilicity

Significance We developed antimicrobial polypeptides (AMPs) with unprecedented radial amphiphilicity. Unlike typical AMPs characterized by facial amphiphilicity or biomimetic antimicrobial polymers with randomly distributed charged and hydrophobic groups, this class of AMPs is made up of homo-polypeptides that feature a radially amphiphilic (RA) structure and adopt a stable α-helical conformation with a hydrophobic helical core and a charged exterior shell, which is formed by flexible hydrophobic side chains with terminal charge group. The RA polypeptides appear to offer several advantages over conventional AMPs with regard to stability against proteases and simplicity of design. They also exhibit high antibacterial activity against both gram-negative and gram-positive bacteria and low hemolytic activity. This design may become a general platform for developing AMPs to treat drug-resistant bacteria. α-Helical antimicrobial peptides (AMPs) generally have facially amphiphilic structures that may lead to undesired peptide interactions with blood proteins and self-aggregation due to exposed hydrophobic surfaces. Here we report the design of a class of cationic, helical homo-polypeptide antimicrobials with a hydrophobic internal helical core and a charged exterior shell, possessing unprecedented radial amphiphilicity. The radially amphiphilic structure enables the polypeptide to bind effectively to the negatively charged bacterial surface and exhibit high antimicrobial activity against both gram-positive and gram-negative bacteria. Moreover, the shielding of the hydrophobic core by the charged exterior shell decreases nonspecific interactions with eukaryotic cells, as evidenced by low hemolytic activity, and protects the polypeptide backbone from proteolytic degradation. The radially amphiphilic polypeptides can also be used as effective adjuvants, allowing improved permeation of commercial antibiotics in bacteria and enhanced antimicrobial activity by one to two orders of magnitude. Designing AMPs bearing this unprecedented, unique radially amphiphilic structure represents an alternative direction of AMP development; radially amphiphilic polypeptides may become a general platform for developing AMPs to treat drug-resistant bacteria.

Thought disorder and nucleus accumbens in childhood: a structural MRI study

Thought disorder has been described as a hallmark feature in both adult and childhood-onset schizophrenia. The nucleus accumbens (NAc) has been repeatedly proposed as a critical station for modulating gating of information flow and processing of information within the thalamocortical circuitry. The aim of the present study was to investigate the relationship of thought disorder measures, which were administered to 12 children with schizophrenia and 15 healthy age-matched controls, and NAc volumes obtained from high-resolution volumetric magnetic resonance imaging analyses. The propensity for specific thought disorder features was significantly related to NAc volumes, despite no statistically significant differences in the NAc volumes of children with schizophrenia and normal children. Smaller left NAc volumes were significantly related to poor on-line revision of linguistic errors in word choice, syntax and reference. On the other hand, underuse of on-line repair of errors in planning and organizing thinking was significantly associated with decreased right NAc volumes. The results of this pilot study suggest that the NAc is implicated in specific thought patterns of childhood. They also suggest that subcortical function in the NAc might reflect hemispheric specialization patterns with left lateralization for revision of linguistic errors and right lateralization for repair strategies involved in the organization of thinking.

Viral fusion protein transmembrane domain adopts β-strand structure to facilitate membrane topological changes for virus–cell fusion

Significance Enveloped viruses enter cells by fusing their lipid envelope with the cell membrane. The transmembrane domain (TMD) of viral fusion proteins is traditionally envisioned as a passive α-helical membrane anchor during the protein-mediated membrane fusion. Using solid-state NMR, we show that a parainfluenza virus fusion protein TMD exhibits lipid-dependent conformations. α-Helical structure dominates in phosphocholine and phosphoglycerol membranes, whereas β-strand conformation dominates in phosphoethanolamine membranes. Importantly, the β-strand–rich conformation quantitatively transforms the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) membrane to a bicontinuous cubic phase, which is rich in the saddle-splay curvature in hemifusion intermediates and fusion pores. Thus, viral fusion protein TMDs play an active role in virus entry by mediating the necessary membrane topological changes. The C-terminal transmembrane domain (TMD) of viral fusion proteins such as HIV gp41 and influenza hemagglutinin (HA) is traditionally viewed as a passive α-helical anchor of the protein to the virus envelope during its merger with the cell membrane. The conformation, dynamics, and lipid interaction of these fusion protein TMDs have so far eluded high-resolution structure characterization because of their highly hydrophobic nature. Using magic-angle-spinning solid-state NMR spectroscopy, we show that the TMD of the parainfluenza virus 5 (PIV5) fusion protein adopts lipid-dependent conformations and interactions with the membrane and water. In phosphatidylcholine (PC) and phosphatidylglycerol (PG) membranes, the TMD is predominantly α-helical, but in phosphatidylethanolamine (PE) membranes, the TMD changes significantly to the β-strand conformation. Measured order parameters indicate that the strand segments are immobilized and thus oligomerized. 31P NMR spectra and small-angle X-ray scattering (SAXS) data show that this β-strand–rich conformation converts the PE membrane to a bicontinuous cubic phase, which is rich in negative Gaussian curvature that is characteristic of hemifusion intermediates and fusion pores. 1H-31P 2D correlation spectra and 2H spectra show that the PE membrane with or without the TMD is much less hydrated than PC and PG membranes, suggesting that the TMD works with the natural dehydration tendency of PE to facilitate membrane merger. These results suggest a new viral-fusion model in which the TMD actively promotes membrane topological changes during fusion using the β-strand as the fusogenic conformation.

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

Antimicrobial peptides (AMPs) are a diverse class of well-studied membrane-permeating peptides with important functions in innate host defense. In this short review, we provide a historical overview of AMPs, summarize previous applications of machine learning to AMPs, and discuss the results of our studies in the context of the latest AMP literature. Much work has been recently done in leveraging computational tools to design new AMP candidates with high therapeutic efficacies for drug-resistant infections. We show that machine learning on AMPs can be used to identify essential physico-chemical determinants of AMP functionality, and identify and design peptide sequences to generate membrane curvature. In a broader scope, we discuss the implications of our findings for the discovery of membrane-active peptides in general, and uncovering membrane activity in new and existing peptide taxonomies.

Direct Antimicrobial Activity of IFN-β

Type I IFNs are a cytokine family essential for antiviral defense. More recently, type I IFNs were shown to be important during bacterial infections. In this article, we show that, in addition to known cytokine functions, IFN-β is antimicrobial. Parts of the IFN-β molecular surface (especially helix 4) are cationic and amphipathic, both classic characteristics of antimicrobial peptides, and we observed that IFN-β can directly kill Staphylococcus aureus. Further, a mutant S. aureus that is more sensitive to antimicrobial peptides was killed more efficiently by IFN-β than was the wild-type S. aureus, and immunoblotting showed that IFN-β interacts with the bacterial cell surface. To determine whether specific parts of IFN-β are antimicrobial, we synthesized IFN-β helix 4 and found that it is sufficient to permeate model prokaryotic membranes using synchrotron x-ray diffraction and that it is sufficient to kill S. aureus. These results suggest that, in addition to its well-known signaling activity, IFN-β may be directly antimicrobial and be part of a growing family of cytokines and chemokines, called kinocidins, that also have antimicrobial properties.

What Can Pleiotropic Proteins in Innate Immunity Teach Us about Bioconjugation and Molecular Design

A common bioengineering strategy to add function to a given molecule is by conjugation of a new moiety onto that molecule. Adding multiple functions in this way becomes increasingly challenging and leads to composite molecules with larger molecular weights. In this review, we attempt to gain a new perspective by looking at this problem in reverse, by examining natures strategies of multiplexing different functions into the same pleiotropic molecule using emerging analysis techniques such as machine learning. We concentrate on examples from the innate immune system, which employs a finite repertoire of molecules for a broad range of tasks. An improved understanding of how diverse functions are multiplexed into a single molecule can inspire new approaches for the deterministic design of multifunctional molecules.

Molecular Motor Dnm1 Synergistically Induces Membrane Curvature To Facilitate Mitochondrial Fission

Dnm1 and Fis1 are prototypical proteins that regulate yeast mitochondrial morphology by controlling fission, the dysregulation of which can result in developmental disorders and neurodegenerative diseases in humans. Loss of Dnm1 blocks the formation of fission complexes and leads to elongated mitochondria in the form of interconnected networks, while overproduction of Dnm1 results in excessive mitochondrial fragmentation. In the current model, Dnm1 is essentially a GTP hydrolysis-driven molecular motor that self-assembles into ring-like oligomeric structures that encircle and pinch the outer mitochondrial membrane at sites of fission. In this work, we use machine learning and synchrotron small-angle X-ray scattering (SAXS) to investigate whether the motor Dnm1 can synergistically facilitate mitochondrial fission by membrane remodeling. A support vector machine (SVM)-based classifier trained to detect sequences with membrane-restructuring activity identifies a helical Dnm1 domain capable of generating negative Gaussian curvature (NGC), the type of saddle-shaped local surface curvature found on scission necks during fission events. Furthermore, this domain is highly conserved in Dnm1 homologues with fission activity. Synchrotron SAXS measurements reveal that Dnm1 restructures membranes into phases rich in NGC, and is capable of inducing a fission neck with a diameter of 12.6 nm. Through in silico mutational analysis, we find that the helical Dnm1 domain is locally optimized for membrane curvature generation, and phylogenetic analysis suggests that dynamin superfamily proteins that are close relatives of human dynamin Dyn1 have evolved the capacity to restructure membranes via the induction of curvature mitochondrial fission. In addition, we observe that Fis1, an adaptor protein, is able to inhibit the pro-fission membrane activity of Dnm1, which points to the antagonistic roles of the two proteins in the regulation of mitochondrial fission.

Modulation of toll-like receptor signaling by antimicrobial peptides

Antimicrobial peptides (AMPs) are typically thought of as molecular hole punchers that directly kill pathogens by membrane permeation. However, recent work has shown that AMPs are pleiotropic, multifunctional molecules that can strongly modulate immune responses. In this review, we provide a historical overview of the immunomodulatory properties of natural and synthetic antimicrobial peptides, with a special focus on human cathelicidin and defensins. We also summarize the various mechanisms of AMP immune modulation and outline key structural rules underlying the recently-discovered phenomenon of AMP-mediated Toll-like receptor (TLR) signaling. In particular, we describe several complementary studies demonstrating how AMPs self-assemble with nucleic acids to form nanocrystalline complexes that amplify TLR-mediated inflammation. In a broader scope, we discuss how this new conceptual framework allows for the prediction of immunomodulatory behavior in AMPs, how the discovery of hidden antimicrobial activity in known immune signaling proteins can inform these predictions, and how these findings reshape our understanding of AMPs in normal host defense and autoimmune disease.

How to Teach Old Antibiotics New Tricks

Antimicrobial peptides (AMPs), or more generally host defense peptides, have broad-spectrum antimicrobial activity and use nonspecific interactions to target generic features common to the membranes of many pathogens. As a result, development of resistance to such natural defenses is inhibited compared to conventional antibiotics. The disadvantage of AMPs, however, is that they are often not very potent. In contrast, traditional antibiotics typically have strong potency, but due to a broad range of bacterial defense mechanisms, there are many examples of resistance. Here, we explore the possibility of combining these two classes of molecules. In the first half of this chapter, we review the fundamentals of membrane curvature generation and the various strategies recently used to mimic this membrane activity of AMPs using different classes of synthetic molecules. In the second half, we show that it is possible to impart membrane activity to molecules with no previous membrane activity, and summarize some of our recent works which aim to combine advantages of traditional antibiotics and AMPs into a single molecule with multiple mechanisms of killing as well as multiple mechanisms of specificity.